├── pymican ├── __init__.py └── bin │ └── mican_x86_64_linux ├── requirements.txt ├── MANIFEST.in ├── src ├── main.h ├── Makefile ├── print_progress.c ├── chain_break_check.c ├── calc_maxdist.c ├── distmat.c ├── make_pdbdat.c ├── utils.c ├── hres2trans.c └── coord_definition.c ├── .gitignore ├── scripts └── mican ├── Makefile ├── Makefile_gcc11 ├── tests ├── dataset │ ├── MALIDUP-ns │ │ └── reference │ │ │ ├── d1kg1a_.aln │ │ │ ├── d1ckv__.aln │ │ │ ├── d1hg7a_.aln │ │ │ ├── d1lpba1.aln │ │ │ ├── d2bn2a_.aln │ │ │ ├── d1df9c_.aln │ │ │ ├── d1d4va1.aln │ │ │ ├── d1f53a_.aln │ │ │ ├── d1fwqa_.aln │ │ │ ├── d1o9sa2.aln │ │ │ ├── d1a4pa_.aln │ │ │ ├── d1ciy_2_3.aln │ │ │ ├── d1fga___2.aln │ │ │ ├── d1fga___3.aln │ │ │ ├── d1ycqa_.aln │ │ │ ├── d1ciy_2_1.aln │ │ │ ├── d1isva1_1.aln │ │ │ ├── d1isva1_2.aln │ │ │ ├── d1utaa_.aln │ │ │ ├── d1yua_1.aln │ │ │ ├── d1i50h_.aln │ │ │ ├── d1ttua3.aln │ │ │ ├── d1cy8a__2.aln │ │ │ ├── d1fga___1.aln │ │ │ ├── d1emn_1.aln │ │ │ ├── d1s3na_.aln │ │ │ ├── d1g61a__2.aln │ │ │ ├── d1jlya1_1.aln │ │ │ ├── d1jlya1_2.aln │ │ │ ├── d1isva1_3.aln │ │ │ ├── d1wba___3.aln │ │ │ ├── d1c3ma__3.aln │ │ │ ├── d1vjla_.aln │ │ │ ├── d1exja2.aln │ │ │ ├── d1jsg__.aln │ │ │ ├── d2g3pa1.aln │ │ │ ├── d1c3ma__1.aln │ │ │ ├── d1g61a__1.aln │ │ │ ├── d1c3ma__2.aln │ │ │ ├── d1fjra_.aln │ │ │ ├── d1ahja_.aln │ │ │ ├── d1ce8a1.aln │ │ │ ├── d1tocr1.aln │ │ │ ├── d1wba___2.aln │ │ │ ├── d1jlya1_3.aln │ │ │ ├── d1tbrr1.aln │ │ │ ├── d1ciy_2_2.aln │ │ │ ├── d1f34b_.aln │ │ │ ├── d1nol_2.aln │ │ │ ├── d1d5ya1.aln │ │ │ ├── d1n0fg_.aln │ │ │ ├── d1pg6a_.aln │ │ │ ├── d1skz_1.aln │ │ │ ├── d1wba___1.aln │ │ │ ├── d2pspa1.aln │ │ │ ├── d1n2ma_.aln │ │ │ ├── d3ezma_.aln │ │ │ ├── d1b3qa2.aln │ │ │ ├── d1cpo_1.aln │ │ │ ├── d1vmoa__3.aln │ │ │ ├── d4proc1.aln │ │ │ ├── d1foka1_2.aln │ │ │ ├── d1g1ba_.aln │ │ │ ├── d1vmoa__1.aln │ │ │ ├── d1vmoa__2.aln │ │ │ ├── d1f9za_.aln │ │ │ ├── d1guwa_.aln │ │ │ ├── d1sr9b3.aln │ │ │ ├── d2bs2c1.aln │ │ │ ├── d1rwtj_.aln │ │ │ ├── d1squa_.aln │ │ │ ├── d1t3ta3.aln │ │ │ ├── d1vlya2.aln │ │ │ ├── d8gep_1.aln │ │ │ ├── d1ck7a3.aln │ │ │ ├── d1foka1_3.aln │ │ │ ├── d1fyze_.aln │ │ │ ├── d1qmea1.aln │ │ │ ├── d2bmia_.aln │ │ │ ├── d1qmha2_2.aln │ │ │ ├── d1d8ha_.aln │ │ │ ├── d1hazb_.aln │ │ │ ├── d1m98a1.aln │ │ │ ├── d1qm4a1.aln │ │ │ ├── d1qtqa1.aln │ │ │ ├── d1anv_2.aln │ │ │ ├── d1dgsa1.aln │ │ │ ├── d1pv5a_.aln │ │ │ ├── d1k2yx1_2.aln │ │ │ ├── d1qmha2_1.aln │ │ │ ├── d1k2yx1_1.aln │ │ │ ├── d1at0__.aln │ │ │ ├── d1hh2p2.aln │ │ │ ├── d1hs6a2.aln │ │ │ ├── d1k28d1.aln │ │ │ ├── d1k6ka_.aln │ │ │ ├── d1avk_2.aln │ │ │ ├── d1kapp1.aln │ │ │ ├── d1b70b2.aln │ │ │ ├── d1jh7a_.aln │ │ │ ├── d1tdj_2.aln │ │ │ ├── d1a6da1.aln │ │ │ ├── d1efud4.aln │ │ │ ├── d1f52a2.aln │ │ │ ├── d1rl6a1.aln │ │ │ ├── d1i1qa__1.aln │ │ │ ├── d1in0b1.aln │ │ │ ├── d1jtgb_.aln │ │ │ ├── d1b24a1.aln │ │ │ ├── d1foka1_1.aln │ │ │ ├── d1hxpa1.aln │ │ │ ├── d1m9sa2.aln │ │ │ └── d1vk6a1.aln │ └── MALISAM-ns │ │ └── reference │ │ ├── d1h6da2d1kjka_.aln │ │ ├── d1oi2a_d1uw1a_.aln │ │ ├── d1qo0d_d1hjp_1.aln │ │ ├── d1ogsa2d1is1a_.aln │ │ ├── d1ce8a6d1di2a_.aln │ │ ├── d1efdn_d1r0va3.aln │ │ ├── d1uw1a_d1q9ua_.aln │ │ ├── d1b3qa2d1bia_2.aln │ │ ├── d1efdn_d1d1ra_.aln │ │ ├── d1qnia1d1k4za_.aln │ │ ├── d1jdbc2d1r9ca_.aln │ │ ├── d1ogsa2d1dq3a4.aln │ │ ├── d1ac5__d1jroa3.aln │ │ ├── d1axn__d1sf9a_.aln │ │ ├── d1chma1d1g62a_.aln │ │ ├── d1qd1b1d1n62c2.aln │ │ ├── d1vk3a3d1lbu_2.aln │ │ ├── d1fy2a_d1qmha1.aln │ │ ├── d3pmga1d1e8ca1.aln │ │ ├── d1axn__d1nkta3.aln │ │ ├── d1a05a_d1j71a_.aln │ │ ├── d1b05a_d1lc0a2.aln │ │ ├── d1lci__d1lla_1.aln │ │ ├── d1ps6a_d1f9za_.aln │ │ ├── d1b05a_d1nkia_.aln │ │ ├── d1gxja_d1p5dx3.aln │ │ ├── d1miwa2d1gyfa_.aln │ │ ├── d1dzta_d1kpf__.aln │ │ ├── d1ogqa_d1fjgc1.aln │ │ ├── d1qd1b1d1itwa_.aln │ │ ├── d1b0pa2d1k0da2.aln │ │ ├── d1h0hb_d1hz6b_.aln │ │ ├── d1ihoa_d1ep7a_.aln │ │ ├── d1qh4a2d1ekga_.aln │ │ ├── d2onea1d1hz6b_.aln │ │ ├── d1g99a1d1gqyb3.aln │ │ ├── d1mw5a_d1bco_1.aln │ │ ├── d1is8a_d1umwa1.aln │ │ ├── d1nkta3d1ldja1.aln │ │ ├── d1dmza_d1hdha_.aln │ │ ├── d1l6ra_d1nrva_.aln │ │ ├── d1pqsa_d1i7la2.aln │ │ ├── d1l6ra_d1ir6a_.aln │ │ ├── d1nf2a_d1ptma_.aln │ │ ├── d1ovma1d1914_2.aln │ │ ├── d1smta_d1b7ta4.aln │ │ ├── d1vk3a3d1w2ia_.aln │ │ ├── d2gaw.1d1nppa1.aln │ │ ├── d1ert__d1jr3d2.aln │ │ ├── d1fbxa_d1o08a_.aln │ │ ├── d1i9ea_d1nppa1.aln │ │ ├── d1piea1d1q0qa1.aln │ │ ├── d1a7j__d1kafa_.aln │ │ ├── d1hbnb2d1aisb2.aln │ │ ├── d1n00a_d1aa7a_.aln │ │ ├── d1okra_d1v9da_.aln │ │ ├── d1ac5__d1vk0a_.aln │ │ ├── d1cs1a_d1q8ia1.aln │ │ ├── d1dc1a_d1nf2a_.aln │ │ ├── d1dc1a_d1rblm_.aln │ │ ├── d1pqsa_d1poh__.aln │ │ ├── d1a2za_d1ghha_.aln │ │ ├── d1b62a2d1i6pa_.aln │ │ ├── d1htjf_d1gnla_.aln │ │ ├── d1j22a_d1m2aa_.aln │ │ ├── d1d7ba_d1svb_2.aln │ │ ├── d1izna_d1gkza1.aln │ │ ├── d1piea1d1nxha_.aln │ │ ├── d1ur3m_d1k87a1.aln │ │ ├── d1vaoa2d1no5a_.aln │ │ ├── d1jnwa_d1ew4a_.aln │ │ ├── d1n7va_d1izna_.aln │ │ ├── d1uoua1d1fs1b1.aln │ │ ├── d1a7j__d2if1__.aln │ │ ├── d1ds1a_d1tig__.aln │ │ ├── d1hrda1d1rp3a3.aln │ │ ├── d1i9ea_d1mzka_.aln │ │ ├── d1o02a_d1ihna_.aln │ │ ├── d1okra_d1m98a1.aln │ │ ├── d1aa7a_d1b68a_.aln │ │ ├── d1st6a8d1gvna_.aln │ │ ├── d1ukfa_d1gsa_2.aln │ │ ├── d1aora2d1dkza2.aln │ │ ├── d1b6ra1d1v97a4.aln │ │ ├── d1lq7a_d1gqea_.aln │ │ ├── d2csta_d1j4wa1.aln │ │ ├── d1b6ra1d1k8kd1.aln │ │ ├── d1hi9a_d1rpua_.aln │ │ ├── d1o17d2d1ir6a_.aln │ │ ├── d1o17d2d1jyra_.aln │ │ ├── d1pdz_1d1irum_.aln │ │ ├── d1dzka_d1qd1b2.aln │ │ ├── d1izna_d1keka2.aln │ │ ├── d1izna_d2gsca_.aln │ │ ├── d1p5gx1d1xppa_.aln │ │ ├── d1a05a_d1dgsa3.aln │ │ ├── d1e3pa3d1tis__.aln │ │ ├── d1htjf_d1nhua_.aln │ │ ├── d1m9na2d1j27a_.aln │ │ ├── d1tv8a_d1nbwb_.aln │ │ ├── d1e3pa3d1gpqa_.aln │ │ ├── d1eg3a1d1paqa_.aln │ │ └── d1gc5a_d1omha_.aln └── fastcheck │ └── testrun.py ├── .github └── workflows │ └── build_and_test.yml └── LICENSE /pymican/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | from pymican.main import BINFILEPATH, mican 3 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | numpy==1.22.0 2 | pandas==1.2.4 3 | memory-tempfile==2.2.3 4 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include src/*.c src/*.h Makefile 2 | include pymican/bin/* 3 | recursive-exclude tests * -------------------------------------------------------------------------------- /src/main.h: -------------------------------------------------------------------------------- 1 | #include "mican.h" 2 | extern INPUT_DATA input; 3 | extern clock_t time_init, time_end, time_tmp; 4 | -------------------------------------------------------------------------------- /pymican/bin/mican_x86_64_linux: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShintaroMinami/mican/HEAD/pymican/bin/mican_x86_64_linux -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # compiled files 2 | */*.o 3 | # pypi 4 | dist 5 | *.egg-info 6 | *.eggs 7 | build 8 | # pycache 9 | */__pycache__/* 10 | # debug 11 | debug -------------------------------------------------------------------------------- /scripts/mican: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python 2 | 3 | import subprocess 4 | import sys 5 | from pymican import BINFILEPATH 6 | 7 | subprocess.run([BINFILEPATH, *sys.argv[1:]]) 8 | -------------------------------------------------------------------------------- /src/Makefile: -------------------------------------------------------------------------------- 1 | CC = gcc 2 | CFLAGS = -O3 -Wall 3 | LIBS = -lm 4 | SRC = $(shell ls *.c) 5 | HEADERS = $(shell ls *.h) 6 | OBJS = $(SRC:.c=.o) 7 | 8 | TARGET = mican 9 | 10 | $(TARGET): $(OBJS) 11 | $(CC) $(CFLAGS) -o $(TARGET) $(OBJS) $(LIBS) 12 | 13 | $(OBJS): $(HEADERS) 14 | 15 | clean: 16 | rm -f $(OBJS) $(TARGET) 17 | -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | CC = gcc 2 | CFLAGS = -O3 -Wall 3 | LIBS = -lm 4 | VPATH = src 5 | SRC = $(shell ls $(VPATH)/*.c) 6 | HEADERS = $(shell ls $(VPATH)/*.h) 7 | OBJS = $(SRC:.c=.o) 8 | 9 | TARGET = mican 10 | 11 | $(TARGET): $(OBJS) 12 | $(CC) $(CFLAGS) -o $(TARGET) $(OBJS) $(LIBS) 13 | 14 | $(OBJS): $(HEADERS) 15 | 16 | clean: 17 | rm -f $(OBJS) $(TARGET) $(TARGETLIB) 18 | -------------------------------------------------------------------------------- /Makefile_gcc11: -------------------------------------------------------------------------------- 1 | CC = gcc-11 2 | CFLAGS = -O3 -Wall 3 | LIBS = -lm 4 | VPATH = src 5 | SRC = $(shell ls $(VPATH)/*.c) 6 | HEADERS = $(shell ls $(VPATH)/*.h) 7 | OBJS = $(SRC:.c=.o) 8 | 9 | TARGET = mican 10 | 11 | $(TARGET): $(OBJS) 12 | $(CC) $(CFLAGS) -o $(TARGET) $(OBJS) $(LIBS) 13 | 14 | $(OBJS): $(HEADERS) 15 | 16 | clean: 17 | rm -f $(OBJS) $(TARGET) $(TARGETLIB) 18 | -------------------------------------------------------------------------------- /src/print_progress.c: -------------------------------------------------------------------------------- 1 | #include "mican.h" 2 | 3 | void print_progress(char *progress_name, int numerator, int denominator) { 4 | 5 | float progress; 6 | progress = (float)(100 * numerator / denominator); 7 | fprintf(stderr, "%18s ... %4d /%4d (%3.0f%%) in sec.\n", progress_name, 8 | numerator, denominator, progress); 9 | fprintf(stderr, "\033[1A"); 10 | 11 | return; 12 | } 13 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1kg1a_.aln: -------------------------------------------------------------------------------- 1 | 4 15 2 | 5 16 3 | 6 17 4 | 7 18 5 | 8 19 6 | 9 20 7 | 10 21 8 | 11 22 9 | 14 24 10 | 15 25 11 | 16 26 12 | 17 27 13 | 18 28 14 | 19 29 15 | 20 30 16 | 21 31 17 | 22 32 18 | 23 4 19 | 24 5 20 | 25 6 21 | 26 7 22 | 27 8 23 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1ckv__.aln: -------------------------------------------------------------------------------- 1 | 38 38 2 | 39 39 3 | 40 40 4 | 41 41 5 | 42 42 6 | 43 43 7 | 44 44 8 | 45 45 9 | 68 10 10 | 69 11 11 | 70 12 12 | 71 13 13 | 72 14 14 | 73 15 15 | 74 16 16 | 75 17 17 | 76 18 18 | 77 19 19 | 78 20 20 | 79 21 21 | 80 22 22 | 81 23 23 | 82 24 24 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1hg7a_.aln: -------------------------------------------------------------------------------- 1 | 5 17 2 | 6 18 3 | 7 19 4 | 8 20 5 | 9 21 6 | 10 22 7 | 11 23 8 | 12 24 9 | 13 25 10 | 14 26 11 | 15 27 12 | 16 28 13 | 17 1 14 | 18 2 15 | 19 3 16 | 20 4 17 | 21 5 18 | 22 6 19 | 23 7 20 | 24 8 21 | 25 9 22 | 26 10 23 | 27 11 24 | 28 12 25 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1lpba1.aln: -------------------------------------------------------------------------------- 1 | 6 10 2 | 7 11 3 | 8 12 4 | 9 13 5 | 10 14 6 | 11 15 7 | 12 16 8 | 13 17 9 | 14 18 10 | 17 29 11 | 18 30 12 | 19 31 13 | 21 34 14 | 22 35 15 | 23 36 16 | 24 37 17 | 25 38 18 | 31 3 19 | 32 4 20 | 33 5 21 | 34 6 22 | 35 7 23 | 36 8 24 | 37 9 25 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d2bn2a_.aln: -------------------------------------------------------------------------------- 1 | 10 15 2 | 11 16 3 | 12 17 4 | 13 18 5 | 14 19 6 | 15 20 7 | 18 21 8 | 19 22 9 | 20 23 10 | 21 24 11 | 22 25 12 | 23 26 13 | 24 27 14 | 25 28 15 | 26 29 16 | 27 30 17 | 28 31 18 | 29 32 19 | 30 33 20 | 31 34 21 | 33 1 22 | 34 2 23 | 35 3 24 | 36 4 25 | 37 5 26 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1df9c_.aln: -------------------------------------------------------------------------------- 1 | 12 12 2 | 13 13 3 | 14 14 4 | 15 15 5 | 16 16 6 | 17 17 7 | 18 18 8 | 19 19 9 | 20 20 10 | 21 21 11 | 22 22 12 | 23 23 13 | 24 24 14 | 25 25 15 | 26 26 16 | 27 27 17 | 28 28 18 | 29 29 19 | 30 30 20 | 31 31 21 | 32 32 22 | 33 33 23 | 34 34 24 | 36 1 25 | 37 2 26 | 38 3 27 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1d4va1.aln: -------------------------------------------------------------------------------- 1 | 8 36 2 | 9 37 3 | 10 38 4 | 11 39 5 | 12 40 6 | 13 41 7 | 14 2 8 | 15 3 9 | 16 4 10 | 17 5 11 | 18 6 12 | 19 7 13 | 20 8 14 | 21 9 15 | 22 10 16 | 23 11 17 | 24 12 18 | 25 13 19 | 26 14 20 | 27 15 21 | 28 16 22 | 29 17 23 | 30 18 24 | 31 19 25 | 32 20 26 | 33 21 27 | 34 22 28 | 35 23 29 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1f53a_.aln: -------------------------------------------------------------------------------- 1 | 12 13 2 | 13 14 3 | 14 15 4 | 15 16 5 | 16 17 6 | 17 18 7 | 18 19 8 | 23 21 9 | 24 22 10 | 25 23 11 | 26 24 12 | 27 25 13 | 28 26 14 | 29 27 15 | 30 28 16 | 31 29 17 | 32 30 18 | 33 31 19 | 34 32 20 | 35 33 21 | 36 34 22 | 41 4 23 | 42 5 24 | 43 6 25 | 44 7 26 | 45 8 27 | 46 9 28 | 47 10 29 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1fwqa_.aln: -------------------------------------------------------------------------------- 1 | 10 2 2 | 11 3 3 | 12 4 4 | 13 5 5 | 14 6 6 | 15 7 7 | 16 8 8 | 17 9 9 | 18 10 10 | 19 11 11 | 20 12 12 | 21 33 13 | 22 34 14 | 23 35 15 | 24 36 16 | 25 37 17 | 59 26 18 | 60 27 19 | 61 28 20 | 62 29 21 | 63 30 22 | 64 31 23 | 71 13 24 | 72 14 25 | 73 15 26 | 74 16 27 | 75 17 28 | 76 18 29 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1o9sa2.aln: -------------------------------------------------------------------------------- 1 | 21 66 2 | 22 67 3 | 23 68 4 | 24 69 5 | 25 70 6 | 26 71 7 | 27 72 8 | 28 73 9 | 29 74 10 | 30 75 11 | 31 76 12 | 32 77 13 | 33 78 14 | 34 3 15 | 35 4 16 | 36 5 17 | 37 6 18 | 38 7 19 | 39 8 20 | 40 9 21 | 41 10 22 | 42 11 23 | 43 12 24 | 44 13 25 | 45 14 26 | 46 15 27 | 47 16 28 | 48 17 29 | 49 18 30 | 50 19 31 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1a4pa_.aln: -------------------------------------------------------------------------------- 1 | 7 34 2 | 8 35 3 | 9 36 4 | 10 37 5 | 11 38 6 | 12 39 7 | 13 40 8 | 14 41 9 | 15 42 10 | 16 43 11 | 17 44 12 | 18 45 13 | 19 46 14 | 20 47 15 | 21 2 16 | 22 3 17 | 23 4 18 | 24 5 19 | 25 6 20 | 26 7 21 | 27 8 22 | 28 9 23 | 29 10 24 | 30 11 25 | 31 12 26 | 32 13 27 | 33 14 28 | 34 15 29 | 35 16 30 | 36 17 31 | 37 18 32 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1ciy_2_3.aln: -------------------------------------------------------------------------------- 1 | 2 57 2 | 3 58 3 | 4 59 4 | 5 60 5 | 6 61 6 | 7 62 7 | 8 63 8 | 9 64 9 | 10 65 10 | 11 66 11 | 12 67 12 | 13 68 13 | 21 47 14 | 22 48 15 | 23 49 16 | 24 50 17 | 25 51 18 | 26 52 19 | 27 53 20 | 28 54 21 | 29 55 22 | 30 56 23 | 42 1 24 | 43 2 25 | 44 3 26 | 45 4 27 | 46 5 28 | 47 6 29 | 48 7 30 | 49 8 31 | 50 9 32 | 51 10 33 | 52 11 34 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1fga___2.aln: -------------------------------------------------------------------------------- 1 | 3 32 2 | 4 33 3 | 5 34 4 | 6 35 5 | 7 36 6 | 8 37 7 | 9 38 8 | 10 39 9 | 11 40 10 | 12 41 11 | 13 42 12 | 14 2 13 | 15 3 14 | 16 4 15 | 17 5 16 | 18 6 17 | 19 7 18 | 20 8 19 | 21 9 20 | 22 10 21 | 23 11 22 | 24 12 23 | 29 30 24 | 30 31 25 | 31 15 26 | 32 16 27 | 33 17 28 | 34 18 29 | 35 19 30 | 36 20 31 | 37 21 32 | 38 22 33 | 39 23 34 | 40 24 35 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1fga___3.aln: -------------------------------------------------------------------------------- 1 | 1 33 2 | 2 34 3 | 3 35 4 | 4 36 5 | 5 37 6 | 6 38 7 | 7 39 8 | 8 40 9 | 9 41 10 | 10 42 11 | 11 20 12 | 12 21 13 | 13 22 14 | 14 23 15 | 15 24 16 | 16 25 17 | 17 26 18 | 18 27 19 | 19 28 20 | 20 29 21 | 21 30 22 | 26 6 23 | 27 7 24 | 28 8 25 | 29 9 26 | 30 10 27 | 31 11 28 | 32 12 29 | 33 13 30 | 34 14 31 | 35 15 32 | 36 16 33 | 37 17 34 | 38 18 35 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1ycqa_.aln: -------------------------------------------------------------------------------- 1 | 2 19 2 | 3 20 3 | 4 21 4 | 5 22 5 | 6 23 6 | 7 2 7 | 8 3 8 | 9 4 9 | 10 5 10 | 11 6 11 | 12 7 12 | 13 8 13 | 14 9 14 | 15 10 15 | 21 36 16 | 22 37 17 | 23 38 18 | 24 39 19 | 25 40 20 | 26 41 21 | 27 42 22 | 28 43 23 | 29 27 24 | 30 28 25 | 31 29 26 | 32 30 27 | 33 31 28 | 34 32 29 | 35 33 30 | 36 34 31 | 37 35 32 | 42 12 33 | 43 13 34 | 44 14 35 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1ciy_2_1.aln: -------------------------------------------------------------------------------- 1 | 1 27 2 | 2 28 3 | 3 29 4 | 4 30 5 | 5 31 6 | 6 32 7 | 7 33 8 | 8 34 9 | 9 35 10 | 10 36 11 | 11 37 12 | 12 38 13 | 21 47 14 | 22 48 15 | 23 49 16 | 24 50 17 | 25 51 18 | 26 52 19 | 27 53 20 | 28 54 21 | 29 55 22 | 30 56 23 | 31 57 24 | 32 58 25 | 42 1 26 | 43 2 27 | 44 3 28 | 45 4 29 | 46 5 30 | 47 6 31 | 48 7 32 | 49 9 33 | 50 10 34 | 51 11 35 | 52 12 36 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1isva1_1.aln: -------------------------------------------------------------------------------- 1 | 10 29 2 | 11 30 3 | 12 31 4 | 13 32 5 | 14 33 6 | 19 37 7 | 20 38 8 | 21 39 9 | 22 40 10 | 23 41 11 | 24 42 12 | 27 1 13 | 28 2 14 | 29 3 15 | 30 4 16 | 31 5 17 | 32 6 18 | 33 7 19 | 34 8 20 | 35 9 21 | 36 10 22 | 37 11 23 | 38 12 24 | 39 13 25 | 40 14 26 | 41 15 27 | 42 16 28 | 43 17 29 | 44 18 30 | 45 19 31 | 46 20 32 | 47 21 33 | 48 22 34 | 49 23 35 | 50 24 36 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1isva1_2.aln: -------------------------------------------------------------------------------- 1 | 3 36 2 | 4 37 3 | 5 38 4 | 6 39 5 | 7 40 6 | 11 4 7 | 12 5 8 | 13 6 9 | 14 7 10 | 15 8 11 | 16 9 12 | 17 12 13 | 18 13 14 | 19 14 15 | 20 15 16 | 21 16 17 | 22 17 18 | 23 18 19 | 24 19 20 | 25 20 21 | 26 21 22 | 27 22 23 | 28 23 24 | 29 24 25 | 30 25 26 | 31 26 27 | 32 27 28 | 33 28 29 | 34 29 30 | 35 30 31 | 36 31 32 | 37 32 33 | 38 33 34 | 39 34 35 | 40 35 36 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1h6da2d1kjka_.aln: -------------------------------------------------------------------------------- 1 | 3 21 2 | 4 22 3 | 5 23 4 | 6 24 5 | 7 25 6 | 8 26 7 | 9 27 8 | 10 28 9 | 11 29 10 | 12 30 11 | 13 31 12 | 14 32 13 | 20 15 14 | 21 16 15 | 22 17 16 | 23 18 17 | 24 19 18 | 25 20 19 | 31 40 20 | 32 41 21 | 33 42 22 | 34 43 23 | 35 44 24 | 36 45 25 | 37 46 26 | 38 47 27 | 39 48 28 | 40 2 29 | 41 3 30 | 42 4 31 | 43 5 32 | 44 6 33 | 45 7 34 | 46 8 35 | 47 9 36 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1oi2a_d1uw1a_.aln: -------------------------------------------------------------------------------- 1 | 1 52 2 | 2 53 3 | 3 54 4 | 4 55 5 | 5 56 6 | 6 57 7 | 7 58 8 | 8 59 9 | 9 60 10 | 10 61 11 | 11 62 12 | 12 63 13 | 13 64 14 | 14 65 15 | 15 66 16 | 16 23 17 | 17 24 18 | 18 25 19 | 19 26 20 | 20 27 21 | 21 28 22 | 22 29 23 | 23 32 24 | 24 33 25 | 25 34 26 | 26 35 27 | 27 36 28 | 28 37 29 | 29 38 30 | 61 6 31 | 62 7 32 | 63 8 33 | 64 9 34 | 65 10 35 | 66 11 36 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1utaa_.aln: -------------------------------------------------------------------------------- 1 | 4 9 2 | 5 10 3 | 6 11 4 | 7 12 5 | 8 13 6 | 9 14 7 | 10 15 8 | 11 16 9 | 12 17 10 | 13 18 11 | 14 19 12 | 15 20 13 | 16 21 14 | 17 22 15 | 18 23 16 | 19 24 17 | 20 25 18 | 21 26 19 | 22 27 20 | 23 28 21 | 24 29 22 | 25 30 23 | 26 31 24 | 27 32 25 | 28 33 26 | 29 34 27 | 30 35 28 | 31 36 29 | 33 1 30 | 34 2 31 | 35 3 32 | 36 4 33 | 37 5 34 | 38 6 35 | 39 7 36 | 40 8 37 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1yua_1.aln: -------------------------------------------------------------------------------- 1 | 18 13 2 | 19 14 3 | 20 15 4 | 21 16 5 | 23 17 6 | 24 18 7 | 25 19 8 | 26 20 9 | 27 21 10 | 28 22 11 | 29 23 12 | 30 24 13 | 31 25 14 | 32 26 15 | 33 27 16 | 34 50 17 | 35 51 18 | 36 52 19 | 37 53 20 | 38 54 21 | 39 55 22 | 40 56 23 | 41 57 24 | 42 58 25 | 45 31 26 | 46 32 27 | 47 33 28 | 48 34 29 | 49 35 30 | 50 36 31 | 51 37 32 | 52 38 33 | 53 39 34 | 54 40 35 | 55 41 36 | 56 42 37 | -------------------------------------------------------------------------------- /src/chain_break_check.c: -------------------------------------------------------------------------------- 1 | #include "mican.h" 2 | 3 | void chain_break_check(int naa, RESDAT *resdat) { 4 | 5 | int iaa; 6 | 7 | for (iaa = 2; iaa <= naa - 1; iaa++) { 8 | /* chain break check */ 9 | if (distance_2(resdat[iaa - 1].cacoord, resdat[iaa].cacoord) > 16.0) { 10 | resdat[iaa].chain_break = ON; 11 | } else if (distance_2(resdat[iaa + 1].cacoord, resdat[iaa].cacoord) > 12 | 16.0) { 13 | resdat[iaa].chain_break = ON; 14 | } else { 15 | resdat[iaa].chain_break = OFF; 16 | } 17 | } 18 | resdat[1].chain_break = ON; 19 | resdat[naa].chain_break = ON; 20 | 21 | return; 22 | } 23 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1qo0d_d1hjp_1.aln: -------------------------------------------------------------------------------- 1 | 4 2 2 | 5 3 3 | 6 4 4 | 7 5 5 | 8 6 6 | 9 7 7 | 10 8 8 | 11 9 9 | 12 10 10 | 13 11 11 | 14 12 12 | 15 13 13 | 17 19 14 | 18 20 15 | 19 21 16 | 20 22 17 | 21 23 18 | 22 24 19 | 23 25 20 | 24 26 21 | 25 27 22 | 26 28 23 | 33 33 24 | 34 34 25 | 35 35 26 | 36 36 27 | 37 37 28 | 38 38 29 | 39 39 30 | 40 40 31 | 41 41 32 | 42 42 33 | 43 43 34 | 44 44 35 | 45 45 36 | 46 46 37 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1ogsa2d1is1a_.aln: -------------------------------------------------------------------------------- 1 | 5 30 2 | 6 31 3 | 7 32 4 | 14 51 5 | 15 52 6 | 16 53 7 | 17 54 8 | 18 55 9 | 19 56 10 | 20 57 11 | 21 35 12 | 22 36 13 | 23 37 14 | 24 38 15 | 25 39 16 | 26 40 17 | 27 41 18 | 28 42 19 | 29 43 20 | 30 44 21 | 31 45 22 | 32 46 23 | 33 47 24 | 34 48 25 | 42 62 26 | 43 63 27 | 44 64 28 | 45 65 29 | 46 66 30 | 47 67 31 | 50 68 32 | 51 69 33 | 52 70 34 | 53 71 35 | 54 72 36 | 55 73 37 | 56 74 38 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1i50h_.aln: -------------------------------------------------------------------------------- 1 | 3 28 2 | 4 29 3 | 5 30 4 | 6 31 5 | 7 32 6 | 8 33 7 | 9 34 8 | 10 35 9 | 11 36 10 | 12 37 11 | 13 38 12 | 21 1 13 | 22 2 14 | 23 3 15 | 24 4 16 | 25 5 17 | 26 6 18 | 27 7 19 | 28 8 20 | 29 9 21 | 35 60 22 | 36 61 23 | 37 62 24 | 38 63 25 | 39 64 26 | 40 65 27 | 41 66 28 | 42 67 29 | 43 68 30 | 52 50 31 | 53 51 32 | 54 52 33 | 55 53 34 | 56 54 35 | 57 55 36 | 58 56 37 | 59 57 38 | 60 58 39 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1ttua3.aln: -------------------------------------------------------------------------------- 1 | 4 5 2 | 5 6 3 | 6 7 4 | 7 8 5 | 8 9 6 | 9 10 7 | 10 11 8 | 11 12 9 | 12 13 10 | 13 14 11 | 14 15 12 | 15 16 13 | 16 17 14 | 17 18 15 | 25 22 16 | 26 23 17 | 27 24 18 | 28 25 19 | 29 26 20 | 30 27 21 | 31 28 22 | 32 29 23 | 33 30 24 | 34 31 25 | 35 32 26 | 36 33 27 | 37 34 28 | 38 35 29 | 39 36 30 | 40 37 31 | 43 51 32 | 44 52 33 | 45 53 34 | 46 54 35 | 47 55 36 | 48 56 37 | 49 57 38 | 50 58 39 | -------------------------------------------------------------------------------- /src/calc_maxdist.c: -------------------------------------------------------------------------------- 1 | #include "mican.h" 2 | 3 | float calc_maxdist(int nsse, SSEDAT *ssedat) { 4 | int icoord; 5 | int isse, jsse; 6 | float dist; 7 | float max_dist = 0.0f; 8 | 9 | for (isse = 1; isse <= nsse - 1; isse++) { 10 | for (jsse = isse + 1; jsse <= nsse; jsse++) { 11 | dist = 0; 12 | for (icoord = 1; icoord <= Ncoord; icoord++) { 13 | dist += (ssedat[isse].mid[icoord] - ssedat[jsse].mid[icoord]) * 14 | (ssedat[isse].mid[icoord] - ssedat[jsse].mid[icoord]); 15 | } 16 | if (dist > max_dist) { 17 | max_dist = dist; 18 | } 19 | } 20 | } 21 | 22 | return ((float)sqrt(max_dist)); 23 | } 24 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1cy8a__2.aln: -------------------------------------------------------------------------------- 1 | 1 55 2 | 2 56 3 | 3 57 4 | 4 58 5 | 5 59 6 | 6 60 7 | 7 61 8 | 8 62 9 | 9 63 10 | 10 64 11 | 11 65 12 | 12 66 13 | 13 67 14 | 14 68 15 | 15 69 16 | 16 70 17 | 18 1 18 | 19 2 19 | 20 3 20 | 21 4 21 | 22 5 22 | 23 6 23 | 51 39 24 | 52 40 25 | 53 41 26 | 54 42 27 | 55 43 28 | 56 44 29 | 57 45 30 | 58 46 31 | 59 47 32 | 60 48 33 | 61 49 34 | 62 50 35 | 63 51 36 | 64 52 37 | 65 53 38 | 66 54 39 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1fga___1.aln: -------------------------------------------------------------------------------- 1 | 1 17 2 | 2 18 3 | 3 19 4 | 4 20 5 | 5 21 6 | 6 22 7 | 7 23 8 | 8 24 9 | 9 25 10 | 10 26 11 | 11 27 12 | 12 28 13 | 13 29 14 | 14 30 15 | 15 31 16 | 16 32 17 | 17 33 18 | 18 34 19 | 19 35 20 | 20 36 21 | 21 37 22 | 22 38 23 | 23 39 24 | 24 40 25 | 25 41 26 | 26 42 27 | 27 43 28 | 29 1 29 | 30 2 30 | 31 3 31 | 32 4 32 | 33 5 33 | 34 6 34 | 35 7 35 | 36 8 36 | 37 9 37 | 38 10 38 | 39 11 39 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1ce8a6d1di2a_.aln: -------------------------------------------------------------------------------- 1 | 4 18 2 | 5 19 3 | 6 20 4 | 7 21 5 | 8 22 6 | 9 23 7 | 15 32 8 | 16 33 9 | 17 34 10 | 18 35 11 | 19 36 12 | 20 37 13 | 21 38 14 | 22 39 15 | 23 40 16 | 24 41 17 | 43 42 18 | 44 43 19 | 45 44 20 | 46 45 21 | 47 46 22 | 48 47 23 | 49 48 24 | 50 49 25 | 51 50 26 | 52 51 27 | 53 52 28 | 54 53 29 | 55 54 30 | 56 55 31 | 57 56 32 | 58 57 33 | 59 58 34 | 60 59 35 | 61 60 36 | 62 61 37 | 63 62 38 | 64 63 39 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1efdn_d1r0va3.aln: -------------------------------------------------------------------------------- 1 | 1 51 2 | 2 52 3 | 3 53 4 | 4 54 5 | 5 55 6 | 6 56 7 | 7 57 8 | 8 58 9 | 9 59 10 | 10 60 11 | 11 61 12 | 13 62 13 | 14 63 14 | 15 64 15 | 16 65 16 | 17 66 17 | 18 67 18 | 19 68 19 | 45 8 20 | 46 9 21 | 47 10 22 | 48 11 23 | 49 12 24 | 50 13 25 | 51 14 26 | 52 15 27 | 53 16 28 | 54 17 29 | 55 18 30 | 56 19 31 | 57 20 32 | 58 21 33 | 61 25 34 | 62 26 35 | 63 27 36 | 64 28 37 | 65 29 38 | 66 30 39 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1emn_1.aln: -------------------------------------------------------------------------------- 1 | 3 5 2 | 4 6 3 | 5 7 4 | 6 8 5 | 7 9 6 | 8 10 7 | 9 11 8 | 10 12 9 | 11 13 10 | 12 14 11 | 13 15 12 | 14 16 13 | 15 17 14 | 16 18 15 | 17 19 16 | 18 20 17 | 19 21 18 | 20 22 19 | 21 23 20 | 22 24 21 | 23 25 22 | 24 26 23 | 25 27 24 | 26 28 25 | 27 29 26 | 28 30 27 | 29 31 28 | 30 32 29 | 31 33 30 | 32 34 31 | 33 35 32 | 34 36 33 | 35 37 34 | 36 38 35 | 37 39 36 | 38 40 37 | 39 41 38 | 40 2 39 | 41 3 40 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1s3na_.aln: -------------------------------------------------------------------------------- 1 | 1 53 2 | 2 54 3 | 3 55 4 | 4 56 5 | 5 57 6 | 6 58 7 | 7 59 8 | 8 60 9 | 11 31 10 | 12 32 11 | 13 33 12 | 14 34 13 | 15 35 14 | 16 36 15 | 17 37 16 | 18 38 17 | 19 39 18 | 20 40 19 | 21 41 20 | 22 42 21 | 23 43 22 | 27 20 23 | 28 21 24 | 29 22 25 | 30 23 26 | 31 24 27 | 32 25 28 | 33 26 29 | 34 27 30 | 35 28 31 | 36 29 32 | 50 9 33 | 51 10 34 | 52 11 35 | 53 12 36 | 54 13 37 | 55 14 38 | 56 15 39 | 57 16 40 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1uw1a_d1q9ua_.aln: -------------------------------------------------------------------------------- 1 | 3 113 2 | 4 114 3 | 5 115 4 | 6 116 5 | 7 117 6 | 8 118 7 | 9 119 8 | 10 120 9 | 11 121 10 | 12 122 11 | 13 123 12 | 14 124 13 | 15 125 14 | 16 126 15 | 21 85 16 | 22 86 17 | 23 87 18 | 24 88 19 | 25 89 20 | 26 90 21 | 27 91 22 | 28 92 23 | 29 93 24 | 30 94 25 | 31 95 26 | 32 6 27 | 33 7 28 | 34 8 29 | 35 9 30 | 36 10 31 | 37 11 32 | 38 12 33 | 56 33 34 | 57 34 35 | 58 35 36 | 59 36 37 | 60 37 38 | 61 38 39 | 62 39 40 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1g61a__2.aln: -------------------------------------------------------------------------------- 1 | 6 25 2 | 7 26 3 | 8 27 4 | 9 28 5 | 10 29 6 | 11 30 7 | 14 3 8 | 15 4 9 | 16 5 10 | 17 6 11 | 18 7 12 | 19 8 13 | 20 9 14 | 21 10 15 | 22 11 16 | 23 12 17 | 24 13 18 | 25 14 19 | 26 15 20 | 27 16 21 | 28 17 22 | 29 18 23 | 30 19 24 | 31 20 25 | 32 21 26 | 33 22 27 | 34 23 28 | 35 24 29 | 36 33 30 | 37 34 31 | 38 35 32 | 39 36 33 | 40 37 34 | 41 38 35 | 42 39 36 | 43 40 37 | 44 41 38 | 45 42 39 | 46 43 40 | 47 44 41 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1jlya1_1.aln: -------------------------------------------------------------------------------- 1 | 5 35 2 | 6 36 3 | 7 37 4 | 8 38 5 | 9 39 6 | 10 40 7 | 11 41 8 | 12 42 9 | 13 43 10 | 14 44 11 | 15 45 12 | 16 46 13 | 17 47 14 | 18 48 15 | 19 49 16 | 20 50 17 | 21 51 18 | 22 52 19 | 28 2 20 | 29 3 21 | 30 4 22 | 31 5 23 | 32 6 24 | 33 7 25 | 34 8 26 | 35 9 27 | 36 10 28 | 37 11 29 | 38 12 30 | 39 13 31 | 42 21 32 | 43 22 33 | 44 23 34 | 45 24 35 | 46 25 36 | 47 26 37 | 48 27 38 | 49 28 39 | 50 29 40 | 51 30 41 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1jlya1_2.aln: -------------------------------------------------------------------------------- 1 | 1 9 2 | 2 10 3 | 3 11 4 | 4 12 5 | 5 13 6 | 6 14 7 | 7 15 8 | 8 16 9 | 9 17 10 | 10 18 11 | 11 19 12 | 12 20 13 | 13 21 14 | 14 22 15 | 15 23 16 | 16 24 17 | 17 25 18 | 18 26 19 | 22 33 20 | 23 34 21 | 24 35 22 | 25 36 23 | 26 37 24 | 27 38 25 | 28 39 26 | 29 40 27 | 30 41 28 | 31 42 29 | 32 43 30 | 33 44 31 | 34 45 32 | 35 46 33 | 41 1 34 | 42 2 35 | 43 3 36 | 44 4 37 | 45 5 38 | 46 6 39 | 47 7 40 | 48 8 41 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1b3qa2d1bia_2.aln: -------------------------------------------------------------------------------- 1 | 6 20 2 | 7 21 3 | 8 22 4 | 9 23 5 | 10 24 6 | 11 25 7 | 12 26 8 | 13 27 9 | 14 28 10 | 15 29 11 | 16 30 12 | 17 31 13 | 18 32 14 | 19 33 15 | 27 36 16 | 28 37 17 | 29 38 18 | 30 39 19 | 31 40 20 | 35 1 21 | 36 2 22 | 37 3 23 | 38 4 24 | 39 5 25 | 40 6 26 | 41 7 27 | 42 8 28 | 43 9 29 | 48 10 30 | 49 11 31 | 50 12 32 | 51 13 33 | 52 14 34 | 53 15 35 | 54 42 36 | 55 43 37 | 56 44 38 | 57 45 39 | 58 46 40 | 59 47 41 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1efdn_d1d1ra_.aln: -------------------------------------------------------------------------------- 1 | 3 33 2 | 4 34 3 | 5 35 4 | 6 36 5 | 7 37 6 | 8 38 7 | 9 39 8 | 10 40 9 | 11 41 10 | 13 5 11 | 14 6 12 | 15 7 13 | 16 8 14 | 17 9 15 | 18 10 16 | 19 11 17 | 45 53 18 | 46 54 19 | 47 55 20 | 48 56 21 | 49 57 22 | 50 58 23 | 51 59 24 | 52 60 25 | 53 61 26 | 54 62 27 | 55 63 28 | 56 64 29 | 57 65 30 | 58 72 31 | 59 73 32 | 60 74 33 | 61 75 34 | 62 76 35 | 63 77 36 | 64 78 37 | 65 79 38 | 66 80 39 | 67 81 40 | 68 82 41 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1qnia1d1k4za_.aln: -------------------------------------------------------------------------------- 1 | 5 1 2 | 6 2 3 | 7 3 4 | 8 4 5 | 9 5 6 | 10 6 7 | 11 7 8 | 12 8 9 | 13 9 10 | 14 10 11 | 15 11 12 | 16 12 13 | 17 13 14 | 18 14 15 | 19 15 16 | 20 16 17 | 30 151 18 | 31 152 19 | 32 153 20 | 33 154 21 | 34 155 22 | 35 156 23 | 36 22 24 | 37 23 25 | 38 24 26 | 39 25 27 | 40 26 28 | 41 27 29 | 42 28 30 | 43 29 31 | 44 30 32 | 62 33 33 | 63 34 34 | 64 35 35 | 65 36 36 | 66 37 37 | 67 38 38 | 68 39 39 | 69 40 40 | 70 41 41 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1isva1_3.aln: -------------------------------------------------------------------------------- 1 | 10 22 2 | 11 23 3 | 12 24 4 | 13 25 5 | 14 26 6 | 15 27 7 | 16 28 8 | 17 29 9 | 18 30 10 | 19 31 11 | 20 32 12 | 21 33 13 | 22 34 14 | 23 35 15 | 24 36 16 | 25 37 17 | 26 38 18 | 27 39 19 | 28 40 20 | 29 41 21 | 30 1 22 | 31 2 23 | 32 3 24 | 33 4 25 | 34 5 26 | 35 6 27 | 36 7 28 | 37 8 29 | 38 9 30 | 39 10 31 | 40 11 32 | 41 12 33 | 42 13 34 | 43 14 35 | 44 15 36 | 45 16 37 | 46 17 38 | 47 18 39 | 48 19 40 | 49 20 41 | 50 21 42 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1wba___3.aln: -------------------------------------------------------------------------------- 1 | 16 2 2 | 17 3 3 | 18 4 4 | 19 5 5 | 20 6 6 | 21 7 7 | 22 8 8 | 23 9 9 | 24 10 10 | 25 14 11 | 26 15 12 | 27 16 13 | 28 17 14 | 29 18 15 | 30 19 16 | 31 20 17 | 32 21 18 | 33 22 19 | 34 23 20 | 35 24 21 | 36 25 22 | 37 26 23 | 43 28 24 | 44 29 25 | 45 30 26 | 46 31 27 | 47 32 28 | 48 33 29 | 49 34 30 | 50 35 31 | 51 36 32 | 52 37 33 | 53 38 34 | 54 39 35 | 55 40 36 | 56 41 37 | 57 42 38 | 58 43 39 | 59 44 40 | 60 45 41 | 61 46 42 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1jdbc2d1r9ca_.aln: -------------------------------------------------------------------------------- 1 | 3 35 2 | 4 36 3 | 5 37 4 | 6 38 5 | 7 39 6 | 8 40 7 | 9 45 8 | 10 46 9 | 11 47 10 | 12 48 11 | 13 49 12 | 14 50 13 | 15 51 14 | 16 52 15 | 17 53 16 | 18 54 17 | 19 55 18 | 22 57 19 | 23 58 20 | 24 60 21 | 25 61 22 | 26 62 23 | 33 4 24 | 34 5 25 | 35 6 26 | 37 7 27 | 38 8 28 | 39 9 29 | 40 10 30 | 41 11 31 | 42 14 32 | 43 15 33 | 44 16 34 | 45 17 35 | 46 18 36 | 47 19 37 | 48 20 38 | 49 21 39 | 50 22 40 | 51 23 41 | 52 24 42 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1ogsa2d1dq3a4.aln: -------------------------------------------------------------------------------- 1 | 5 50 2 | 6 51 3 | 7 52 4 | 8 53 5 | 9 54 6 | 14 1 7 | 15 2 8 | 16 3 9 | 17 4 10 | 18 5 11 | 19 6 12 | 20 7 13 | 21 10 14 | 22 11 15 | 23 12 16 | 24 13 17 | 25 14 18 | 26 15 19 | 27 16 20 | 28 17 21 | 29 18 22 | 30 19 23 | 31 20 24 | 32 21 25 | 33 22 26 | 34 23 27 | 42 56 28 | 43 57 29 | 44 58 30 | 45 59 31 | 46 60 32 | 47 61 33 | 48 62 34 | 49 69 35 | 50 70 36 | 51 71 37 | 52 72 38 | 53 73 39 | 54 74 40 | 55 75 41 | 56 76 42 | -------------------------------------------------------------------------------- /src/distmat.c: -------------------------------------------------------------------------------- 1 | #include "mican.h" 2 | 3 | void calc_distmat(int naa, RESDAT *resdat, float **distmat){ 4 | int iaa, jaa; 5 | float dist; 6 | 7 | for(iaa=1; iaa<=naa; iaa++){ 8 | for(jaa=iaa+1; jaa<=naa; jaa++){ 9 | dist = 10 | (resdat[iaa].cacoord[1] - resdat[jaa].cacoord[1]) 11 | * (resdat[iaa].cacoord[1] - resdat[jaa].cacoord[1]) 12 | + (resdat[iaa].cacoord[2] - resdat[jaa].cacoord[2]) 13 | * (resdat[iaa].cacoord[2] - resdat[jaa].cacoord[2]) 14 | + (resdat[iaa].cacoord[3] - resdat[jaa].cacoord[3]) 15 | * (resdat[iaa].cacoord[3] - resdat[jaa].cacoord[3]); 16 | dist = sqrt(dist); 17 | distmat[iaa][jaa] = dist; 18 | distmat[jaa][iaa] = dist; 19 | } 20 | } 21 | 22 | return; 23 | } 24 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1c3ma__3.aln: -------------------------------------------------------------------------------- 1 | 5 29 2 | 6 30 3 | 7 31 4 | 8 32 5 | 9 33 6 | 10 34 7 | 11 35 8 | 12 36 9 | 13 37 10 | 14 38 11 | 15 39 12 | 16 40 13 | 17 41 14 | 18 42 15 | 19 43 16 | 20 44 17 | 21 45 18 | 22 46 19 | 23 47 20 | 24 48 21 | 25 2 22 | 26 3 23 | 27 4 24 | 28 5 25 | 29 6 26 | 30 7 27 | 31 8 28 | 32 9 29 | 33 10 30 | 34 11 31 | 35 12 32 | 36 18 33 | 37 19 34 | 38 20 35 | 39 21 36 | 40 22 37 | 41 23 38 | 42 24 39 | 43 25 40 | 44 26 41 | 45 27 42 | 46 28 43 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1vjla_.aln: -------------------------------------------------------------------------------- 1 | 2 48 2 | 3 49 3 | 4 50 4 | 5 51 5 | 6 52 6 | 7 53 7 | 8 54 8 | 9 55 9 | 10 56 10 | 11 57 11 | 12 58 12 | 16 65 13 | 17 66 14 | 18 67 15 | 19 68 16 | 20 69 17 | 21 70 18 | 22 71 19 | 23 72 20 | 24 73 21 | 25 74 22 | 26 75 23 | 29 2 24 | 30 3 25 | 31 4 26 | 32 5 27 | 33 6 28 | 34 7 29 | 35 8 30 | 36 9 31 | 37 10 32 | 38 11 33 | 39 12 34 | 40 13 35 | 41 14 36 | 42 15 37 | 43 16 38 | 44 17 39 | 45 18 40 | 46 19 41 | 47 20 42 | 48 21 43 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1ac5__d1jroa3.aln: -------------------------------------------------------------------------------- 1 | 2 1 2 | 3 2 3 | 4 3 4 | 5 4 5 | 6 5 6 | 7 6 7 | 8 7 8 | 9 8 9 | 10 9 10 | 11 10 11 | 20 15 12 | 21 16 13 | 22 17 14 | 23 18 15 | 24 19 16 | 25 20 17 | 26 21 18 | 27 22 19 | 28 23 20 | 29 24 21 | 30 25 22 | 31 35 23 | 32 36 24 | 33 37 25 | 34 38 26 | 35 39 27 | 36 40 28 | 37 41 29 | 48 87 30 | 49 88 31 | 50 89 32 | 51 90 33 | 52 91 34 | 53 92 35 | 54 93 36 | 55 94 37 | 56 95 38 | 57 96 39 | 58 97 40 | 59 98 41 | 60 99 42 | 61 100 43 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1axn__d1sf9a_.aln: -------------------------------------------------------------------------------- 1 | 1 57 2 | 2 58 3 | 3 59 4 | 4 60 5 | 5 61 6 | 6 62 7 | 7 63 8 | 8 64 9 | 9 65 10 | 10 66 11 | 11 67 12 | 12 68 13 | 13 69 14 | 14 70 15 | 15 1 16 | 16 2 17 | 17 3 18 | 18 4 19 | 19 5 20 | 20 6 21 | 21 7 22 | 22 8 23 | 23 9 24 | 24 10 25 | 25 11 26 | 26 12 27 | 27 13 28 | 28 14 29 | 29 15 30 | 35 32 31 | 36 33 32 | 37 34 33 | 38 35 34 | 39 36 35 | 40 37 36 | 41 38 37 | 42 39 38 | 43 40 39 | 44 41 40 | 45 42 41 | 46 43 42 | 47 44 43 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1chma1d1g62a_.aln: -------------------------------------------------------------------------------- 1 | 4 5 2 | 5 6 3 | 6 7 4 | 7 8 5 | 8 9 6 | 9 10 7 | 14 11 8 | 15 12 9 | 16 13 10 | 17 14 11 | 18 15 12 | 19 16 13 | 20 17 14 | 21 18 15 | 22 19 16 | 23 20 17 | 24 21 18 | 25 22 19 | 26 23 20 | 27 24 21 | 28 25 22 | 29 26 23 | 30 27 24 | 33 35 25 | 34 36 26 | 35 37 27 | 36 38 28 | 37 39 29 | 38 40 30 | 39 41 31 | 40 42 32 | 44 67 33 | 45 68 34 | 46 69 35 | 47 70 36 | 48 71 37 | 49 72 38 | 50 73 39 | 51 74 40 | 52 75 41 | 53 76 42 | 54 77 43 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1qd1b1d1n62c2.aln: -------------------------------------------------------------------------------- 1 | 7 50 2 | 8 51 3 | 9 52 4 | 10 53 5 | 11 54 6 | 12 55 7 | 22 16 8 | 23 17 9 | 24 18 10 | 25 19 11 | 26 20 12 | 27 21 13 | 28 22 14 | 29 23 15 | 30 24 16 | 31 25 17 | 32 26 18 | 33 27 19 | 34 28 20 | 40 56 21 | 41 57 22 | 42 58 23 | 43 59 24 | 44 60 25 | 45 61 26 | 55 30 27 | 56 31 28 | 57 32 29 | 58 33 30 | 59 34 31 | 60 35 32 | 61 36 33 | 62 37 34 | 63 38 35 | 91 3 36 | 92 4 37 | 93 5 38 | 94 6 39 | 95 7 40 | 96 8 41 | 97 9 42 | 98 10 43 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1vk3a3d1lbu_2.aln: -------------------------------------------------------------------------------- 1 | 4 13 2 | 5 14 3 | 6 15 4 | 7 16 5 | 8 17 6 | 9 18 7 | 10 19 8 | 11 20 9 | 12 21 10 | 13 22 11 | 23 23 12 | 24 24 13 | 25 25 14 | 26 26 15 | 27 27 16 | 28 28 17 | 29 29 18 | 30 30 19 | 31 31 20 | 32 32 21 | 33 33 22 | 34 34 23 | 35 35 24 | 36 36 25 | 37 37 26 | 38 51 27 | 39 52 28 | 40 53 29 | 41 54 30 | 42 55 31 | 55 6 32 | 56 7 33 | 57 8 34 | 58 9 35 | 59 10 36 | 60 11 37 | 61 39 38 | 62 40 39 | 63 41 40 | 64 42 41 | 65 43 42 | 66 44 43 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1exja2.aln: -------------------------------------------------------------------------------- 1 | 3 20 2 | 4 21 3 | 5 22 4 | 6 23 5 | 7 24 6 | 8 25 7 | 9 26 8 | 10 27 9 | 11 28 10 | 12 29 11 | 13 30 12 | 14 31 13 | 15 32 14 | 16 33 15 | 17 34 16 | 18 35 17 | 32 47 18 | 33 48 19 | 34 49 20 | 35 50 21 | 36 51 22 | 37 52 23 | 38 53 24 | 39 54 25 | 40 55 26 | 41 56 27 | 42 57 28 | 43 58 29 | 49 64 30 | 50 65 31 | 51 66 32 | 52 67 33 | 53 68 34 | 54 69 35 | 55 70 36 | 68 7 37 | 69 8 38 | 70 9 39 | 71 10 40 | 72 11 41 | 73 12 42 | 74 13 43 | 75 14 44 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1jsg__.aln: -------------------------------------------------------------------------------- 1 | 10 27 2 | 11 28 3 | 12 29 4 | 13 30 5 | 14 31 6 | 15 32 7 | 16 33 8 | 17 34 9 | 18 35 10 | 19 36 11 | 20 37 12 | 21 38 13 | 22 39 14 | 23 40 15 | 24 41 16 | 25 42 17 | 26 43 18 | 27 44 19 | 28 45 20 | 29 46 21 | 30 47 22 | 31 48 23 | 32 49 24 | 33 50 25 | 34 51 26 | 35 52 27 | 36 53 28 | 37 54 29 | 38 55 30 | 39 56 31 | 40 57 32 | 42 1 33 | 43 2 34 | 44 3 35 | 45 4 36 | 46 5 37 | 47 6 38 | 48 7 39 | 49 8 40 | 50 9 41 | 51 10 42 | 52 11 43 | 53 12 44 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d2g3pa1.aln: -------------------------------------------------------------------------------- 1 | 9 108 2 | 10 109 3 | 11 110 4 | 12 111 5 | 13 112 6 | 14 113 7 | 15 62 8 | 16 63 9 | 17 64 10 | 18 65 11 | 19 66 12 | 20 67 13 | 21 68 14 | 22 69 15 | 25 70 16 | 26 71 17 | 27 72 18 | 28 73 19 | 29 74 20 | 30 75 21 | 31 76 22 | 32 77 23 | 33 78 24 | 34 79 25 | 35 80 26 | 36 81 27 | 37 82 28 | 38 83 29 | 39 84 30 | 40 85 31 | 41 86 32 | 42 87 33 | 43 88 34 | 44 89 35 | 45 90 36 | 46 91 37 | 54 7 38 | 55 8 39 | 56 9 40 | 57 10 41 | 58 11 42 | 59 12 43 | 60 13 44 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1c3ma__1.aln: -------------------------------------------------------------------------------- 1 | 5 29 2 | 6 30 3 | 7 31 4 | 8 32 5 | 9 33 6 | 10 34 7 | 11 35 8 | 12 36 9 | 13 37 10 | 14 38 11 | 15 39 12 | 16 40 13 | 17 41 14 | 18 42 15 | 19 43 16 | 20 44 17 | 21 45 18 | 22 46 19 | 23 47 20 | 24 48 21 | 25 2 22 | 26 3 23 | 27 4 24 | 28 5 25 | 29 6 26 | 30 7 27 | 31 8 28 | 32 9 29 | 33 10 30 | 34 11 31 | 35 12 32 | 36 13 33 | 37 14 34 | 38 15 35 | 39 16 36 | 40 17 37 | 41 18 38 | 42 19 39 | 43 20 40 | 44 21 41 | 45 22 42 | 46 23 43 | 47 24 44 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1g61a__1.aln: -------------------------------------------------------------------------------- 1 | 1 16 2 | 2 17 3 | 3 18 4 | 4 19 5 | 5 20 6 | 6 21 7 | 7 22 8 | 8 23 9 | 9 24 10 | 10 25 11 | 11 26 12 | 12 27 13 | 13 28 14 | 14 29 15 | 15 30 16 | 16 31 17 | 17 32 18 | 18 33 19 | 19 34 20 | 20 35 21 | 21 36 22 | 22 37 23 | 23 38 24 | 24 39 25 | 25 40 26 | 26 41 27 | 27 42 28 | 28 43 29 | 29 1 30 | 30 2 31 | 31 3 32 | 32 4 33 | 33 5 34 | 34 6 35 | 35 7 36 | 36 8 37 | 37 9 38 | 38 10 39 | 39 11 40 | 40 12 41 | 41 13 42 | 42 14 43 | 43 15 44 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1fy2a_d1qmha1.aln: -------------------------------------------------------------------------------- 1 | 1 7 2 | 2 8 3 | 3 9 4 | 4 10 5 | 5 11 6 | 6 12 7 | 7 13 8 | 8 14 9 | 17 84 10 | 18 85 11 | 19 86 12 | 20 87 13 | 21 88 14 | 22 89 15 | 23 90 16 | 24 91 17 | 25 92 18 | 26 93 19 | 27 94 20 | 28 95 21 | 33 18 22 | 34 19 23 | 35 20 24 | 36 21 25 | 37 22 26 | 38 23 27 | 39 32 28 | 40 33 29 | 41 34 30 | 42 35 31 | 43 36 32 | 44 37 33 | 45 38 34 | 46 39 35 | 47 40 36 | 48 45 37 | 49 46 38 | 50 47 39 | 51 48 40 | 52 49 41 | 53 50 42 | 54 51 43 | 55 52 44 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d3pmga1d1e8ca1.aln: -------------------------------------------------------------------------------- 1 | 1 57 2 | 2 58 3 | 3 59 4 | 4 60 5 | 5 61 6 | 6 62 7 | 7 63 8 | 16 68 9 | 17 69 10 | 18 70 11 | 19 71 12 | 20 72 13 | 21 73 14 | 22 74 15 | 23 75 16 | 24 76 17 | 25 77 18 | 26 78 19 | 27 79 20 | 28 80 21 | 29 81 22 | 30 82 23 | 31 83 24 | 32 84 25 | 33 85 26 | 34 86 27 | 35 87 28 | 36 88 29 | 40 96 30 | 41 97 31 | 42 98 32 | 43 99 33 | 44 100 34 | 45 101 35 | 52 1 36 | 53 2 37 | 54 3 38 | 55 4 39 | 56 5 40 | 57 6 41 | 58 7 42 | 59 8 43 | 60 9 44 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1c3ma__2.aln: -------------------------------------------------------------------------------- 1 | 1 22 2 | 2 23 3 | 3 24 4 | 4 25 5 | 5 26 6 | 6 27 7 | 7 28 8 | 8 29 9 | 9 30 10 | 10 31 11 | 11 32 12 | 12 33 13 | 13 39 14 | 14 40 15 | 15 41 16 | 16 42 17 | 17 43 18 | 18 44 19 | 19 45 20 | 20 46 21 | 21 47 22 | 22 48 23 | 23 49 24 | 29 1 25 | 30 2 26 | 31 3 27 | 32 4 28 | 33 5 29 | 34 6 30 | 35 7 31 | 36 8 32 | 37 9 33 | 38 10 34 | 39 11 35 | 40 12 36 | 41 13 37 | 42 14 38 | 43 15 39 | 44 16 40 | 45 17 41 | 46 18 42 | 47 19 43 | 48 20 44 | 49 21 45 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1fjra_.aln: -------------------------------------------------------------------------------- 1 | 9 8 2 | 10 9 3 | 11 10 4 | 12 11 5 | 13 12 6 | 14 13 7 | 15 55 8 | 16 56 9 | 17 57 10 | 18 58 11 | 19 59 12 | 20 60 13 | 21 61 14 | 22 62 15 | 23 63 16 | 24 64 17 | 25 65 18 | 26 66 19 | 27 67 20 | 28 31 21 | 29 32 22 | 30 33 23 | 31 34 24 | 32 35 25 | 33 36 26 | 34 37 27 | 35 38 28 | 36 39 29 | 37 40 30 | 38 41 31 | 39 42 32 | 40 43 33 | 41 44 34 | 52 19 35 | 53 20 36 | 54 21 37 | 55 22 38 | 56 23 39 | 57 24 40 | 58 25 41 | 59 26 42 | 60 27 43 | 61 28 44 | 62 29 45 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1axn__d1nkta3.aln: -------------------------------------------------------------------------------- 1 | 2 49 2 | 3 50 3 | 4 51 4 | 5 52 5 | 6 53 6 | 7 54 7 | 8 55 8 | 9 56 9 | 10 57 10 | 11 58 11 | 12 59 12 | 13 60 13 | 14 61 14 | 15 62 15 | 16 63 16 | 17 64 17 | 18 65 18 | 19 66 19 | 20 67 20 | 21 68 21 | 22 69 22 | 23 70 23 | 24 71 24 | 25 72 25 | 26 73 26 | 27 74 27 | 28 75 28 | 29 76 29 | 35 8 30 | 36 9 31 | 37 10 32 | 38 11 33 | 39 12 34 | 40 13 35 | 41 14 36 | 42 15 37 | 43 16 38 | 44 17 39 | 45 18 40 | 46 19 41 | 47 20 42 | 48 21 43 | 49 22 44 | 50 23 45 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1ahja_.aln: -------------------------------------------------------------------------------- 1 | 53 61 2 | 54 62 3 | 55 63 4 | 56 64 5 | 57 65 6 | 58 66 7 | 59 67 8 | 60 68 9 | 61 69 10 | 62 70 11 | 63 71 12 | 64 72 13 | 65 73 14 | 66 74 15 | 67 75 16 | 68 76 17 | 69 77 18 | 70 78 19 | 71 79 20 | 72 80 21 | 73 81 22 | 74 82 23 | 75 83 24 | 76 84 25 | 77 85 26 | 78 86 27 | 79 87 28 | 84 4 29 | 85 5 30 | 86 6 31 | 87 7 32 | 88 8 33 | 89 9 34 | 90 10 35 | 91 11 36 | 92 12 37 | 93 13 38 | 94 14 39 | 95 15 40 | 96 16 41 | 97 17 42 | 98 18 43 | 99 19 44 | 100 20 45 | 101 21 46 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1ce8a1.aln: -------------------------------------------------------------------------------- 1 | 8 28 2 | 9 29 3 | 10 30 4 | 11 31 5 | 12 32 6 | 13 33 7 | 14 34 8 | 15 35 9 | 16 36 10 | 17 37 11 | 18 38 12 | 22 44 13 | 23 45 14 | 24 46 15 | 25 47 16 | 26 48 17 | 27 49 18 | 28 50 19 | 29 51 20 | 30 52 21 | 31 53 22 | 32 54 23 | 33 55 24 | 34 56 25 | 35 1 26 | 36 2 27 | 37 3 28 | 38 4 29 | 39 5 30 | 40 6 31 | 41 7 32 | 42 8 33 | 43 9 34 | 44 10 35 | 45 11 36 | 46 12 37 | 47 13 38 | 48 14 39 | 49 15 40 | 50 16 41 | 51 17 42 | 52 18 43 | 53 19 44 | 54 20 45 | 55 21 46 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1tocr1.aln: -------------------------------------------------------------------------------- 1 | 2 21 2 | 3 22 3 | 4 23 4 | 5 24 5 | 6 25 6 | 7 26 7 | 8 27 8 | 12 57 9 | 13 58 10 | 14 59 11 | 15 60 12 | 18 45 13 | 19 46 14 | 20 47 15 | 21 48 16 | 22 49 17 | 23 50 18 | 24 51 19 | 25 52 20 | 26 53 21 | 27 30 22 | 28 31 23 | 29 32 24 | 30 33 25 | 31 34 26 | 32 35 27 | 33 36 28 | 34 37 29 | 35 39 30 | 36 40 31 | 37 41 32 | 38 42 33 | 40 2 34 | 41 3 35 | 42 4 36 | 43 5 37 | 44 6 38 | 45 7 39 | 46 8 40 | 47 9 41 | 48 10 42 | 49 11 43 | 50 12 44 | 51 13 45 | 52 14 46 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1wba___2.aln: -------------------------------------------------------------------------------- 1 | 10 15 2 | 11 16 3 | 12 17 4 | 13 18 5 | 14 19 6 | 15 20 7 | 16 21 8 | 17 22 9 | 18 23 10 | 19 24 11 | 20 25 12 | 21 26 13 | 22 27 14 | 23 28 15 | 24 29 16 | 25 30 17 | 26 31 18 | 27 32 19 | 28 33 20 | 29 34 21 | 30 35 22 | 31 36 23 | 32 37 24 | 33 38 25 | 34 39 26 | 35 40 27 | 36 41 28 | 37 42 29 | 38 43 30 | 39 44 31 | 40 45 32 | 41 46 33 | 45 1 34 | 46 2 35 | 47 3 36 | 48 4 37 | 49 5 38 | 50 6 39 | 51 7 40 | 52 8 41 | 53 9 42 | 54 10 43 | 55 11 44 | 56 12 45 | 57 13 46 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1a05a_d1j71a_.aln: -------------------------------------------------------------------------------- 1 | 1 137 2 | 2 138 3 | 3 139 4 | 4 140 5 | 5 141 6 | 6 142 7 | 7 143 8 | 16 1 9 | 17 2 10 | 18 3 11 | 19 4 12 | 20 5 13 | 21 6 14 | 22 7 15 | 24 39 16 | 25 40 17 | 26 41 18 | 27 42 19 | 28 43 20 | 29 44 21 | 30 45 22 | 31 46 23 | 32 47 24 | 33 48 25 | 34 49 26 | 43 18 27 | 44 19 28 | 45 20 29 | 46 21 30 | 47 22 31 | 48 23 32 | 49 24 33 | 50 25 34 | 51 26 35 | 52 27 36 | 53 28 37 | 54 63 38 | 55 64 39 | 56 65 40 | 57 66 41 | 58 67 42 | 59 68 43 | 60 69 44 | 61 70 45 | 62 71 46 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1b05a_d1lc0a2.aln: -------------------------------------------------------------------------------- 1 | 5 106 2 | 6 107 3 | 7 108 4 | 8 109 5 | 9 110 6 | 10 111 7 | 11 112 8 | 12 113 9 | 21 77 10 | 22 78 11 | 23 79 12 | 24 80 13 | 25 81 14 | 26 82 15 | 27 83 16 | 28 84 17 | 29 85 18 | 30 86 19 | 31 87 20 | 35 1 21 | 36 2 22 | 37 3 23 | 38 4 24 | 39 5 25 | 40 6 26 | 41 7 27 | 42 8 28 | 43 9 29 | 44 10 30 | 45 20 31 | 46 21 32 | 47 22 33 | 48 23 34 | 49 24 35 | 50 25 36 | 51 26 37 | 52 27 38 | 56 31 39 | 57 32 40 | 58 33 41 | 59 34 42 | 60 35 43 | 61 36 44 | 62 37 45 | 63 38 46 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1lci__d1lla_1.aln: -------------------------------------------------------------------------------- 1 | 3 23 2 | 4 24 3 | 5 25 4 | 6 26 5 | 7 27 6 | 8 28 7 | 9 29 8 | 10 30 9 | 11 31 10 | 12 32 11 | 13 33 12 | 14 34 13 | 15 35 14 | 16 36 15 | 17 37 16 | 19 67 17 | 20 68 18 | 21 69 19 | 22 70 20 | 23 71 21 | 24 72 22 | 25 73 23 | 26 74 24 | 27 75 25 | 28 76 26 | 29 77 27 | 30 78 28 | 31 79 29 | 32 80 30 | 41 39 31 | 42 40 32 | 43 41 33 | 44 42 34 | 45 43 35 | 46 44 36 | 47 45 37 | 48 46 38 | 49 47 39 | 50 48 40 | 51 49 41 | 52 50 42 | 53 51 43 | 54 52 44 | 55 53 45 | 56 54 46 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1ps6a_d1f9za_.aln: -------------------------------------------------------------------------------- 1 | 3 61 2 | 4 62 3 | 5 63 4 | 6 64 5 | 7 65 6 | 8 66 7 | 9 67 8 | 10 68 9 | 11 69 10 | 15 24 11 | 16 25 12 | 17 26 13 | 18 27 14 | 19 28 15 | 20 29 16 | 21 30 17 | 22 31 18 | 23 32 19 | 24 33 20 | 25 34 21 | 26 35 22 | 27 36 23 | 30 39 24 | 31 40 25 | 32 41 26 | 33 42 27 | 34 43 28 | 35 44 29 | 36 45 30 | 37 46 31 | 38 47 32 | 39 48 33 | 40 49 34 | 41 50 35 | 42 51 36 | 43 52 37 | 46 8 38 | 47 9 39 | 48 10 40 | 49 11 41 | 50 12 42 | 51 13 43 | 52 14 44 | 53 15 45 | 54 16 46 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1jlya1_3.aln: -------------------------------------------------------------------------------- 1 | 4 13 2 | 5 14 3 | 6 15 4 | 7 16 5 | 8 17 6 | 9 18 7 | 10 19 8 | 11 20 9 | 12 21 10 | 13 22 11 | 14 23 12 | 15 24 13 | 16 25 14 | 17 26 15 | 18 27 16 | 19 28 17 | 20 29 18 | 21 30 19 | 22 31 20 | 23 32 21 | 24 33 22 | 25 34 23 | 26 35 24 | 27 36 25 | 28 37 26 | 29 38 27 | 30 39 28 | 31 40 29 | 32 41 30 | 33 42 31 | 34 43 32 | 35 44 33 | 36 45 34 | 37 46 35 | 38 47 36 | 39 2 37 | 40 3 38 | 41 4 39 | 42 5 40 | 43 6 41 | 44 7 42 | 45 8 43 | 46 9 44 | 47 10 45 | 48 11 46 | 49 12 47 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1tbrr1.aln: -------------------------------------------------------------------------------- 1 | 5 1 2 | 6 2 3 | 7 4 4 | 8 5 5 | 9 6 6 | 10 8 7 | 11 9 8 | 12 10 9 | 13 11 10 | 14 12 11 | 15 13 12 | 16 14 13 | 17 15 14 | 18 16 15 | 19 17 16 | 20 18 17 | 21 19 18 | 22 20 19 | 23 21 20 | 24 22 21 | 25 23 22 | 26 24 23 | 27 25 24 | 28 26 25 | 29 27 26 | 30 28 27 | 31 29 28 | 32 30 29 | 33 31 30 | 34 32 31 | 35 33 32 | 36 34 33 | 37 35 34 | 38 36 35 | 39 37 36 | 40 38 37 | 41 39 38 | 42 40 39 | 43 41 40 | 44 42 41 | 45 43 42 | 46 44 43 | 47 45 44 | 48 46 45 | 49 47 46 | 50 48 47 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1b05a_d1nkia_.aln: -------------------------------------------------------------------------------- 1 | 6 51 2 | 7 52 3 | 8 53 4 | 9 54 5 | 10 55 6 | 11 56 7 | 12 57 8 | 20 33 9 | 21 34 10 | 22 35 11 | 23 36 12 | 24 37 13 | 25 38 14 | 26 39 15 | 27 40 16 | 28 41 17 | 29 42 18 | 30 43 19 | 31 44 20 | 34 13 21 | 35 14 22 | 36 15 23 | 37 16 24 | 38 17 25 | 39 18 26 | 40 19 27 | 41 20 28 | 42 21 29 | 43 22 30 | 45 23 31 | 46 24 32 | 47 25 33 | 48 26 34 | 49 27 35 | 50 28 36 | 51 29 37 | 53 31 38 | 54 32 39 | 56 1 40 | 57 2 41 | 58 3 42 | 59 4 43 | 60 5 44 | 61 6 45 | 62 7 46 | 63 8 47 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1gxja_d1p5dx3.aln: -------------------------------------------------------------------------------- 1 | 6 61 2 | 7 62 3 | 8 63 4 | 9 64 5 | 10 65 6 | 11 66 7 | 12 67 8 | 13 68 9 | 14 80 10 | 15 81 11 | 16 82 12 | 17 83 13 | 18 84 14 | 19 85 15 | 20 22 16 | 21 23 17 | 22 24 18 | 23 25 19 | 24 26 20 | 25 27 21 | 26 28 22 | 27 29 23 | 28 30 24 | 29 31 25 | 30 32 26 | 31 33 27 | 32 34 28 | 33 35 29 | 34 36 30 | 35 37 31 | 37 87 32 | 38 88 33 | 39 89 34 | 40 90 35 | 41 91 36 | 42 92 37 | 43 93 38 | 44 94 39 | 45 95 40 | 46 96 41 | 47 97 42 | 48 98 43 | 50 41 44 | 51 42 45 | 52 43 46 | 53 44 47 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1miwa2d1gyfa_.aln: -------------------------------------------------------------------------------- 1 | 1 19 2 | 2 20 3 | 3 21 4 | 4 22 5 | 5 23 6 | 6 24 7 | 7 25 8 | 8 26 9 | 9 50 10 | 10 51 11 | 11 52 12 | 12 53 13 | 13 54 14 | 14 55 15 | 15 56 16 | 16 57 17 | 17 59 18 | 18 60 19 | 19 61 20 | 20 62 21 | 22 38 22 | 23 39 23 | 24 40 24 | 25 41 25 | 26 42 26 | 27 43 27 | 28 44 28 | 29 45 29 | 30 46 30 | 31 47 31 | 32 48 32 | 36 31 33 | 37 32 34 | 38 33 35 | 39 34 36 | 40 35 37 | 41 36 38 | 42 3 39 | 43 4 40 | 44 5 41 | 45 6 42 | 46 7 43 | 47 8 44 | 48 9 45 | 49 10 46 | 50 11 47 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1ciy_2_2.aln: -------------------------------------------------------------------------------- 1 | 2 1 2 | 3 2 3 | 4 3 4 | 5 4 5 | 6 5 6 | 7 6 7 | 8 7 8 | 9 8 9 | 10 9 10 | 11 10 11 | 12 11 12 | 13 12 13 | 14 13 14 | 15 14 15 | 16 25 16 | 17 26 17 | 18 27 18 | 19 28 19 | 20 29 20 | 21 30 21 | 22 31 22 | 23 32 23 | 24 33 24 | 25 34 25 | 26 35 26 | 27 36 27 | 28 37 28 | 29 38 29 | 32 39 30 | 33 40 31 | 34 41 32 | 35 42 33 | 36 43 34 | 37 44 35 | 38 45 36 | 39 46 37 | 41 47 38 | 42 48 39 | 43 49 40 | 44 50 41 | 45 51 42 | 46 52 43 | 51 53 44 | 52 54 45 | 53 55 46 | 54 56 47 | 55 57 48 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1f34b_.aln: -------------------------------------------------------------------------------- 1 | 12 21 2 | 13 22 3 | 14 23 4 | 15 24 5 | 16 25 6 | 17 26 7 | 18 27 8 | 19 28 9 | 20 29 10 | 21 30 11 | 22 31 12 | 23 32 13 | 24 33 14 | 25 34 15 | 26 35 16 | 27 36 17 | 28 37 18 | 29 38 19 | 30 39 20 | 31 40 21 | 32 41 22 | 33 42 23 | 34 43 24 | 35 44 25 | 36 45 26 | 37 46 27 | 38 47 28 | 39 48 29 | 40 49 30 | 41 50 31 | 42 51 32 | 43 52 33 | 44 53 34 | 45 54 35 | 46 55 36 | 47 56 37 | 48 57 38 | 49 58 39 | 50 59 40 | 61 10 41 | 62 11 42 | 63 12 43 | 64 13 44 | 65 14 45 | 66 15 46 | 67 16 47 | 68 17 48 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1nol_2.aln: -------------------------------------------------------------------------------- 1 | 1 45 2 | 2 46 3 | 3 47 4 | 4 48 5 | 5 49 6 | 6 50 7 | 7 51 8 | 8 52 9 | 9 53 10 | 10 54 11 | 11 55 12 | 12 56 13 | 13 57 14 | 18 72 15 | 19 73 16 | 20 74 17 | 21 75 18 | 22 76 19 | 23 77 20 | 24 78 21 | 25 79 22 | 26 80 23 | 27 81 24 | 28 82 25 | 44 107 26 | 45 108 27 | 46 109 28 | 47 110 29 | 48 111 30 | 49 112 31 | 50 113 32 | 51 114 33 | 52 115 34 | 53 116 35 | 54 117 36 | 55 118 37 | 56 119 38 | 57 120 39 | 58 121 40 | 59 122 41 | 60 123 42 | 61 124 43 | 62 125 44 | 63 126 45 | 64 127 46 | 65 128 47 | 66 129 48 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1dzta_d1kpf__.aln: -------------------------------------------------------------------------------- 1 | 1 86 2 | 2 87 3 | 3 88 4 | 4 89 5 | 5 90 6 | 6 91 7 | 7 92 8 | 8 93 9 | 11 99 10 | 12 100 11 | 13 101 12 | 14 102 13 | 15 103 14 | 16 104 15 | 17 105 16 | 18 106 17 | 19 107 18 | 32 31 19 | 33 32 20 | 34 33 21 | 35 34 22 | 36 35 23 | 37 36 24 | 38 37 25 | 39 38 26 | 40 39 27 | 41 40 28 | 50 3 29 | 51 4 30 | 52 5 31 | 53 6 32 | 54 7 33 | 55 8 34 | 56 9 35 | 57 10 36 | 58 11 37 | 59 12 38 | 60 47 39 | 61 48 40 | 62 49 41 | 63 50 42 | 64 51 43 | 65 52 44 | 66 53 45 | 67 54 46 | 68 55 47 | 69 56 48 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1ogqa_d1fjgc1.aln: -------------------------------------------------------------------------------- 1 | 4 86 2 | 5 87 3 | 6 88 4 | 7 89 5 | 8 90 6 | 9 91 7 | 10 92 8 | 11 93 9 | 12 94 10 | 13 95 11 | 14 96 12 | 15 97 13 | 16 98 14 | 17 99 15 | 18 100 16 | 19 101 17 | 40 4 18 | 41 5 19 | 42 6 20 | 43 7 21 | 44 8 22 | 50 10 23 | 51 11 24 | 52 12 25 | 54 13 26 | 55 14 27 | 56 15 28 | 57 16 29 | 58 17 30 | 59 18 31 | 69 37 32 | 70 38 33 | 71 39 34 | 72 40 35 | 73 41 36 | 74 42 37 | 75 43 38 | 76 44 39 | 77 45 40 | 78 46 41 | 79 47 42 | 80 48 43 | 81 49 44 | 82 50 45 | 83 51 46 | 84 52 47 | 85 53 48 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1qd1b1d1itwa_.aln: -------------------------------------------------------------------------------- 1 | 7 178 2 | 8 179 3 | 9 180 4 | 10 181 5 | 11 182 6 | 19 140 7 | 20 141 8 | 21 142 9 | 22 143 10 | 23 144 11 | 24 145 12 | 25 146 13 | 26 147 14 | 27 148 15 | 28 149 16 | 29 150 17 | 30 151 18 | 31 152 19 | 32 153 20 | 33 154 21 | 34 155 22 | 35 156 23 | 36 157 24 | 37 158 25 | 38 159 26 | 39 160 27 | 40 161 28 | 41 162 29 | 42 163 30 | 43 164 31 | 44 165 32 | 45 166 33 | 55 93 34 | 56 94 35 | 57 95 36 | 58 96 37 | 59 97 38 | 60 98 39 | 61 99 40 | 90 207 41 | 91 208 42 | 92 209 43 | 93 210 44 | 94 211 45 | 95 212 46 | 96 213 47 | 97 214 48 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1d5ya1.aln: -------------------------------------------------------------------------------- 1 | 3 14 2 | 4 15 3 | 5 16 4 | 6 17 5 | 7 18 6 | 8 19 7 | 9 20 8 | 10 21 9 | 11 22 10 | 12 23 11 | 13 24 12 | 14 25 13 | 15 26 14 | 20 1 15 | 21 2 16 | 22 3 17 | 23 4 18 | 24 5 19 | 25 6 20 | 26 7 21 | 27 8 22 | 28 10 23 | 29 11 24 | 30 12 25 | 31 13 26 | 32 28 27 | 33 29 28 | 34 30 29 | 35 31 30 | 36 32 31 | 37 33 32 | 38 34 33 | 39 35 34 | 40 36 35 | 41 37 36 | 42 38 37 | 43 39 38 | 44 40 39 | 45 41 40 | 46 42 41 | 47 43 42 | 48 44 43 | 49 45 44 | 50 46 45 | 51 47 46 | 52 48 47 | 53 49 48 | 54 50 49 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1n0fg_.aln: -------------------------------------------------------------------------------- 1 | 10 14 2 | 11 15 3 | 12 16 4 | 13 17 5 | 14 18 6 | 15 19 7 | 16 20 8 | 17 21 9 | 18 22 10 | 19 23 11 | 20 24 12 | 21 25 13 | 22 26 14 | 23 27 15 | 24 28 16 | 25 29 17 | 26 30 18 | 27 31 19 | 28 32 20 | 29 2 21 | 30 3 22 | 31 4 23 | 32 5 24 | 33 6 25 | 34 7 26 | 35 8 27 | 36 9 28 | 37 10 29 | 38 11 30 | 39 12 31 | 40 13 32 | 42 34 33 | 43 35 34 | 44 36 35 | 45 37 36 | 46 38 37 | 47 39 38 | 48 40 39 | 49 41 40 | 50 42 41 | 51 43 42 | 52 44 43 | 53 45 44 | 54 46 45 | 55 47 46 | 56 48 47 | 57 49 48 | 58 50 49 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1pg6a_.aln: -------------------------------------------------------------------------------- 1 | 12 37 2 | 13 38 3 | 14 39 4 | 15 40 5 | 16 41 6 | 17 42 7 | 18 43 8 | 19 44 9 | 20 45 10 | 22 1 11 | 23 2 12 | 24 3 13 | 25 4 14 | 26 5 15 | 27 6 16 | 28 7 17 | 29 8 18 | 30 9 19 | 31 10 20 | 32 11 21 | 33 12 22 | 34 13 23 | 35 14 24 | 36 15 25 | 37 16 26 | 38 17 27 | 39 18 28 | 40 19 29 | 41 20 30 | 42 21 31 | 43 22 32 | 44 23 33 | 66 51 34 | 67 52 35 | 68 53 36 | 69 54 37 | 70 55 38 | 71 56 39 | 72 57 40 | 75 27 41 | 76 28 42 | 77 29 43 | 78 30 44 | 79 31 45 | 80 32 46 | 81 33 47 | 82 34 48 | 83 35 49 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1skz_1.aln: -------------------------------------------------------------------------------- 1 | 1 27 2 | 2 28 3 | 3 29 4 | 4 30 5 | 5 31 6 | 6 32 7 | 7 33 8 | 8 34 9 | 9 35 10 | 10 36 11 | 11 37 12 | 12 38 13 | 13 39 14 | 14 40 15 | 15 41 16 | 16 42 17 | 17 43 18 | 18 44 19 | 19 45 20 | 20 46 21 | 21 47 22 | 22 48 23 | 23 49 24 | 25 2 25 | 26 3 26 | 27 4 27 | 28 5 28 | 29 6 29 | 30 7 30 | 31 8 31 | 32 9 32 | 33 10 33 | 34 11 34 | 35 12 35 | 36 13 36 | 37 14 37 | 38 15 38 | 39 16 39 | 40 17 40 | 41 18 41 | 42 19 42 | 43 20 43 | 44 21 44 | 45 22 45 | 46 23 46 | 47 24 47 | 48 25 48 | 49 26 49 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1b0pa2d1k0da2.aln: -------------------------------------------------------------------------------- 1 | 1 83 2 | 2 84 3 | 3 85 4 | 4 86 5 | 5 87 6 | 6 88 7 | 7 89 8 | 8 90 9 | 9 91 10 | 10 92 11 | 13 42 12 | 14 43 13 | 15 44 14 | 16 45 15 | 17 46 16 | 18 47 17 | 19 48 18 | 20 49 19 | 21 50 20 | 22 51 21 | 23 52 22 | 24 53 23 | 25 54 24 | 26 55 25 | 27 56 26 | 28 57 27 | 29 58 28 | 30 59 29 | 31 60 30 | 32 61 31 | 33 62 32 | 34 63 33 | 35 64 34 | 36 65 35 | 49 33 36 | 50 34 37 | 51 35 38 | 52 36 39 | 53 37 40 | 54 38 41 | 55 39 42 | 56 40 43 | 57 41 44 | 63 2 45 | 64 3 46 | 65 4 47 | 66 5 48 | 67 6 49 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1h0hb_d1hz6b_.aln: -------------------------------------------------------------------------------- 1 | 1 54 2 | 2 55 3 | 3 56 4 | 4 57 5 | 5 58 6 | 6 59 7 | 7 60 8 | 8 61 9 | 9 62 10 | 18 5 11 | 19 6 12 | 20 7 13 | 21 8 14 | 22 9 15 | 23 12 16 | 24 13 17 | 25 14 18 | 26 15 19 | 27 16 20 | 28 17 21 | 29 18 22 | 30 19 23 | 31 20 24 | 32 21 25 | 33 22 26 | 34 23 27 | 35 24 28 | 36 25 29 | 37 26 30 | 38 27 31 | 39 28 32 | 40 29 33 | 41 30 34 | 42 31 35 | 43 32 36 | 45 34 37 | 46 35 38 | 47 36 39 | 48 37 40 | 49 38 41 | 53 42 42 | 54 43 43 | 55 44 44 | 56 45 45 | 57 46 46 | 58 47 47 | 59 48 48 | 60 49 49 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1ihoa_d1ep7a_.aln: -------------------------------------------------------------------------------- 1 | 2 34 2 | 3 35 3 | 4 36 4 | 5 37 5 | 6 38 6 | 7 41 7 | 8 42 8 | 9 43 9 | 10 44 10 | 11 45 11 | 12 46 12 | 13 47 13 | 14 48 14 | 15 49 15 | 16 50 16 | 17 51 17 | 18 52 18 | 19 53 19 | 20 54 20 | 21 55 21 | 25 23 22 | 26 24 23 | 27 25 24 | 28 26 25 | 29 27 26 | 30 28 27 | 31 29 28 | 32 30 29 | 36 9 30 | 37 10 31 | 38 11 32 | 39 12 33 | 40 13 34 | 41 14 35 | 42 15 36 | 43 16 37 | 44 17 38 | 45 18 39 | 46 19 40 | 47 20 41 | 48 21 42 | 51 58 43 | 52 59 44 | 53 60 45 | 54 61 46 | 55 62 47 | 56 63 48 | 57 64 49 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1qh4a2d1ekga_.aln: -------------------------------------------------------------------------------- 1 | 11 85 2 | 12 86 3 | 13 87 4 | 14 88 5 | 15 89 6 | 16 90 7 | 17 91 8 | 18 92 9 | 19 93 10 | 20 94 11 | 21 95 12 | 22 96 13 | 23 97 14 | 24 98 15 | 25 99 16 | 26 100 17 | 27 101 18 | 28 102 19 | 29 103 20 | 30 104 21 | 35 113 22 | 36 114 23 | 37 115 24 | 38 116 25 | 39 117 26 | 40 118 27 | 41 119 28 | 51 1 29 | 52 2 30 | 53 3 31 | 54 4 32 | 55 5 33 | 56 6 34 | 57 7 35 | 58 8 36 | 59 9 37 | 60 10 38 | 61 11 39 | 62 12 40 | 63 13 41 | 64 14 42 | 65 15 43 | 66 16 44 | 67 17 45 | 72 27 46 | 73 28 47 | 74 29 48 | 75 30 49 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d2onea1d1hz6b_.aln: -------------------------------------------------------------------------------- 1 | 4 1 2 | 5 2 3 | 6 3 4 | 7 4 5 | 8 5 6 | 9 6 7 | 10 7 8 | 11 8 9 | 12 9 10 | 27 57 11 | 28 58 12 | 29 59 13 | 30 60 14 | 31 61 15 | 32 62 16 | 33 63 17 | 36 13 18 | 37 14 19 | 38 15 20 | 39 16 21 | 40 17 22 | 41 18 23 | 42 19 24 | 43 20 25 | 44 21 26 | 45 22 27 | 46 23 28 | 47 24 29 | 48 25 30 | 49 26 31 | 50 27 32 | 51 28 33 | 52 29 34 | 53 30 35 | 54 31 36 | 55 32 37 | 56 33 38 | 65 34 39 | 66 35 40 | 67 36 41 | 68 37 42 | 69 38 43 | 70 48 44 | 71 49 45 | 72 50 46 | 73 51 47 | 74 52 48 | 75 53 49 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1wba___1.aln: -------------------------------------------------------------------------------- 1 | 10 4 2 | 11 5 3 | 12 6 4 | 13 7 5 | 14 8 6 | 15 9 7 | 16 10 8 | 17 11 9 | 18 12 10 | 19 13 11 | 20 14 12 | 21 15 13 | 22 16 14 | 23 17 15 | 24 18 16 | 25 22 17 | 26 23 18 | 27 24 19 | 28 25 20 | 29 26 21 | 30 27 22 | 31 28 23 | 32 29 24 | 33 30 25 | 34 31 26 | 35 32 27 | 36 33 28 | 37 34 29 | 38 35 30 | 43 53 31 | 44 54 32 | 45 55 33 | 46 56 34 | 47 57 35 | 48 58 36 | 49 59 37 | 50 38 38 | 51 39 39 | 52 40 40 | 53 41 41 | 54 42 42 | 55 43 43 | 56 44 44 | 57 45 45 | 58 46 46 | 59 47 47 | 60 48 48 | 61 49 49 | 62 50 50 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d2pspa1.aln: -------------------------------------------------------------------------------- 1 | 4 37 2 | 5 38 3 | 6 39 4 | 7 40 5 | 8 41 6 | 10 42 7 | 11 43 8 | 12 44 9 | 13 45 10 | 14 46 11 | 15 47 12 | 16 48 13 | 17 49 14 | 18 50 15 | 19 51 16 | 20 52 17 | 21 1 18 | 22 2 19 | 23 3 20 | 24 4 21 | 25 5 22 | 26 6 23 | 27 7 24 | 28 8 25 | 29 9 26 | 30 10 27 | 31 11 28 | 32 12 29 | 33 13 30 | 34 14 31 | 35 15 32 | 36 16 33 | 37 17 34 | 38 18 35 | 39 19 36 | 40 20 37 | 41 21 38 | 42 22 39 | 43 23 40 | 44 24 41 | 45 25 42 | 46 26 43 | 47 27 44 | 48 28 45 | 49 29 46 | 50 30 47 | 51 31 48 | 52 32 49 | 53 33 50 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1g99a1d1gqyb3.aln: -------------------------------------------------------------------------------- 1 | 14 69 2 | 15 70 3 | 16 71 4 | 17 72 5 | 18 73 6 | 19 74 7 | 20 75 8 | 21 77 9 | 22 78 10 | 24 1 11 | 25 2 12 | 26 3 13 | 27 4 14 | 28 5 15 | 29 6 16 | 30 7 17 | 31 8 18 | 32 9 19 | 33 10 20 | 34 11 21 | 35 12 22 | 36 13 23 | 37 14 24 | 38 15 25 | 39 16 26 | 40 17 27 | 41 18 28 | 42 19 29 | 43 20 30 | 44 21 31 | 45 22 32 | 46 23 33 | 47 24 34 | 48 25 35 | 49 26 36 | 50 27 37 | 51 28 38 | 52 29 39 | 53 30 40 | 54 31 41 | 55 32 42 | 56 33 43 | 57 34 44 | 58 35 45 | 59 36 46 | 60 37 47 | 61 38 48 | 62 39 49 | 63 40 50 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1mw5a_d1bco_1.aln: -------------------------------------------------------------------------------- 1 | 1 74 2 | 2 75 3 | 3 76 4 | 4 77 5 | 5 78 6 | 6 79 7 | 7 80 8 | 11 1 9 | 12 2 10 | 13 3 11 | 14 4 12 | 15 5 13 | 16 6 14 | 17 7 15 | 18 8 16 | 21 48 17 | 22 49 18 | 23 50 19 | 24 51 20 | 25 52 21 | 26 53 22 | 27 54 23 | 28 55 24 | 29 56 25 | 30 57 26 | 34 24 27 | 35 25 28 | 36 26 29 | 37 27 30 | 38 28 31 | 39 29 32 | 40 30 33 | 45 37 34 | 46 38 35 | 47 39 36 | 48 40 37 | 49 41 38 | 50 42 39 | 51 43 40 | 52 44 41 | 53 45 42 | 56 13 43 | 57 14 44 | 58 15 45 | 59 16 46 | 60 17 47 | 61 18 48 | 62 19 49 | 63 20 50 | -------------------------------------------------------------------------------- /src/make_pdbdat.c: -------------------------------------------------------------------------------- 1 | #include "mican.h" 2 | 3 | void make_pdbdat(int naa, RESDAT *resdat, PDBDAT *pdbdat) { 4 | 5 | int iaa; 6 | int nchain; 7 | 8 | /* get chainID_org */ 9 | /* get naa */ 10 | nchain = 0; 11 | for (iaa = 1; iaa <= naa; iaa++) { 12 | if (nchain < resdat[iaa].chainID) { 13 | nchain = resdat[iaa].chainID; 14 | strcpy(pdbdat->chainID_org[nchain], resdat[iaa].chainID_org); 15 | pdbdat->chainID[nchain] = nchain; 16 | pdbdat->naa[nchain] = 0; 17 | } 18 | pdbdat->naa[nchain]++; 19 | } 20 | 21 | return; 22 | } 23 | 24 | int count_chain(int naa, RESDAT *resdat) { 25 | 26 | int iaa; 27 | int nchain; 28 | 29 | nchain = 0; 30 | for (iaa = 1; iaa <= naa; iaa++) { 31 | if (nchain < resdat[iaa].chainID) { 32 | nchain = resdat[iaa].chainID; 33 | } 34 | } 35 | return (nchain); 36 | } 37 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1n2ma_.aln: -------------------------------------------------------------------------------- 1 | 12 23 2 | 13 24 3 | 14 25 4 | 15 26 5 | 16 27 6 | 17 28 7 | 18 29 8 | 19 30 9 | 20 31 10 | 21 32 11 | 22 33 12 | 23 2 13 | 24 3 14 | 25 4 15 | 26 5 16 | 27 6 17 | 28 7 18 | 29 8 19 | 30 9 20 | 31 10 21 | 32 11 22 | 33 12 23 | 34 13 24 | 35 14 25 | 36 15 26 | 66 35 27 | 67 36 28 | 68 37 29 | 69 38 30 | 70 40 31 | 71 41 32 | 72 42 33 | 73 43 34 | 74 44 35 | 75 45 36 | 76 46 37 | 77 47 38 | 78 48 39 | 79 56 40 | 80 57 41 | 81 58 42 | 82 59 43 | 83 60 44 | 84 61 45 | 85 62 46 | 86 63 47 | 87 64 48 | 88 65 49 | 89 66 50 | 90 67 51 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d3ezma_.aln: -------------------------------------------------------------------------------- 1 | 1 37 2 | 2 38 3 | 3 39 4 | 4 40 5 | 5 41 6 | 6 42 7 | 7 43 8 | 8 44 9 | 9 45 10 | 10 46 11 | 11 47 12 | 12 48 13 | 13 49 14 | 14 50 15 | 15 51 16 | 16 2 17 | 17 3 18 | 18 4 19 | 19 5 20 | 20 6 21 | 21 7 22 | 22 8 23 | 23 9 24 | 24 10 25 | 25 11 26 | 26 12 27 | 27 13 28 | 28 14 29 | 29 15 30 | 30 16 31 | 31 17 32 | 32 18 33 | 33 19 34 | 34 20 35 | 35 21 36 | 36 22 37 | 37 23 38 | 38 24 39 | 39 25 40 | 40 26 41 | 41 27 42 | 42 28 43 | 43 29 44 | 44 30 45 | 45 31 46 | 46 32 47 | 47 33 48 | 48 34 49 | 49 35 50 | 50 36 51 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1is8a_d1umwa1.aln: -------------------------------------------------------------------------------- 1 | 3 25 2 | 4 26 3 | 5 27 4 | 6 28 5 | 7 29 6 | 8 30 7 | 9 31 8 | 10 32 9 | 12 33 10 | 13 34 11 | 27 35 12 | 28 36 13 | 29 37 14 | 30 38 15 | 31 39 16 | 32 40 17 | 33 41 18 | 34 42 19 | 35 43 20 | 36 44 21 | 40 87 22 | 41 88 23 | 42 89 24 | 43 90 25 | 44 91 26 | 45 92 27 | 46 93 28 | 47 94 29 | 56 2 30 | 57 3 31 | 58 4 32 | 59 5 33 | 60 6 34 | 61 7 35 | 62 8 36 | 63 9 37 | 68 58 38 | 69 59 39 | 70 60 40 | 71 61 41 | 72 62 42 | 73 63 43 | 74 64 44 | 75 65 45 | 76 66 46 | 77 67 47 | 78 68 48 | 79 69 49 | 80 70 50 | 81 71 51 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1nkta3d1ldja1.aln: -------------------------------------------------------------------------------- 1 | 1 18 2 | 2 19 3 | 3 20 4 | 4 21 5 | 5 22 6 | 6 23 7 | 7 24 8 | 8 25 9 | 9 26 10 | 10 27 11 | 11 28 12 | 12 29 13 | 13 30 14 | 14 31 15 | 15 32 16 | 16 33 17 | 17 34 18 | 24 76 19 | 25 77 20 | 26 78 21 | 27 79 22 | 28 80 23 | 29 81 24 | 30 82 25 | 31 83 26 | 32 84 27 | 33 85 28 | 34 86 29 | 35 87 30 | 36 88 31 | 37 89 32 | 38 90 33 | 41 39 34 | 42 40 35 | 43 41 36 | 44 42 37 | 45 43 38 | 46 44 39 | 47 45 40 | 48 46 41 | 49 47 42 | 50 48 43 | 51 49 44 | 52 50 45 | 53 51 46 | 54 52 47 | 55 53 48 | 56 54 49 | 57 55 50 | 58 56 51 | -------------------------------------------------------------------------------- /.github/workflows/build_and_test.yml: -------------------------------------------------------------------------------- 1 | name: Action Sample 2 | 3 | on: 4 | push: 5 | branches: 6 | - master 7 | - working 8 | release: 9 | types: [released] 10 | workflow_dispatch: 11 | 12 | jobs: 13 | build_and_test: 14 | runs-on: ubuntu-latest 15 | steps: 16 | - name: Checking out code from repository 17 | uses: actions/checkout@v2 18 | 19 | - name: Setting up Python 3.8 20 | uses: actions/setup-python@v2 21 | with: 22 | python-version: 3.8 23 | 24 | - name: Install dependencies 25 | run: | 26 | python -m pip install --upgrade pip 27 | pip install -r requirements.txt 28 | pip install tqdm 29 | 30 | - name: Install pymican 31 | run: python setup.py install 32 | 33 | - name: Test 34 | run: python tests/test_malisam.py 35 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1b3qa2.aln: -------------------------------------------------------------------------------- 1 | 3 23 2 | 4 24 3 | 5 25 4 | 6 26 5 | 7 27 6 | 8 28 7 | 9 29 8 | 10 30 9 | 11 31 10 | 12 32 11 | 13 33 12 | 14 34 13 | 15 35 14 | 16 36 15 | 17 37 16 | 18 38 17 | 19 39 18 | 20 40 19 | 21 41 20 | 22 42 21 | 23 43 22 | 24 44 23 | 25 45 24 | 26 46 25 | 27 47 26 | 28 48 27 | 29 49 28 | 30 50 29 | 34 62 30 | 35 63 31 | 36 64 32 | 37 65 33 | 42 56 34 | 43 57 35 | 44 58 36 | 45 59 37 | 46 60 38 | 47 1 39 | 48 2 40 | 49 3 41 | 50 4 42 | 51 5 43 | 52 6 44 | 53 7 45 | 54 8 46 | 55 9 47 | 56 10 48 | 57 11 49 | 58 12 50 | 59 13 51 | 60 14 52 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1cpo_1.aln: -------------------------------------------------------------------------------- 1 | 4 4 2 | 5 5 3 | 6 6 4 | 7 7 5 | 8 8 6 | 9 9 7 | 10 10 8 | 11 11 9 | 12 12 10 | 21 68 11 | 22 69 12 | 23 70 13 | 24 71 14 | 25 72 15 | 26 73 16 | 27 74 17 | 28 75 18 | 29 76 19 | 30 77 20 | 31 78 21 | 32 79 22 | 33 80 23 | 35 81 24 | 36 82 25 | 37 83 26 | 39 20 27 | 40 21 28 | 41 22 29 | 42 23 30 | 43 24 31 | 44 25 32 | 45 26 33 | 46 27 34 | 47 28 35 | 48 29 36 | 49 30 37 | 50 31 38 | 51 32 39 | 52 33 40 | 53 34 41 | 54 35 42 | 64 47 43 | 65 48 44 | 66 49 45 | 67 50 46 | 69 51 47 | 70 52 48 | 71 53 49 | 72 54 50 | 73 55 51 | 74 56 52 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1vmoa__3.aln: -------------------------------------------------------------------------------- 1 | 5 1 2 | 6 2 3 | 7 3 4 | 8 4 5 | 9 5 6 | 10 6 7 | 11 7 8 | 13 8 9 | 14 9 10 | 15 10 11 | 16 11 12 | 17 12 13 | 18 13 14 | 19 14 15 | 20 15 16 | 21 16 17 | 22 17 18 | 23 18 19 | 24 19 20 | 25 20 21 | 26 21 22 | 27 22 23 | 29 24 24 | 30 25 25 | 31 26 26 | 32 27 27 | 33 28 28 | 34 29 29 | 35 30 30 | 36 31 31 | 37 32 32 | 38 33 33 | 39 34 34 | 40 35 35 | 41 36 36 | 42 37 37 | 43 38 38 | 44 39 39 | 45 40 40 | 46 41 41 | 47 42 42 | 48 43 43 | 49 44 44 | 50 45 45 | 51 46 46 | 52 47 47 | 53 48 48 | 54 49 49 | 55 50 50 | 56 51 51 | 57 52 52 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d4proc1.aln: -------------------------------------------------------------------------------- 1 | 20 1 2 | 21 2 3 | 22 3 4 | 23 4 5 | 24 5 6 | 25 6 7 | 26 7 8 | 27 8 9 | 28 9 10 | 29 10 11 | 30 11 12 | 31 12 13 | 32 13 14 | 33 14 15 | 34 15 16 | 35 16 17 | 36 17 18 | 37 18 19 | 40 20 20 | 41 21 21 | 42 22 22 | 43 23 23 | 44 24 24 | 45 25 25 | 46 26 26 | 47 27 27 | 48 28 28 | 49 29 29 | 50 30 30 | 51 31 31 | 55 32 32 | 56 33 33 | 57 34 34 | 58 35 35 | 59 36 36 | 60 37 37 | 61 38 38 | 62 39 39 | 63 40 40 | 64 41 41 | 71 58 42 | 72 59 43 | 73 60 44 | 74 61 45 | 75 62 46 | 76 63 47 | 77 64 48 | 78 65 49 | 79 66 50 | 80 67 51 | 81 68 52 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1dmza_d1hdha_.aln: -------------------------------------------------------------------------------- 1 | 4 21 2 | 5 22 3 | 6 23 4 | 7 24 5 | 8 25 6 | 9 26 7 | 10 27 8 | 12 56 9 | 13 57 10 | 14 58 11 | 18 41 12 | 19 42 13 | 20 43 14 | 21 44 15 | 22 45 16 | 23 46 17 | 43 47 18 | 44 48 19 | 45 49 20 | 46 50 21 | 47 51 22 | 48 52 23 | 49 53 24 | 50 54 25 | 51 33 26 | 52 34 27 | 53 35 28 | 54 36 29 | 55 37 30 | 56 38 31 | 57 39 32 | 58 40 33 | 65 3 34 | 66 4 35 | 67 5 36 | 68 6 37 | 69 7 38 | 70 8 39 | 71 9 40 | 72 10 41 | 74 64 42 | 75 65 43 | 76 66 44 | 77 67 45 | 78 68 46 | 79 69 47 | 80 70 48 | 81 71 49 | 82 72 50 | 83 73 51 | 84 74 52 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1l6ra_d1nrva_.aln: -------------------------------------------------------------------------------- 1 | 5 40 2 | 6 41 3 | 7 42 4 | 8 43 5 | 9 84 6 | 10 85 7 | 11 86 8 | 12 87 9 | 13 88 10 | 14 89 11 | 15 90 12 | 16 91 13 | 17 92 14 | 18 93 15 | 19 94 16 | 20 95 17 | 21 96 18 | 22 97 19 | 23 98 20 | 25 26 21 | 26 27 22 | 27 28 23 | 28 29 24 | 29 30 25 | 30 31 26 | 33 6 27 | 34 7 28 | 35 8 29 | 36 9 30 | 37 10 31 | 38 11 32 | 39 15 33 | 40 16 34 | 41 17 35 | 42 18 36 | 43 19 37 | 44 20 38 | 45 21 39 | 46 22 40 | 50 58 41 | 51 59 42 | 52 60 43 | 53 61 44 | 54 62 45 | 55 63 46 | 56 64 47 | 57 65 48 | 58 66 49 | 59 67 50 | 60 68 51 | 61 69 52 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1pqsa_d1i7la2.aln: -------------------------------------------------------------------------------- 1 | 1 14 2 | 2 15 3 | 3 16 4 | 4 17 5 | 5 18 6 | 6 19 7 | 7 21 8 | 8 22 9 | 9 23 10 | 35 29 11 | 36 30 12 | 37 31 13 | 38 32 14 | 39 33 15 | 40 34 16 | 41 35 17 | 42 36 18 | 43 37 19 | 44 38 20 | 45 39 21 | 46 40 22 | 47 45 23 | 48 46 24 | 49 47 25 | 50 48 26 | 51 49 27 | 52 50 28 | 53 51 29 | 54 52 30 | 55 53 31 | 56 54 32 | 57 55 33 | 58 56 34 | 59 57 35 | 60 58 36 | 61 59 37 | 62 60 38 | 63 61 39 | 64 62 40 | 65 63 41 | 66 64 42 | 67 65 43 | 68 66 44 | 69 67 45 | 71 1 46 | 72 2 47 | 73 3 48 | 74 4 49 | 75 5 50 | 76 6 51 | 77 7 52 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1foka1_2.aln: -------------------------------------------------------------------------------- 1 | 16 41 2 | 17 42 3 | 18 43 4 | 19 44 5 | 20 45 6 | 21 46 7 | 22 47 8 | 23 48 9 | 24 49 10 | 25 50 11 | 26 51 12 | 27 52 13 | 30 2 14 | 31 3 15 | 32 4 16 | 33 5 17 | 34 6 18 | 35 7 19 | 36 8 20 | 37 9 21 | 38 10 22 | 39 11 23 | 40 12 24 | 41 13 25 | 80 84 26 | 81 85 27 | 82 86 28 | 83 87 29 | 84 88 30 | 85 89 31 | 86 90 32 | 87 91 33 | 88 92 34 | 89 93 35 | 90 94 36 | 91 95 37 | 92 96 38 | 93 97 39 | 94 98 40 | 95 99 41 | 96 100 42 | 97 79 43 | 98 80 44 | 99 81 45 | 100 82 46 | 101 83 47 | 117 54 48 | 118 55 49 | 119 56 50 | 120 57 51 | 121 58 52 | 122 59 53 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1g1ba_.aln: -------------------------------------------------------------------------------- 1 | 22 2 2 | 23 3 3 | 24 4 4 | 25 5 5 | 26 6 6 | 27 7 7 | 28 8 8 | 29 9 9 | 30 10 10 | 31 11 11 | 32 12 12 | 42 22 13 | 43 23 14 | 44 24 15 | 45 25 16 | 46 26 17 | 47 27 18 | 48 29 19 | 49 30 20 | 51 31 21 | 52 32 22 | 53 33 23 | 54 34 24 | 55 35 25 | 56 36 26 | 72 37 27 | 73 38 28 | 74 39 29 | 75 40 30 | 76 41 31 | 77 42 32 | 78 43 33 | 79 44 34 | 80 45 35 | 81 46 36 | 82 47 37 | 83 48 38 | 84 49 39 | 85 50 40 | 86 51 41 | 88 52 42 | 89 53 43 | 90 54 44 | 91 55 45 | 92 56 46 | 93 57 47 | 94 58 48 | 95 59 49 | 96 60 50 | 97 61 51 | 98 62 52 | 99 63 53 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1vmoa__1.aln: -------------------------------------------------------------------------------- 1 | 5 31 2 | 6 32 3 | 7 33 4 | 8 34 5 | 9 35 6 | 10 36 7 | 11 37 8 | 13 38 9 | 14 39 10 | 15 40 11 | 16 41 12 | 17 42 13 | 18 43 14 | 19 44 15 | 20 45 16 | 21 46 17 | 22 47 18 | 23 48 19 | 24 49 20 | 25 50 21 | 26 51 22 | 27 52 23 | 28 53 24 | 29 2 25 | 30 3 26 | 31 4 27 | 32 5 28 | 33 6 29 | 34 7 30 | 35 8 31 | 36 9 32 | 37 10 33 | 38 11 34 | 39 12 35 | 40 13 36 | 41 14 37 | 42 15 38 | 43 16 39 | 44 17 40 | 45 18 41 | 46 19 42 | 47 20 43 | 48 21 44 | 49 22 45 | 50 23 46 | 51 24 47 | 52 25 48 | 53 26 49 | 54 27 50 | 55 28 51 | 56 29 52 | 57 30 53 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1vmoa__2.aln: -------------------------------------------------------------------------------- 1 | 1 33 2 | 2 34 3 | 3 35 4 | 4 36 5 | 5 37 6 | 6 38 7 | 7 39 8 | 8 40 9 | 9 41 10 | 10 42 11 | 11 43 12 | 12 44 13 | 13 45 14 | 14 46 15 | 15 47 16 | 16 48 17 | 17 49 18 | 18 50 19 | 19 51 20 | 20 52 21 | 21 1 22 | 22 2 23 | 23 3 24 | 24 4 25 | 25 5 26 | 26 6 27 | 27 7 28 | 28 8 29 | 29 9 30 | 30 10 31 | 31 11 32 | 32 12 33 | 33 13 34 | 34 14 35 | 35 15 36 | 36 16 37 | 37 17 38 | 38 18 39 | 39 19 40 | 40 20 41 | 41 21 42 | 42 22 43 | 43 23 44 | 44 24 45 | 45 25 46 | 46 26 47 | 47 27 48 | 48 28 49 | 49 29 50 | 50 30 51 | 51 31 52 | 52 32 53 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1l6ra_d1ir6a_.aln: -------------------------------------------------------------------------------- 1 | 3 98 2 | 4 99 3 | 5 100 4 | 6 101 5 | 7 102 6 | 8 103 7 | 9 104 8 | 10 66 9 | 11 67 10 | 12 68 11 | 13 69 12 | 14 70 13 | 15 71 14 | 16 72 15 | 17 73 16 | 18 74 17 | 19 75 18 | 20 76 19 | 21 77 20 | 22 78 21 | 25 79 22 | 26 80 23 | 27 81 24 | 28 82 25 | 29 83 26 | 30 84 27 | 33 89 28 | 34 90 29 | 35 91 30 | 36 92 31 | 37 93 32 | 38 94 33 | 41 22 34 | 42 23 35 | 43 24 36 | 44 25 37 | 45 26 38 | 46 27 39 | 50 33 40 | 51 34 41 | 52 35 42 | 53 36 43 | 54 37 44 | 55 38 45 | 56 39 46 | 57 40 47 | 58 41 48 | 59 42 49 | 60 43 50 | 61 44 51 | 62 45 52 | 63 46 53 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1nf2a_d1ptma_.aln: -------------------------------------------------------------------------------- 1 | 1 40 2 | 2 41 3 | 3 42 4 | 4 43 5 | 5 44 6 | 6 45 7 | 7 46 8 | 8 47 9 | 9 48 10 | 10 49 11 | 11 50 12 | 12 51 13 | 13 52 14 | 14 53 15 | 15 54 16 | 16 55 17 | 18 77 18 | 19 78 19 | 20 79 20 | 21 80 21 | 22 81 22 | 23 82 23 | 24 83 24 | 25 84 25 | 26 85 26 | 27 86 27 | 28 87 28 | 29 88 29 | 31 7 30 | 32 8 31 | 33 9 32 | 34 10 33 | 35 11 34 | 36 12 35 | 37 13 36 | 38 17 37 | 39 18 38 | 40 19 39 | 41 20 40 | 42 21 41 | 43 22 42 | 44 23 43 | 45 24 44 | 46 25 45 | 48 29 46 | 49 30 47 | 50 31 48 | 51 32 49 | 52 33 50 | 53 34 51 | 54 35 52 | 55 36 53 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1ovma1d1914_2.aln: -------------------------------------------------------------------------------- 1 | 10 44 2 | 11 45 3 | 12 46 4 | 13 47 5 | 14 48 6 | 15 49 7 | 16 50 8 | 17 51 9 | 18 52 10 | 19 53 11 | 20 54 12 | 21 55 13 | 22 56 14 | 23 57 15 | 24 58 16 | 25 59 17 | 26 60 18 | 28 31 19 | 29 32 20 | 30 33 21 | 31 34 22 | 32 35 23 | 33 36 24 | 34 37 25 | 35 10 26 | 36 11 27 | 37 12 28 | 38 13 29 | 39 14 30 | 40 15 31 | 41 20 32 | 42 21 33 | 43 22 34 | 44 23 35 | 45 24 36 | 48 63 37 | 49 64 38 | 50 65 39 | 51 66 40 | 52 67 41 | 53 68 42 | 54 69 43 | 55 70 44 | 56 71 45 | 57 72 46 | 58 73 47 | 59 74 48 | 60 75 49 | 61 76 50 | 62 77 51 | 63 78 52 | 64 79 53 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1smta_d1b7ta4.aln: -------------------------------------------------------------------------------- 1 | 2 63 2 | 3 64 3 | 4 65 4 | 5 66 5 | 6 67 6 | 7 68 7 | 8 69 8 | 9 70 9 | 10 71 10 | 11 72 11 | 12 73 12 | 13 74 13 | 14 75 14 | 15 76 15 | 16 77 16 | 17 78 17 | 38 100 18 | 39 101 19 | 40 102 20 | 41 103 21 | 42 104 22 | 43 105 23 | 44 106 24 | 45 107 25 | 46 108 26 | 47 109 27 | 48 110 28 | 49 111 29 | 58 6 30 | 59 7 31 | 60 8 32 | 61 9 33 | 62 10 34 | 63 11 35 | 64 12 36 | 65 13 37 | 66 14 38 | 67 15 39 | 68 16 40 | 69 17 41 | 70 18 42 | 71 19 43 | 90 132 44 | 91 133 45 | 92 134 46 | 93 135 47 | 94 136 48 | 95 137 49 | 96 138 50 | 97 139 51 | 98 140 52 | 99 141 53 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1vk3a3d1w2ia_.aln: -------------------------------------------------------------------------------- 1 | 5 29 2 | 6 30 3 | 7 31 4 | 8 32 5 | 9 33 6 | 10 34 7 | 11 35 8 | 12 36 9 | 13 37 10 | 14 38 11 | 15 39 12 | 16 40 13 | 17 41 14 | 23 68 15 | 24 69 16 | 25 70 17 | 26 71 18 | 27 72 19 | 28 73 20 | 29 74 21 | 30 75 22 | 31 76 23 | 32 77 24 | 33 78 25 | 34 79 26 | 35 80 27 | 36 81 28 | 37 82 29 | 38 83 30 | 39 84 31 | 40 85 32 | 41 86 33 | 42 87 34 | 43 88 35 | 44 89 36 | 50 42 37 | 51 43 38 | 52 44 39 | 53 45 40 | 54 46 41 | 56 47 42 | 57 48 43 | 58 49 44 | 59 50 45 | 60 51 46 | 62 20 47 | 63 21 48 | 64 22 49 | 65 23 50 | 66 24 51 | 67 25 52 | 68 26 53 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d2gaw.1d1nppa1.aln: -------------------------------------------------------------------------------- 1 | 3 40 2 | 4 41 3 | 5 42 4 | 6 43 5 | 7 44 6 | 8 45 7 | 9 46 8 | 11 50 9 | 12 51 10 | 13 53 11 | 14 54 12 | 15 55 13 | 16 56 14 | 17 57 15 | 56 60 16 | 57 61 17 | 58 62 18 | 59 63 19 | 60 64 20 | 61 65 21 | 62 66 22 | 63 67 23 | 64 68 24 | 70 1 25 | 71 2 26 | 72 3 27 | 73 4 28 | 74 5 29 | 75 6 30 | 76 7 31 | 77 8 32 | 78 9 33 | 80 70 34 | 81 71 35 | 82 72 36 | 83 73 37 | 84 74 38 | 85 75 39 | 86 77 40 | 87 78 41 | 88 79 42 | 89 80 43 | 90 30 44 | 91 31 45 | 92 32 46 | 93 33 47 | 94 34 48 | 95 35 49 | 96 36 50 | 97 37 51 | 98 38 52 | 99 39 53 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1f9za_.aln: -------------------------------------------------------------------------------- 1 | 2 16 2 | 3 17 3 | 4 18 4 | 5 19 5 | 6 20 6 | 7 21 7 | 8 22 8 | 9 23 9 | 10 24 10 | 11 25 11 | 12 26 12 | 13 27 13 | 14 28 14 | 15 29 15 | 16 30 16 | 17 31 17 | 18 32 18 | 19 33 19 | 20 34 20 | 21 35 21 | 22 36 22 | 23 37 23 | 25 38 24 | 26 39 25 | 27 40 26 | 28 41 27 | 29 42 28 | 30 43 29 | 31 45 30 | 32 46 31 | 33 47 32 | 34 48 33 | 35 49 34 | 36 50 35 | 37 51 36 | 38 52 37 | 39 53 38 | 40 54 39 | 41 55 40 | 42 56 41 | 43 57 42 | 44 58 43 | 45 59 44 | 46 60 45 | 52 2 46 | 53 3 47 | 54 4 48 | 55 5 49 | 56 6 50 | 57 7 51 | 58 8 52 | 59 9 53 | 60 10 54 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1guwa_.aln: -------------------------------------------------------------------------------- 1 | 1 30 2 | 2 31 3 | 3 32 4 | 4 33 5 | 5 34 6 | 6 35 7 | 7 36 8 | 8 37 9 | 9 38 10 | 10 39 11 | 11 40 12 | 12 41 13 | 13 42 14 | 14 43 15 | 15 44 16 | 16 45 17 | 17 46 18 | 18 47 19 | 19 48 20 | 20 49 21 | 21 50 22 | 22 51 23 | 23 52 24 | 24 53 25 | 25 54 26 | 26 55 27 | 27 56 28 | 28 57 29 | 31 1 30 | 32 2 31 | 33 3 32 | 34 4 33 | 35 5 34 | 36 6 35 | 37 7 36 | 38 8 37 | 39 9 38 | 40 10 39 | 41 13 40 | 42 14 41 | 43 15 42 | 44 16 43 | 45 17 44 | 46 18 45 | 47 19 46 | 48 20 47 | 49 21 48 | 50 22 49 | 51 23 50 | 52 24 51 | 53 25 52 | 54 26 53 | 55 27 54 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1sr9b3.aln: -------------------------------------------------------------------------------- 1 | 3 49 2 | 4 50 3 | 5 51 4 | 6 52 5 | 7 53 6 | 8 54 7 | 9 55 8 | 10 56 9 | 11 57 10 | 12 58 11 | 13 59 12 | 14 1 13 | 15 2 14 | 16 3 15 | 17 4 16 | 18 5 17 | 19 6 18 | 20 7 19 | 21 8 20 | 22 9 21 | 23 10 22 | 24 11 23 | 25 12 24 | 26 13 25 | 27 14 26 | 28 15 27 | 29 16 28 | 30 17 29 | 31 19 30 | 32 20 31 | 33 21 32 | 34 22 33 | 35 23 34 | 36 24 35 | 37 25 36 | 38 26 37 | 39 27 38 | 40 28 39 | 41 29 40 | 42 30 41 | 43 31 42 | 44 32 43 | 45 33 44 | 46 34 45 | 47 35 46 | 48 36 47 | 49 37 48 | 50 38 49 | 51 39 50 | 52 40 51 | 53 41 52 | 54 42 53 | 55 43 54 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d2bs2c1.aln: -------------------------------------------------------------------------------- 1 | 21 117 2 | 22 118 3 | 23 119 4 | 24 120 5 | 25 121 6 | 26 122 7 | 27 123 8 | 28 124 9 | 29 125 10 | 30 126 11 | 31 127 12 | 32 128 13 | 33 129 14 | 34 130 15 | 35 131 16 | 36 132 17 | 37 133 18 | 38 134 19 | 39 135 20 | 40 136 21 | 41 137 22 | 42 138 23 | 43 139 24 | 44 140 25 | 45 141 26 | 46 142 27 | 47 143 28 | 48 144 29 | 49 145 30 | 50 146 31 | 79 14 32 | 80 15 33 | 81 16 34 | 82 17 35 | 83 18 36 | 84 19 37 | 85 20 38 | 86 21 39 | 87 22 40 | 88 23 41 | 89 24 42 | 90 25 43 | 91 26 44 | 92 27 45 | 93 28 46 | 94 29 47 | 95 30 48 | 96 31 49 | 97 32 50 | 98 33 51 | 99 34 52 | 100 35 53 | 101 36 54 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1ert__d1jr3d2.aln: -------------------------------------------------------------------------------- 1 | 1 61 2 | 2 62 3 | 3 63 4 | 4 64 5 | 5 65 6 | 6 66 7 | 7 86 8 | 8 87 9 | 9 88 10 | 10 89 11 | 11 90 12 | 12 91 13 | 13 92 14 | 14 93 15 | 15 94 16 | 16 95 17 | 17 96 18 | 18 97 19 | 19 98 20 | 21 48 21 | 22 49 22 | 23 50 23 | 24 51 24 | 25 52 25 | 26 53 26 | 27 54 27 | 28 55 28 | 29 56 29 | 32 3 30 | 33 4 31 | 34 5 32 | 35 6 33 | 36 7 34 | 37 8 35 | 38 9 36 | 39 10 37 | 40 11 38 | 41 12 39 | 42 13 40 | 43 14 41 | 44 15 42 | 45 16 43 | 46 17 44 | 49 68 45 | 50 69 46 | 51 70 47 | 52 71 48 | 53 72 49 | 54 73 50 | 55 74 51 | 56 75 52 | 57 76 53 | 58 77 54 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1fbxa_d1o08a_.aln: -------------------------------------------------------------------------------- 1 | 4 16 2 | 5 17 3 | 6 18 4 | 7 19 5 | 8 20 6 | 9 21 7 | 10 22 8 | 11 23 9 | 12 24 10 | 13 25 11 | 14 26 12 | 15 27 13 | 16 28 14 | 17 29 15 | 18 30 16 | 19 31 17 | 20 32 18 | 21 33 19 | 28 5 20 | 29 6 21 | 30 7 22 | 31 8 23 | 32 9 24 | 33 10 25 | 43 68 26 | 44 69 27 | 45 70 28 | 46 71 29 | 47 72 30 | 48 73 31 | 49 74 32 | 50 75 33 | 51 76 34 | 52 77 35 | 53 38 36 | 54 39 37 | 55 40 38 | 56 41 39 | 57 42 40 | 58 43 41 | 59 44 42 | 60 45 43 | 61 46 44 | 62 47 45 | 63 48 46 | 64 49 47 | 65 50 48 | 66 51 49 | 67 52 50 | 68 53 51 | 69 54 52 | 70 55 53 | 71 56 54 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1i9ea_d1nppa1.aln: -------------------------------------------------------------------------------- 1 | 2 73 2 | 3 74 3 | 4 75 4 | 5 76 5 | 6 77 6 | 7 78 7 | 8 79 8 | 9 80 9 | 10 81 10 | 16 64 11 | 17 65 12 | 18 66 13 | 19 67 14 | 20 68 15 | 21 69 16 | 22 70 17 | 23 71 18 | 24 43 19 | 25 44 20 | 26 45 21 | 27 46 22 | 28 47 23 | 29 48 24 | 30 49 25 | 31 50 26 | 32 51 27 | 33 55 28 | 34 56 29 | 35 57 30 | 36 58 31 | 37 59 32 | 38 60 33 | 39 61 34 | 40 62 35 | 41 63 36 | 44 25 37 | 45 26 38 | 46 27 39 | 47 28 40 | 48 29 41 | 49 31 42 | 50 32 43 | 51 33 44 | 59 15 45 | 60 16 46 | 61 17 47 | 62 18 48 | 63 19 49 | 64 20 50 | 65 21 51 | 66 22 52 | 67 23 53 | 68 24 54 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1piea1d1q0qa1.aln: -------------------------------------------------------------------------------- 1 | 4 61 2 | 5 62 3 | 6 63 4 | 7 64 5 | 8 65 6 | 9 66 7 | 10 67 8 | 11 68 9 | 12 69 10 | 13 70 11 | 14 71 12 | 15 72 13 | 16 73 14 | 17 74 15 | 18 75 16 | 19 76 17 | 20 77 18 | 31 32 19 | 32 33 20 | 33 34 21 | 34 35 22 | 35 36 23 | 36 37 24 | 37 38 25 | 38 39 26 | 39 40 27 | 40 41 28 | 41 42 29 | 42 43 30 | 43 44 31 | 44 45 32 | 45 46 33 | 46 47 34 | 47 48 35 | 48 49 36 | 52 79 37 | 53 80 38 | 54 81 39 | 55 82 40 | 56 83 41 | 57 84 42 | 58 85 43 | 59 86 44 | 60 87 45 | 61 88 46 | 62 89 47 | 63 90 48 | 64 91 49 | 65 92 50 | 66 93 51 | 67 94 52 | 68 95 53 | 69 96 54 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1rwtj_.aln: -------------------------------------------------------------------------------- 1 | 33 56 2 | 34 57 3 | 35 58 4 | 36 59 5 | 37 60 6 | 38 61 7 | 39 62 8 | 40 63 9 | 41 64 10 | 42 65 11 | 43 66 12 | 44 67 13 | 45 68 14 | 46 69 15 | 47 70 16 | 48 71 17 | 49 72 18 | 50 73 19 | 51 74 20 | 52 75 21 | 53 76 22 | 54 77 23 | 55 78 24 | 56 79 25 | 57 80 26 | 58 81 27 | 59 82 28 | 60 83 29 | 61 84 30 | 62 85 31 | 63 86 32 | 64 87 33 | 65 88 34 | 66 89 35 | 67 90 36 | 68 91 37 | 69 92 38 | 70 93 39 | 71 94 40 | 72 95 41 | 73 96 42 | 74 97 43 | 82 1 44 | 83 2 45 | 84 3 46 | 85 4 47 | 86 5 48 | 87 6 49 | 88 7 50 | 89 8 51 | 90 9 52 | 91 10 53 | 92 11 54 | 93 12 55 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1squa_.aln: -------------------------------------------------------------------------------- 1 | 2 71 2 | 3 72 3 | 4 73 4 | 5 74 5 | 6 75 6 | 7 76 7 | 8 77 8 | 9 78 9 | 10 79 10 | 11 80 11 | 12 81 12 | 13 82 13 | 14 83 14 | 15 84 15 | 16 85 16 | 17 86 17 | 18 87 18 | 19 88 19 | 20 89 20 | 22 1 21 | 23 2 22 | 24 3 23 | 25 4 24 | 26 5 25 | 27 6 26 | 28 7 27 | 29 8 28 | 30 9 29 | 31 10 30 | 32 11 31 | 33 12 32 | 34 13 33 | 40 22 34 | 41 23 35 | 42 24 36 | 43 25 37 | 44 26 38 | 45 27 39 | 46 28 40 | 47 29 41 | 48 30 42 | 49 31 43 | 50 32 44 | 51 33 45 | 52 34 46 | 55 35 47 | 56 36 48 | 57 37 49 | 58 38 50 | 59 39 51 | 60 40 52 | 61 41 53 | 62 42 54 | 63 43 55 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1t3ta3.aln: -------------------------------------------------------------------------------- 1 | 2 38 2 | 3 39 3 | 4 40 4 | 5 41 5 | 6 42 6 | 7 43 7 | 8 44 8 | 13 67 9 | 14 68 10 | 15 69 11 | 16 70 12 | 17 71 13 | 18 72 14 | 19 73 15 | 20 74 16 | 21 75 17 | 22 76 18 | 23 77 19 | 24 78 20 | 25 79 21 | 26 80 22 | 27 81 23 | 28 82 24 | 29 83 25 | 30 49 26 | 31 50 27 | 32 51 28 | 33 52 29 | 34 53 30 | 35 54 31 | 36 55 32 | 37 56 33 | 38 57 34 | 39 58 35 | 40 59 36 | 41 60 37 | 42 61 38 | 43 62 39 | 44 63 40 | 46 1 41 | 47 2 42 | 48 3 43 | 49 4 44 | 50 5 45 | 51 6 46 | 52 7 47 | 53 8 48 | 54 9 49 | 55 10 50 | 56 11 51 | 57 12 52 | 58 13 53 | 59 14 54 | 60 15 55 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1vlya2.aln: -------------------------------------------------------------------------------- 1 | 1 65 2 | 2 66 3 | 3 67 4 | 4 68 5 | 5 69 6 | 6 70 7 | 7 71 8 | 8 72 9 | 9 73 10 | 10 74 11 | 11 75 12 | 12 76 13 | 13 77 14 | 14 78 15 | 15 79 16 | 16 80 17 | 17 81 18 | 18 82 19 | 19 83 20 | 20 84 21 | 21 85 22 | 28 20 23 | 29 21 24 | 30 22 25 | 31 23 26 | 32 24 27 | 33 25 28 | 34 8 29 | 35 9 30 | 36 10 31 | 37 11 32 | 38 12 33 | 39 13 34 | 40 14 35 | 41 15 36 | 45 29 37 | 46 30 38 | 47 31 39 | 48 32 40 | 49 33 41 | 50 34 42 | 51 35 43 | 52 36 44 | 53 37 45 | 54 39 46 | 55 40 47 | 56 41 48 | 57 42 49 | 58 43 50 | 59 44 51 | 60 45 52 | 61 46 53 | 62 47 54 | 63 48 55 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1a7j__d1kafa_.aln: -------------------------------------------------------------------------------- 1 | 1 73 2 | 2 74 3 | 3 76 4 | 4 77 5 | 5 78 6 | 6 79 7 | 7 80 8 | 8 81 9 | 9 82 10 | 27 18 11 | 28 19 12 | 29 20 13 | 30 21 14 | 31 22 15 | 32 23 16 | 33 24 17 | 34 25 18 | 35 26 19 | 36 27 20 | 37 28 21 | 40 3 22 | 41 4 23 | 42 5 24 | 43 6 25 | 44 7 26 | 45 8 27 | 46 9 28 | 47 10 29 | 50 11 30 | 51 12 31 | 52 13 32 | 53 14 33 | 55 15 34 | 56 16 35 | 57 87 36 | 58 88 37 | 59 89 38 | 60 90 39 | 61 91 40 | 62 92 41 | 63 93 42 | 64 94 43 | 65 97 44 | 66 98 45 | 67 99 46 | 68 100 47 | 69 101 48 | 70 102 49 | 71 103 50 | 72 104 51 | 73 105 52 | 74 106 53 | 75 107 54 | 76 108 55 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1hbnb2d1aisb2.aln: -------------------------------------------------------------------------------- 1 | 1 33 2 | 2 34 3 | 3 35 4 | 4 36 5 | 5 37 6 | 6 38 7 | 7 39 8 | 8 40 9 | 9 41 10 | 10 42 11 | 17 43 12 | 18 44 13 | 19 45 14 | 20 46 15 | 21 47 16 | 22 48 17 | 23 49 18 | 24 50 19 | 25 51 20 | 26 52 21 | 27 53 22 | 28 54 23 | 29 55 24 | 30 56 25 | 31 57 26 | 32 58 27 | 33 59 28 | 34 60 29 | 35 61 30 | 57 4 31 | 58 5 32 | 59 6 33 | 60 7 34 | 61 8 35 | 62 9 36 | 63 10 37 | 64 11 38 | 65 12 39 | 66 13 40 | 67 14 41 | 68 15 42 | 69 16 43 | 70 17 44 | 71 18 45 | 76 68 46 | 77 69 47 | 78 70 48 | 79 71 49 | 80 72 50 | 81 73 51 | 82 74 52 | 83 75 53 | 84 76 54 | 85 77 55 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1n00a_d1aa7a_.aln: -------------------------------------------------------------------------------- 1 | 1 3 2 | 2 4 3 | 3 5 4 | 4 6 5 | 5 7 6 | 6 8 7 | 7 9 8 | 8 10 9 | 9 11 10 | 10 12 11 | 11 13 12 | 12 14 13 | 13 15 14 | 14 16 15 | 21 22 16 | 22 23 17 | 23 24 18 | 24 25 19 | 25 26 20 | 26 27 21 | 27 28 22 | 28 29 23 | 29 30 24 | 30 31 25 | 31 32 26 | 36 38 27 | 37 39 28 | 38 40 29 | 39 41 30 | 40 42 31 | 41 43 32 | 42 44 33 | 43 45 34 | 44 46 35 | 45 47 36 | 46 48 37 | 47 49 38 | 48 50 39 | 49 51 40 | 51 54 41 | 52 55 42 | 53 56 43 | 54 57 44 | 55 58 45 | 56 59 46 | 57 60 47 | 58 61 48 | 59 62 49 | 60 63 50 | 61 64 51 | 62 65 52 | 63 66 53 | 64 67 54 | 65 68 55 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1okra_d1v9da_.aln: -------------------------------------------------------------------------------- 1 | 4 8 2 | 5 9 3 | 6 10 4 | 7 11 5 | 8 12 6 | 9 13 7 | 10 14 8 | 11 15 9 | 12 16 10 | 13 17 11 | 14 18 12 | 15 19 13 | 16 20 14 | 17 21 15 | 18 22 16 | 19 23 17 | 21 102 18 | 22 103 19 | 23 104 20 | 24 105 21 | 25 106 22 | 26 107 23 | 27 108 24 | 28 109 25 | 29 110 26 | 30 111 27 | 31 112 28 | 32 113 29 | 33 114 30 | 40 120 31 | 41 121 32 | 42 122 33 | 43 123 34 | 44 124 35 | 45 125 36 | 46 126 37 | 47 127 38 | 48 128 39 | 49 129 40 | 50 130 41 | 51 131 42 | 59 24 43 | 60 25 44 | 61 26 45 | 62 27 46 | 63 28 47 | 64 29 48 | 65 30 49 | 66 31 50 | 67 32 51 | 68 33 52 | 69 34 53 | 70 35 54 | 71 36 55 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d8gep_1.aln: -------------------------------------------------------------------------------- 1 | 1 12 2 | 2 13 3 | 3 14 4 | 4 15 5 | 5 16 6 | 6 17 7 | 7 18 8 | 8 19 9 | 9 20 10 | 10 21 11 | 11 22 12 | 12 23 13 | 13 69 14 | 14 70 15 | 15 71 16 | 16 72 17 | 17 73 18 | 18 74 19 | 19 75 20 | 20 76 21 | 21 77 22 | 22 78 23 | 23 79 24 | 24 80 25 | 30 24 26 | 31 25 27 | 32 26 28 | 33 27 29 | 34 28 30 | 35 29 31 | 36 30 32 | 37 31 33 | 38 32 34 | 39 33 35 | 40 34 36 | 41 35 37 | 42 36 38 | 43 37 39 | 44 38 40 | 45 39 41 | 46 40 42 | 47 46 43 | 48 47 44 | 49 48 45 | 50 49 46 | 51 50 47 | 52 51 48 | 53 52 49 | 54 53 50 | 55 54 51 | 56 55 52 | 57 56 53 | 58 57 54 | 59 58 55 | 60 59 56 | -------------------------------------------------------------------------------- /tests/fastcheck/testrun.py: -------------------------------------------------------------------------------- 1 | #! /usr/bin/env python 2 | 3 | import sys 4 | sys.path.append("../../") 5 | import numpy as np 6 | # import mican class 7 | from pymican import mican 8 | 9 | # setup mican object 10 | mican = mican() 11 | 12 | # calculate mican alignment for two pdb files 13 | aln = mican.align('test1.1.pdb', 'test1.2.pdb') 14 | 15 | # calculate mican alignment for pdb line and pdb file 16 | pdbline1 = "".join(open('test1.1.pdb', 'r').readlines()) 17 | pdbline2 = "".join(open('test1.2.pdb', 'r').readlines()) 18 | aln = mican.align(pdbline1, pdbline2) 19 | 20 | # print summary 21 | print(aln) 22 | 23 | # print TM-score 24 | print(aln.TMscore) 25 | 26 | # print the first 10 aligned residue-pairs 27 | for a in aln[0:10]: 28 | print(a.residue1, a.residue2, a.distance) 29 | 30 | # translate coordinates by superposition matrix 31 | xyz = np.random.rand(10,3) 32 | print(xyz) 33 | xyz_translated = aln.translate_xyz(xyz) 34 | print(xyz_translated) -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1ac5__d1vk0a_.aln: -------------------------------------------------------------------------------- 1 | 1 157 2 | 2 158 3 | 3 159 4 | 4 160 5 | 5 161 6 | 6 162 7 | 7 163 8 | 8 164 9 | 9 165 10 | 10 166 11 | 15 170 12 | 16 171 13 | 17 172 14 | 18 173 15 | 19 174 16 | 20 175 17 | 21 176 18 | 22 177 19 | 23 178 20 | 24 179 21 | 25 180 22 | 26 181 23 | 36 188 24 | 37 189 25 | 38 190 26 | 39 191 27 | 40 192 28 | 41 193 29 | 42 194 30 | 43 195 31 | 44 196 32 | 45 197 33 | 46 198 34 | 47 199 35 | 48 200 36 | 54 6 37 | 55 7 38 | 56 8 39 | 57 9 40 | 58 10 41 | 59 11 42 | 60 12 43 | 61 13 44 | 62 14 45 | 63 15 46 | 64 16 47 | 65 17 48 | 66 18 49 | 67 19 50 | 68 20 51 | 69 21 52 | 70 22 53 | 71 23 54 | 72 24 55 | 73 25 56 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1cs1a_d1q8ia1.aln: -------------------------------------------------------------------------------- 1 | 1 2 2 | 2 3 3 | 3 4 4 | 4 5 5 | 5 6 6 | 6 7 7 | 7 8 8 | 9 9 9 | 10 10 10 | 11 11 11 | 12 12 12 | 13 13 13 | 14 14 14 | 15 15 15 | 16 16 16 | 17 17 17 | 18 18 18 | 19 19 19 | 20 20 20 | 22 24 21 | 23 25 22 | 24 26 23 | 25 27 24 | 26 28 25 | 27 29 26 | 28 30 27 | 29 31 28 | 38 38 29 | 39 39 30 | 40 40 31 | 41 41 32 | 42 42 33 | 43 43 34 | 44 44 35 | 45 45 36 | 46 46 37 | 47 47 38 | 48 48 39 | 49 49 40 | 50 50 41 | 51 51 42 | 52 52 43 | 53 53 44 | 54 54 45 | 55 55 46 | 56 56 47 | 57 57 48 | 58 58 49 | 59 59 50 | 60 60 51 | 61 61 52 | 62 62 53 | 63 63 54 | 64 64 55 | 65 65 56 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1dc1a_d1nf2a_.aln: -------------------------------------------------------------------------------- 1 | 5 32 2 | 6 33 3 | 7 34 4 | 8 35 5 | 9 36 6 | 10 37 7 | 11 38 8 | 12 39 9 | 13 40 10 | 14 41 11 | 15 42 12 | 16 43 13 | 17 44 14 | 18 45 15 | 19 46 16 | 20 47 17 | 21 48 18 | 22 49 19 | 23 50 20 | 24 51 21 | 25 52 22 | 26 53 23 | 27 54 24 | 28 55 25 | 34 75 26 | 35 76 27 | 36 77 28 | 37 78 29 | 38 79 30 | 39 80 31 | 40 19 32 | 41 20 33 | 42 21 34 | 43 22 35 | 44 23 36 | 45 24 37 | 46 25 38 | 47 26 39 | 49 83 40 | 50 84 41 | 51 85 42 | 52 86 43 | 53 87 44 | 54 88 45 | 55 89 46 | 56 90 47 | 57 91 48 | 58 92 49 | 60 65 50 | 61 66 51 | 62 67 52 | 63 68 53 | 64 69 54 | 65 70 55 | 66 71 56 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1dc1a_d1rblm_.aln: -------------------------------------------------------------------------------- 1 | 5 51 2 | 6 52 3 | 7 53 4 | 8 54 5 | 9 55 6 | 10 56 7 | 11 57 8 | 12 58 9 | 13 59 10 | 14 60 11 | 15 61 12 | 16 62 13 | 17 63 14 | 18 64 15 | 19 65 16 | 20 66 17 | 21 67 18 | 22 68 19 | 23 69 20 | 24 70 21 | 25 71 22 | 26 72 23 | 27 73 24 | 28 74 25 | 34 7 26 | 35 8 27 | 36 9 28 | 37 10 29 | 38 13 30 | 39 14 31 | 40 15 32 | 41 16 33 | 42 17 34 | 45 84 35 | 46 85 36 | 47 86 37 | 48 87 38 | 49 88 39 | 50 89 40 | 51 22 41 | 52 23 42 | 53 24 43 | 54 25 44 | 55 26 45 | 56 27 46 | 57 28 47 | 58 29 48 | 59 96 49 | 60 97 50 | 61 98 51 | 62 100 52 | 63 101 53 | 64 102 54 | 65 103 55 | 66 104 56 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1pqsa_d1poh__.aln: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 2 3 | 3 3 4 | 4 4 5 | 5 5 6 | 6 6 7 | 7 7 8 | 8 8 9 | 9 9 10 | 10 10 11 | 13 46 12 | 14 47 13 | 15 48 14 | 16 49 15 | 17 50 16 | 18 51 17 | 19 52 18 | 20 53 19 | 21 54 20 | 22 55 21 | 23 56 22 | 24 57 23 | 25 58 24 | 37 78 25 | 38 79 26 | 39 80 27 | 40 81 28 | 41 82 29 | 42 83 30 | 43 84 31 | 44 85 32 | 46 59 33 | 47 60 34 | 48 61 35 | 49 62 36 | 50 63 37 | 51 64 38 | 52 65 39 | 53 66 40 | 54 67 41 | 55 68 42 | 56 69 43 | 57 70 44 | 58 71 45 | 59 72 46 | 60 73 47 | 61 74 48 | 70 14 49 | 71 15 50 | 72 16 51 | 73 17 52 | 74 18 53 | 75 19 54 | 76 20 55 | 77 21 56 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1ck7a3.aln: -------------------------------------------------------------------------------- 1 | 5 26 2 | 6 27 3 | 7 28 4 | 8 29 5 | 9 30 6 | 10 31 7 | 11 32 8 | 12 33 9 | 13 34 10 | 14 35 11 | 15 36 12 | 16 37 13 | 17 38 14 | 18 39 15 | 19 40 16 | 20 41 17 | 21 42 18 | 22 43 19 | 23 44 20 | 24 45 21 | 25 46 22 | 26 47 23 | 27 48 24 | 28 49 25 | 29 50 26 | 30 51 27 | 31 52 28 | 32 53 29 | 33 54 30 | 34 55 31 | 35 56 32 | 36 1 33 | 37 2 34 | 38 3 35 | 39 4 36 | 40 5 37 | 41 6 38 | 42 7 39 | 43 8 40 | 44 9 41 | 45 10 42 | 46 11 43 | 47 12 44 | 48 13 45 | 49 14 46 | 50 15 47 | 51 16 48 | 52 17 49 | 53 18 50 | 54 19 51 | 55 20 52 | 56 21 53 | 57 22 54 | 58 23 55 | 59 24 56 | 60 25 57 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1foka1_3.aln: -------------------------------------------------------------------------------- 1 | 13 87 2 | 14 88 3 | 15 89 4 | 16 90 5 | 17 91 6 | 18 92 7 | 19 93 8 | 20 94 9 | 21 95 10 | 22 96 11 | 23 97 12 | 24 98 13 | 25 99 14 | 26 100 15 | 61 2 16 | 62 3 17 | 63 4 18 | 64 5 19 | 65 6 20 | 66 7 21 | 67 8 22 | 68 9 23 | 86 10 24 | 87 11 25 | 88 12 26 | 89 13 27 | 98 19 28 | 99 20 29 | 100 21 30 | 101 22 31 | 102 23 32 | 103 24 33 | 104 25 34 | 105 26 35 | 106 27 36 | 107 28 37 | 108 29 38 | 109 30 39 | 110 31 40 | 111 32 41 | 112 33 42 | 113 34 43 | 114 35 44 | 115 36 45 | 116 38 46 | 117 39 47 | 118 40 48 | 119 41 49 | 120 42 50 | 121 43 51 | 124 44 52 | 125 45 53 | 126 46 54 | 127 47 55 | 128 48 56 | 129 49 57 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1fyze_.aln: -------------------------------------------------------------------------------- 1 | 7 57 2 | 8 58 3 | 9 59 4 | 10 60 5 | 11 61 6 | 12 62 7 | 13 63 8 | 14 64 9 | 15 65 10 | 16 66 11 | 17 67 12 | 18 68 13 | 19 69 14 | 20 70 15 | 21 71 16 | 22 72 17 | 23 73 18 | 24 74 19 | 25 75 20 | 26 76 21 | 27 77 22 | 28 78 23 | 29 79 24 | 30 80 25 | 31 81 26 | 32 82 27 | 33 83 28 | 34 84 29 | 35 85 30 | 36 86 31 | 37 87 32 | 38 88 33 | 48 4 34 | 49 5 35 | 50 6 36 | 51 7 37 | 52 8 38 | 53 9 39 | 54 10 40 | 55 11 41 | 56 12 42 | 57 13 43 | 58 14 44 | 59 15 45 | 60 16 46 | 61 17 47 | 62 18 48 | 63 19 49 | 64 20 50 | 65 21 51 | 66 22 52 | 67 23 53 | 68 24 54 | 69 25 55 | 70 26 56 | 71 27 57 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1qmea1.aln: -------------------------------------------------------------------------------- 1 | 5 29 2 | 6 30 3 | 7 31 4 | 8 32 5 | 9 33 6 | 10 34 7 | 11 35 8 | 12 36 9 | 13 37 10 | 14 38 11 | 15 39 12 | 16 40 13 | 17 41 14 | 18 42 15 | 19 43 16 | 20 44 17 | 21 45 18 | 22 46 19 | 23 47 20 | 24 48 21 | 25 49 22 | 26 50 23 | 27 51 24 | 28 52 25 | 29 53 26 | 30 54 27 | 31 55 28 | 32 56 29 | 33 57 30 | 34 58 31 | 35 1 32 | 36 2 33 | 37 3 34 | 38 4 35 | 39 5 36 | 40 6 37 | 41 7 38 | 42 8 39 | 43 9 40 | 44 10 41 | 45 11 42 | 46 12 43 | 47 13 44 | 48 14 45 | 49 15 46 | 50 16 47 | 51 17 48 | 52 18 49 | 53 19 50 | 54 20 51 | 55 21 52 | 56 22 53 | 57 23 54 | 58 24 55 | 59 25 56 | 60 26 57 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d2bmia_.aln: -------------------------------------------------------------------------------- 1 | 9 9 2 | 10 10 3 | 11 11 4 | 12 12 5 | 13 13 6 | 14 14 7 | 16 19 8 | 17 20 9 | 18 21 10 | 19 22 11 | 20 23 12 | 21 24 13 | 22 25 14 | 23 26 15 | 24 27 16 | 32 31 17 | 33 32 18 | 34 33 19 | 35 34 20 | 36 35 21 | 37 36 22 | 38 37 23 | 39 38 24 | 40 39 25 | 41 40 26 | 45 42 27 | 46 43 28 | 47 44 29 | 48 45 30 | 49 46 31 | 53 65 32 | 54 66 33 | 55 67 34 | 56 68 35 | 57 69 36 | 58 70 37 | 59 71 38 | 60 72 39 | 61 73 40 | 62 74 41 | 63 75 42 | 64 76 43 | 65 77 44 | 66 78 45 | 67 79 46 | 68 80 47 | 69 81 48 | 71 82 49 | 72 83 50 | 73 84 51 | 74 85 52 | 75 86 53 | 76 87 54 | 77 88 55 | 78 89 56 | 79 90 57 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1a2za_d1ghha_.aln: -------------------------------------------------------------------------------- 1 | 2 73 2 | 3 74 3 | 4 75 4 | 5 76 5 | 6 77 6 | 7 78 7 | 8 79 8 | 12 16 9 | 13 17 10 | 14 18 11 | 15 19 12 | 16 20 13 | 17 21 14 | 18 22 15 | 19 23 16 | 20 24 17 | 21 25 18 | 22 26 19 | 23 27 20 | 24 28 21 | 25 37 22 | 26 38 23 | 27 39 24 | 28 40 25 | 29 41 26 | 30 42 27 | 31 43 28 | 32 44 29 | 38 1 30 | 39 2 31 | 40 3 32 | 41 4 33 | 42 5 34 | 43 6 35 | 44 7 36 | 45 8 37 | 64 46 38 | 65 47 39 | 66 48 40 | 67 49 41 | 68 50 42 | 69 51 43 | 70 52 44 | 71 53 45 | 72 54 46 | 73 55 47 | 74 56 48 | 75 57 49 | 76 58 50 | 77 59 51 | 78 60 52 | 79 61 53 | 80 62 54 | 81 63 55 | 82 64 56 | 83 65 57 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1b62a2d1i6pa_.aln: -------------------------------------------------------------------------------- 1 | 1 22 2 | 2 23 3 | 3 24 4 | 4 25 5 | 5 26 6 | 6 27 7 | 7 28 8 | 8 29 9 | 9 30 10 | 10 31 11 | 14 75 12 | 15 76 13 | 16 77 14 | 17 78 15 | 18 79 16 | 19 80 17 | 20 81 18 | 21 82 19 | 22 83 20 | 23 84 21 | 24 85 22 | 25 86 23 | 26 87 24 | 27 88 25 | 28 89 26 | 29 90 27 | 30 91 28 | 31 92 29 | 32 93 30 | 35 3 31 | 36 4 32 | 37 5 33 | 38 6 34 | 39 7 35 | 40 8 36 | 41 9 37 | 42 10 38 | 43 11 39 | 44 18 40 | 45 19 41 | 46 20 42 | 47 21 43 | 48 104 44 | 49 105 45 | 50 106 46 | 51 107 47 | 58 108 48 | 59 109 49 | 60 110 50 | 61 111 51 | 62 112 52 | 63 113 53 | 64 114 54 | 65 115 55 | 66 116 56 | 67 117 57 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1htjf_d1gnla_.aln: -------------------------------------------------------------------------------- 1 | 2 32 2 | 3 33 3 | 4 34 4 | 5 35 5 | 6 36 6 | 7 37 7 | 8 38 8 | 9 39 9 | 10 40 10 | 11 41 11 | 12 42 12 | 13 43 13 | 14 44 14 | 15 45 15 | 16 46 16 | 17 47 17 | 18 48 18 | 20 115 19 | 21 116 20 | 22 117 21 | 23 118 22 | 24 119 23 | 25 120 24 | 26 121 25 | 27 122 26 | 28 123 27 | 29 124 28 | 30 125 29 | 31 126 30 | 32 127 31 | 33 128 32 | 34 129 33 | 36 130 34 | 37 131 35 | 38 132 36 | 39 133 37 | 40 134 38 | 41 135 39 | 44 56 40 | 45 57 41 | 46 58 42 | 47 59 43 | 48 60 44 | 49 61 45 | 50 62 46 | 51 63 47 | 52 64 48 | 53 65 49 | 54 66 50 | 55 67 51 | 56 68 52 | 57 69 53 | 58 70 54 | 59 71 55 | 60 72 56 | 61 73 57 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1j22a_d1m2aa_.aln: -------------------------------------------------------------------------------- 1 | 1 34 2 | 2 35 3 | 3 36 4 | 4 37 5 | 5 38 6 | 6 39 7 | 7 40 8 | 8 41 9 | 12 66 10 | 13 67 11 | 14 68 12 | 15 69 13 | 16 70 14 | 17 71 15 | 18 72 16 | 19 73 17 | 20 74 18 | 21 75 19 | 22 76 20 | 23 9 21 | 24 10 22 | 25 11 23 | 26 12 24 | 27 13 25 | 28 14 26 | 29 15 27 | 30 25 28 | 31 26 29 | 32 27 30 | 34 18 31 | 35 19 32 | 36 20 33 | 37 21 34 | 38 22 35 | 39 23 36 | 40 44 37 | 41 45 38 | 42 46 39 | 43 47 40 | 44 48 41 | 45 49 42 | 49 78 43 | 50 79 44 | 51 80 45 | 52 81 46 | 53 82 47 | 54 83 48 | 55 84 49 | 56 85 50 | 57 86 51 | 58 87 52 | 59 89 53 | 60 90 54 | 61 91 55 | 62 92 56 | 63 93 57 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1qmha2_2.aln: -------------------------------------------------------------------------------- 1 | 1 139 2 | 2 140 3 | 3 141 4 | 4 142 5 | 5 143 6 | 6 144 7 | 11 81 8 | 12 82 9 | 13 83 10 | 14 84 11 | 15 85 12 | 16 86 13 | 17 87 14 | 18 88 15 | 19 89 16 | 20 90 17 | 21 91 18 | 22 92 19 | 23 93 20 | 24 94 21 | 25 95 22 | 26 96 23 | 27 97 24 | 29 106 25 | 30 107 26 | 31 108 27 | 32 109 28 | 33 110 29 | 34 111 30 | 43 113 31 | 44 114 32 | 45 115 33 | 46 116 34 | 47 117 35 | 48 118 36 | 49 119 37 | 50 120 38 | 51 121 39 | 52 122 40 | 53 123 41 | 54 124 42 | 55 125 43 | 56 126 44 | 57 127 45 | 58 128 46 | 59 129 47 | 60 130 48 | 61 131 49 | 62 132 50 | 63 133 51 | 64 134 52 | 65 135 53 | 71 101 54 | 72 102 55 | 73 103 56 | 74 104 57 | 75 105 58 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1d7ba_d1svb_2.aln: -------------------------------------------------------------------------------- 1 | 7 51 2 | 8 52 3 | 9 53 4 | 10 54 5 | 11 55 6 | 12 56 7 | 13 57 8 | 14 58 9 | 15 59 10 | 16 60 11 | 17 61 12 | 19 216 13 | 20 217 14 | 21 218 15 | 22 219 16 | 23 220 17 | 24 221 18 | 25 222 19 | 30 62 20 | 31 63 21 | 32 64 22 | 33 65 23 | 34 66 24 | 35 67 25 | 36 68 26 | 37 69 27 | 38 70 28 | 39 71 29 | 40 72 30 | 41 288 31 | 42 289 32 | 43 290 33 | 44 291 34 | 45 292 35 | 46 293 36 | 47 294 37 | 48 295 38 | 49 296 39 | 50 297 40 | 64 28 41 | 65 29 42 | 66 30 43 | 67 31 44 | 68 32 45 | 71 99 46 | 72 100 47 | 73 101 48 | 76 199 49 | 77 200 50 | 78 201 51 | 79 202 52 | 80 203 53 | 81 204 54 | 82 205 55 | 83 206 56 | 84 207 57 | 85 208 58 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1izna_d1gkza1.aln: -------------------------------------------------------------------------------- 1 | 3 74 2 | 4 75 3 | 5 76 4 | 6 77 5 | 7 78 6 | 8 79 7 | 9 80 8 | 10 81 9 | 11 82 10 | 12 83 11 | 13 84 12 | 14 85 13 | 23 30 14 | 24 31 15 | 25 32 16 | 26 33 17 | 27 34 18 | 28 35 19 | 29 36 20 | 30 37 21 | 31 38 22 | 32 39 23 | 33 40 24 | 34 41 25 | 35 42 26 | 37 51 27 | 38 52 28 | 39 53 29 | 40 54 30 | 41 55 31 | 42 56 32 | 43 57 33 | 44 58 34 | 45 59 35 | 46 60 36 | 47 61 37 | 48 62 38 | 49 63 39 | 50 64 40 | 51 65 41 | 52 5 42 | 53 6 43 | 54 7 44 | 55 8 45 | 56 9 46 | 57 10 47 | 58 11 48 | 59 12 49 | 60 13 50 | 61 14 51 | 62 15 52 | 63 16 53 | 64 17 54 | 65 18 55 | 66 19 56 | 67 20 57 | 68 21 58 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1piea1d1nxha_.aln: -------------------------------------------------------------------------------- 1 | 3 22 2 | 4 23 3 | 5 24 4 | 6 25 5 | 7 26 6 | 8 27 7 | 9 28 8 | 10 29 9 | 11 30 10 | 12 31 11 | 13 32 12 | 14 33 13 | 15 34 14 | 16 35 15 | 17 36 16 | 18 37 17 | 19 38 18 | 20 39 19 | 31 104 20 | 32 105 21 | 33 106 22 | 34 107 23 | 35 108 24 | 36 109 25 | 37 110 26 | 38 111 27 | 39 112 28 | 40 113 29 | 41 114 30 | 42 117 31 | 43 118 32 | 44 119 33 | 45 120 34 | 46 121 35 | 47 122 36 | 48 123 37 | 49 124 38 | 51 1 39 | 52 2 40 | 53 3 41 | 54 4 42 | 55 5 43 | 56 6 44 | 57 7 45 | 58 8 46 | 59 9 47 | 60 10 48 | 61 11 49 | 62 12 50 | 63 13 51 | 64 14 52 | 65 15 53 | 66 16 54 | 67 17 55 | 68 18 56 | 69 19 57 | 70 20 58 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1ur3m_d1k87a1.aln: -------------------------------------------------------------------------------- 1 | 8 77 2 | 9 78 3 | 10 79 4 | 11 80 5 | 12 81 6 | 13 82 7 | 14 83 8 | 15 84 9 | 16 85 10 | 17 86 11 | 18 87 12 | 19 88 13 | 20 89 14 | 21 90 15 | 22 91 16 | 23 92 17 | 24 93 18 | 25 94 19 | 27 95 20 | 28 96 21 | 29 97 22 | 30 98 23 | 31 99 24 | 32 100 25 | 33 101 26 | 34 102 27 | 35 103 28 | 36 104 29 | 37 105 30 | 38 106 31 | 39 107 32 | 40 108 33 | 47 61 34 | 48 62 35 | 49 63 36 | 50 64 37 | 51 65 38 | 52 66 39 | 53 67 40 | 54 69 41 | 55 70 42 | 56 71 43 | 57 72 44 | 60 7 45 | 61 8 46 | 62 9 47 | 63 10 48 | 64 11 49 | 65 12 50 | 66 13 51 | 67 14 52 | 68 15 53 | 69 16 54 | 70 17 55 | 71 18 56 | 72 19 57 | 73 20 58 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1vaoa2d1no5a_.aln: -------------------------------------------------------------------------------- 1 | 8 68 2 | 9 69 3 | 10 70 4 | 11 71 5 | 12 72 6 | 13 73 7 | 14 74 8 | 15 75 9 | 16 76 10 | 17 77 11 | 18 78 12 | 19 79 13 | 20 80 14 | 21 81 15 | 22 82 16 | 23 83 17 | 24 84 18 | 25 85 19 | 26 86 20 | 27 87 21 | 28 88 22 | 31 91 23 | 32 92 24 | 33 93 25 | 34 94 26 | 35 95 27 | 36 96 28 | 38 10 29 | 39 11 30 | 40 12 31 | 41 13 32 | 42 14 33 | 43 15 34 | 44 16 35 | 45 17 36 | 46 18 37 | 47 19 38 | 48 20 39 | 49 21 40 | 50 22 41 | 51 23 42 | 52 24 43 | 53 25 44 | 54 26 45 | 55 27 46 | 56 28 47 | 57 29 48 | 58 30 49 | 59 31 50 | 60 32 51 | 62 40 52 | 63 41 53 | 64 42 54 | 65 43 55 | 66 44 56 | 67 45 57 | 68 46 58 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1d8ha_.aln: -------------------------------------------------------------------------------- 1 | 4 58 2 | 5 59 3 | 6 60 4 | 7 61 5 | 8 62 6 | 9 63 7 | 10 64 8 | 11 65 9 | 12 66 10 | 13 67 11 | 14 68 12 | 49 2 13 | 50 3 14 | 51 4 15 | 52 5 16 | 53 6 17 | 54 7 18 | 55 8 19 | 56 9 20 | 57 10 21 | 72 13 22 | 73 14 23 | 74 15 24 | 75 16 25 | 76 17 26 | 77 18 27 | 78 19 28 | 79 20 29 | 80 21 30 | 81 22 31 | 82 23 32 | 83 24 33 | 84 25 34 | 85 26 35 | 86 29 36 | 87 30 37 | 88 31 38 | 89 32 39 | 90 33 40 | 91 34 41 | 92 35 42 | 93 36 43 | 94 37 44 | 95 38 45 | 96 39 46 | 97 42 47 | 98 43 48 | 99 44 49 | 100 45 50 | 102 46 51 | 103 47 52 | 104 48 53 | 105 49 54 | 106 50 55 | 107 51 56 | 108 52 57 | 109 53 58 | 110 54 59 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1hazb_.aln: -------------------------------------------------------------------------------- 1 | 14 11 2 | 15 12 3 | 16 13 4 | 17 14 5 | 18 15 6 | 19 16 7 | 20 17 8 | 21 18 9 | 24 57 10 | 25 58 11 | 26 59 12 | 27 60 13 | 28 61 14 | 30 62 15 | 31 63 16 | 32 64 17 | 33 65 18 | 34 66 19 | 35 67 20 | 36 68 21 | 38 113 22 | 39 114 23 | 40 115 24 | 41 116 25 | 42 117 26 | 43 118 27 | 44 119 28 | 45 120 29 | 46 121 30 | 47 122 31 | 48 123 32 | 49 124 33 | 50 125 34 | 52 22 35 | 53 23 36 | 54 24 37 | 55 25 38 | 56 26 39 | 57 27 40 | 58 28 41 | 68 32 42 | 69 33 43 | 70 34 44 | 71 35 45 | 72 37 46 | 73 38 47 | 74 39 48 | 75 40 49 | 76 41 50 | 77 42 51 | 94 78 52 | 95 79 53 | 96 80 54 | 97 81 55 | 98 82 56 | 99 83 57 | 100 84 58 | 101 85 59 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1m98a1.aln: -------------------------------------------------------------------------------- 1 | 21 52 2 | 22 53 3 | 23 54 4 | 24 55 5 | 25 56 6 | 26 57 7 | 27 58 8 | 28 59 9 | 29 60 10 | 30 61 11 | 31 62 12 | 32 63 13 | 33 64 14 | 34 65 15 | 35 66 16 | 36 67 17 | 37 68 18 | 38 69 19 | 39 70 20 | 40 71 21 | 41 72 22 | 42 73 23 | 43 74 24 | 44 75 25 | 45 76 26 | 46 77 27 | 47 78 28 | 48 79 29 | 49 80 30 | 60 7 31 | 61 8 32 | 62 9 33 | 63 10 34 | 64 11 35 | 65 12 36 | 66 13 37 | 67 14 38 | 68 15 39 | 69 16 40 | 70 17 41 | 71 18 42 | 72 19 43 | 73 20 44 | 74 21 45 | 75 22 46 | 76 23 47 | 77 24 48 | 78 25 49 | 79 26 50 | 80 27 51 | 81 28 52 | 82 29 53 | 83 30 54 | 84 31 55 | 85 32 56 | 86 33 57 | 87 34 58 | 88 35 59 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1qm4a1.aln: -------------------------------------------------------------------------------- 1 | 14 86 2 | 15 87 3 | 16 88 4 | 17 89 5 | 18 90 6 | 19 91 7 | 20 92 8 | 21 93 9 | 22 94 10 | 23 95 11 | 24 96 12 | 25 97 13 | 26 98 14 | 27 99 15 | 28 100 16 | 29 101 17 | 30 102 18 | 31 103 19 | 32 104 20 | 33 105 21 | 39 28 22 | 40 29 23 | 41 30 24 | 42 31 25 | 43 32 26 | 44 33 27 | 45 34 28 | 46 35 29 | 47 36 30 | 48 11 31 | 49 12 32 | 50 13 33 | 51 14 34 | 52 15 35 | 53 16 36 | 54 17 37 | 55 18 38 | 56 19 39 | 57 20 40 | 63 48 41 | 64 49 42 | 65 50 43 | 66 51 44 | 67 53 45 | 68 54 46 | 69 55 47 | 70 56 48 | 71 57 49 | 72 58 50 | 86 110 51 | 87 111 52 | 88 112 53 | 89 113 54 | 90 114 55 | 91 115 56 | 92 116 57 | 93 117 58 | 94 118 59 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1qtqa1.aln: -------------------------------------------------------------------------------- 1 | 2 56 2 | 3 57 3 | 4 58 4 | 5 59 5 | 6 60 6 | 7 61 7 | 8 62 8 | 9 84 9 | 10 85 10 | 11 86 11 | 12 87 12 | 13 88 13 | 14 89 14 | 15 90 15 | 16 91 16 | 17 92 17 | 45 26 18 | 46 27 19 | 47 28 20 | 48 29 21 | 49 30 22 | 50 31 23 | 51 32 24 | 52 33 25 | 53 34 26 | 54 35 27 | 55 36 28 | 65 37 29 | 66 38 30 | 67 39 31 | 68 40 32 | 69 41 33 | 70 42 34 | 71 43 35 | 72 44 36 | 73 45 37 | 74 46 38 | 75 47 39 | 76 48 40 | 77 49 41 | 78 50 42 | 79 51 43 | 80 52 44 | 81 53 45 | 82 54 46 | 83 79 47 | 84 80 48 | 85 81 49 | 86 82 50 | 93 64 51 | 94 65 52 | 95 66 53 | 96 67 54 | 97 68 55 | 98 69 56 | 99 70 57 | 100 71 58 | 101 72 59 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1jnwa_d1ew4a_.aln: -------------------------------------------------------------------------------- 1 | 5 30 2 | 6 31 3 | 7 32 4 | 8 33 5 | 9 34 6 | 10 35 7 | 11 36 8 | 12 37 9 | 13 38 10 | 14 39 11 | 15 40 12 | 16 41 13 | 17 42 14 | 18 43 15 | 19 44 16 | 21 45 17 | 22 46 18 | 23 47 19 | 24 48 20 | 25 49 21 | 26 50 22 | 27 51 23 | 28 52 24 | 29 53 25 | 30 60 26 | 31 61 27 | 32 62 28 | 33 63 29 | 34 64 30 | 35 65 31 | 45 90 32 | 46 91 33 | 47 92 34 | 48 93 35 | 49 94 36 | 50 95 37 | 51 96 38 | 52 97 39 | 53 102 40 | 54 103 41 | 55 104 42 | 56 105 43 | 73 68 44 | 74 69 45 | 75 70 46 | 76 71 47 | 77 72 48 | 78 73 49 | 79 74 50 | 80 75 51 | 81 76 52 | 82 77 53 | 83 78 54 | 84 79 55 | 85 80 56 | 86 81 57 | 87 82 58 | 88 83 59 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1n7va_d1izna_.aln: -------------------------------------------------------------------------------- 1 | 3 117 2 | 4 118 3 | 5 119 4 | 6 120 5 | 7 121 6 | 8 122 7 | 9 123 8 | 10 124 9 | 11 134 10 | 12 135 11 | 13 136 12 | 14 137 13 | 15 138 14 | 16 139 15 | 17 140 16 | 18 141 17 | 19 142 18 | 20 143 19 | 21 144 20 | 22 145 21 | 23 65 22 | 24 66 23 | 25 67 24 | 26 68 25 | 27 69 26 | 28 70 27 | 29 71 28 | 30 72 29 | 31 73 30 | 32 74 31 | 33 75 32 | 34 154 33 | 35 155 34 | 36 156 35 | 38 157 36 | 39 158 37 | 40 159 38 | 41 160 39 | 42 161 40 | 43 162 41 | 44 163 42 | 45 164 43 | 46 165 44 | 50 1 45 | 51 2 46 | 52 3 47 | 53 4 48 | 54 5 49 | 55 6 50 | 56 7 51 | 57 8 52 | 58 9 53 | 59 10 54 | 60 11 55 | 61 12 56 | 62 13 57 | 63 14 58 | 64 15 59 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1uoua1d1fs1b1.aln: -------------------------------------------------------------------------------- 1 | 3 66 2 | 4 67 3 | 5 68 4 | 6 69 5 | 7 70 6 | 8 71 7 | 9 72 8 | 10 73 9 | 11 74 10 | 12 75 11 | 13 76 12 | 14 77 13 | 15 78 14 | 16 79 15 | 17 80 16 | 18 81 17 | 24 46 18 | 25 47 19 | 26 48 20 | 27 49 21 | 28 50 22 | 29 51 23 | 30 52 24 | 31 53 25 | 32 54 26 | 33 55 27 | 46 2 28 | 47 3 29 | 48 4 30 | 49 5 31 | 50 6 32 | 51 7 33 | 52 8 34 | 53 9 35 | 54 10 36 | 55 11 37 | 56 12 38 | 57 13 39 | 58 14 40 | 59 15 41 | 60 16 42 | 64 17 43 | 65 18 44 | 66 19 45 | 67 20 46 | 68 21 47 | 69 22 48 | 70 23 49 | 71 24 50 | 72 25 51 | 73 26 52 | 74 27 53 | 75 28 54 | 76 29 55 | 77 30 56 | 78 31 57 | 79 32 58 | 80 33 59 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1anv_2.aln: -------------------------------------------------------------------------------- 1 | 15 133 2 | 16 134 3 | 17 135 4 | 18 122 5 | 19 123 6 | 20 124 7 | 21 125 8 | 22 126 9 | 23 21 10 | 24 22 11 | 25 23 12 | 26 24 13 | 27 25 14 | 28 26 15 | 29 27 16 | 30 28 17 | 31 29 18 | 38 118 19 | 39 119 20 | 40 120 21 | 42 94 22 | 43 95 23 | 44 96 24 | 45 97 25 | 46 98 26 | 47 99 27 | 48 100 28 | 49 101 29 | 60 3 30 | 61 4 31 | 62 5 32 | 63 6 33 | 64 7 34 | 65 8 35 | 66 9 36 | 67 10 37 | 69 37 38 | 70 38 39 | 71 39 40 | 72 40 41 | 73 41 42 | 74 42 43 | 75 43 44 | 76 44 45 | 77 45 46 | 78 46 47 | 79 47 48 | 80 48 49 | 81 49 50 | 82 50 51 | 83 51 52 | 84 52 53 | 85 53 54 | 86 54 55 | 87 55 56 | 88 56 57 | 89 57 58 | 90 58 59 | 91 59 60 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1dgsa1.aln: -------------------------------------------------------------------------------- 1 | 4 9 2 | 5 10 3 | 6 11 4 | 7 12 5 | 8 13 6 | 9 14 7 | 10 15 8 | 11 16 9 | 12 17 10 | 13 18 11 | 20 19 12 | 21 20 13 | 22 21 14 | 23 22 15 | 24 23 16 | 25 24 17 | 26 25 18 | 27 26 19 | 28 27 20 | 29 28 21 | 30 29 22 | 31 30 23 | 32 31 24 | 33 32 25 | 34 33 26 | 37 34 27 | 38 35 28 | 39 36 29 | 40 37 30 | 41 38 31 | 42 39 32 | 43 40 33 | 44 41 34 | 45 42 35 | 46 43 36 | 48 1 37 | 49 2 38 | 50 3 39 | 51 4 40 | 52 5 41 | 53 6 42 | 54 7 43 | 55 44 44 | 56 45 45 | 57 46 46 | 58 47 47 | 59 48 48 | 60 49 49 | 61 50 50 | 62 51 51 | 63 52 52 | 64 53 53 | 65 54 54 | 66 55 55 | 67 56 56 | 68 57 57 | 69 58 58 | 70 59 59 | 71 60 60 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1pv5a_.aln: -------------------------------------------------------------------------------- 1 | 2 21 2 | 3 22 3 | 4 23 4 | 5 24 5 | 6 25 6 | 7 26 7 | 45 1 8 | 46 2 9 | 47 3 10 | 48 4 11 | 49 5 12 | 50 6 13 | 51 7 14 | 52 8 15 | 53 9 16 | 54 10 17 | 55 11 18 | 56 12 19 | 57 13 20 | 58 14 21 | 71 34 22 | 72 35 23 | 73 36 24 | 74 37 25 | 75 38 26 | 76 39 27 | 77 40 28 | 78 41 29 | 79 42 30 | 80 43 31 | 88 71 32 | 89 72 33 | 90 73 34 | 91 74 35 | 92 75 36 | 93 76 37 | 94 77 38 | 95 78 39 | 96 79 40 | 97 80 41 | 98 81 42 | 99 82 43 | 100 83 44 | 101 84 45 | 102 85 46 | 109 57 47 | 110 58 48 | 111 59 49 | 112 60 50 | 113 61 51 | 114 62 52 | 115 63 53 | 116 64 54 | 117 65 55 | 138 114 56 | 139 115 57 | 140 116 58 | 141 117 59 | 142 118 60 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1a7j__d2if1__.aln: -------------------------------------------------------------------------------- 1 | 1 80 2 | 2 81 3 | 3 82 4 | 4 83 5 | 5 84 6 | 6 85 7 | 7 86 8 | 8 87 9 | 9 88 10 | 10 89 11 | 25 29 12 | 26 30 13 | 27 31 14 | 28 32 15 | 29 33 16 | 30 34 17 | 31 35 18 | 32 36 19 | 33 37 20 | 37 12 21 | 38 13 22 | 39 14 23 | 40 15 24 | 41 16 25 | 42 17 26 | 43 18 27 | 44 19 28 | 45 20 29 | 46 21 30 | 47 22 31 | 48 23 32 | 49 24 33 | 50 2 34 | 51 3 35 | 52 4 36 | 53 5 37 | 54 6 38 | 55 7 39 | 57 94 40 | 58 95 41 | 59 96 42 | 60 97 43 | 61 98 44 | 62 99 45 | 63 100 46 | 64 101 47 | 65 102 48 | 66 103 49 | 67 104 50 | 68 105 51 | 69 106 52 | 70 107 53 | 71 108 54 | 72 109 55 | 73 110 56 | 74 111 57 | 75 112 58 | 76 113 59 | 77 114 60 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1ds1a_d1tig__.aln: -------------------------------------------------------------------------------- 1 | 1 81 2 | 2 82 3 | 3 83 4 | 4 84 5 | 5 85 6 | 6 86 7 | 8 63 8 | 9 64 9 | 10 65 10 | 11 66 11 | 12 67 12 | 13 68 13 | 14 69 14 | 15 70 15 | 16 71 16 | 17 72 17 | 18 73 18 | 19 74 19 | 20 75 20 | 21 76 21 | 22 77 22 | 26 21 23 | 27 22 24 | 28 23 25 | 29 24 26 | 30 25 27 | 31 26 28 | 32 27 29 | 57 6 30 | 58 7 31 | 59 8 32 | 60 9 33 | 61 10 34 | 62 11 35 | 63 12 36 | 64 13 37 | 65 14 38 | 66 15 39 | 67 16 40 | 68 17 41 | 69 18 42 | 70 19 43 | 73 34 44 | 74 35 45 | 75 36 46 | 76 37 47 | 77 39 48 | 78 40 49 | 79 42 50 | 80 43 51 | 87 48 52 | 88 49 53 | 89 50 54 | 90 51 55 | 91 52 56 | 92 53 57 | 93 54 58 | 94 55 59 | 95 56 60 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1hrda1d1rp3a3.aln: -------------------------------------------------------------------------------- 1 | 10 14 2 | 11 15 3 | 12 16 4 | 13 17 5 | 14 18 6 | 15 19 7 | 16 20 8 | 17 21 9 | 18 22 10 | 19 23 11 | 20 24 12 | 21 25 13 | 22 26 14 | 23 27 15 | 24 28 16 | 25 29 17 | 26 30 18 | 27 31 19 | 28 32 20 | 29 33 21 | 33 66 22 | 34 67 23 | 35 68 24 | 36 69 25 | 37 70 26 | 38 72 27 | 39 73 28 | 40 74 29 | 41 75 30 | 42 76 31 | 43 77 32 | 44 78 33 | 45 79 34 | 46 80 35 | 47 81 36 | 48 82 37 | 49 83 38 | 50 84 39 | 58 42 40 | 59 43 41 | 60 44 42 | 61 45 43 | 62 46 44 | 63 47 45 | 64 48 46 | 65 49 47 | 66 50 48 | 67 51 49 | 68 52 50 | 69 53 51 | 70 54 52 | 71 55 53 | 72 56 54 | 73 57 55 | 74 58 56 | 75 59 57 | 76 60 58 | 77 61 59 | 78 62 60 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1i9ea_d1mzka_.aln: -------------------------------------------------------------------------------- 1 | 2 3 2 | 3 4 3 | 4 5 4 | 5 6 5 | 6 7 6 | 7 8 7 | 8 9 8 | 9 10 9 | 10 11 10 | 11 12 11 | 13 64 12 | 14 65 13 | 15 66 14 | 16 67 15 | 17 68 16 | 18 69 17 | 20 70 18 | 21 71 19 | 22 72 20 | 23 73 21 | 26 55 22 | 27 56 23 | 28 57 24 | 29 58 25 | 30 59 26 | 31 60 27 | 32 61 28 | 35 30 29 | 36 31 30 | 37 32 31 | 38 33 32 | 39 34 33 | 40 35 34 | 41 36 35 | 42 37 36 | 43 38 37 | 44 39 38 | 45 40 39 | 46 41 40 | 47 42 41 | 48 43 42 | 49 44 43 | 50 45 44 | 51 46 45 | 52 47 46 | 53 48 47 | 54 49 48 | 55 50 49 | 58 110 50 | 59 111 51 | 60 112 52 | 61 113 53 | 62 114 54 | 63 115 55 | 64 116 56 | 65 117 57 | 66 118 58 | 67 119 59 | 68 120 60 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1o02a_d1ihna_.aln: -------------------------------------------------------------------------------- 1 | 1 22 2 | 2 23 3 | 3 24 4 | 4 25 5 | 5 26 6 | 6 27 7 | 7 98 8 | 8 99 9 | 9 100 10 | 10 101 11 | 11 102 12 | 12 103 13 | 13 84 14 | 14 85 15 | 15 86 16 | 16 87 17 | 17 88 18 | 18 89 19 | 19 90 20 | 20 91 21 | 21 92 22 | 22 93 23 | 23 94 24 | 24 95 25 | 25 96 26 | 35 29 27 | 36 30 28 | 37 31 29 | 38 32 30 | 39 33 31 | 40 34 32 | 41 35 33 | 42 36 34 | 43 37 35 | 44 63 36 | 45 64 37 | 46 65 38 | 47 66 39 | 48 67 40 | 49 68 41 | 50 69 42 | 51 70 43 | 52 71 44 | 53 72 45 | 54 73 46 | 55 74 47 | 56 75 48 | 57 76 49 | 58 77 50 | 59 78 51 | 60 79 52 | 64 39 53 | 65 40 54 | 66 41 55 | 67 42 56 | 68 43 57 | 69 44 58 | 70 45 59 | 71 46 60 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1okra_d1m98a1.aln: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 2 3 | 3 3 4 | 4 4 5 | 5 5 6 | 6 6 7 | 7 7 8 | 8 8 9 | 9 9 10 | 10 10 11 | 11 11 12 | 12 12 13 | 13 13 14 | 14 14 15 | 17 15 16 | 18 16 17 | 19 17 18 | 20 18 19 | 21 19 20 | 22 20 21 | 23 21 22 | 24 22 23 | 25 23 24 | 26 24 25 | 27 25 26 | 28 26 27 | 29 27 28 | 30 28 29 | 31 29 30 | 32 30 31 | 33 37 32 | 34 38 33 | 35 39 34 | 36 40 35 | 37 41 36 | 38 42 37 | 39 43 38 | 40 44 39 | 41 45 40 | 42 46 41 | 43 47 42 | 44 48 43 | 45 49 44 | 46 50 45 | 47 51 46 | 50 52 47 | 51 53 48 | 52 54 49 | 53 55 50 | 54 56 51 | 55 57 52 | 56 58 53 | 57 59 54 | 58 60 55 | 59 61 56 | 60 62 57 | 61 63 58 | 62 64 59 | 63 65 60 | -------------------------------------------------------------------------------- /src/utils.c: -------------------------------------------------------------------------------- 1 | #include "mican.h" 2 | 3 | /** function : distance^2 **/ 4 | float distance_2(float *a, float *b) { 5 | 6 | float sum = 0.0; 7 | 8 | sum = (a[1] - b[1]) * (a[1] - b[1]) 9 | + (a[2] - b[2]) * (a[2] - b[2]) 10 | + (a[3] - b[3]) * (a[3] - b[3]); 11 | 12 | return (sum); 13 | } 14 | 15 | /** function : angle **/ 16 | float angle(float *a1, float *a2, float *a3, float *b1, float *b2, float *b3) { 17 | float v1[3+1]; 18 | float v2[3+1]; 19 | float size_v1; 20 | float size_v2; 21 | float ip; 22 | float ang; 23 | int i; 24 | 25 | size_v1 = 0.0; 26 | size_v2 = 0.0; 27 | ip = 0; 28 | for (i = 1; i <= 3; i++) { 29 | v1[i] = (a2[i] - a1[i]) + (a2[i] - a3[i]); 30 | v2[i] = (b2[i] - b1[i]) + (b2[i] - b3[i]); 31 | size_v1 += v1[i] * v1[i]; 32 | size_v2 += v2[i] * v2[i]; 33 | ip += v1[i] * v2[i]; 34 | } 35 | ip /= (float)sqrt(size_v1 * size_v2); 36 | 37 | if(ip > 1.0) ip = 1.0; 38 | if(ip < -1.0) ip = -1.0; 39 | 40 | ang = (float)acos(ip); 41 | 42 | return (ang); 43 | } 44 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1k2yx1_2.aln: -------------------------------------------------------------------------------- 1 | 19 38 2 | 20 39 3 | 21 40 4 | 22 41 5 | 23 42 6 | 24 43 7 | 25 44 8 | 26 45 9 | 27 46 10 | 28 47 11 | 33 49 12 | 34 50 13 | 35 51 14 | 36 52 15 | 37 53 16 | 38 54 17 | 39 55 18 | 40 56 19 | 41 57 20 | 42 58 21 | 43 59 22 | 44 60 23 | 45 61 24 | 46 62 25 | 47 63 26 | 48 64 27 | 49 65 28 | 50 66 29 | 51 67 30 | 70 1 31 | 71 2 32 | 72 3 33 | 73 4 34 | 74 5 35 | 75 6 36 | 76 7 37 | 77 8 38 | 78 9 39 | 79 10 40 | 80 11 41 | 81 12 42 | 82 13 43 | 83 14 44 | 84 15 45 | 85 16 46 | 86 17 47 | 87 18 48 | 88 19 49 | 89 20 50 | 96 70 51 | 97 71 52 | 98 72 53 | 99 73 54 | 100 74 55 | 101 75 56 | 102 79 57 | 103 80 58 | 104 81 59 | 105 82 60 | 106 83 61 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1qmha2_1.aln: -------------------------------------------------------------------------------- 1 | 1 54 2 | 2 55 3 | 3 56 4 | 4 57 5 | 5 58 6 | 6 59 7 | 7 60 8 | 12 67 9 | 13 68 10 | 14 69 11 | 15 70 12 | 16 71 13 | 17 72 14 | 18 73 15 | 19 74 16 | 20 75 17 | 21 76 18 | 22 77 19 | 23 78 20 | 24 79 21 | 25 80 22 | 26 81 23 | 27 82 24 | 28 83 25 | 29 84 26 | 30 85 27 | 31 86 28 | 32 87 29 | 33 88 30 | 34 89 31 | 45 28 32 | 46 29 33 | 47 30 34 | 48 31 35 | 49 33 36 | 50 34 37 | 51 35 38 | 52 36 39 | 53 37 40 | 54 38 41 | 55 39 42 | 56 40 43 | 57 41 44 | 58 42 45 | 60 43 46 | 61 44 47 | 62 45 48 | 63 46 49 | 64 47 50 | 65 48 51 | 71 10 52 | 72 11 53 | 73 12 54 | 74 13 55 | 75 14 56 | 76 15 57 | 77 16 58 | 78 17 59 | 79 18 60 | 80 19 61 | -------------------------------------------------------------------------------- /src/hres2trans.c: -------------------------------------------------------------------------------- 1 | #include "mican.h" 2 | 3 | int hres2trans(SSEDAT *ssedat_q, SSEDAT *ssedat_t, ALIGN align) { 4 | int i, j; 5 | int isse_q, isse_t; 6 | float xq[4], yq[4], zq[4]; 7 | float xt[4], yt[4], zt[4]; 8 | 9 | isse_q = align.isse_q; 10 | isse_t = align.isse_t; 11 | 12 | /**** coordinate difinition ****/ 13 | coord_definition(xq, yq, zq, ssedat_q, isse_q); 14 | if (align.coord_mode == FORWARD) { 15 | coord_definition(xt, yt, zt, ssedat_t, isse_t); 16 | } else { 17 | coord_definition_r(xt, yt, zt, ssedat_t, isse_t); 18 | } 19 | 20 | /**** rotation matrix ****/ 21 | for (i = 1; i <= 3; i++) { 22 | for (j = 1; j <= 3; j++) { 23 | align.rot[i][j] = xq[i] * xt[j] + yq[i] * yt[j] + zq[i] * zt[j]; 24 | } 25 | } 26 | /**** translation vector ****/ 27 | for (i = 1; i <= 3; i++) { 28 | align.vec[i] = ssedat_q[isse_q].mid[i]; 29 | for (j = 1; j <= 3; j++) { 30 | align.vec[i] += -align.rot[i][j] * ssedat_t[isse_t].mid[j]; 31 | } 32 | } 33 | 34 | return (TRUE); 35 | } 36 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1aa7a_d1b68a_.aln: -------------------------------------------------------------------------------- 1 | 3 86 2 | 4 87 3 | 5 88 4 | 6 89 5 | 7 90 6 | 8 91 7 | 9 92 8 | 10 93 9 | 11 94 10 | 12 95 11 | 13 96 12 | 14 97 13 | 15 98 14 | 16 99 15 | 17 100 16 | 18 101 17 | 27 115 18 | 28 116 19 | 29 117 20 | 30 118 21 | 31 119 22 | 32 120 23 | 33 121 24 | 34 122 25 | 35 123 26 | 39 21 27 | 40 22 28 | 41 23 29 | 42 24 30 | 43 25 31 | 44 26 32 | 45 27 33 | 46 28 34 | 47 29 35 | 48 30 36 | 49 31 37 | 50 32 38 | 51 33 39 | 52 34 40 | 53 35 41 | 58 55 42 | 59 56 43 | 60 57 44 | 61 58 45 | 62 59 46 | 63 60 47 | 64 61 48 | 65 62 49 | 66 63 50 | 67 64 51 | 68 65 52 | 69 66 53 | 70 67 54 | 71 68 55 | 72 69 56 | 73 70 57 | 74 71 58 | 75 72 59 | 76 73 60 | 77 74 61 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1st6a8d1gvna_.aln: -------------------------------------------------------------------------------- 1 | 22 14 2 | 23 15 3 | 24 16 4 | 25 17 5 | 26 18 6 | 27 19 7 | 28 20 8 | 29 21 9 | 30 22 10 | 31 23 11 | 32 24 12 | 33 25 13 | 34 26 14 | 35 27 15 | 36 28 16 | 37 29 17 | 38 30 18 | 39 31 19 | 40 32 20 | 41 33 21 | 47 68 22 | 48 69 23 | 49 70 24 | 50 71 25 | 51 72 26 | 52 73 27 | 53 74 28 | 54 75 29 | 55 76 30 | 56 77 31 | 57 78 32 | 58 79 33 | 59 80 34 | 60 81 35 | 61 82 36 | 62 83 37 | 75 36 38 | 76 37 39 | 77 38 40 | 78 39 41 | 79 40 42 | 80 41 43 | 81 42 44 | 82 43 45 | 83 44 46 | 84 45 47 | 85 46 48 | 86 47 49 | 87 48 50 | 88 49 51 | 89 50 52 | 90 51 53 | 91 52 54 | 92 53 55 | 93 54 56 | 94 55 57 | 95 56 58 | 96 57 59 | 97 58 60 | 98 59 61 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1ukfa_d1gsa_2.aln: -------------------------------------------------------------------------------- 1 | 7 31 2 | 8 32 3 | 9 33 4 | 10 34 5 | 11 35 6 | 12 36 7 | 20 37 8 | 21 38 9 | 22 39 10 | 23 40 11 | 24 41 12 | 25 42 13 | 26 43 14 | 27 44 15 | 28 45 16 | 29 46 17 | 30 47 18 | 31 48 19 | 33 49 20 | 34 50 21 | 35 51 22 | 36 52 23 | 37 53 24 | 38 54 25 | 39 55 26 | 40 56 27 | 41 57 28 | 46 62 29 | 47 63 30 | 48 64 31 | 49 65 32 | 50 66 33 | 51 67 34 | 52 68 35 | 53 69 36 | 58 70 37 | 59 71 38 | 77 72 39 | 78 73 40 | 79 74 41 | 80 75 42 | 81 76 43 | 82 77 44 | 83 78 45 | 84 79 46 | 85 80 47 | 86 81 48 | 87 82 49 | 88 83 50 | 93 2 51 | 94 3 52 | 95 4 53 | 96 5 54 | 97 6 55 | 98 7 56 | 99 8 57 | 100 9 58 | 101 10 59 | 102 11 60 | 103 12 61 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1k2yx1_1.aln: -------------------------------------------------------------------------------- 1 | 45 97 2 | 46 98 3 | 47 99 4 | 48 100 5 | 49 101 6 | 50 102 7 | 51 103 8 | 52 104 9 | 53 105 10 | 54 106 11 | 59 1 12 | 60 2 13 | 61 3 14 | 62 4 15 | 63 5 16 | 64 6 17 | 65 7 18 | 66 8 19 | 67 9 20 | 68 10 21 | 69 11 22 | 70 12 23 | 71 13 24 | 72 14 25 | 73 15 26 | 74 16 27 | 75 17 28 | 76 18 29 | 77 19 30 | 78 20 31 | 79 21 32 | 82 40 33 | 83 41 34 | 84 42 35 | 85 43 36 | 86 44 37 | 87 45 38 | 88 46 39 | 89 47 40 | 90 48 41 | 91 49 42 | 92 50 43 | 93 51 44 | 94 52 45 | 95 53 46 | 96 54 47 | 97 55 48 | 98 56 49 | 99 57 50 | 100 58 51 | 101 59 52 | 102 60 53 | 111 64 54 | 112 65 55 | 113 66 56 | 114 67 57 | 115 68 58 | 116 69 59 | 117 70 60 | 118 71 61 | 119 72 62 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1aora2d1dkza2.aln: -------------------------------------------------------------------------------- 1 | 4 87 2 | 5 88 3 | 6 89 4 | 7 90 5 | 8 91 6 | 9 92 7 | 10 93 8 | 11 94 9 | 16 18 10 | 17 19 11 | 18 20 12 | 19 21 13 | 20 22 14 | 22 23 15 | 23 24 16 | 24 25 17 | 25 26 18 | 26 27 19 | 27 28 20 | 28 29 21 | 29 30 22 | 36 38 23 | 37 39 24 | 38 40 25 | 39 42 26 | 40 43 27 | 41 44 28 | 42 45 29 | 43 46 30 | 44 47 31 | 45 55 32 | 46 56 33 | 47 57 34 | 48 58 35 | 49 59 36 | 50 60 37 | 51 61 38 | 52 62 39 | 53 63 40 | 54 64 41 | 55 65 42 | 59 66 43 | 60 67 44 | 61 68 45 | 62 69 46 | 63 70 47 | 64 71 48 | 65 72 49 | 66 73 50 | 67 74 51 | 68 75 52 | 69 76 53 | 70 107 54 | 71 108 55 | 72 109 56 | 73 110 57 | 74 111 58 | 75 112 59 | 76 113 60 | 77 114 61 | 78 115 62 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1b6ra1d1v97a4.aln: -------------------------------------------------------------------------------- 1 | 1 73 2 | 2 74 3 | 3 75 4 | 4 76 5 | 5 77 6 | 6 78 7 | 7 79 8 | 8 80 9 | 9 81 10 | 13 106 11 | 14 107 12 | 15 108 13 | 16 109 14 | 17 110 15 | 18 111 16 | 19 112 17 | 20 33 18 | 21 34 19 | 22 35 20 | 23 36 21 | 24 37 22 | 25 38 23 | 26 39 24 | 27 40 25 | 31 83 26 | 32 84 27 | 33 85 28 | 34 86 29 | 35 87 30 | 36 88 31 | 37 89 32 | 41 9 33 | 42 10 34 | 43 11 35 | 44 12 36 | 45 13 37 | 46 14 38 | 47 15 39 | 48 16 40 | 49 17 41 | 50 18 42 | 51 19 43 | 52 20 44 | 53 21 45 | 54 22 46 | 57 48 47 | 58 49 48 | 59 50 49 | 60 51 50 | 61 52 51 | 62 53 52 | 63 54 53 | 64 55 54 | 65 56 55 | 66 57 56 | 67 58 57 | 68 59 58 | 69 60 59 | 70 61 60 | 71 62 61 | 72 63 62 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1lq7a_d1gqea_.aln: -------------------------------------------------------------------------------- 1 | 5 76 2 | 6 77 3 | 7 78 4 | 8 79 5 | 9 80 6 | 10 81 7 | 11 82 8 | 12 83 9 | 13 84 10 | 14 85 11 | 15 86 12 | 16 87 13 | 17 88 14 | 18 89 15 | 19 90 16 | 20 91 17 | 21 92 18 | 22 93 19 | 24 24 20 | 25 25 21 | 26 26 22 | 27 27 23 | 28 28 24 | 29 29 25 | 30 30 26 | 31 31 27 | 32 32 28 | 33 33 29 | 34 34 30 | 35 35 31 | 36 36 32 | 37 37 33 | 38 38 34 | 39 39 35 | 40 40 36 | 41 41 37 | 42 42 38 | 43 43 39 | 44 44 40 | 46 48 41 | 47 49 42 | 48 50 43 | 49 52 44 | 50 53 45 | 51 54 46 | 52 55 47 | 53 56 48 | 54 57 49 | 55 58 50 | 56 59 51 | 57 60 52 | 58 61 53 | 59 62 54 | 60 63 55 | 61 64 56 | 62 65 57 | 63 66 58 | 64 67 59 | 65 68 60 | 66 69 61 | 67 70 62 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d2csta_d1j4wa1.aln: -------------------------------------------------------------------------------- 1 | 26 3 2 | 27 4 3 | 28 5 4 | 29 6 5 | 30 7 6 | 31 8 7 | 32 9 8 | 33 10 9 | 34 11 10 | 37 12 11 | 38 13 12 | 39 14 13 | 40 15 14 | 41 16 15 | 42 17 16 | 43 18 17 | 44 24 18 | 45 25 19 | 46 26 20 | 47 27 21 | 48 28 22 | 49 29 23 | 50 30 24 | 54 65 25 | 55 66 26 | 56 67 27 | 57 68 28 | 58 69 29 | 59 70 30 | 60 71 31 | 61 72 32 | 70 35 33 | 71 36 34 | 72 37 35 | 73 38 36 | 74 39 37 | 75 40 38 | 76 41 39 | 77 42 40 | 78 43 41 | 79 44 42 | 81 45 43 | 82 46 44 | 83 47 45 | 84 48 46 | 85 49 47 | 86 50 48 | 87 51 49 | 88 52 50 | 89 53 51 | 90 54 52 | 91 55 53 | 92 56 54 | 93 57 55 | 94 58 56 | 95 59 57 | 96 60 58 | 97 61 59 | 98 62 60 | 99 63 61 | 100 64 62 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1at0__.aln: -------------------------------------------------------------------------------- 1 | 1 67 2 | 2 68 3 | 3 69 4 | 4 70 5 | 5 71 6 | 6 72 7 | 7 73 8 | 8 74 9 | 9 75 10 | 10 76 11 | 11 77 12 | 12 46 13 | 13 47 14 | 14 48 15 | 15 49 16 | 16 50 17 | 17 51 18 | 18 52 19 | 19 53 20 | 20 54 21 | 21 55 22 | 22 56 23 | 23 57 24 | 24 58 25 | 25 59 26 | 26 60 27 | 27 61 28 | 28 62 29 | 29 63 30 | 30 64 31 | 31 65 32 | 32 66 33 | 33 30 34 | 34 31 35 | 35 32 36 | 36 33 37 | 37 34 38 | 38 35 39 | 39 36 40 | 40 37 41 | 41 38 42 | 42 39 43 | 43 40 44 | 44 41 45 | 45 42 46 | 50 24 47 | 51 25 48 | 52 26 49 | 53 27 50 | 54 28 51 | 55 2 52 | 56 3 53 | 57 4 54 | 58 5 55 | 59 6 56 | 60 7 57 | 61 8 58 | 62 9 59 | 63 10 60 | 64 11 61 | 65 12 62 | 66 13 63 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1hh2p2.aln: -------------------------------------------------------------------------------- 1 | 2 21 2 | 3 22 3 | 4 23 4 | 5 24 5 | 6 25 6 | 7 26 7 | 8 27 8 | 9 28 9 | 10 29 10 | 11 30 11 | 21 31 12 | 22 32 13 | 23 33 14 | 24 34 15 | 25 35 16 | 26 36 17 | 27 37 18 | 28 38 19 | 29 39 20 | 30 41 21 | 31 42 22 | 32 43 23 | 34 2 24 | 35 3 25 | 36 4 26 | 37 5 27 | 38 6 28 | 39 7 29 | 40 8 30 | 47 45 31 | 48 46 32 | 49 47 33 | 50 48 34 | 51 49 35 | 52 50 36 | 53 51 37 | 54 52 38 | 55 53 39 | 56 54 40 | 57 55 41 | 58 56 42 | 59 57 43 | 60 58 44 | 61 59 45 | 62 60 46 | 63 61 47 | 64 62 48 | 65 63 49 | 66 64 50 | 67 65 51 | 68 66 52 | 70 10 53 | 71 11 54 | 72 12 55 | 73 13 56 | 74 14 57 | 75 15 58 | 76 16 59 | 77 17 60 | 78 18 61 | 79 19 62 | 80 20 63 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1hs6a2.aln: -------------------------------------------------------------------------------- 1 | 22 1 2 | 23 2 3 | 24 3 4 | 25 4 5 | 26 5 6 | 27 6 7 | 28 7 8 | 32 60 9 | 33 61 10 | 34 62 11 | 35 63 12 | 36 64 13 | 37 65 14 | 38 66 15 | 39 67 16 | 40 68 17 | 41 69 18 | 42 70 19 | 50 49 20 | 51 50 21 | 52 51 22 | 53 52 23 | 54 53 24 | 55 54 25 | 56 55 26 | 57 11 27 | 58 12 28 | 59 13 29 | 60 14 30 | 61 15 31 | 63 16 32 | 64 17 33 | 65 18 34 | 71 19 35 | 72 20 36 | 73 21 37 | 74 23 38 | 75 24 39 | 76 25 40 | 77 26 41 | 78 27 42 | 79 28 43 | 80 29 44 | 81 30 45 | 83 84 46 | 84 85 47 | 85 86 48 | 86 87 49 | 87 88 50 | 88 89 51 | 89 90 52 | 90 91 53 | 91 92 54 | 92 93 55 | 101 75 56 | 102 76 57 | 103 77 58 | 104 78 59 | 105 79 60 | 106 80 61 | 107 81 62 | 108 82 63 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1k28d1.aln: -------------------------------------------------------------------------------- 1 | 3 30 2 | 4 31 3 | 5 32 4 | 6 33 5 | 7 34 6 | 8 35 7 | 9 36 8 | 10 38 9 | 11 39 10 | 12 40 11 | 16 124 12 | 17 125 13 | 18 126 14 | 19 127 15 | 20 128 16 | 21 129 17 | 22 130 18 | 23 131 19 | 24 132 20 | 25 133 21 | 30 12 22 | 31 13 23 | 32 14 24 | 33 15 25 | 34 16 26 | 35 17 27 | 36 18 28 | 37 19 29 | 38 20 30 | 39 21 31 | 40 22 32 | 41 23 33 | 42 24 34 | 43 25 35 | 44 26 36 | 51 10 37 | 52 11 38 | 53 59 39 | 54 60 40 | 55 61 41 | 56 62 42 | 57 63 43 | 58 64 44 | 59 65 45 | 60 66 46 | 61 67 47 | 62 68 48 | 63 69 49 | 64 70 50 | 65 71 51 | 66 72 52 | 67 73 53 | 68 74 54 | 72 1 55 | 73 2 56 | 74 3 57 | 75 4 58 | 76 5 59 | 77 6 60 | 78 7 61 | 79 8 62 | 80 9 63 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1k6ka_.aln: -------------------------------------------------------------------------------- 1 | 1 32 2 | 2 33 3 | 3 34 4 | 4 35 5 | 5 36 6 | 6 37 7 | 7 38 8 | 8 39 9 | 9 40 10 | 10 41 11 | 11 42 12 | 12 43 13 | 13 44 14 | 14 45 15 | 15 46 16 | 16 47 17 | 17 48 18 | 18 49 19 | 19 50 20 | 20 51 21 | 21 52 22 | 22 53 23 | 23 54 24 | 24 55 25 | 25 56 26 | 26 57 27 | 27 58 28 | 28 59 29 | 29 60 30 | 30 61 31 | 31 62 32 | 32 63 33 | 33 64 34 | 34 65 35 | 35 66 36 | 36 67 37 | 37 68 38 | 38 15 39 | 39 16 40 | 40 17 41 | 41 18 42 | 42 19 43 | 43 20 44 | 44 21 45 | 45 22 46 | 46 23 47 | 47 24 48 | 48 25 49 | 49 26 50 | 54 1 51 | 55 2 52 | 56 3 53 | 57 4 54 | 58 5 55 | 59 6 56 | 60 7 57 | 61 8 58 | 62 9 59 | 63 10 60 | 64 11 61 | 65 12 62 | 66 13 63 | -------------------------------------------------------------------------------- /src/coord_definition.c: -------------------------------------------------------------------------------- 1 | #include "mican.h" 2 | 3 | void coord_definition(float *x, float *y, float *z, SSEDAT *ssedat, int isse) { 4 | int i; 5 | 6 | /** coordinate x **/ 7 | for (i = 1; i <= 3; i++) { 8 | x[i] = ssedat[isse].para[i]; 9 | } 10 | /** coordinate y **/ 11 | for (i = 1; i <= 3; i++) { 12 | y[i] = ssedat[isse].perp[i]; 13 | } 14 | /** coordinate z **/ 15 | z[1] = x[2] * y[3] - x[3] * y[2]; 16 | z[2] = x[3] * y[1] - x[1] * y[3]; 17 | z[3] = x[1] * y[2] - x[2] * y[1]; 18 | 19 | return; 20 | } 21 | 22 | void coord_definition_r(float *x, float *y, float *z, SSEDAT *ssedat, 23 | int isse) { 24 | int i; 25 | 26 | /** coordinate x **/ 27 | for (i = 1; i <= 3; i++) { 28 | x[i] = -ssedat[isse].para[i]; 29 | } 30 | /** coordinate y **/ 31 | for (i = 1; i <= 3; i++) { 32 | y[i] = ssedat[isse].perp[i]; 33 | } 34 | /** coordinate z **/ 35 | z[1] = x[2] * y[3] - x[3] * y[2]; 36 | z[2] = x[3] * y[1] - x[1] * y[3]; 37 | z[3] = x[1] * y[2] - x[2] * y[1]; 38 | 39 | return; 40 | } 41 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1b6ra1d1k8kd1.aln: -------------------------------------------------------------------------------- 1 | 1 110 2 | 2 111 3 | 3 112 4 | 4 113 5 | 5 114 6 | 6 115 7 | 7 116 8 | 8 117 9 | 9 118 10 | 10 98 11 | 11 99 12 | 12 100 13 | 14 101 14 | 15 102 15 | 16 103 16 | 17 104 17 | 18 105 18 | 21 2 19 | 22 3 20 | 23 4 21 | 24 5 22 | 25 6 23 | 26 7 24 | 27 8 25 | 28 9 26 | 29 10 27 | 30 83 28 | 31 84 29 | 32 85 30 | 33 86 31 | 34 87 32 | 35 88 33 | 36 89 34 | 37 90 35 | 38 91 36 | 39 92 37 | 44 39 38 | 45 40 39 | 46 41 40 | 47 42 41 | 48 43 42 | 49 44 43 | 50 45 44 | 51 46 45 | 52 47 46 | 53 48 47 | 54 49 48 | 55 50 49 | 56 51 50 | 60 62 51 | 61 63 52 | 62 64 53 | 63 65 54 | 64 66 55 | 65 67 56 | 66 68 57 | 67 69 58 | 68 70 59 | 69 71 60 | 70 72 61 | 71 73 62 | 72 74 63 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1hi9a_d1rpua_.aln: -------------------------------------------------------------------------------- 1 | 4 81 2 | 5 82 3 | 6 83 4 | 7 84 5 | 8 85 6 | 9 86 7 | 10 91 8 | 11 92 9 | 12 93 10 | 13 94 11 | 17 15 12 | 18 16 13 | 19 17 14 | 20 18 15 | 21 19 16 | 22 20 17 | 23 21 18 | 24 22 19 | 25 23 20 | 26 24 21 | 27 25 22 | 33 32 23 | 34 33 24 | 35 34 25 | 36 35 26 | 37 36 27 | 38 37 28 | 39 38 29 | 40 39 30 | 41 40 31 | 42 41 32 | 43 42 33 | 44 43 34 | 45 44 35 | 46 45 36 | 47 46 37 | 48 47 38 | 49 48 39 | 50 49 40 | 51 50 41 | 52 53 42 | 53 54 43 | 54 55 44 | 55 56 45 | 56 57 46 | 57 58 47 | 58 59 48 | 59 60 49 | 60 61 50 | 61 62 51 | 62 63 52 | 63 64 53 | 64 65 54 | 65 66 55 | 66 67 56 | 67 68 57 | 68 69 58 | 69 70 59 | 70 71 60 | 71 72 61 | 72 73 62 | 73 74 63 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1o17d2d1ir6a_.aln: -------------------------------------------------------------------------------- 1 | 4 19 2 | 5 20 3 | 6 21 4 | 7 22 5 | 8 23 6 | 9 24 7 | 10 25 8 | 11 26 9 | 12 2 10 | 13 3 11 | 14 4 12 | 15 5 13 | 16 6 14 | 17 7 15 | 18 8 16 | 19 9 17 | 20 10 18 | 21 11 19 | 22 12 20 | 23 13 21 | 24 14 22 | 25 15 23 | 26 16 24 | 27 17 25 | 28 58 26 | 29 59 27 | 31 60 28 | 32 61 29 | 33 62 30 | 34 63 31 | 35 64 32 | 36 65 33 | 37 66 34 | 50 67 35 | 51 68 36 | 52 69 37 | 53 70 38 | 54 71 39 | 55 72 40 | 56 73 41 | 57 74 42 | 59 98 43 | 60 99 44 | 61 100 45 | 62 101 46 | 63 102 47 | 64 103 48 | 65 104 49 | 66 105 50 | 76 28 51 | 77 29 52 | 78 30 53 | 79 31 54 | 80 32 55 | 81 33 56 | 82 34 57 | 83 35 58 | 84 36 59 | 85 37 60 | 86 38 61 | 87 39 62 | 88 40 63 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1o17d2d1jyra_.aln: -------------------------------------------------------------------------------- 1 | 9 28 2 | 10 29 3 | 11 30 4 | 12 31 5 | 13 32 6 | 14 33 7 | 16 34 8 | 17 35 9 | 18 36 10 | 19 37 11 | 20 38 12 | 21 39 13 | 22 40 14 | 23 41 15 | 24 42 16 | 25 43 17 | 26 44 18 | 27 45 19 | 28 46 20 | 29 47 21 | 30 48 22 | 31 49 23 | 32 50 24 | 33 51 25 | 34 52 26 | 35 53 27 | 36 54 28 | 37 55 29 | 38 56 30 | 39 57 31 | 48 3 32 | 49 4 33 | 50 5 34 | 51 6 35 | 52 7 36 | 53 8 37 | 54 9 38 | 55 10 39 | 56 11 40 | 57 12 41 | 58 13 42 | 59 14 43 | 60 15 44 | 61 16 45 | 62 17 46 | 63 18 47 | 64 19 48 | 65 20 49 | 66 21 50 | 67 22 51 | 74 72 52 | 75 73 53 | 76 74 54 | 77 75 55 | 78 76 56 | 79 77 57 | 80 78 58 | 81 79 59 | 82 80 60 | 83 81 61 | 84 82 62 | 85 83 63 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1pdz_1d1irum_.aln: -------------------------------------------------------------------------------- 1 | 1 52 2 | 2 53 3 | 3 54 4 | 4 55 5 | 5 56 6 | 6 57 7 | 7 58 8 | 19 83 9 | 20 84 10 | 22 41 11 | 23 42 12 | 24 43 13 | 25 44 14 | 26 45 15 | 27 46 16 | 36 16 17 | 37 17 18 | 38 18 19 | 39 19 20 | 40 20 21 | 41 21 22 | 42 22 23 | 43 23 24 | 44 24 25 | 45 25 26 | 46 26 27 | 47 27 28 | 48 28 29 | 49 29 30 | 50 30 31 | 51 31 32 | 52 32 33 | 53 33 34 | 54 34 35 | 55 35 36 | 56 36 37 | 73 64 38 | 74 65 39 | 75 66 40 | 76 67 41 | 77 68 42 | 78 69 43 | 79 70 44 | 80 71 45 | 81 72 46 | 82 73 47 | 83 74 48 | 84 75 49 | 85 76 50 | 86 77 51 | 87 78 52 | 88 79 53 | 89 80 54 | 90 81 55 | 94 4 56 | 95 5 57 | 96 6 58 | 97 7 59 | 98 8 60 | 99 9 61 | 100 10 62 | 101 11 63 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1avk_2.aln: -------------------------------------------------------------------------------- 1 | 4 16 2 | 5 17 3 | 6 18 4 | 7 19 5 | 8 20 6 | 9 21 7 | 10 22 8 | 11 23 9 | 12 24 10 | 13 25 11 | 14 26 12 | 15 27 13 | 16 28 14 | 17 29 15 | 18 30 16 | 19 31 17 | 20 32 18 | 21 33 19 | 22 34 20 | 29 100 21 | 30 101 22 | 31 102 23 | 32 103 24 | 33 104 25 | 34 105 26 | 35 106 27 | 36 107 28 | 37 108 29 | 38 109 30 | 39 110 31 | 40 111 32 | 48 3 33 | 49 4 34 | 50 5 35 | 51 6 36 | 52 7 37 | 53 8 38 | 54 9 39 | 55 10 40 | 56 11 41 | 57 12 42 | 58 13 43 | 59 14 44 | 64 57 45 | 65 58 46 | 66 59 47 | 67 60 48 | 68 61 49 | 69 62 50 | 70 63 51 | 71 64 52 | 72 65 53 | 73 66 54 | 74 67 55 | 75 68 56 | 76 69 57 | 77 70 58 | 78 71 59 | 79 72 60 | 80 73 61 | 81 74 62 | 82 75 63 | 83 76 64 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1kapp1.aln: -------------------------------------------------------------------------------- 1 | 1 18 2 | 2 19 3 | 3 20 4 | 4 21 5 | 5 22 6 | 6 23 7 | 7 24 8 | 19 76 9 | 20 77 10 | 21 78 11 | 22 79 12 | 23 80 13 | 24 81 14 | 25 82 15 | 26 83 16 | 27 3 17 | 28 4 18 | 29 5 19 | 30 6 20 | 31 7 21 | 32 8 22 | 33 9 23 | 37 87 24 | 38 88 25 | 39 89 26 | 40 90 27 | 41 91 28 | 42 92 29 | 43 93 30 | 44 94 31 | 45 95 32 | 46 96 33 | 47 57 34 | 48 58 35 | 49 59 36 | 50 60 37 | 51 61 38 | 52 62 39 | 53 63 40 | 54 64 41 | 55 65 42 | 56 35 43 | 57 36 44 | 58 37 45 | 59 38 46 | 60 39 47 | 61 40 48 | 62 41 49 | 63 73 50 | 64 74 51 | 65 75 52 | 68 29 53 | 69 30 54 | 70 31 55 | 71 32 56 | 74 25 57 | 75 26 58 | 76 27 59 | 77 28 60 | 78 14 61 | 79 15 62 | 80 16 63 | 81 17 64 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1dzka_d1qd1b2.aln: -------------------------------------------------------------------------------- 1 | 6 17 2 | 7 18 3 | 8 19 4 | 9 20 5 | 11 21 6 | 12 22 7 | 13 23 8 | 14 24 9 | 15 25 10 | 16 26 11 | 17 54 12 | 18 55 13 | 19 56 14 | 20 57 15 | 21 58 16 | 22 59 17 | 23 60 18 | 24 61 19 | 25 62 20 | 26 63 21 | 27 64 22 | 31 1 23 | 32 2 24 | 33 3 25 | 34 4 26 | 35 5 27 | 36 6 28 | 37 7 29 | 38 8 30 | 39 9 31 | 40 10 32 | 41 11 33 | 42 12 34 | 43 13 35 | 44 14 36 | 45 15 37 | 46 66 38 | 47 67 39 | 48 68 40 | 49 69 41 | 50 70 42 | 51 71 43 | 52 72 44 | 53 73 45 | 54 74 46 | 55 75 47 | 56 76 48 | 57 77 49 | 58 78 50 | 59 79 51 | 60 80 52 | 61 81 53 | 62 82 54 | 63 83 55 | 64 84 56 | 65 85 57 | 66 86 58 | 67 87 59 | 68 88 60 | 69 89 61 | 70 90 62 | 71 91 63 | 72 92 64 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1izna_d1keka2.aln: -------------------------------------------------------------------------------- 1 | 3 35 2 | 4 36 3 | 5 37 4 | 6 38 5 | 7 39 6 | 8 40 7 | 9 41 8 | 10 42 9 | 11 43 10 | 12 44 11 | 13 45 12 | 14 46 13 | 15 47 14 | 16 48 15 | 17 49 16 | 18 50 17 | 19 72 18 | 20 73 19 | 21 74 20 | 22 75 21 | 23 77 22 | 24 78 23 | 25 79 24 | 26 80 25 | 27 81 26 | 28 82 27 | 29 83 28 | 30 84 29 | 31 85 30 | 32 86 31 | 33 87 32 | 34 88 33 | 37 2 34 | 38 3 35 | 39 4 36 | 40 5 37 | 41 6 38 | 42 7 39 | 43 8 40 | 44 9 41 | 45 10 42 | 46 11 43 | 47 12 44 | 48 13 45 | 49 14 46 | 50 15 47 | 51 16 48 | 52 17 49 | 54 54 50 | 55 55 51 | 56 56 52 | 57 57 53 | 58 58 54 | 59 59 55 | 60 60 56 | 61 61 57 | 62 62 58 | 63 63 59 | 64 64 60 | 65 65 61 | 66 66 62 | 67 67 63 | 68 68 64 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1izna_d2gsca_.aln: -------------------------------------------------------------------------------- 1 | 3 64 2 | 4 65 3 | 5 66 4 | 6 67 5 | 7 68 6 | 8 69 7 | 9 70 8 | 10 71 9 | 11 72 10 | 12 73 11 | 13 74 12 | 14 75 13 | 15 76 14 | 16 77 15 | 17 78 16 | 18 79 17 | 19 80 18 | 22 8 19 | 23 9 20 | 24 10 21 | 25 11 22 | 26 12 23 | 27 13 24 | 28 14 25 | 29 15 26 | 30 16 27 | 31 17 28 | 32 18 29 | 33 19 30 | 34 20 31 | 35 21 32 | 37 39 33 | 38 40 34 | 39 41 35 | 40 42 36 | 41 43 37 | 42 44 38 | 43 45 39 | 44 46 40 | 45 47 41 | 46 48 42 | 47 49 43 | 48 50 44 | 49 51 45 | 50 52 46 | 51 53 47 | 52 85 48 | 53 86 49 | 54 87 50 | 55 88 51 | 56 89 52 | 57 90 53 | 58 91 54 | 59 92 55 | 60 93 56 | 61 94 57 | 62 95 58 | 63 96 59 | 64 97 60 | 65 98 61 | 66 99 62 | 67 100 63 | 68 101 64 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1p5gx1d1xppa_.aln: -------------------------------------------------------------------------------- 1 | 5 94 2 | 6 95 3 | 7 97 4 | 8 98 5 | 9 4 6 | 10 5 7 | 11 6 8 | 12 7 9 | 13 8 10 | 14 9 11 | 15 10 12 | 19 11 13 | 20 12 14 | 21 13 15 | 22 14 16 | 23 15 17 | 24 16 18 | 25 17 19 | 26 18 20 | 27 19 21 | 28 20 22 | 29 21 23 | 30 22 24 | 31 23 25 | 32 24 26 | 33 25 27 | 34 26 28 | 35 27 29 | 43 81 30 | 44 82 31 | 45 83 32 | 46 84 33 | 47 85 34 | 48 86 35 | 49 87 36 | 55 32 37 | 56 33 38 | 57 34 39 | 58 35 40 | 59 36 41 | 60 37 42 | 61 38 43 | 62 39 44 | 63 40 45 | 64 41 46 | 65 42 47 | 66 43 48 | 67 44 49 | 69 45 50 | 70 46 51 | 71 47 52 | 72 48 53 | 73 49 54 | 74 50 55 | 75 51 56 | 76 52 57 | 77 53 58 | 78 54 59 | 79 55 60 | 80 56 61 | 81 57 62 | 82 58 63 | 83 59 64 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1b70b2.aln: -------------------------------------------------------------------------------- 1 | 1 40 2 | 2 41 3 | 3 42 4 | 4 43 5 | 5 44 6 | 6 45 7 | 7 46 8 | 8 47 9 | 9 48 10 | 10 49 11 | 11 50 12 | 12 51 13 | 13 52 14 | 14 53 15 | 15 54 16 | 16 55 17 | 17 56 18 | 18 57 19 | 19 58 20 | 20 59 21 | 21 60 22 | 22 61 23 | 23 62 24 | 24 63 25 | 25 64 26 | 26 65 27 | 27 66 28 | 28 67 29 | 29 68 30 | 30 69 31 | 31 70 32 | 32 71 33 | 33 72 34 | 34 73 35 | 35 74 36 | 36 75 37 | 41 1 38 | 42 2 39 | 43 3 40 | 44 4 41 | 45 5 42 | 46 6 43 | 47 7 44 | 48 8 45 | 49 9 46 | 50 10 47 | 51 11 48 | 52 12 49 | 53 13 50 | 54 14 51 | 55 15 52 | 56 16 53 | 57 17 54 | 58 18 55 | 59 19 56 | 60 20 57 | 61 21 58 | 62 22 59 | 63 23 60 | 64 24 61 | 65 25 62 | 66 26 63 | 67 27 64 | 68 28 65 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1jh7a_.aln: -------------------------------------------------------------------------------- 1 | 10 1 2 | 11 2 3 | 12 3 4 | 13 4 5 | 14 5 6 | 15 6 7 | 16 7 8 | 17 8 9 | 18 9 10 | 21 44 11 | 22 45 12 | 23 46 13 | 24 47 14 | 25 48 15 | 26 49 16 | 27 50 17 | 28 51 18 | 29 52 19 | 30 53 20 | 31 54 21 | 32 55 22 | 39 16 23 | 40 17 24 | 41 18 25 | 42 19 26 | 43 20 27 | 44 21 28 | 45 22 29 | 46 23 30 | 47 24 31 | 49 25 32 | 50 26 33 | 51 27 34 | 52 28 35 | 53 29 36 | 54 30 37 | 55 31 38 | 56 32 39 | 57 33 40 | 58 34 41 | 59 35 42 | 60 36 43 | 61 37 44 | 62 38 45 | 63 39 46 | 64 40 47 | 65 41 48 | 66 42 49 | 67 61 50 | 68 62 51 | 69 63 52 | 70 64 53 | 71 65 54 | 72 66 55 | 73 67 56 | 74 68 57 | 75 69 58 | 76 70 59 | 77 71 60 | 78 72 61 | 79 73 62 | 80 74 63 | 81 75 64 | 82 76 65 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1tdj_2.aln: -------------------------------------------------------------------------------- 1 | 2 52 2 | 3 53 3 | 4 54 4 | 5 55 5 | 6 56 6 | 7 57 7 | 8 58 8 | 9 59 9 | 10 60 10 | 11 61 11 | 12 62 12 | 13 63 13 | 14 64 14 | 15 65 15 | 16 66 16 | 17 67 17 | 18 68 18 | 19 69 19 | 20 70 20 | 21 71 21 | 22 72 22 | 23 73 23 | 24 74 24 | 25 75 25 | 26 20 26 | 27 21 27 | 28 22 28 | 29 23 29 | 30 24 30 | 31 25 31 | 32 26 32 | 33 27 33 | 34 28 34 | 35 29 35 | 36 30 36 | 37 31 37 | 38 32 38 | 39 33 39 | 40 34 40 | 41 35 41 | 42 36 42 | 43 37 43 | 44 38 44 | 45 39 45 | 46 40 46 | 47 41 47 | 48 42 48 | 49 43 49 | 68 1 50 | 69 2 51 | 70 3 52 | 71 4 53 | 72 5 54 | 73 6 55 | 74 7 56 | 76 8 57 | 77 9 58 | 78 10 59 | 79 11 60 | 80 12 61 | 81 13 62 | 82 14 63 | 83 15 64 | 84 16 65 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1a6da1.aln: -------------------------------------------------------------------------------- 1 | 7 51 2 | 8 52 3 | 9 53 4 | 10 54 5 | 11 55 6 | 12 56 7 | 13 57 8 | 14 58 9 | 15 59 10 | 16 60 11 | 17 61 12 | 18 62 13 | 19 63 14 | 20 64 15 | 21 65 16 | 22 66 17 | 23 67 18 | 24 68 19 | 25 69 20 | 26 70 21 | 47 8 22 | 48 9 23 | 49 10 24 | 50 11 25 | 51 12 26 | 52 13 27 | 53 14 28 | 54 15 29 | 55 16 30 | 59 28 31 | 60 29 32 | 61 30 33 | 62 31 34 | 63 32 35 | 64 33 36 | 65 34 37 | 66 35 38 | 67 36 39 | 68 37 40 | 69 38 41 | 70 39 42 | 71 40 43 | 72 41 44 | 77 119 45 | 78 120 46 | 79 121 47 | 80 122 48 | 81 123 49 | 82 124 50 | 83 125 51 | 84 126 52 | 85 127 53 | 86 128 54 | 87 129 55 | 88 130 56 | 89 131 57 | 90 132 58 | 91 133 59 | 92 134 60 | 93 135 61 | 94 136 62 | 95 137 63 | 96 138 64 | 97 139 65 | 98 140 66 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1efud4.aln: -------------------------------------------------------------------------------- 1 | 5 102 2 | 6 103 3 | 7 104 4 | 8 105 5 | 9 106 6 | 10 107 7 | 11 108 8 | 12 109 9 | 13 110 10 | 14 46 11 | 15 47 12 | 16 48 13 | 17 49 14 | 18 50 15 | 19 51 16 | 20 52 17 | 21 53 18 | 22 54 19 | 23 55 20 | 34 57 21 | 35 58 22 | 36 59 23 | 37 60 24 | 38 61 25 | 39 62 26 | 40 63 27 | 41 64 28 | 42 65 29 | 43 66 30 | 44 67 31 | 45 68 32 | 46 69 33 | 47 70 34 | 48 71 35 | 49 72 36 | 50 73 37 | 51 74 38 | 52 75 39 | 53 76 40 | 54 77 41 | 55 39 42 | 56 40 43 | 57 41 44 | 58 42 45 | 59 43 46 | 60 9 47 | 61 10 48 | 62 11 49 | 63 12 50 | 64 13 51 | 65 14 52 | 66 15 53 | 67 16 54 | 68 17 55 | 75 111 56 | 76 112 57 | 77 113 58 | 78 114 59 | 79 115 60 | 80 116 61 | 81 117 62 | 82 118 63 | 83 119 64 | 84 120 65 | 85 121 66 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1f52a2.aln: -------------------------------------------------------------------------------- 1 | 22 6 2 | 23 7 3 | 24 8 4 | 25 9 5 | 26 10 6 | 27 11 7 | 28 12 8 | 29 13 9 | 30 14 10 | 31 15 11 | 32 16 12 | 33 17 13 | 34 18 14 | 35 19 15 | 36 20 16 | 86 73 17 | 87 74 18 | 88 75 19 | 89 76 20 | 90 77 21 | 91 78 22 | 92 79 23 | 93 80 24 | 94 81 25 | 95 82 26 | 96 83 27 | 97 84 28 | 98 85 29 | 99 86 30 | 100 87 31 | 101 88 32 | 102 89 33 | 107 57 34 | 108 58 35 | 109 59 36 | 110 60 37 | 111 61 38 | 112 62 39 | 113 63 40 | 114 64 41 | 115 65 42 | 116 97 43 | 117 98 44 | 118 99 45 | 119 100 46 | 120 101 47 | 121 102 48 | 122 103 49 | 133 109 50 | 134 110 51 | 135 111 52 | 136 112 53 | 137 113 54 | 138 114 55 | 139 115 56 | 140 116 57 | 141 117 58 | 142 118 59 | 143 119 60 | 144 120 61 | 145 121 62 | 146 122 63 | 147 123 64 | 148 124 65 | 149 125 66 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1rl6a1.aln: -------------------------------------------------------------------------------- 1 | 1 70 2 | 2 71 3 | 3 72 4 | 4 73 5 | 5 75 6 | 6 76 7 | 7 77 8 | 8 78 9 | 9 79 10 | 10 80 11 | 11 81 12 | 12 82 13 | 13 83 14 | 14 84 15 | 15 85 16 | 16 86 17 | 17 87 18 | 18 88 19 | 19 89 20 | 20 90 21 | 21 91 22 | 22 92 23 | 23 93 24 | 24 37 25 | 25 38 26 | 26 39 27 | 27 40 28 | 28 41 29 | 29 42 30 | 30 43 31 | 31 44 32 | 32 45 33 | 33 46 34 | 34 47 35 | 35 48 36 | 36 49 37 | 37 50 38 | 38 51 39 | 39 52 40 | 40 54 41 | 41 55 42 | 42 56 43 | 43 57 44 | 44 58 45 | 45 59 46 | 46 60 47 | 47 61 48 | 48 62 49 | 54 1 50 | 55 2 51 | 56 3 52 | 57 4 53 | 58 5 54 | 59 6 55 | 60 7 56 | 61 8 57 | 62 9 58 | 63 10 59 | 64 11 60 | 65 12 61 | 66 13 62 | 67 14 63 | 68 15 64 | 69 16 65 | 70 17 66 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1i1qa__1.aln: -------------------------------------------------------------------------------- 1 | 7 50 2 | 8 51 3 | 9 52 4 | 10 53 5 | 11 54 6 | 12 55 7 | 13 56 8 | 16 73 9 | 17 74 10 | 18 75 11 | 19 76 12 | 20 77 13 | 21 78 14 | 22 79 15 | 23 80 16 | 24 81 17 | 25 82 18 | 26 83 19 | 29 35 20 | 30 36 21 | 31 37 22 | 32 38 23 | 33 39 24 | 34 40 25 | 35 41 26 | 36 42 27 | 37 43 28 | 46 99 29 | 47 100 30 | 48 101 31 | 49 102 32 | 50 103 33 | 51 104 34 | 55 105 35 | 56 106 36 | 57 107 37 | 58 108 38 | 59 109 39 | 60 110 40 | 61 111 41 | 62 112 42 | 65 113 43 | 66 114 44 | 67 115 45 | 68 116 46 | 69 117 47 | 70 118 48 | 71 119 49 | 72 120 50 | 81 1 51 | 82 2 52 | 83 3 53 | 84 4 54 | 85 5 55 | 86 6 56 | 87 7 57 | 88 8 58 | 89 9 59 | 90 10 60 | 91 11 61 | 92 12 62 | 93 13 63 | 94 14 64 | 95 15 65 | 96 16 66 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1a05a_d1dgsa3.aln: -------------------------------------------------------------------------------- 1 | 5 43 2 | 6 44 3 | 7 45 4 | 8 46 5 | 9 47 6 | 10 48 7 | 11 49 8 | 12 50 9 | 13 51 10 | 14 52 11 | 15 53 12 | 16 54 13 | 17 55 14 | 18 56 15 | 20 3 16 | 21 4 17 | 22 5 18 | 23 6 19 | 24 7 20 | 25 8 21 | 26 9 22 | 27 10 23 | 28 11 24 | 29 12 25 | 30 31 26 | 31 32 27 | 32 33 28 | 33 34 29 | 34 35 30 | 35 36 31 | 36 37 32 | 37 38 33 | 38 39 34 | 41 58 35 | 42 59 36 | 43 60 37 | 44 61 38 | 45 62 39 | 46 63 40 | 47 64 41 | 48 65 42 | 49 66 43 | 50 67 44 | 51 68 45 | 52 69 46 | 53 70 47 | 54 71 48 | 55 72 49 | 56 73 50 | 61 82 51 | 62 83 52 | 63 84 53 | 64 85 54 | 65 86 55 | 66 87 56 | 67 88 57 | 68 89 58 | 73 22 59 | 74 23 60 | 75 24 61 | 76 25 62 | 77 26 63 | 78 27 64 | 79 28 65 | 80 29 66 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1e3pa3d1tis__.aln: -------------------------------------------------------------------------------- 1 | 3 12 2 | 4 13 3 | 5 14 4 | 6 72 5 | 7 73 6 | 8 74 7 | 9 75 8 | 10 76 9 | 11 77 10 | 18 92 11 | 19 93 12 | 20 94 13 | 21 95 14 | 22 96 15 | 23 97 16 | 24 98 17 | 25 99 18 | 33 1 19 | 34 2 20 | 35 3 21 | 36 4 22 | 37 5 23 | 38 6 24 | 39 7 25 | 40 8 26 | 47 24 27 | 48 25 28 | 49 26 29 | 50 27 30 | 51 28 31 | 52 29 32 | 53 30 33 | 54 31 34 | 55 32 35 | 56 33 36 | 57 34 37 | 58 35 38 | 59 36 39 | 60 37 40 | 61 38 41 | 62 39 42 | 63 40 43 | 73 45 44 | 74 46 45 | 75 47 46 | 76 48 47 | 77 49 48 | 78 50 49 | 79 51 50 | 80 52 51 | 81 53 52 | 83 57 53 | 84 58 54 | 85 59 55 | 86 60 56 | 87 61 57 | 88 62 58 | 89 63 59 | 90 64 60 | 91 65 61 | 92 66 62 | 93 67 63 | 94 68 64 | 95 69 65 | 96 70 66 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1htjf_d1nhua_.aln: -------------------------------------------------------------------------------- 1 | 1 37 2 | 2 38 3 | 3 39 4 | 4 40 5 | 5 41 6 | 6 42 7 | 7 43 8 | 8 44 9 | 9 45 10 | 10 46 11 | 11 47 12 | 12 48 13 | 13 49 14 | 14 50 15 | 15 51 16 | 16 52 17 | 17 70 18 | 18 71 19 | 19 72 20 | 20 73 21 | 21 74 22 | 22 75 23 | 23 76 24 | 24 77 25 | 25 78 26 | 26 79 27 | 27 80 28 | 28 81 29 | 29 82 30 | 30 83 31 | 39 111 32 | 40 112 33 | 41 113 34 | 42 114 35 | 43 115 36 | 44 116 37 | 45 117 38 | 46 118 39 | 47 119 40 | 48 120 41 | 49 121 42 | 50 122 43 | 51 123 44 | 52 124 45 | 53 125 46 | 54 126 47 | 55 127 48 | 56 128 49 | 57 129 50 | 59 130 51 | 60 131 52 | 61 132 53 | 62 133 54 | 63 134 55 | 64 135 56 | 65 136 57 | 66 137 58 | 67 138 59 | 68 139 60 | 69 140 61 | 70 141 62 | 71 142 63 | 72 143 64 | 73 144 65 | 74 145 66 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1m9na2d1j27a_.aln: -------------------------------------------------------------------------------- 1 | 3 5 2 | 4 6 3 | 5 7 4 | 6 8 5 | 7 9 6 | 8 10 7 | 9 11 8 | 10 12 9 | 11 13 10 | 12 14 11 | 13 15 12 | 14 16 13 | 15 17 14 | 16 18 15 | 17 19 16 | 18 20 17 | 19 21 18 | 20 22 19 | 27 90 20 | 28 91 21 | 29 92 22 | 30 93 23 | 31 94 24 | 32 95 25 | 38 60 26 | 39 61 27 | 40 62 28 | 41 63 29 | 42 64 30 | 43 65 31 | 44 66 32 | 45 70 33 | 46 71 34 | 47 72 35 | 48 73 36 | 49 74 37 | 50 75 38 | 51 76 39 | 52 77 40 | 53 78 41 | 54 79 42 | 55 80 43 | 56 81 44 | 57 82 45 | 58 83 46 | 59 84 47 | 60 85 48 | 61 86 49 | 62 87 50 | 63 88 51 | 64 89 52 | 67 26 53 | 68 27 54 | 69 28 55 | 70 29 56 | 71 30 57 | 72 31 58 | 73 42 59 | 74 43 60 | 75 44 61 | 77 45 62 | 78 46 63 | 79 47 64 | 80 48 65 | 81 49 66 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1tv8a_d1nbwb_.aln: -------------------------------------------------------------------------------- 1 | 2 36 2 | 3 37 3 | 4 38 4 | 5 39 5 | 6 40 6 | 7 41 7 | 8 42 8 | 9 43 9 | 39 57 10 | 40 58 11 | 41 59 12 | 42 60 13 | 43 61 14 | 44 62 15 | 45 63 16 | 46 64 17 | 47 65 18 | 48 66 19 | 49 67 20 | 50 68 21 | 51 69 22 | 52 70 23 | 53 71 24 | 54 72 25 | 55 73 26 | 56 19 27 | 57 20 28 | 58 21 29 | 59 22 30 | 60 23 31 | 61 24 32 | 62 25 33 | 63 30 34 | 64 31 35 | 65 32 36 | 66 33 37 | 67 34 38 | 69 81 39 | 70 82 40 | 71 83 41 | 72 84 42 | 73 85 43 | 74 47 44 | 75 48 45 | 76 49 46 | 77 50 47 | 78 51 48 | 86 87 49 | 87 88 50 | 88 89 51 | 89 90 52 | 90 91 53 | 91 92 54 | 92 93 55 | 93 94 56 | 94 95 57 | 95 96 58 | 96 97 59 | 97 98 60 | 98 99 61 | 99 100 62 | 100 101 63 | 101 102 64 | 102 103 65 | 103 104 66 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1in0b1.aln: -------------------------------------------------------------------------------- 1 | 2 68 2 | 3 69 3 | 4 70 4 | 5 71 5 | 6 72 6 | 7 73 7 | 8 74 8 | 9 75 9 | 10 76 10 | 11 77 11 | 12 78 12 | 13 79 13 | 14 80 14 | 15 81 15 | 16 82 16 | 17 83 17 | 18 84 18 | 20 60 19 | 21 61 20 | 22 62 21 | 23 63 22 | 24 64 23 | 25 65 24 | 26 66 25 | 27 29 26 | 28 30 27 | 29 31 28 | 30 32 29 | 31 33 30 | 32 34 31 | 33 35 32 | 34 36 33 | 35 37 34 | 36 38 35 | 37 39 36 | 38 40 37 | 39 41 38 | 40 42 39 | 41 43 40 | 42 44 41 | 43 45 42 | 44 46 43 | 45 47 44 | 46 48 45 | 47 49 46 | 48 50 47 | 49 51 48 | 50 52 49 | 51 53 50 | 55 23 51 | 56 24 52 | 57 25 53 | 58 26 54 | 59 27 55 | 60 2 56 | 61 3 57 | 62 4 58 | 63 5 59 | 64 10 60 | 65 11 61 | 66 12 62 | 67 13 63 | 68 14 64 | 69 15 65 | 70 16 66 | 71 17 67 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1jtgb_.aln: -------------------------------------------------------------------------------- 1 | 3 25 2 | 4 26 3 | 5 27 4 | 6 28 5 | 7 29 6 | 8 30 7 | 9 31 8 | 10 32 9 | 11 33 10 | 12 34 11 | 13 35 12 | 14 36 13 | 15 37 14 | 16 38 15 | 17 39 16 | 18 40 17 | 19 41 18 | 20 42 19 | 21 43 20 | 22 44 21 | 23 45 22 | 24 46 23 | 25 47 24 | 26 48 25 | 27 49 26 | 28 50 27 | 29 51 28 | 30 52 29 | 31 53 30 | 32 54 31 | 33 55 32 | 38 11 33 | 39 12 34 | 40 13 35 | 41 14 36 | 42 15 37 | 43 16 38 | 44 17 39 | 45 18 40 | 46 19 41 | 47 20 42 | 48 21 43 | 49 63 44 | 50 64 45 | 51 65 46 | 52 66 47 | 53 67 48 | 54 68 49 | 55 69 50 | 56 70 51 | 57 71 52 | 58 72 53 | 59 73 54 | 60 74 55 | 65 75 56 | 66 76 57 | 67 77 58 | 68 78 59 | 69 79 60 | 70 80 61 | 71 81 62 | 72 82 63 | 73 83 64 | 74 84 65 | 75 85 66 | 76 86 67 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1e3pa3d1gpqa_.aln: -------------------------------------------------------------------------------- 1 | 1 104 2 | 2 105 3 | 3 106 4 | 4 107 5 | 5 108 6 | 6 109 7 | 7 110 8 | 8 111 9 | 9 112 10 | 10 113 11 | 11 114 12 | 17 115 13 | 18 116 14 | 19 117 15 | 20 118 16 | 21 119 17 | 22 120 18 | 23 121 19 | 24 122 20 | 25 123 21 | 32 34 22 | 33 35 23 | 34 36 24 | 35 37 25 | 36 38 26 | 37 39 27 | 38 40 28 | 39 41 29 | 40 42 30 | 42 45 31 | 43 46 32 | 44 47 33 | 45 48 34 | 46 49 35 | 47 50 36 | 48 51 37 | 49 52 38 | 50 53 39 | 51 54 40 | 52 55 41 | 53 56 42 | 54 57 43 | 55 58 44 | 56 59 45 | 57 60 46 | 58 61 47 | 59 62 48 | 60 63 49 | 61 64 50 | 62 65 51 | 63 66 52 | 64 67 53 | 73 5 54 | 74 6 55 | 75 7 56 | 76 8 57 | 77 9 58 | 78 10 59 | 79 11 60 | 80 12 61 | 81 13 62 | 82 14 63 | 83 15 64 | 84 16 65 | 85 17 66 | 86 18 67 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1eg3a1d1paqa_.aln: -------------------------------------------------------------------------------- 1 | 3 144 2 | 4 145 3 | 5 146 4 | 6 147 5 | 7 148 6 | 8 149 7 | 9 150 8 | 10 151 9 | 11 152 10 | 12 153 11 | 13 154 12 | 14 155 13 | 15 156 14 | 16 157 15 | 17 158 16 | 20 3 17 | 21 4 18 | 22 5 19 | 25 6 20 | 26 7 21 | 27 8 22 | 28 9 23 | 29 10 24 | 30 11 25 | 31 12 26 | 32 13 27 | 33 14 28 | 34 15 29 | 35 16 30 | 36 17 31 | 37 18 32 | 40 37 33 | 41 38 34 | 42 39 35 | 43 40 36 | 44 41 37 | 45 42 38 | 46 43 39 | 47 44 40 | 48 45 41 | 49 46 42 | 50 47 43 | 51 48 44 | 52 49 45 | 53 50 46 | 60 51 47 | 61 52 48 | 62 53 49 | 63 54 50 | 64 55 51 | 65 56 52 | 66 57 53 | 67 58 54 | 68 59 55 | 69 60 56 | 70 61 57 | 71 62 58 | 72 63 59 | 73 64 60 | 74 65 61 | 75 66 62 | 76 67 63 | 77 68 64 | 78 69 65 | 79 70 66 | 80 71 67 | -------------------------------------------------------------------------------- /tests/dataset/MALISAM-ns/reference/d1gc5a_d1omha_.aln: -------------------------------------------------------------------------------- 1 | 5 1 2 | 6 2 3 | 7 3 4 | 8 4 5 | 9 5 6 | 10 264 7 | 11 265 8 | 12 266 9 | 13 267 10 | 14 268 11 | 15 269 12 | 16 270 13 | 17 271 14 | 20 48 15 | 21 49 16 | 22 50 17 | 23 51 18 | 24 52 19 | 25 53 20 | 26 54 21 | 27 55 22 | 28 56 23 | 29 57 24 | 30 58 25 | 31 59 26 | 32 60 27 | 33 61 28 | 34 62 29 | 35 63 30 | 45 34 31 | 46 35 32 | 47 36 33 | 48 37 34 | 49 38 35 | 50 193 36 | 51 194 37 | 52 195 38 | 53 196 39 | 54 197 40 | 55 198 41 | 56 199 42 | 57 200 43 | 58 201 44 | 59 202 45 | 60 203 46 | 61 204 47 | 62 205 48 | 71 84 49 | 72 85 50 | 73 86 51 | 74 87 52 | 75 88 53 | 76 89 54 | 77 90 55 | 78 91 56 | 79 92 57 | 80 93 58 | 81 94 59 | 82 95 60 | 83 96 61 | 84 97 62 | 85 98 63 | 86 99 64 | 87 100 65 | 88 101 66 | 89 102 67 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2021 Shintaro Minami 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1b24a1.aln: -------------------------------------------------------------------------------- 1 | 2 1 2 | 3 2 3 | 4 3 4 | 5 4 5 | 6 5 6 | 7 6 7 | 8 7 8 | 9 8 9 | 10 9 10 | 11 10 11 | 12 11 12 | 13 12 13 | 14 13 14 | 15 14 15 | 16 15 16 | 17 16 17 | 30 20 18 | 31 21 19 | 32 22 20 | 33 23 21 | 34 24 22 | 35 25 23 | 36 26 24 | 37 27 25 | 38 28 26 | 39 29 27 | 40 30 28 | 41 31 29 | 42 32 30 | 43 33 31 | 44 34 32 | 46 35 33 | 47 36 34 | 48 37 35 | 49 38 36 | 50 39 37 | 51 40 38 | 52 41 39 | 53 42 40 | 54 43 41 | 61 44 42 | 62 45 43 | 63 46 44 | 64 47 45 | 65 48 46 | 66 49 47 | 67 50 48 | 68 51 49 | 69 52 50 | 70 56 51 | 71 57 52 | 72 58 53 | 73 59 54 | 74 60 55 | 75 61 56 | 76 62 57 | 77 63 58 | 78 66 59 | 79 67 60 | 80 68 61 | 81 69 62 | 82 70 63 | 83 71 64 | 84 72 65 | 85 73 66 | 86 74 67 | 87 75 68 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1foka1_1.aln: -------------------------------------------------------------------------------- 1 | 14 123 2 | 15 124 3 | 16 125 4 | 17 126 5 | 18 127 6 | 19 128 7 | 20 129 8 | 21 130 9 | 22 131 10 | 23 132 11 | 24 133 12 | 25 134 13 | 26 135 14 | 60 55 15 | 61 56 16 | 62 57 17 | 63 58 18 | 64 59 19 | 65 60 20 | 66 61 21 | 67 62 22 | 68 63 23 | 86 93 24 | 87 94 25 | 88 95 26 | 89 96 27 | 90 97 28 | 100 28 29 | 101 29 30 | 102 30 31 | 103 31 32 | 104 32 33 | 105 33 34 | 106 34 35 | 107 35 36 | 108 36 37 | 109 37 38 | 110 38 39 | 111 39 40 | 112 40 41 | 113 41 42 | 114 42 43 | 115 43 44 | 116 44 45 | 117 45 46 | 118 46 47 | 119 47 48 | 120 48 49 | 121 49 50 | 122 50 51 | 123 73 52 | 124 74 53 | 125 75 54 | 126 76 55 | 127 77 56 | 128 78 57 | 129 79 58 | 130 80 59 | 131 81 60 | 132 82 61 | 133 83 62 | 134 84 63 | 135 85 64 | 136 86 65 | 137 87 66 | 138 88 67 | 139 89 68 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1hxpa1.aln: -------------------------------------------------------------------------------- 1 | 28 93 2 | 29 94 3 | 30 95 4 | 31 96 5 | 32 97 6 | 33 98 7 | 34 99 8 | 35 100 9 | 36 101 10 | 37 102 11 | 38 103 12 | 39 104 13 | 40 105 14 | 62 166 15 | 63 167 16 | 64 168 17 | 65 169 18 | 66 170 19 | 67 171 20 | 74 6 21 | 75 7 22 | 76 8 23 | 77 9 24 | 78 10 25 | 79 11 26 | 80 12 27 | 81 13 28 | 82 14 29 | 83 15 30 | 84 16 31 | 85 17 32 | 86 18 33 | 87 19 34 | 88 20 35 | 89 21 36 | 90 22 37 | 91 23 38 | 92 24 39 | 93 25 40 | 94 26 41 | 95 27 42 | 96 28 43 | 97 29 44 | 98 30 45 | 99 31 46 | 100 32 47 | 101 33 48 | 104 39 49 | 105 40 50 | 106 41 51 | 107 42 52 | 108 43 53 | 109 44 54 | 110 45 55 | 111 46 56 | 112 47 57 | 120 110 58 | 121 111 59 | 122 112 60 | 123 113 61 | 124 114 62 | 125 115 63 | 126 116 64 | 127 117 65 | 128 118 66 | 129 119 67 | 130 120 68 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1m9sa2.aln: -------------------------------------------------------------------------------- 1 | 1 82 2 | 2 83 3 | 3 84 4 | 4 85 5 | 5 86 6 | 7 68 7 | 8 69 8 | 9 70 9 | 10 71 10 | 11 72 11 | 12 73 12 | 13 74 13 | 14 75 14 | 18 2 15 | 19 3 16 | 20 4 17 | 21 5 18 | 22 6 19 | 23 7 20 | 24 8 21 | 25 9 22 | 26 10 23 | 27 11 24 | 32 17 25 | 33 18 26 | 34 19 27 | 35 20 28 | 36 21 29 | 37 22 30 | 38 23 31 | 39 24 32 | 40 25 33 | 41 26 34 | 42 27 35 | 43 28 36 | 44 29 37 | 45 30 38 | 46 31 39 | 47 32 40 | 48 33 41 | 49 34 42 | 50 35 43 | 51 36 44 | 52 37 45 | 53 38 46 | 54 39 47 | 55 40 48 | 56 41 49 | 57 42 50 | 58 43 51 | 59 44 52 | 60 45 53 | 61 46 54 | 62 47 55 | 63 52 56 | 64 53 57 | 65 54 58 | 66 55 59 | 67 56 60 | 68 57 61 | 69 58 62 | 70 59 63 | 71 60 64 | 72 61 65 | 73 62 66 | 74 63 67 | 75 64 68 | -------------------------------------------------------------------------------- /tests/dataset/MALIDUP-ns/reference/d1vk6a1.aln: -------------------------------------------------------------------------------- 1 | 11 45 2 | 12 46 3 | 13 47 4 | 14 48 5 | 15 49 6 | 16 50 7 | 17 51 8 | 18 52 9 | 19 53 10 | 20 54 11 | 21 55 12 | 22 56 13 | 23 57 14 | 24 58 15 | 25 59 16 | 26 90 17 | 27 91 18 | 28 92 19 | 29 93 20 | 30 94 21 | 31 95 22 | 32 111 23 | 33 112 24 | 34 113 25 | 35 114 26 | 36 115 27 | 37 116 28 | 38 117 29 | 39 118 30 | 40 119 31 | 41 120 32 | 42 121 33 | 43 122 34 | 44 123 35 | 45 124 36 | 46 125 37 | 47 126 38 | 48 127 39 | 49 128 40 | 50 129 41 | 51 66 42 | 52 67 43 | 53 68 44 | 54 69 45 | 55 70 46 | 56 71 47 | 57 72 48 | 58 73 49 | 59 74 50 | 76 22 51 | 77 23 52 | 78 24 53 | 79 25 54 | 80 26 55 | 81 27 56 | 82 28 57 | 83 29 58 | 84 30 59 | 85 31 60 | 86 32 61 | 87 33 62 | 88 34 63 | 89 35 64 | 90 36 65 | 91 37 66 | 92 38 67 | 93 39 68 | --------------------------------------------------------------------------------