29 | */
30 | public class HeaderParseException extends Error{
31 |
32 | private static final long serialVersionUID = -8356845980320906455L;
33 |
34 | public HeaderParseException(String error){
35 | super(error);
36 | }
37 | }
38 |
--------------------------------------------------------------------------------
/biojava3-core/src/main/java/org/biojava3/core/exceptions/SequenceLengthError.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on DATE
21 | *
22 | */
23 |
24 | package org.biojava3.core.exceptions;
25 |
26 | /**
27 | * Currently not used
28 | * @author Scooter Willis
29 | */
30 | public class SequenceLengthError extends Error{
31 |
32 | private static final long serialVersionUID = -5486504706601790351L;
33 |
34 | public SequenceLengthError(String message){
35 | super(message);
36 | }
37 | }
38 |
--------------------------------------------------------------------------------
/biojava3-core/src/main/java/org/biojava3/core/sequence/DataSource.java:
--------------------------------------------------------------------------------
1 | /*
2 | * To change this template, choose Tools | Templates
3 | * and open the template in the editor.
4 | */
5 | package org.biojava3.core.sequence;
6 |
7 | /**
8 | *
9 | * GenBank gi|gi-number|gb|accession|locus
10 | * ENA Data Library gi|gi-number|emb|accession|locus
11 | * DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus
12 | * NBRF PIR pir||entry
13 | * Protein Research Foundation prf||name
14 | * SWISS-PROT UNIPROT sp|accession|name
15 | * Brookhaven Protein Data Bank (1) pdb|entry|chain
16 | * Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE
17 | * Patents pat|country|number
18 | * GenInfo Backbone Id bbs|number
19 | * General database identifier gnl|database|identifier
20 | * NCBI Reference Sequence ref|accession|locus
21 | * Local Sequence identifier lcl|identifier
22 | *
23 | * @author Scooter Willis
24 | */
25 |
26 | public enum DataSource {
27 |
28 | GENBANK, ENA, DDBJ, NBRF, PRF, PDB1, PDB2, PDBe, PATENTS, GENINFO, GENERAL, NCBI, UNIPROT, PFAM, LOCAL, UNKNOWN
29 | }
30 |
--------------------------------------------------------------------------------
/biojava3-core/src/main/java/org/biojava3/core/sequence/SequenceComparator.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on DATE
21 | *
22 | */
23 | package org.biojava3.core.sequence;
24 |
25 | import java.util.Comparator;
26 |
27 | import org.biojava3.core.sequence.template.AbstractSequence;
28 |
29 | /**
30 | * Used to sort sequences
31 | * @author Scooter Willis
32 | */
33 | public class SequenceComparator implements Comparator>{
34 |
35 |
36 | public int compare(AbstractSequence o1, AbstractSequence o2) {
37 | return o1.getBioBegin() - o2.getBioBegin();
38 | }
39 |
40 | }
41 |
--------------------------------------------------------------------------------
/biojava3-core/src/main/java/org/biojava3/core/sequence/Strand.java:
--------------------------------------------------------------------------------
1 | package org.biojava3.core.sequence;
2 |
3 | /**
4 | * Provides a way of representing the strand of a sequence, location
5 | * hit or feature.
6 | *
7 | * @author ayates
8 | */
9 | public enum Strand {
10 |
11 | POSITIVE("+", 1), NEGATIVE("-", -1), UNDEFINED(".", 0);
12 | private final String stringRepresentation;
13 | private final int numericRepresentation;
14 |
15 | private Strand(String stringRepresentation, int numericRepresentation) {
16 | this.stringRepresentation = stringRepresentation;
17 | this.numericRepresentation = numericRepresentation;
18 | }
19 |
20 | public int getNumericRepresentation() {
21 | return numericRepresentation;
22 | }
23 |
24 | public String getStringRepresentation() {
25 | return stringRepresentation;
26 | }
27 |
28 | public Strand getReverse() {
29 | switch (this) {
30 | case POSITIVE:
31 | return NEGATIVE;
32 | case NEGATIVE:
33 | return POSITIVE;
34 | default:
35 | return UNDEFINED;
36 | }
37 | }
38 | }
39 |
--------------------------------------------------------------------------------
/biojava3-core/src/main/java/org/biojava3/core/sequence/compound/RNACompoundSet.java:
--------------------------------------------------------------------------------
1 | package org.biojava3.core.sequence.compound;
2 |
3 | import org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet;
4 |
5 | /**
6 | *
7 | * @author Andy Yates
8 | */
9 | public class RNACompoundSet extends AbstractNucleotideCompoundSet {
10 |
11 | private static class InitaliseOnDemand {
12 | public static final RNACompoundSet INSTANCE = new RNACompoundSet();
13 | }
14 | public static RNACompoundSet getRNACompoundSet() {
15 | return InitaliseOnDemand.INSTANCE;
16 | }
17 |
18 | public RNACompoundSet() {
19 | addNucleotideCompound("A", "U");
20 | addNucleotideCompound("U", "A");
21 | addNucleotideCompound("G", "C");
22 | addNucleotideCompound("C", "G");
23 | addNucleotideCompound("N", "N");
24 | addNucleotideCompound("-", "-");
25 | }
26 |
27 | public NucleotideCompound newNucleotideCompound(String base, String complement, String... equivalents) {
28 | return new NucleotideCompound(base, this, complement);
29 | }
30 | }
--------------------------------------------------------------------------------
/biojava3-core/src/main/java/org/biojava3/core/sequence/features/DatabaseReferenceInterface.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on 01-21-2010
21 | */
22 |
23 | package org.biojava3.core.sequence.features;
24 |
25 | import java.util.ArrayList;
26 | import java.util.LinkedHashMap;
27 |
28 | /**
29 | * If a SequenceProxyReader implements this interface then that external source
30 | * has a list of cross reference id(s)
31 | * @author Scooter Willis
32 | */
33 | public interface DatabaseReferenceInterface {
34 |
35 | public LinkedHashMap> getDatabaseReferences() throws Exception;
36 | }
37 |
--------------------------------------------------------------------------------
/biojava3-core/src/main/java/org/biojava3/core/sequence/io/template/FastaHeaderFormatInterface.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on 01-21-2010
21 | */
22 |
23 | package org.biojava3.core.sequence.io.template;
24 |
25 | import org.biojava3.core.sequence.template.Compound;
26 | import org.biojava3.core.sequence.template.Sequence;
27 |
28 | /**
29 | *
30 | * @author Scooter Willis
31 | */
32 | public interface FastaHeaderFormatInterface, C extends Compound> {
33 | /**
34 | *
35 | * @param sequence
36 | * @return
37 | */
38 | public String getHeader(S sequence);
39 | }
40 |
--------------------------------------------------------------------------------
/biojava3-core/src/main/java/org/biojava3/core/sequence/io/template/FastaHeaderParserInterface.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on 01-21-2010
21 | */
22 |
23 | package org.biojava3.core.sequence.io.template;
24 |
25 | import org.biojava3.core.sequence.template.Compound;
26 | import org.biojava3.core.sequence.template.Sequence;
27 |
28 | /**
29 | *
30 | * @author Scooter Willis
31 | */
32 | public interface FastaHeaderParserInterface, C extends Compound> {
33 | /**
34 | *
35 | * @param header
36 | * @param sequence
37 | */
38 | public void parseHeader(String header, S sequence);
39 | }
40 |
--------------------------------------------------------------------------------
/biojava3-core/src/main/java/org/biojava3/core/sequence/io/template/SequenceParserInterface.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on 01-21-2010
21 | */
22 |
23 | package org.biojava3.core.sequence.io.template;
24 |
25 | import java.io.DataInput;
26 |
27 | /**
28 | *
29 | * @author Scooter Willis
30 | */
31 | public interface SequenceParserInterface {
32 | /**
33 | *
34 | * @param dataInput
35 | * @param sequenceLength
36 | * @return
37 | * @throws Exception
38 | */
39 | public String getSequence(DataInput dataInput,int sequenceLength) throws Exception;
40 | }
41 |
--------------------------------------------------------------------------------
/biojava3-core/src/main/java/org/biojava3/core/sequence/loader/ArrayListProxySequenceReader.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on 01-21-2010
21 | */
22 | package org.biojava3.core.sequence.loader;
23 |
24 | import org.biojava3.core.sequence.storage.ArrayListSequenceReader;
25 | import org.biojava3.core.sequence.template.Compound;
26 | import org.biojava3.core.sequence.template.ProxySequenceReader;
27 |
28 | /**
29 | *
30 | *
31 | * @param
32 | */
33 | public class ArrayListProxySequenceReader
34 | extends ArrayListSequenceReader implements ProxySequenceReader{
35 |
36 | }
37 |
--------------------------------------------------------------------------------
/biojava3-core/src/main/java/org/biojava3/core/sequence/template/Accessioned.java:
--------------------------------------------------------------------------------
1 | package org.biojava3.core.sequence.template;
2 |
3 | import org.biojava3.core.sequence.AccessionID;
4 |
5 | /**
6 | * Indicates an entity is accessioned
7 | *
8 | * @author ayates
9 | */
10 | public interface Accessioned {
11 |
12 | /**
13 | * Returns the AccessionID this location is currently bound with
14 | */
15 | AccessionID getAccession();
16 |
17 | }
18 |
--------------------------------------------------------------------------------
/biojava3-core/src/main/java/org/biojava3/core/sequence/template/ComplementCompound.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on 01-21-2010
21 | *
22 | * @author Richard Holland
23 | * @auther Scooter Willis
24 | *
25 | */
26 |
27 | package org.biojava3.core.sequence.template;
28 |
29 | public interface ComplementCompound extends Compound {
30 |
31 | public ComplementCompound getComplement();
32 | }
33 |
--------------------------------------------------------------------------------
/biojava3-core/src/main/java/org/biojava3/core/sequence/template/CompoundTranslator.java:
--------------------------------------------------------------------------------
1 | package org.biojava3.core.sequence.template;
2 |
3 | import java.util.List;
4 |
5 | public interface CompoundTranslator {
6 |
7 | T translate(F fromCompound);
8 |
9 | List translateMany(F fromCompound);
10 |
11 | Sequence createSequence(Sequence originalSequence);
12 |
13 | List> createSequences(Sequence originalSequence);
14 |
15 | }
16 |
--------------------------------------------------------------------------------
/biojava3-core/src/main/java/org/biojava3/core/sequence/template/ProxySequenceReader.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on 01-21-2010
21 | *
22 | * @author Richard Holland
23 | * @auther Scooter Willis
24 | *
25 | */
26 | package org.biojava3.core.sequence.template;
27 |
28 | public interface ProxySequenceReader extends SequenceReader {
29 |
30 | }
31 |
--------------------------------------------------------------------------------
/biojava3-core/src/main/java/org/biojava3/core/sequence/template/SequenceReader.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on 01-21-2010
21 | *
22 | * @author Richard Holland
23 | *
24 | *
25 | */
26 | package org.biojava3.core.sequence.template;
27 |
28 | public interface SequenceReader extends Sequence {
29 |
30 | public void setCompoundSet(CompoundSet compoundSet);
31 |
32 | public void setContents(String sequence);
33 | }
34 |
--------------------------------------------------------------------------------
/biojava3-core/src/main/java/org/biojava3/core/sequence/template/SequenceView.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on 01-21-2010
21 | *
22 | * @author Richard Holland
23 | *
24 | *
25 | */
26 | package org.biojava3.core.sequence.template;
27 |
28 | public interface SequenceView extends Sequence {
29 |
30 | public Sequence getViewedSequence();
31 |
32 | /**
33 | * 1-indexed, inclusive.
34 | */
35 | public Integer getBioStart();
36 |
37 | /**
38 | * 1-indexed, inclusive.
39 | */
40 | public Integer getBioEnd();
41 | }
42 |
--------------------------------------------------------------------------------
/biojava3-core/src/test/java/org/biojava3/core/sequence/compound/AmbiguityDNACompoundTest.java:
--------------------------------------------------------------------------------
1 | package org.biojava3.core.sequence.compound;
2 |
3 | import static org.junit.Assert.assertEquals;
4 |
5 | import java.util.ArrayList;
6 | import java.util.List;
7 |
8 | import org.junit.Test;
9 |
10 | public class AmbiguityDNACompoundTest {
11 |
12 | private AmbiguityDNACompoundSet set = AmbiguityDNACompoundSet.getDNACompoundSet();
13 |
14 | @Test
15 | public void testAmbiguity() {
16 | NucleotideCompound actual = set.getAmbiguity(getCompounds("M","V"));
17 | assertEquals("Checking M & G = V", getCompounds("V")[0], actual);
18 | }
19 |
20 | @Test
21 | public void testBasicAmbiguity() {
22 | NucleotideCompound actual = set.getAmbiguity(getCompounds("A","C"));
23 | assertEquals("Checking A & C = M", getCompounds("M")[0], actual);
24 | }
25 |
26 | private NucleotideCompound[] getCompounds(String... compoundStrings) {
27 | List c = new ArrayList();
28 | for(String s: compoundStrings) {
29 | c.add(set.getCompoundForString(s));
30 | }
31 | return c.toArray(new NucleotideCompound[0]);
32 | }
33 | }
34 |
--------------------------------------------------------------------------------
/biojava3-core/src/test/resources/org/biojava3/core/sequence/volvox-peptide.fasta:
--------------------------------------------------------------------------------
1 | >rna-Apple3
2 | FLGFASDSNFRRQ*R*YFIRLSLPSAPSGPVALLLNVPCTMLAVPTPPRALWVDRLAL*G
3 | CVFNWFQVRRLWIYDATSNIIPMSRLSSKTSKP*N*GRSFF*MKGSVIAIHVSAYSIACR
4 | LSCYRCRKFVNIKYNTF*V*QGLFTATYWCR**NEKPQHREEENGIPTNLIST*RTKRAV
5 | HGADENESPNGPS*TPQPVEKLRSARS*STDLKKKRRSLPER*AQPVPGCCRILPHGGAI
6 | WTTPYFGHSRLPTANASRSCAKFSLDRSHVRFALRKYGILEVLSGLA*GLSGTGAHRSSP
7 | SR*RGD*IRNMLVPGFGTNQSR*RYKKPFLLVLCLKRTPVTIRRQPEEATWFSFISTLFA
8 | ISNVILCGDLNAFW*NHTEIQRTRHSDRSRFGGQPRTLHCSARGVSYPEVPVV*RVVTGA
9 | GPTLPTVKEGNKFDPRVRPGSGGMAYIPYAHSACTFLAHAGILQAGQSVLWPLSYTSNAR
10 | SMFANIAPVAYSTV*PLHHVM
--------------------------------------------------------------------------------
/biojava3-genome/nb-configuration.xml:
--------------------------------------------------------------------------------
1 |
2 |
3 |
9 |
10 |
16 |
17 |
18 |
--------------------------------------------------------------------------------
/biojava3-genome/src/main/java/org/biojava3/genome/App.java:
--------------------------------------------------------------------------------
1 | package org.biojava3.genome;
2 |
3 | /**
4 | * Hello world!
5 | *
6 | */
7 | public class App
8 | {
9 | public static void main( String[] args )
10 | {
11 | System.out.println( "Hello World!" );
12 | }
13 | }
14 |
--------------------------------------------------------------------------------
/biojava3-genome/src/test/java/org/biojava3/genome/AppTest.java:
--------------------------------------------------------------------------------
1 | package org.biojava3.genome;
2 |
3 | import junit.framework.Test;
4 | import junit.framework.TestCase;
5 | import junit.framework.TestSuite;
6 |
7 | /**
8 | * Unit test for simple App.
9 | */
10 | public class AppTest
11 | extends TestCase
12 | {
13 | /**
14 | * Create the test case
15 | *
16 | * @param testName name of the test case
17 | */
18 | public AppTest( String testName )
19 | {
20 | super( testName );
21 | }
22 |
23 | /**
24 | * @return the suite of tests being tested
25 | */
26 | public static Test suite()
27 | {
28 | return new TestSuite( AppTest.class );
29 | }
30 |
31 | /**
32 | * Rigourous Test :-)
33 | */
34 | public void testApp()
35 | {
36 | assertTrue( true );
37 | }
38 | }
39 |
--------------------------------------------------------------------------------
/biojava3-genome/src/test/resources/amphimedon.gff3:
--------------------------------------------------------------------------------
1 | ##gff-version 3
2 | Contig13175 JGI gene 1 1864985 . - . ID=Aqu1;Name=Aqu1
3 | Contig100 JGI mRNA 27 746 . - . ID=PAC:15698561;Name=Aqu1.200033;PACid=15698561;Parent=Aqu1
--------------------------------------------------------------------------------
/biojava3-genome/src/test/resources/volvox_length.gff3:
--------------------------------------------------------------------------------
1 | ##gff-version 3
2 | ctgA volvox_all.fna contig 1 50001 . . . Name=ctgA
3 | agt830.5 volvox_all.fna contig 1 654 . . . Name=agt830.5
4 | agt830.3 volvox_all.fna contig 1 595 . . . Name=agt830.3
5 | agt767.5 volvox_all.fna contig 1 1053 . . . Name=agt767.5
6 | agt221.5 volvox_all.fna contig 1 1253 . . . Name=agt221.5
7 | agt221.3 volvox_all.fna contig 1 501 . . . Name=agt221.3
8 | agt767.3 volvox_all.fna contig 1 1001 . . . Name=agt767.3
9 |
--------------------------------------------------------------------------------
/biojava3-genome/src/test/resources/volvox_length_reference.gff3:
--------------------------------------------------------------------------------
1 | ##gff-version 3
2 | ctgA volvox_all.fna contig 1 50001 . . . Name=ctgA
3 | agt830.5 volvox_all.fna contig 1 654 . . . Name=agt830.5
4 | agt830.3 volvox_all.fna contig 1 595 . . . Name=agt830.3
5 | agt767.5 volvox_all.fna contig 1 1053 . . . Name=agt767.5
6 | agt221.5 volvox_all.fna contig 1 1253 . . . Name=agt221.5
7 | agt221.3 volvox_all.fna contig 1 501 . . . Name=agt221.3
8 | agt767.3 volvox_all.fna contig 1 1001 . . . Name=agt767.3
9 |
--------------------------------------------------------------------------------
/biojava3-phylo/src/main/java/org/biojava3/phylo/App.java:
--------------------------------------------------------------------------------
1 | package org.biojava3.phylo;
2 |
3 | /**
4 | * Hello world!
5 | *
6 | */
7 | public class App
8 | {
9 | public static void main( String[] args )
10 | {
11 | System.out.println( "Hello World!" );
12 | }
13 | }
14 |
--------------------------------------------------------------------------------
/biojava3-phylo/src/main/java/org/biojava3/phylo/NJTreeProgressListener.java:
--------------------------------------------------------------------------------
1 | /*
2 | * To change this template, choose Tools | Templates
3 | * and open the template in the editor.
4 | */
5 |
6 | package org.biojava3.phylo;
7 |
8 | //import org.biojavax.bio.phylo.jalview.NJTree;
9 |
10 |
11 | /**
12 | *
13 | * @author willishf
14 | */
15 | public interface NJTreeProgressListener {
16 | public void progress(Object njtree,String state, int percentageComplete);
17 | public void progress(Object njtree,String state, int currentCount,int totalCount);
18 | public void complete(Object njtree);
19 | public void canceled(Object njtree);
20 | }
21 |
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/biojava3-phylo/src/main/java/org/biojava3/phylo/ProgessListenerStub.java:
--------------------------------------------------------------------------------
1 | /*
2 | * To change this template, choose Tools | Templates
3 | * and open the template in the editor.
4 | */
5 |
6 | package org.biojava3.phylo;
7 |
8 |
9 | /**
10 | *
11 | * @author willishf
12 | */
13 | public class ProgessListenerStub implements NJTreeProgressListener {
14 | String priorState = "";
15 | public void progress(Object njtree,String state, int percentageComplete) {
16 | if(!priorState.equals(state)){
17 | priorState = state;
18 | System.out.println();
19 | }
20 |
21 | System.out.println("\n" + state + ":" + percentageComplete);
22 | }
23 |
24 |
25 |
26 | public void progress(Object njtree,String state, int currentCount, int totalCount) {
27 | if (!priorState.equals(state)){
28 | priorState = state;
29 | System.out.println();
30 | }
31 |
32 | System.out.println("\n" + state + ":" + currentCount + "/" + totalCount);
33 | }
34 |
35 | public void complete(Object njtree) {
36 |
37 | }
38 |
39 | public void canceled(Object njtree) {
40 |
41 | }
42 |
43 | }
44 |
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/biojava3-phylo/src/main/java/org/biojava3/phylo/TreeConstructionAlgorithm.java:
--------------------------------------------------------------------------------
1 | /*
2 | * To change this template, choose Tools | Templates
3 | * and open the template in the editor.
4 | */
5 |
6 | package org.biojava3.phylo;
7 |
8 | /**
9 | *
10 | * @author willishf
11 | */
12 | public enum TreeConstructionAlgorithm {
13 | PID, BLOSUM62;
14 | }
15 |
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/biojava3-phylo/src/main/java/org/biojava3/phylo/TreeType.java:
--------------------------------------------------------------------------------
1 | /*
2 | * To change this template, choose Tools | Templates
3 | * and open the template in the editor.
4 | */
5 |
6 | package org.biojava3.phylo;
7 |
8 | /**
9 | *
10 | * @author willishf
11 | */
12 | public enum TreeType {
13 | AV, NJ;
14 | }
15 |
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/biojava3-phylo/src/test/java/org/biojava3/phylo/AppTest.java:
--------------------------------------------------------------------------------
1 | package org.biojava3.phylo;
2 |
3 | import junit.framework.Test;
4 | import junit.framework.TestCase;
5 | import junit.framework.TestSuite;
6 |
7 | /**
8 | * Unit test for simple App.
9 | */
10 | public class AppTest
11 | extends TestCase
12 | {
13 | /**
14 | * Create the test case
15 | *
16 | * @param testName name of the test case
17 | */
18 | public AppTest( String testName )
19 | {
20 | super( testName );
21 | }
22 |
23 | /**
24 | * @return the suite of tests being tested
25 | */
26 | public static Test suite()
27 | {
28 | return new TestSuite( AppTest.class );
29 | }
30 |
31 | /**
32 | * Rigourous Test :-)
33 | */
34 | public void testApp()
35 | {
36 | assertTrue( true );
37 | }
38 | }
39 |
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/biojava3-protein-disorder/src/main/java/org/biojava3/data/sequence/package-info.java:
--------------------------------------------------------------------------------
1 | /**
2 | * Set of classes that responsible for data handling.
3 | * Classes in this package have no dependencies to other sources in the project.
4 | *
5 | * @author Peter Troshin
6 | *
7 | * @version 1.0 January 2010
8 | */
9 | package org.biojava3.data.sequence;
10 |
11 |
--------------------------------------------------------------------------------
/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/JronnTest.java:
--------------------------------------------------------------------------------
1 | package org.biojava3.ronn;
2 |
3 | import static org.junit.Assert.assertEquals;
4 |
5 | import org.biojava3.data.sequence.FastaSequence;
6 | import org.biojava3.ronn.Jronn.Range;
7 | import org.junit.Test;
8 |
9 |
10 | public class JronnTest {
11 |
12 | @Test
13 | public void verifyRanges() {
14 |
15 | Range[] ranges = Jronn.getDisorder(new FastaSequence("name", "LLRGRHLMNGTMIMRPWNFLNDHHFPKFFPHLIEQQAIWLADWWRKKHC" +
16 | "RPLPTRAPTMDQWDHFALIQKHWTANLWFLTFPFNDKWGWIWFLKDWTPGSADQAQRACTWFFCHGHDTN" +
17 | "CQIIFEGRNAPERADPMWTGGLNKHIIARGHFFQSNKFHFLERKFCEMAEIERPNFTCRTLDCQKFPWDDP" +
18 | "CSSTHSDCPKLEDLISFTETHGCSAADNADRPSQACHIGWAAMCEPTAMFMLMGSRCRCSFWPQNNAARHR" +
19 | "NFLIQIEMHSHLEHWIQTLHPQRPFLCNTWDDNWPICQFASQARGNSPDHHP"));
20 | assertEquals(4, ranges.length);
21 | assertEquals(53, ranges[0].from);
22 | assertEquals(59, ranges[0].to);
23 |
24 | assertEquals(190, ranges[1].from);
25 | assertEquals(196, ranges[1].to);
26 |
27 | assertEquals(210, ranges[2].from);
28 | assertEquals(226, ranges[2].to);
29 |
30 | assertEquals(305, ranges[3].from);
31 | assertEquals(313, ranges[3].to);
32 | //System.out.println(Arrays.toString(ranges));
33 | }
34 | }
35 |
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/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/IlluminaFastqReader.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | */
21 | package org.biojava3.sequencing.io.fastq;
22 |
23 | /**
24 | * Reader for {@link FastqVariant#FASTQ_ILLUMINA} formatted sequences.
25 | *
26 | * @since 3.0.3
27 | */
28 | public final class IlluminaFastqReader
29 | extends AbstractFastqReader
30 | {
31 |
32 | /** {@inheritDoc} */
33 | protected FastqVariant getVariant()
34 | {
35 | return FastqVariant.FASTQ_ILLUMINA;
36 | }
37 | }
--------------------------------------------------------------------------------
/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/SangerFastqReader.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | */
21 | package org.biojava3.sequencing.io.fastq;
22 |
23 | /**
24 | * Reader for {@link FastqVariant#FASTQ_SANGER} formatted sequences.
25 | *
26 | * @since 3.0.3
27 | */
28 | public final class SangerFastqReader
29 | extends AbstractFastqReader
30 | {
31 |
32 | /** {@inheritDoc} */
33 | protected FastqVariant getVariant()
34 | {
35 | return FastqVariant.FASTQ_SANGER;
36 | }
37 | }
--------------------------------------------------------------------------------
/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/SolexaFastqReader.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | */
21 | package org.biojava3.sequencing.io.fastq;
22 |
23 | /**
24 | * Reader for {@link FastqVariant#FASTQ_SOLEXA} formatted sequences.
25 | *
26 | * @since 3.0.3
27 | */
28 | public final class SolexaFastqReader
29 | extends AbstractFastqReader
30 | {
31 |
32 | /** {@inheritDoc} */
33 | protected FastqVariant getVariant()
34 | {
35 | return FastqVariant.FASTQ_SOLEXA;
36 | }
37 | }
--------------------------------------------------------------------------------
/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/StreamListener.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | */
21 | package org.biojava3.sequencing.io.fastq;
22 |
23 | /**
24 | * Event based parser callback.
25 | *
26 | * @since 3.0.3
27 | */
28 | public interface StreamListener
29 | {
30 | /**
31 | * Notify this listener of a FASTQ formatted sequence.
32 | *
33 | * @param fastq FASTQ formatted sequence
34 | */
35 | void fastq(Fastq fastq);
36 | }
37 |
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/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/bug2335.fastq:
--------------------------------------------------------------------------------
1 | @DS6BPQV01A2G0A
2 | TTGGAATGTTGCAAATGGGAGGCAGTTTGAAATACTGAATAGGCCTCATCGAGAATGTGAAGTTTCAGTAAAGACTTGAGGAAGTTGAATGAGCTGATGAATGGATATATG
3 | +DS6BPQV01A2G0A
4 | @8A8@7<=A9:8?:#6B>*2B<<<:B>*=A<(<6;6<<2;8@8A9<<=<==<<@88=<+<==B:<<@8C<60,)%"<=:5<
5 | @85@7@8+8<
24 | <3;=4:DA3%<;=8-9.A=):B=*
25 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/example.fastq:
--------------------------------------------------------------------------------
1 | @EAS54_6_R1_2_1_413_324
2 | CCCTTCTTGTCTTCAGCGTTTCTCC
3 | +
4 | ;;3;;;;;;;;;;;;7;;;;;;;88
5 | @EAS54_6_R1_2_1_540_792
6 | TTGGCAGGCCAAGGCCGATGGATCA
7 | +
8 | ;;;;;;;;;;;7;;;;;-;;;3;83
9 | @EAS54_6_R1_2_1_443_348
10 | GTTGCTTCTGGCGTGGGTGGGGGGG
11 | +
12 | ;;;;;;;;;;;9;7;;.7;393333
13 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/illumina-invalid-description.fastq:
--------------------------------------------------------------------------------
1 | invalid description
2 | ACTG
3 | +
4 | ZZZZ
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/illumina-invalid-repeat-description.fastq:
--------------------------------------------------------------------------------
1 | @description
2 | ACTG
3 | +invalid repeat description
4 | ZZZZ
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/illumina_faked.fastq:
--------------------------------------------------------------------------------
1 | @Test PHRED qualities from 40 to 0 inclusive
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTN
3 | +
4 | hgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@
5 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/illumina_full_range_as_illumina.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0005 Original version has PHRED scores from 62 to 0 inclusive (in that order)
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG
3 | +
4 | @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
5 | @FAKE0006 Original version has PHRED scores from 0 to 62 inclusive (in that order)
6 | GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7 | +
8 | ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@
9 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/illumina_full_range_as_sanger.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0005 Original version has PHRED scores from 62 to 0 inclusive (in that order)
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG
3 | +
4 | !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_
5 | @FAKE0006 Original version has PHRED scores from 0 to 62 inclusive (in that order)
6 | GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7 | +
8 | _^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!
9 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/illumina_full_range_as_solexa.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0005 Original version has PHRED scores from 62 to 0 inclusive (in that order)
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG
3 | +
4 | ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
5 | @FAKE0006 Original version has PHRED scores from 0 to 62 inclusive (in that order)
6 | GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7 | +
8 | ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJHGFECB@>;;
9 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/illumina_full_range_original_illumina.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0005 Original version has PHRED scores from 62 to 0 inclusive (in that order)
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG
3 | +
4 | @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
5 | @FAKE0006 Original version has PHRED scores from 0 to 62 inclusive (in that order)
6 | GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7 | +
8 | ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@
9 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/misc_dna_as_illumina.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0007 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA
3 | +
4 | @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
5 | @FAKE0008 Original version has mixed case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
6 | gTcatAGcgTcatAGcgTcatAGcgTcatAGcgTcatAGcg
7 | +
8 | @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
9 | @FAKE0009 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
10 | tcagtcagtcagtcagtcagtcagtcagtcagtcagtcagt
11 | +
12 | @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
13 | @FAKE0010 Original version has mixed case ambiguous DNA and PHRED scores of 40, 30, 20, 10 (cycled)
14 | gatcrywsmkhbvdnGATCRYWSMKHBVDN
15 | +
16 | h^TJh^TJh^TJh^TJh^TJh^TJh^TJh^
17 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/misc_dna_as_sanger.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0007 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA
3 | +
4 | !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
5 | @FAKE0008 Original version has mixed case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
6 | gTcatAGcgTcatAGcgTcatAGcgTcatAGcgTcatAGcg
7 | +
8 | !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
9 | @FAKE0009 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
10 | tcagtcagtcagtcagtcagtcagtcagtcagtcagtcagt
11 | +
12 | !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
13 | @FAKE0010 Original version has mixed case ambiguous DNA and PHRED scores of 40, 30, 20, 10 (cycled)
14 | gatcrywsmkhbvdnGATCRYWSMKHBVDN
15 | +
16 | I?5+I?5+I?5+I?5+I?5+I?5+I?5+I?
17 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/misc_dna_as_solexa.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0007 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA
3 | +
4 | ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
5 | @FAKE0008 Original version has mixed case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
6 | gTcatAGcgTcatAGcgTcatAGcgTcatAGcgTcatAGcg
7 | +
8 | ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
9 | @FAKE0009 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
10 | tcagtcagtcagtcagtcagtcagtcagtcagtcagtcagt
11 | +
12 | ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
13 | @FAKE0010 Original version has mixed case ambiguous DNA and PHRED scores of 40, 30, 20, 10 (cycled)
14 | gatcrywsmkhbvdnGATCRYWSMKHBVDN
15 | +
16 | h^TJh^TJh^TJh^TJh^TJh^TJh^TJh^
17 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/misc_dna_original_sanger.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0007 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA
3 | +
4 | !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
5 | @FAKE0008 Original version has mixed case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
6 | gTcatAGcgTcatAGcgTcatAGcgTcatAGcgTcatAGcg
7 | +
8 | !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
9 | @FAKE0009 Original version has lower case unambiguous DNA with PHRED scores from 0 to 40 inclusive (in that order)
10 | tcagtcagtcagtcagtcagtcagtcagtcagtcagtcagt
11 | +
12 | !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
13 | @FAKE0010 Original version has mixed case ambiguous DNA and PHRED scores of 40, 30, 20, 10 (cycled)
14 | gatcrywsmkhbvdnGATCRYWSMKHBVDN
15 | +
16 | I?5+I?5+I?5+I?5+I?5+I?5+I?5+I?
17 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/misc_rna_as_illumina.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0011 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
2 | ACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUA
3 | +
4 | @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
5 | @FAKE0012 Original version has mixed case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
6 | gUcauAGcgUcauAGcgUcauAGcgUcauAGcgUcauAGcg
7 | +
8 | @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
9 | @FAKE0013 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
10 | ucagucagucagucagucagucagucagucagucagucagu
11 | +
12 | @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
13 | @FAKE0014 Original version has mixed case ambiguous RNA with PHRED scores from 35 to 40 inclusive (cycled)
14 | gaucrywsmkhbvdnGAUCRYWSMKHBVDN
15 | +
16 | cdefghcdefghcdefghcdefghcdefgh
17 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/misc_rna_as_sanger.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0011 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
2 | ACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUA
3 | +
4 | !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
5 | @FAKE0012 Original version has mixed case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
6 | gUcauAGcgUcauAGcgUcauAGcgUcauAGcgUcauAGcg
7 | +
8 | !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
9 | @FAKE0013 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
10 | ucagucagucagucagucagucagucagucagucagucagu
11 | +
12 | !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
13 | @FAKE0014 Original version has mixed case ambiguous RNA with PHRED scores from 35 to 40 inclusive (cycled)
14 | gaucrywsmkhbvdnGAUCRYWSMKHBVDN
15 | +
16 | DEFGHIDEFGHIDEFGHIDEFGHIDEFGHI
17 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/misc_rna_as_solexa.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0011 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
2 | ACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUA
3 | +
4 | ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
5 | @FAKE0012 Original version has mixed case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
6 | gUcauAGcgUcauAGcgUcauAGcgUcauAGcgUcauAGcg
7 | +
8 | ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
9 | @FAKE0013 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
10 | ucagucagucagucagucagucagucagucagucagucagu
11 | +
12 | ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
13 | @FAKE0014 Original version has mixed case ambiguous RNA with PHRED scores from 35 to 40 inclusive (cycled)
14 | gaucrywsmkhbvdnGAUCRYWSMKHBVDN
15 | +
16 | cdefghcdefghcdefghcdefghcdefgh
17 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/misc_rna_original_sanger.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0011 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
2 | ACGUACGUACGUACGUACGUACGUACGUACGUACGUACGUA
3 | +
4 | !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
5 | @FAKE0012 Original version has mixed case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
6 | gUcauAGcgUcauAGcgUcauAGcgUcauAGcgUcauAGcg
7 | +
8 | !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
9 | @FAKE0013 Original version has lower case unambiguous RNA with PHRED scores from 0 to 40 inclusive (in that order)
10 | ucagucagucagucagucagucagucagucagucagucagu
11 | +
12 | !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
13 | @FAKE0014 Original version has mixed case ambiguous RNA with PHRED scores from 35 to 40 inclusive (cycled)
14 | gaucrywsmkhbvdnGAUCRYWSMKHBVDN
15 | +
16 | DEFGHIDEFGHIDEFGHIDEFGHIDEFGHI
17 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/multiple-wrapped-quality.fastq:
--------------------------------------------------------------------------------
1 | @description
2 | AC
3 | T
4 | G
5 | +
6 | ZZ
7 | Z
8 | Z
9 | @description
10 | AC
11 | T
12 | G
13 | +
14 | ZZ
15 | Z
16 | Z
17 | @description
18 | AC
19 | T
20 | G
21 | +
22 | ZZ
23 | Z
24 | Z
25 | @description
26 | AC
27 | T
28 | G
29 | +
30 | ZZ
31 | Z
32 | Z
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/sanger-invalid-description.fastq:
--------------------------------------------------------------------------------
1 | invalid description
2 | ACTG
3 | +
4 | ZZZZ
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/sanger-invalid-repeat-description.fastq:
--------------------------------------------------------------------------------
1 | @description
2 | ACTG
3 | +invalid repeat description
4 | ZZZZ
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/sanger_93.fastq:
--------------------------------------------------------------------------------
1 | @Test PHRED qualities from 93 to 0 inclusive
2 | ACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGAN
3 | +
4 | ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!
5 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/sanger_faked.fastq:
--------------------------------------------------------------------------------
1 | @Test PHRED qualities from 40 to 0 inclusive
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTN
3 | +
4 | IHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!
5 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/sanger_full_range_as_illumina.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0001 Original version has PHRED scores from 93 to 0 inclusive (in that order)
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
3 | +
4 | @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5 | @FAKE0002 Original version has PHRED scores from 0 to 93 inclusive (in that order)
6 | CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7 | +
8 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@
9 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/sanger_full_range_as_sanger.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0001 Original version has PHRED scores from 93 to 0 inclusive (in that order)
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
3 | +
4 | !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
5 | @FAKE0002 Original version has PHRED scores from 0 to 93 inclusive (in that order)
6 | CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7 | +
8 | ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!
9 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/sanger_full_range_as_solexa.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0001 Original version has PHRED scores from 93 to 0 inclusive (in that order)
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
3 | +
4 | ;;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5 | @FAKE0002 Original version has PHRED scores from 0 to 93 inclusive (in that order)
6 | CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7 | +
8 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJHGFECB@>;;
9 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/sanger_full_range_original_sanger.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0001 Original version has PHRED scores from 93 to 0 inclusive (in that order)
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
3 | +
4 | !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
5 | @FAKE0002 Original version has PHRED scores from 0 to 93 inclusive (in that order)
6 | CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7 | +
8 | ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,+*)('&%$#"!
9 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/solexa-invalid-description.fastq:
--------------------------------------------------------------------------------
1 | invalid description
2 | ACTG
3 | +
4 | ZZZZ
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/solexa-invalid-repeat-description.fastq:
--------------------------------------------------------------------------------
1 | @description
2 | ACTG
3 | +invalid repeat description
4 | ZZZZ
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/solexa_example.fastq:
--------------------------------------------------------------------------------
1 | @SLXA-B3_649_FC8437_R1_1_1_610_79
2 | GATGTGCAATACCTTTGTAGAGGAA
3 | +SLXA-B3_649_FC8437_R1_1_1_610_79
4 | YYYYYYYYYYYYYYYYYYWYWYYSU
5 | @SLXA-B3_649_FC8437_R1_1_1_397_389
6 | GGTTTGAGAAAGAGAAATGAGATAA
7 | +SLXA-B3_649_FC8437_R1_1_1_397_389
8 | YYYYYYYYYWYYYYWWYYYWYWYWW
9 | @SLXA-B3_649_FC8437_R1_1_1_850_123
10 | GAGGGTGTTGATCATGATGATGGCG
11 | +SLXA-B3_649_FC8437_R1_1_1_850_123
12 | YYYYYYYYYYYYYWYYWYYSYYYSY
13 | @SLXA-B3_649_FC8437_R1_1_1_362_549
14 | GGAAACAAAGTTTTTCTCAACATAG
15 | +SLXA-B3_649_FC8437_R1_1_1_362_549
16 | YYYYYYYYYYYYYYYYYYWWWWYWY
17 | @SLXA-B3_649_FC8437_R1_1_1_183_714
18 | GTATTATTTAATGGCATACACTCAA
19 | +SLXA-B3_649_FC8437_R1_1_1_183_714
20 | YYYYYYYYYYWYYYYWYWWUWWWQQ
21 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/solexa_faked.fastq:
--------------------------------------------------------------------------------
1 | @slxa_0001_1_0001_01
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN
3 | +slxa_0001_1_0001_01
4 | hgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;
5 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/solexa_full_range_as_illumina.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0003 Original version has Solexa scores from 62 to -5 inclusive (in that order)
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
3 | +
4 | AABBCCDDEEFGHIJJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
5 | @FAKE0004 Original version has Solexa scores from -5 to 62 inclusive (in that order)
6 | TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7 | +
8 | ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJJIHGFEEDDCCBBAA
9 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/solexa_full_range_as_sanger.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0003 Original version has Solexa scores from 62 to -5 inclusive (in that order)
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
3 | +
4 | ""##$$%%&&'()*++,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_
5 | @FAKE0004 Original version has Solexa scores from -5 to 62 inclusive (in that order)
6 | TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7 | +
8 | _^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;:9876543210/.-,++*)('&&%%$$##""
9 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/solexa_full_range_as_solexa.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0003 Original version has Solexa scores from 62 to -5 inclusive (in that order)
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
3 | +
4 | ;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
5 | @FAKE0004 Original version has Solexa scores from -5 to 62 inclusive (in that order)
6 | TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7 | +
8 | ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;
9 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/solexa_full_range_original_solexa.fastq:
--------------------------------------------------------------------------------
1 | @FAKE0003 Original version has Solexa scores from 62 to -5 inclusive (in that order)
2 | ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
3 | +
4 | ;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
5 | @FAKE0004 Original version has Solexa scores from -5 to 62 inclusive (in that order)
6 | TGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA
7 | +
8 | ~}|{zyxwvutsrqponmlkjihgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@?>=<;
9 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/test2_solexa.fastq:
--------------------------------------------------------------------------------
1 | @SLXA-B3_649_FC8437_R1_1_1_610_79
2 | GATGTGCAATACCTTTGTAGAGGAA
3 | +
4 | YYYYYYYYYYYYYYYYYYWYWYYSU
5 | @SLXA-B3_649_FC8437_R1_1_1_397_389
6 | GGTTTGAGAAAGAGAAATGAGATAA
7 | +
8 | YYYYYYYYYWYYYYWWYYYWYWYWW
9 | @SLXA-B3_649_FC8437_R1_1_1_850_123
10 | GAGGGTGTTGATCATGATGATGGCG
11 | +SLXA-B3_649_FC8437_R1_1_1_850_123
12 | YYYYYYYYYYYYYWYYWYYSYYYSY
13 | @SLXA-B3_649_FC8437_R1_1_1_362_549
14 | GGAAACAAAGTTTTTCTCAACATAG
15 | +SLXA-B3_649_FC8437_R1_1_1_362_549
16 | YYYYYYYYYYYYYYYYYYWWWWYWY
17 | @SLXA-B3_649_FC8437_R1_1_1_183_714
18 | GTATTATTTAATGGCATACACTCAA
19 | +SLXA-B3_649_FC8437_R1_1_1_183_714
20 | YYYYYYYYYYWYYYYWYWWUWWWQQ
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/tricky.fastq:
--------------------------------------------------------------------------------
1 | @071113_EAS56_0053:1:1:998:236
2 | TTTCTTGCCCCCATAGACTGAGACCTTCCCTAAATA
3 | +071113_EAS56_0053:1:1:998:236
4 | IIIIIIIIIIIIIIIIIIIIIIIIIIIIICII+III
5 | @071113_EAS56_0053:1:1:182:712
6 | ACCCAGCTAATTTTTGTATTTTTGTTAGAGACAGTG
7 | +
8 | @IIIIIIIIIIIIIIICDIIIII<%<6&-*).(*%+
9 | @071113_EAS56_0053:1:1:153:10
10 | TGTTCTGAAGGAAGGTGTGCGTGCGTGTGTGTGTGT
11 | +
12 | IIIIIIIIIIIICIIGIIIII>IAIIIE65I=II:6
13 | @071113_EAS56_0053:1:3:990:501
14 | TGGGAGGTTTTATGTGGA
15 | AAGCAGCAATGTACAAGA
16 | +
17 | IIIIIII.IIIIII1@44
18 | @-7.%<&+/$/%4(++(%
19 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/wrapped-quality.fastq:
--------------------------------------------------------------------------------
1 | @description
2 | AC
3 | T
4 | G
5 | +
6 | ZZ
7 | Z
8 | Z
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/wrapped-sequence.fastq:
--------------------------------------------------------------------------------
1 | @description
2 | AC
3 | T
4 | G
5 | +
6 | ZZZZ
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/wrapping_as_illumina.fastq:
--------------------------------------------------------------------------------
1 | @SRR014849.50939 EIXKN4201BA2EC length=135
2 | GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG
3 | +
4 | Zb^Ld`N\[d`NaZ[aZc]UOKHDA[\YT[_W[aZ\aZ[Zd`SF_WeaUI[Y\[[\\\[\Z\aY`X[[aZ\aZ\d`OY[aY[[\[[e`WPJC^UZ[`X\[R]T_V_W[`[Ga\I`\H[[Q^TVa\Ia\Ic^LY\S
5 | @SRR014849.110027 EIXKN4201APUB0 length=131
6 | CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG
7 | +
8 | \aYY_[FY\T`X^Vd`OY\[[^U_V[R^T[_ZDc^La\HYYO\S[c^Ld`Nc_QAZaZaYaY`XZZ\[aZZ[aZ[aZ[aZY`Z[`ZWeaVJ\[aZaY`X[PY\eaUG[\[[d`OXTUZ[Q\\`W\\\Y_W\
9 | @SRR014849.203935 EIXKN4201B4HU6 length=144
10 | AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT
11 | +
12 | `Z_ZDVT^YB[[Xd`PZ\d`RDaZaZ`ZaZ_ZDXd`Pd`Pd`RD[aZ`ZWd`Oc_RCd`P\aZ`ZaZaZY\YaZYaY`XYd`O`X[e`WPJEAc^LaZS[YYN[Z\Y`XWLT^U\b]JW[[RZ\SYc`RD[Z\WLXM`\HYa\I
13 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/wrapping_as_sanger.fastq:
--------------------------------------------------------------------------------
1 | @SRR014849.50939 EIXKN4201BA2EC length=135
2 | GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG
3 | +
4 | ;C?-EA/=60,)%"<=:5<@85@7@8+8<<3;=4:DA3%<;=8-9.A=):B=*
13 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/wrapping_as_solexa.fastq:
--------------------------------------------------------------------------------
1 | @SRR014849.50939 EIXKN4201BA2EC length=135
2 | GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG
3 | +
4 | Zb^Ld`N\[d`NaZ[aZc]UOKGB;[\YT[_W[aZ\aZ[Zd`SE_WeaUH[Y\[[\\\[\Z\aY`X[[aZ\aZ\d`OY[aY[[\[[e`WPJ@^UZ[`X\[R]T_V_W[`[Fa\H`\G[[Q^TVa\Ha\Hc^LY\S
5 | @SRR014849.110027 EIXKN4201APUB0 length=131
6 | CTTCAAATGATTCCGGGACTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTTCGGTTCCAACTCGCCGTCCGAATAATCCGTTCAAAATCTTGGCCTGTCAAAACGACTTTACGACCAGAACGATCCG
7 | +
8 | \aYY_[EY\T`X^Vd`OY\[[^U_V[R^T[_ZBc^La\GYYO\S[c^Ld`Nc_Q;ZaZaYaY`XZZ\[aZZ[aZ[aZ[aZY`Z[`ZWeaVJ\[aZaY`X[PY\eaUF[\[[d`OXTUZ[Q\\`W\\\Y_W\
9 | @SRR014849.203935 EIXKN4201B4HU6 length=144
10 | AACCCGTCCCATCAAAGATTTTGGTTGGAACCCGAAAGGGTTTTGAATTCAAACCCCTTTCGGTTCCAACTATTCAATTGTTTAACTTTTTTTAAATTGATGGTCTGTTGGACCATTTGTAATAATCCCCATCGGAATTTCTTT
11 | +
12 | `Z_ZBVT^Y>[[Xd`PZ\d`RBaZaZ`ZaZ_ZBXd`Pd`Pd`RB[aZ`ZWd`Oc_R@d`P\aZ`ZaZaZY\YaZYaY`XYd`O`X[e`WPJC;c^LaZS[YYN[Z\Y`XWLT^U\b]JW[[RZ\SYc`RB[Z\WLXM`\GYa\H
13 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/wrapping_issues.fastq:
--------------------------------------------------------------------------------
1 | @SRR014849.50939 EIXKN4201BA2EC length=135
2 | GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG
3 | +
4 | ;C?-EA/=60,)%"<=:5<
5 | @85@7@8+8<
24 | <3;=4:DA3%<;=8-9.A=):B=*
25 |
--------------------------------------------------------------------------------
/biojava3-sequencing/src/test/resources/org/biojava3/sequencing/io/fastq/wrapping_original_sanger.fastq:
--------------------------------------------------------------------------------
1 | @SRR014849.50939 EIXKN4201BA2EC length=135
2 | GAAATTTCAGGGCCACCTTTTTTTTGATAGAATAATGGAGAAAATTAAAAGCTGTACATATACCAATGAACAATAAATCAATACATAAAAAAGGAGAAGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGG
3 | +
4 | ;C?-EA/=60,)%"<=:5<
5 | @85@7@8+8<
24 | <3;=4:DA3%<;=8-9.A=):B=*
25 |
--------------------------------------------------------------------------------
/biojava3-structure-gui/readme.txt:
--------------------------------------------------------------------------------
1 | TODO in order for this to compile:
2 |
3 | Install JmolApplet.jar from the Jmol web site using:
4 |
5 | http://jmol.sourceforge.net/download/
6 |
7 | mvn install:install-file \
8 | -Dfile=/Users/andreas/workspace_mvn/Jmol/build/JmolApplet.jar \
9 | -DgroupId=jmolapplet \
10 | -DartifactId=JmolApplet \
11 | -Dversion=11.8.17 \
12 | -Dpackaging=jar \
13 | -DgeneratePom=true
14 |
15 |
16 | Install Javaws.jar
17 | (probably somewhere in your Java install)
--------------------------------------------------------------------------------
/biojava3-structure-gui/src/main/java/demo/AlignmentGuiDemo.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on 2010-01-21
21 | *
22 | */
23 | package demo;
24 |
25 |
26 | import org.biojava.bio.structure.align.gui.AlignmentGui;
27 |
28 | /**
29 | *
30 | * @author Andreas Prlic
31 | *
32 | */
33 | public class AlignmentGuiDemo {
34 |
35 | /** e.g. try to align 2hyn vs 1zll
36 | *
37 | */
38 | public static void main(String[] args) {
39 |
40 | AlignmentGui.getInstance();
41 |
42 | }
43 | }
44 |
--------------------------------------------------------------------------------
/biojava3-structure-gui/src/main/java/demo/ShowStructureInJmol.java:
--------------------------------------------------------------------------------
1 | package demo;
2 |
3 | import org.biojava.bio.structure.Structure;
4 | import org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol;
5 | import org.biojava.bio.structure.align.util.AtomCache;
6 |
7 |
8 | /** Demo how to load and display a structure in Jmol
9 | *
10 | * @author Andreas Prlic
11 | *
12 | */
13 | public class ShowStructureInJmol {
14 | public static void main(String[] args){
15 | try {
16 |
17 | AtomCache cache = new AtomCache();
18 |
19 | Structure struc = cache.getStructure("1aoi");
20 |
21 | StructureAlignmentJmol jmolPanel = new StructureAlignmentJmol();
22 |
23 | jmolPanel.setStructure(struc);
24 |
25 | // send some RASMOL style commands to Jmol
26 | jmolPanel.evalString("select * ; color chain;");
27 | jmolPanel.evalString("select nucleic; cartoon on;");
28 | jmolPanel.evalString("select *; spacefill off; wireframe off; cartoon on; ");
29 | } catch (Exception e){
30 | e.printStackTrace();
31 | }
32 | }
33 | }
34 |
--------------------------------------------------------------------------------
/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/AlignmentCalculationRunnable.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on Mar 30, 2010
21 | * Author: Andreas Prlic
22 | *
23 | */
24 |
25 | package org.biojava.bio.structure.align.gui;
26 |
27 | public interface AlignmentCalculationRunnable extends Runnable
28 | {
29 |
30 | public void interrupt();
31 | public void cleanup();
32 | public void setNrCPUs(int useNrCPUs);
33 |
34 | }
35 |
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/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/jmol/package.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 | Utility methods for better interaction with Jmol.
7 |
8 |
9 |
--------------------------------------------------------------------------------
/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/webstart/package.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 | Classes related to Java Web Start
7 |
8 |
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/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/events/AlignmentPositionListener.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * created at May 28, 2008
21 | */
22 | package org.biojava.bio.structure.gui.events;
23 |
24 | import org.biojava.bio.structure.gui.util.AlignedPosition;
25 |
26 | public interface AlignmentPositionListener {
27 |
28 | public void mouseOverPosition(AlignedPosition p);
29 | public void positionSelected(AlignedPosition p);
30 | public void toggleSelection(AlignedPosition p);
31 | public void rangeSelected(AlignedPosition start , AlignedPosition end);
32 | public void selectionLocked();
33 | public void selectionUnlocked();
34 |
35 | }
36 |
--------------------------------------------------------------------------------
/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/events/package.html:
--------------------------------------------------------------------------------
1 |
2 |
3 | Some event classes for the protein structure GUIs.
4 |
5 | Possible start classes are one level higher at
6 | org.biojava.bio.structure.gui.BiojavaJmol, and org.biojava.bio.structure.gui.AlignmentGui.
7 |
8 |
9 |
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/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/package.html:
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1 |
2 |
3 | A few convenience classes to view protein structures with Jmol (if it is on the classpath),
4 | to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.
5 |
6 | Possible start classes are BiojavaJmol, AlignmentGui.
7 |
8 |
9 |
--------------------------------------------------------------------------------
/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/StructurePairSelector.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * created at May 25, 2008
21 | */
22 | package org.biojava.bio.structure.gui.util;
23 |
24 | import org.biojava.bio.structure.Structure;
25 | import org.biojava.bio.structure.StructureException;
26 |
27 | /** To be implemented by JPanels that are part of the GUI to trigger structure aligmnents.
28 | *
29 | *
30 | * @author Andreas Prlic
31 | * @since 1.7
32 | *
33 | */
34 | public interface StructurePairSelector {
35 |
36 | public Structure getStructure1() throws StructureException;
37 | public Structure getStructure2() throws StructureException;
38 |
39 | }
40 |
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/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/color/ContinuousColorMapper.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on Aug 3, 2007
21 | */
22 | package org.biojava.bio.structure.gui.util.color;
23 |
24 | import java.awt.Color;
25 |
26 | /**
27 | * Provides a mapping between real numbers and Colors.
28 | * For instance, this could generate a gradient.
29 | *
30 | * @author Spencer Bliven
31 | *
32 | */
33 | public interface ContinuousColorMapper {
34 |
35 | /**
36 | *
37 | * @param value The real to be mapped
38 | * @return The color corresponding to value
39 | */
40 | public Color getColor(double value);
41 | }
42 |
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/biojava3-structure-gui/src/main/java/org/biojava/bio/structure/gui/util/package.html:
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1 |
2 |
3 | Some utility classes for the protein structure GUIs.
4 |
5 | Possible start classes are one level higher at
6 | org.biojava.bio.structure.gui.BiojavaJmol, and org.biojava.bio.structure.gui.AlignmentGui.
7 |
8 |
9 |
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/biojava3-structure-gui/src/main/java/org/biojava3/structure/gui/RenderStyle.java:
--------------------------------------------------------------------------------
1 | package org.biojava3.structure.gui;
2 |
3 | public enum RenderStyle {
4 | WIREFRAME, STICKS, BALL_AND_STICK, SURFACE, RIBBON, CARTOON, SPHERES, MESH
5 |
6 | }
7 |
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/biojava3-structure-gui/src/main/java/org/biojava3/structure/gui/Selection.java:
--------------------------------------------------------------------------------
1 | package org.biojava3.structure.gui;
2 |
3 | import java.util.List;
4 |
5 | import org.biojava.bio.structure.align.gui.jmol.AtomInfo;
6 |
7 | public interface Selection {
8 |
9 |
10 | public void clear();
11 | public List getSelection();
12 | public void setSelection(List selection);
13 |
14 | }
15 |
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/biojava3-structure-gui/src/main/java/org/biojava3/structure/gui/SelectionImpl.java:
--------------------------------------------------------------------------------
1 | package org.biojava3.structure.gui;
2 |
3 | import java.util.List;
4 |
5 | import org.biojava.bio.structure.align.gui.jmol.AtomInfo;
6 |
7 | public class SelectionImpl implements Selection {
8 |
9 | public void clear() {
10 | // TODO Auto-generated method stub
11 |
12 | }
13 |
14 | public List getSelection() {
15 | // TODO Auto-generated method stub
16 | return null;
17 | }
18 |
19 | public void setSelection(List selection) {
20 | // TODO Auto-generated method stub
21 |
22 | }
23 |
24 | }
25 |
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/biojava3-structure-gui/src/main/java/org/biojava3/structure/gui/StructureViewer.java:
--------------------------------------------------------------------------------
1 | package org.biojava3.structure.gui;
2 |
3 | import java.awt.Color;
4 |
5 | import org.biojava.bio.structure.Structure;
6 |
7 | public interface StructureViewer {
8 |
9 | public void setStructure(Structure structure);
10 | public void repaint();
11 | public void setSelection(Selection selection);
12 | public Selection getSelection();
13 |
14 | /** Apply this color to the current Selection
15 | *
16 | * @param red
17 | */
18 | public void setColor(Color red);
19 | public Color getColor();
20 |
21 |
22 | /** Apply this style to the current selection
23 | *
24 | * @param wireframe renderstyle
25 | */
26 | public void setStyle(RenderStyle wireframe);
27 |
28 | /** Clear the current display
29 | *
30 | *
31 | */
32 | public void clear();
33 |
34 | /** Set the Zoom level
35 | *
36 | * @param i
37 | */
38 | public void setZoom(int i);
39 |
40 | }
41 |
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/biojava3-structure-gui/src/main/java/org/biojava3/structure/gui/package.html:
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1 |
2 |
3 | New MVC interface for structure-gui
4 |
5 |
6 |
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/biojava3-structure-gui/src/test/java/org/biojava/structure/gui/RenderStyleTest.java:
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1 | /*
2 | * To change this template, choose Tools | Templates
3 | * and open the template in the editor.
4 | */
5 |
6 | package org.biojava.structure.gui;
7 |
8 | import junit.framework.TestCase;
9 |
10 | /**
11 | *
12 | * @author Jules
13 | */
14 | public class RenderStyleTest extends TestCase {
15 |
16 | public RenderStyleTest(String testName) {
17 | super(testName);
18 | }
19 |
20 | @Override
21 | protected void setUp() throws Exception {
22 | super.setUp();
23 | }
24 |
25 | @Override
26 | protected void tearDown() throws Exception {
27 | super.tearDown();
28 | }
29 |
30 | public void testSomeMethod() {
31 | // TODO review the generated test code and remove the default call to fail.
32 | //fail("The test case is a prototype.");
33 | }
34 |
35 | }
36 |
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/biojava3-structure/src/main/java/META-INF/MANIFEST.MF:
--------------------------------------------------------------------------------
1 | Manifest-Version: 1.0
2 | Class-Path:
3 |
4 |
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/biojava3-structure/src/main/java/demo/ChemCompDistribution.java:
--------------------------------------------------------------------------------
1 | package demo;
2 |
3 | import org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider;
4 |
5 | public class ChemCompDistribution {
6 |
7 | public static void main(String[] args){
8 |
9 |
10 | DownloadChemCompProvider.setPath("/Users/andreas/WORK/PDB/");
11 | DownloadChemCompProvider c = new DownloadChemCompProvider();
12 | c.setDownloadAll(true);
13 | c.checkDoFirstInstall();
14 |
15 | }
16 | }
17 |
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/biojava3-structure/src/main/java/demo/DemoBerkeleyScop.java:
--------------------------------------------------------------------------------
1 | package demo;
2 |
3 | import org.biojava.bio.structure.scop.BerkeleyScopInstallation;
4 | import org.biojava.bio.structure.scop.ScopDatabase;
5 | import org.biojava.bio.structure.scop.ScopFactory;
6 |
7 | /** A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOP
8 | *
9 | * @author andreas
10 | * @since 3.0.4
11 | *
12 | */
13 | public class DemoBerkeleyScop {
14 | public static void main(String[]args){
15 |
16 |
17 | ScopDatabase berkeley = new BerkeleyScopInstallation();
18 |
19 | ScopFactory.setScopDatabase(berkeley);
20 |
21 | // whenever you want to get access to SCOP now request it like this:
22 | ScopDatabase scop = ScopFactory.getSCOP();
23 | // ... and do something with it
24 |
25 |
26 | // eg. you can run all the demos that work for the UK - SCOP (currently at version 1.75)
27 | // this demo no automatically picks up the Berkeley version (currently 1.75A)
28 | DemoSCOP scopDemo = new DemoSCOP();
29 |
30 | scopDemo.getCategories();
31 | scopDemo.printDomainsForPDB();
32 | scopDemo.traverseHierarchy();
33 | scopDemo.alignSuperfamily();
34 |
35 |
36 | }
37 | }
38 |
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/biojava3-structure/src/main/java/org/biojava/bio/structure/BondType.java:
--------------------------------------------------------------------------------
1 | /*
2 | * To change this template, choose Tools | Templates
3 | * and open the template in the editor.
4 | */
5 |
6 | package org.biojava.bio.structure;
7 |
8 | /**
9 | * Work in progress - NOT final!
10 | * @author Jules Jacobsen
11 | */
12 | public enum BondType {
13 | UNDEFINED, COVALENT, IONIC, HBOND, VANDERWAALS, HYDROPHOBIC, METAL, PLANAR, ATOM_PLANE;
14 | }
15 |
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/biojava3-structure/src/main/java/org/biojava/bio/structure/GroupType.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure;
2 |
3 | /** contains only the static declaration of which types of Groups are available
4 | *
5 | * @author Andreas Prlic
6 | * @since 1.7
7 | *
8 | */
9 | public class GroupType {
10 |
11 | /** the type for amino acids
12 | *
13 | */
14 | public static final String AMINOACID = "amino";
15 |
16 | /** the type for hetero groups
17 | *
18 | */
19 | public static final String HETATM = "hetatm";
20 |
21 | /** the type for nucelotide groups
22 | *
23 | */
24 | public static final String NUCLEOTIDE = "nucleotide";
25 | }
26 |
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/biojava3-structure/src/main/java/org/biojava/bio/structure/PDBRecord.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure;
2 |
3 | /** An interface implemented by all classes that represent PDB records
4 | *
5 | * @author Andreas Prlic
6 | * @since 1.6
7 | */
8 | public interface PDBRecord {
9 |
10 | /** Returns a PDB file like representation of this record.
11 | *
12 | * @return a String providing a PDB file like representation of the record.
13 | */
14 | public String toPDB();
15 |
16 |
17 | /** Appends a PDB file like representation of this record to the provided StringBuffer.
18 | *
19 | */
20 | public void toPDB(StringBuffer buf);
21 |
22 |
23 | }
24 |
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/biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/CeCPUserArgumentProcessor.java:
--------------------------------------------------------------------------------
1 | /**
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on Apr 24, 2012
21 | * Created by Andreas Prlic
22 | *
23 | * @since 3.0.2
24 | */
25 | package org.biojava.bio.structure.align.ce;
26 |
27 | import org.biojava.bio.structure.align.StructureAlignment;
28 |
29 | public class CeCPUserArgumentProcessor extends CeUserArgumentProcessor {
30 | public StructureAlignment getAlgorithm() {
31 | return new CeCPMain();
32 | }
33 | }
34 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/CeSideChainUserArgumentProcessor.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.align.ce;
2 |
3 | import org.biojava.bio.structure.align.StructureAlignment;
4 |
5 | public class CeSideChainUserArgumentProcessor extends AbstractUserArgumentProcessor {
6 |
7 | public StructureAlignment getAlgorithm() {
8 | return new CeSideChainMain();
9 | }
10 |
11 |
12 | @Override
13 | public Object getParameters() {
14 |
15 | CeParameters params = new CeParameters();
16 |
17 | params.setScoringStrategy(CeParameters.SIDE_CHAIN_SCORING);
18 | //params.setMaxGapSize(0);
19 | return params;
20 | }
21 |
22 |
23 | public String getDbSearchLegend(){
24 | String legend = "# name1\tname2\tscore\tz-score\trmsd\tlen1\tlen2\tsim1\tsim2\t " ;
25 | return legend;
26 | }
27 |
28 | }
29 |
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/biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/ConfigStrucAligParams.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.align.ce;
2 |
3 |
4 | import java.util.List;
5 |
6 | public interface ConfigStrucAligParams {
7 |
8 |
9 | /** get the list of parameters that the user can change through the user interface.
10 | * Parameter names are the same names as the corresponding Get/Set methods.
11 | *
12 | * @return list of parameters
13 | */
14 | public List getUserConfigParameters();
15 |
16 | /** The labels to be displayed to the user for each parameter
17 | *
18 | * @return list of parameter names
19 | */
20 | public List getUserConfigParameterNames();
21 |
22 | /** Get the data types of the parameters
23 | *
24 | * @return list of parameter classes
25 | */
26 | @SuppressWarnings("rawtypes")
27 | public List getUserConfigTypes();
28 |
29 |
30 | /** The help text for each of these parameters.
31 | *
32 | * @return help strings
33 | */
34 | public List getUserConfigHelp();
35 |
36 |
37 | /** Set the parameters to the default.
38 | *
39 | */
40 | public void reset();
41 | }
42 |
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/biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/MatrixListener.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.align.ce;
2 |
3 |
4 |
5 | public interface MatrixListener {
6 |
7 | public double[][] matrixInOptimizer(double[][] max);
8 |
9 | public boolean[][] initializeBreakFlag(boolean[][] brkFlag);
10 | }
11 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/UserArgumentProcessor.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.align.ce;
2 |
3 | public interface UserArgumentProcessor {
4 |
5 |
6 | /** Process user arguments that have been provided from the command line
7 | *
8 | * @param argv
9 | */
10 | public void process(String[] argv);
11 | }
12 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/align/ce/package.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 | Classes related to the implementation of the CE alignment algorithm, here called jCE.
7 |
8 | CE reference:
9 |
10 | Shindyalov IN, Bourne PE (1998)
11 | Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.
12 | Protein Eng 11: 739-747
13 |
14 |
15 | see also:
16 |
17 | Andreas Prlic; Spencer Bliven; Peter W. Rose; Wolfgang F. Bluhm; Chris Bizon; Adam Godzik; Philip E. Bourne (2010)
18 | Pre-calculated protein structure alignments at the RCSB PDB website
19 | Bioinformatics 26: 2983-2985
20 |
21 |
22 |
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/biojava3-structure/src/main/java/org/biojava/bio/structure/align/client/JobKillException.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on Sep 16, 2009
21 | * Author: Andreas Prlic
22 | *
23 | */
24 |
25 | package org.biojava.bio.structure.align.client;
26 |
27 | public class JobKillException extends Exception {
28 |
29 | /**
30 | *
31 | */
32 | private static final long serialVersionUID = 1L;
33 |
34 | public JobKillException(String message){
35 | super(message);
36 | }
37 | }
38 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/align/client/package.html:
--------------------------------------------------------------------------------
1 |
2 |
3 | This package deals with the server communication for auto-downloading pre-calculated alignments.
4 |
5 |
6 |
7 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/align/events/AlignmentProgressListener.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.align.events;
2 |
3 | public interface AlignmentProgressListener {
4 |
5 | public void alignmentStarted(String name1, String name2);
6 |
7 | public void alignmentEnded();
8 |
9 | public void logStatus(String message);
10 |
11 | public void downloadingStructures(String name);
12 |
13 | public void requestingAlignmentsFromServer(int nrAlignments);
14 |
15 | public void sentResultsToServer(int nrAlignments,String serverMessage);
16 |
17 |
18 | }
19 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/align/fatcat/package.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 | Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.
9 |
10 | FATCAT reference:
11 |
12 | Yuzhen Ye & Adam Godzik (2003)
13 | Flexible structure alignment by chaining aligned fragment pairs allowing twists.
14 | Bioinformatics vol.19 suppl. 2. ii246-ii255.
15 |
16 |
17 | see also:
18 |
19 | Andreas Prlic; Spencer Bliven; Peter W. Rose; Wolfgang F. Bluhm; Chris Bizon; Adam Godzik; Philip E. Bourne (2010)
20 | Pre-calculated protein structure alignments at the RCSB PDB website
21 | Bioinformatics 26: 2983-2985
22 |
23 |
24 |
25 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/align/helper/IdxComparator.java:
--------------------------------------------------------------------------------
1 | /*
2 | * PDB web development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | *
15 | * Created on May 23, 2009
16 | * Created by Andreas Prlic
17 | *
18 | */
19 |
20 | package org.biojava.bio.structure.align.helper;
21 |
22 | import java.util.Comparator;
23 |
24 | public class IdxComparator implements Comparator
25 | {
26 |
27 | public int compare(int[] o1, int[] o2)
28 | {
29 | if (((o1[0]) == (o2[0])) &&
30 | ((o2[1]) == (o2[1])))
31 | return 0;
32 | if ( o1[0] < o2[0])
33 | return -1;
34 |
35 | return 1;
36 | }
37 |
38 | }
39 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/align/helper/package.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 | Helper classes for structural alignment.
9 |
10 |
11 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/align/package.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 | Classes for the alignment of structures. This is the unpublished legacy implementation from the time,
9 | before BioJava supported CE and FATCAT alignments.
10 |
11 | See the StructurePairAligner for an example.
12 |
13 |
14 |
15 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/align/pairwise/package.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 | Classes for the pairwise alignment of structures.
9 |
10 |
11 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/align/seq/SmithWatermanUserArgumentProcessor.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.align.seq;
2 |
3 |
4 | import org.biojava.bio.structure.align.StructureAlignment;
5 | import org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor;
6 |
7 |
8 |
9 | public class SmithWatermanUserArgumentProcessor extends AbstractUserArgumentProcessor{
10 |
11 |
12 |
13 |
14 | public StructureAlignment getAlgorithm() {
15 | return new SmithWaterman3Daligner();
16 | }
17 |
18 |
19 |
20 | @Override
21 | public Object getParameters() {
22 | StructureAlignment alignment = getAlgorithm();
23 |
24 | SmithWaterman3DParameters p = (SmithWaterman3DParameters) alignment.getParameters();
25 |
26 | if ( p == null)
27 | p = new SmithWaterman3DParameters();
28 |
29 |
30 | return p;
31 | }
32 |
33 | public String getDbSearchLegend(){
34 | String legend = "# name1\tname2\tscore\tz-score\trmsd\tlen1\tlen2\tsim1\tsim2\t " ;
35 | return legend;
36 | }
37 |
38 |
39 | }
40 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/CacheFactory.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.align.util;
2 |
3 | import org.biojava3.core.util.SoftHashMap;
4 |
5 |
6 | /** provides a SoftHashMap singleton.
7 | *
8 | *
9 | * @Deprecated find better ways for caching or use a SoftHashMap directly
10 | */
11 |
12 | public class CacheFactory {
13 |
14 | @SuppressWarnings("rawtypes")
15 | private static SoftHashMap cache = new SoftHashMap ();
16 |
17 | // no public constructor;
18 | private CacheFactory(){
19 |
20 | }
21 |
22 | @SuppressWarnings("rawtypes")
23 | public static SoftHashMap getCache(){
24 | return cache;
25 | }
26 |
27 | }
28 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/CollectionTools.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.align.util;
2 |
3 | import java.util.*;
4 |
5 | /**
6 | * Utilities for working with collections.
7 | *
8 | * @author Thomas Down
9 | */
10 | public class CollectionTools {
11 | public static int[] toIntArray(Collection l) {
12 | int[] a = new int[l.size()];
13 | int i = 0;
14 | for (Iterator j = l.iterator(); j.hasNext(); ) {
15 | a[i++] = ( j.next()).intValue();
16 | }
17 | return a;
18 | }
19 |
20 | public static double[] toDoubleArray(Collection l) {
21 | double[] a = new double[l.size()];
22 | int i = 0;
23 | for (Iterator j = l.iterator(); j.hasNext(); ) {
24 | a[i++] = ((Number) j.next()).doubleValue();
25 | }
26 | return a;
27 | }
28 |
29 | public static Object randomPick(Collection col) {
30 | Object[] objs = col.toArray(new Object[col.size()]);
31 | return objs[(int) Math.floor(Math.random() * objs.length)];
32 | }
33 | }
34 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/ConfigurationException.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.align.util;
2 |
3 |
4 | public class ConfigurationException extends Exception {
5 |
6 | /**
7 | *
8 | */
9 | private static final long serialVersionUID = -8047100079715000276L;
10 |
11 | /**
12 | * Constructs a ConfigurationException object.
13 | *
14 | * @param s a String ...
15 | */
16 | public ConfigurationException(String s) {
17 | super(s);
18 | }
19 |
20 | /**
21 | * Constructs a ConfigurationException object.
22 | *
23 | * @param t a Throwable object
24 | */
25 | public ConfigurationException (Throwable t) {
26 | super(t);
27 | }
28 | }
29 |
30 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/align/xml/package.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 | Serialization and deserialization for structure alignment results (as AFPChain object) to XML.
7 |
8 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/domain/DomainProvider.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.domain;
2 |
3 | import java.util.SortedSet;
4 |
5 | public interface DomainProvider {
6 |
7 | public SortedSet getDomainNames(String name);
8 |
9 | public SortedSet getRepresentativeDomains();
10 | }
11 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/domain/DomainProviderFactory.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.domain;
2 |
3 |
4 | /** A simple factory object that returns the system wide default DomainProvider
5 | *
6 | * @author andreas
7 | *
8 | */
9 | public class DomainProviderFactory {
10 |
11 | private DomainProviderFactory(){
12 |
13 | }
14 |
15 | static DomainProvider domainProvider ;
16 |
17 |
18 |
19 | public static void setDomainProvider(DomainProvider provider){
20 | domainProvider = provider;
21 |
22 | }
23 |
24 | public static DomainProvider getDomainProvider(){
25 | if ( domainProvider == null)
26 | domainProvider = new RemoteDomainProvider(true);
27 |
28 | return domainProvider;
29 | }
30 | }
31 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/domain/PDPProvider.java:
--------------------------------------------------------------------------------
1 | /**
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on May 1, 2012
21 | * Created by Andreas Prlic
22 | *
23 | * @since 3.0.2
24 | */
25 | package org.biojava.bio.structure.domain;
26 |
27 | import java.util.SortedSet;
28 |
29 | import org.biojava.bio.structure.Structure;
30 | import org.biojava.bio.structure.align.util.AtomCache;
31 |
32 | public interface PDPProvider {
33 |
34 | public SortedSet getPDPDomainNamesForPDB(String pdbId);
35 | public Structure getDomain(String pdbDomainName, AtomCache cache);
36 |
37 | }
38 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/domain/pdp/CutSites.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.domain.pdp;
2 |
3 | import java.util.Arrays;
4 |
5 |
6 | public class CutSites {
7 | int ncuts;
8 | int[] cut_sites;
9 |
10 | public CutSites(){
11 | ncuts = 0;
12 |
13 | cut_sites = new int[PDPParameters.MAX_CUTS];
14 | }
15 |
16 | @Override
17 | public String toString() {
18 | return "CutSites [ncuts=" + ncuts + ", cut_sites="
19 | + Arrays.toString(cut_sites) + "]";
20 | }
21 | public int getNcuts() {
22 | return ncuts;
23 | }
24 | public void setNcuts(int ncuts) {
25 | this.ncuts = ncuts;
26 | }
27 | public int[] getCut_sites() {
28 | return cut_sites;
29 | }
30 | public void setCut_sites(int[] cut_sites) {
31 | this.cut_sites = cut_sites;
32 | }
33 |
34 |
35 |
36 | }
37 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/domain/pdp/CutValues.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.domain.pdp;
2 |
3 |
4 |
5 | public class CutValues {
6 | public double s_min;
7 | public int site2;
8 | public boolean first_cut;
9 |
10 | public double AD;
11 |
12 | public CutValues(){
13 | s_min = 100;
14 | site2 = 0;
15 | first_cut = true;
16 | }
17 |
18 | @Override
19 | public String toString() {
20 | return "CutValues [s_min=" + s_min + ", site2=" + site2 +
21 | ", AD=" + AD
22 | + "]";
23 | }
24 |
25 |
26 |
27 | }
28 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/domain/pdp/PDPDistanceMatrix.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.domain.pdp;
2 |
3 | public class PDPDistanceMatrix {
4 | int[][] dist;
5 | int nclose;
6 | int[] iclose ;
7 | int[] jclose ;
8 |
9 | public PDPDistanceMatrix(){
10 |
11 | }
12 |
13 | public int[][] getDist() {
14 | return dist;
15 | }
16 |
17 | public void setDist(int[][] dist) {
18 | this.dist = dist;
19 | }
20 |
21 | public int getNclose() {
22 | return nclose;
23 | }
24 |
25 | public void setNclose(int nclose) {
26 | this.nclose = nclose;
27 | }
28 |
29 | public int[] getIclose() {
30 | return iclose;
31 | }
32 |
33 | public void setIclose(int[] iclose) {
34 | this.iclose = iclose;
35 | }
36 |
37 | public int[] getJclose() {
38 | return jclose;
39 | }
40 |
41 | public void setJclose(int[] jclose) {
42 | this.jclose = jclose;
43 | }
44 |
45 |
46 |
47 |
48 | }
49 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/domain/pdp/PDPParameters.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.domain.pdp;
2 |
3 | public class PDPParameters {
4 | public static final int MAXLEN = 3200;
5 | public static final int MAXDOM = 30;
6 | public static final int MAX_CUTS = 80;
7 | public static final int MAXSIZE = 350;
8 | public static final int MIN_DOMAIN_LENGTH = 35;
9 | public static final int ENDS = 12 ;
10 | public static final int ENDSEND = 9;
11 | public static final float RG1 = 1.0f;
12 | public static final float RG = 0.0f;
13 | public static final float TD1 = 40.f;
14 | public static final float TD = 25.f;
15 | public static final float DBL = .05f;
16 | public static final int MAXCONT = 900;
17 |
18 | public static final float CUT_OFF_VALUE=.50f; /* decide to cut */
19 | public static final float CUT_OFF_VALUE1=.29f; /* decide to combine */
20 | public static final float CUT_OFF_VALUE2=.44f; /* decide to double cut */
21 | public static final float CUT_OFF_VALUE1S=.19f; /* decide to combine small domains */
22 | public static final float CUT_OFF_VALUE1M=.21f; /* decide to combine medium domains */
23 |
24 |
25 | }
26 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/domain/pdp/SegmentComparator.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.domain.pdp;
2 |
3 | import java.util.Comparator;
4 |
5 | public class SegmentComparator implements Comparator {
6 |
7 | public int compare(Segment v1, Segment v2) {
8 |
9 | return v1.compareTo(v2);
10 | }
11 | }
12 |
13 |
14 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/domain/pdp/ShortSegmentRemover.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.domain.pdp;
2 |
3 | import java.util.List;
4 |
5 |
6 | public class ShortSegmentRemover {
7 |
8 | public static void cleanup(List domains) {
9 |
10 | int ndom = domains.size();
11 |
12 | for(int j=0;j=30) allshort = false;
20 | n+=seglen;
21 | }
22 |
23 | if(n
2 |
3 |
4 |
5 |
6 |
7 |
8 | Datamodel objects used for processing mmcif files. This are beans that can represent the data from a category in mmcif.
9 |
10 |
11 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/io/mmcif/package.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 | Input and Output of mmcif files
9 |
10 |
11 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/io/package.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 | Input and Output of Structures
9 |
10 |
11 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/jama/Maths.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.jama;
2 |
3 | public class Maths {
4 |
5 | /** sqrt(a^2 + b^2) without under/overflow.
6 | * @param a a double
7 | * @param b a double
8 | * @return a double
9 | * */
10 |
11 | public static double hypot(double a, double b) {
12 | double r;
13 | if (Math.abs(a) > Math.abs(b)) {
14 | r = b/a;
15 | r = Math.abs(a)*Math.sqrt(1+r*r);
16 | } else if (b != 0) {
17 | r = a/b;
18 | r = Math.abs(b)*Math.sqrt(1+r*r);
19 | } else {
20 | r = 0.0;
21 | }
22 | return r;
23 | }
24 | }
25 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/jama/README.txt:
--------------------------------------------------------------------------------
1 | all files in this directory have been downloaded from
2 | the Jama web site at:
3 | http://math.nist.gov/javanumerics/jama/
4 | on Dec. 2nd, 2005.
5 |
6 | they correspond to version 1.0.2 of the Jama package
7 |
8 | This code is under public domain and should therefore be
9 | o.k for inclusion into the biojava code.
10 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/jama/package.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 | Matrix package for from JAMA
9 |
10 |
11 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/package.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 | Parsers and API for SCOP, Structural Classification of Proteins.
7 | See DemoSCOP.java for an example.
8 |
9 |
10 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/BridgeType.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.secstruc;
2 |
3 | import java.io.Serializable;
4 |
5 | public enum BridgeType implements Serializable{
6 |
7 | parallel("parallel",'p'),
8 | antiparallel("antiparallel",'a');
9 |
10 | public final Character type;
11 | public final String name;
12 |
13 |
14 | private BridgeType(String name,Character stype){
15 | this.name = name;
16 | this.type = stype;
17 | }
18 |
19 | public static BridgeType fromCharacter(Character stype){
20 |
21 | for ( BridgeType c : BridgeType.values()){
22 | if ( c.type.equals(stype)){
23 | return c;
24 | }
25 | }
26 |
27 | return null;
28 |
29 | }
30 |
31 | public String toString(){
32 | return type.toString();
33 | }
34 |
35 | }
36 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/DistEn.java:
--------------------------------------------------------------------------------
1 | /*
2 | * PDB web development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | *
15 | * Created on Aug 5, 2009
16 | * Created by ap3
17 | *
18 | */
19 |
20 | package org.biojava.bio.structure.secstruc;
21 |
22 | public class DistEn
23 | {
24 | double distance;
25 | double energy;
26 |
27 | public double getDistance()
28 | {
29 | return distance;
30 | }
31 | public void setDistance(double distance)
32 | {
33 | this.distance = distance;
34 | }
35 | public double getEnergy()
36 | {
37 | return energy;
38 | }
39 | public void setEnergy(double energy)
40 | {
41 | this.energy = energy;
42 | }
43 |
44 |
45 | }
46 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/secstruc/SecStrucType.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure.secstruc;
2 |
3 | import java.io.Serializable;
4 |
5 | public enum SecStrucType implements Serializable{
6 |
7 | coil("Coil",' '),
8 | helix4("alpha Helix",'H'),
9 | helix3("3-10 Helix",'G'),
10 | helix5("pi helix",'I'),
11 | turn("Turn",'T'),
12 | bend("Bend",'S'),
13 | extended("Extended",'E'),
14 | bridge("Bridge",'B');
15 | ;
16 |
17 | public final Character type;
18 | public final String name;
19 |
20 |
21 | private SecStrucType(String name,Character stype){
22 | this.name = name;
23 | this.type = stype;
24 | }
25 |
26 | public static SecStrucType fromCharacter(Character stype){
27 |
28 | for ( SecStrucType c : SecStrucType.values()){
29 | if ( c.type.equals(stype)){
30 | return c;
31 | }
32 | }
33 |
34 | return null;
35 |
36 | }
37 |
38 | public String toString(){
39 | return type.toString();
40 | }
41 |
42 | public boolean isHelixType() {
43 | if ( type.equals(helix4.type) || type.equals(helix3.type) || type.equals(helix5.type))
44 | return true;
45 | return false;
46 | }
47 |
48 |
49 | }
50 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/server/PDBFilter.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * created at Sep 7, 2007
21 | */
22 | package org.biojava.bio.structure.server;
23 |
24 | import org.biojava.bio.structure.PDBHeader;
25 |
26 | /** defines how a filter of PDB files has to behave
27 | *
28 | * @author Andreas Prlic
29 | *
30 | */
31 | public interface PDBFilter {
32 |
33 | /** return true if this PDBHeader is passing this filter.
34 | *
35 | * @param header
36 | * @return flag if this PDBHeader is accepted by this filter
37 | */
38 | public boolean accept(PDBHeader header);
39 | }
40 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/server/StructureEvent.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * created at Sep 7, 2007
21 | */
22 | package org.biojava.bio.structure.server;
23 |
24 | import org.biojava.bio.structure.Structure;
25 |
26 | public interface StructureEvent {
27 |
28 | public Structure getStructure();
29 | public String getPDBCode();
30 | public void setPDBCode(String pdbCode);
31 |
32 | }
33 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/server/StructureListener.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * created at Sep 7, 2007
21 | */
22 | package org.biojava.bio.structure.server;
23 |
24 | public interface StructureListener {
25 |
26 | public void newStructure(StructureEvent event);
27 |
28 | public void modifiedStructure(StructureEvent event);
29 |
30 | public void obsoleteStructure(StructureEvent event);
31 | }
32 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/java/org/biojava/bio/structure/server/package.html:
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1 |
2 |
3 | classes for easier management of PDB installations
4 |
5 | As of BioJava 3.0.2 this package is deprecated. Please use AtomCache instead.
6 |
7 |
8 |
9 |
10 |
--------------------------------------------------------------------------------
/biojava3-structure/src/main/resources/about.properties:
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1 | project_version=${project.version}
2 | build=${timestamp}
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/biojava3-structure/src/main/resources/jfatcat.properties:
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1 | jfatcat.version=1.2
2 | jfatcat.name=JFATCAT
3 | server.url=http://www.rcsb.org/pdb/rest/
4 | connection.timeout=60000
5 | connection.pair.delay=3000
6 | request.pair.size=400
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/biojava3-structure/src/test/java/org/biojava/bio/structure/StructureIOTest.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure;
2 |
3 | import junit.framework.TestCase;
4 |
5 | import org.biojava3.structure.StructureIO;
6 |
7 | public class StructureIOTest extends TestCase {
8 | public void testStructureIO(){
9 |
10 | String pdbId = "1gav";
11 |
12 | int nrAssembls = StructureIO.getNrBiologicalAssemblies(pdbId);
13 | assertEquals(1,nrAssembls);
14 |
15 | pdbId = "1hv4";
16 | nrAssembls = StructureIO.getNrBiologicalAssemblies(pdbId);
17 | assertEquals(2,nrAssembls);
18 |
19 | }
20 | }
21 |
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/biojava3-structure/src/test/java/org/biojava/bio/structure/TestDownloadChemCompProvider.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure;
2 |
3 | import org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider;
4 | import org.biojava.bio.structure.io.mmcif.model.ChemComp;
5 |
6 | import junit.framework.TestCase;
7 |
8 | public class TestDownloadChemCompProvider extends TestCase{
9 |
10 | public void testProtectedIDs(){
11 |
12 | String id = "CON";
13 |
14 | DownloadChemCompProvider prov = new DownloadChemCompProvider();
15 | ChemComp cc = prov.getChemComp(id);
16 | assertNotNull(cc);
17 |
18 | assertEquals(cc.getId(), id);
19 | }
20 |
21 | }
22 |
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/biojava3-structure/src/test/java/org/biojava/bio/structure/TestLoadStructureFromURL.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure;
2 |
3 | import java.io.File;
4 | import java.io.IOException;
5 | import java.net.URL;
6 |
7 | import org.biojava.bio.structure.align.util.AtomCache;
8 |
9 | import junit.framework.TestCase;
10 |
11 |
12 | public class TestLoadStructureFromURL extends TestCase{
13 |
14 | private static final String FILE_SEPARATOR = System.getProperty("file.separator");
15 | public void testLoadStructureFromURL() throws IOException, StructureException{
16 | AtomCache cache = new AtomCache();
17 | String path = cache.getPath();
18 |
19 | path += "SUB DIR" + FILE_SEPARATOR;
20 |
21 | File f = new File(path);
22 | if ( ! f.exists()) {
23 | System.out.println("making dir with space:" + f);
24 | f.mkdir();
25 | }
26 | AtomCache c = new AtomCache(path, true);
27 | // fetch a random small structure
28 |
29 | c.getStructure("1znf");
30 |
31 | //and now create a URL for this file
32 |
33 | File newFile = new File(path+FILE_SEPARATOR+"zn"+ FILE_SEPARATOR + "pdb1znf.ent.gz");
34 |
35 | URL u = newFile.toURI().toURL();
36 |
37 | System.out.println(u);
38 |
39 | Structure s = c.getStructure(u.toString()+"?args=test");
40 |
41 | System.out.println(s);
42 |
43 |
44 | }
45 | }
46 |
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/biojava3-structure/src/test/java/org/biojava/bio/structure/TestVeryLongFileName.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure;
2 |
3 | import junit.framework.TestCase;
4 |
5 |
6 | public class TestVeryLongFileName extends TestCase{
7 |
8 |
9 | public void testVeryLongFilename(){
10 |
11 | try {
12 | PDBHeader header = new PDBHeader();
13 |
14 | header.setTitle("IAMAVERYLONGTITLEWITHOUTANYSPACECHARACTERSJUSTTOMAKESUREWECANTESTWHATISGOINGTOHAPPENIFWETRYTOWRITETHISTOAPDBFILE.");
15 |
16 | header.toPDB();
17 |
18 | String title2 = "jCE V.1.1 : file:/Users/ap3/tmp/mareike/IAMAVERYLONGTITLEWITHOUTANYSPACECHARACTERSJUSTTOMAKESUREWECANTESTWHATISGOINGTOHAPPENIFWETRYTOWRITETHISTOAPDBFILE/pdb1_chainG.pdb vs. file:/Users/ap3/tmp/mareike/IAMAVERYLONGTITLEWITHOUTANYSPACECHARACTERSJUSTTOMAKESUREWECANTESTWHATISGOINGTOHAPPENIFWETRYTOWRITETHISTOAPDBFILE/pdb2_chainB.pdb ";
19 | header.setTitle(title2);
20 | header.toPDB();
21 | } catch(Exception e){
22 | e.printStackTrace();
23 | fail(e.getMessage());
24 | }
25 | }
26 | }
27 |
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/biojava3-structure/src/test/resources/db_search.pairs:
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1 | 4hhb.C 4hhb.D
2 | 4hhb:0 4hhb:1
3 | 1hiv.A 1a4w.H
4 | 1RLW 1BYN
5 | 2sim 1nsb
6 | 1CEW 1mol
7 | 1TEN 3HHR
8 | 4hhb:(A:10-40,B:10-40) 4hhb:(C:10-40,D:10-40)
9 |
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/biojava3-structure/src/test/resources/describeMol/1w0p.xml:
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1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
12 |
13 |
14 |
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/biojava3-structure/src/test/resources/describeMol/almost_empty.xml:
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/biojava3-structure/src/test/resources/describeMol/diff_ecs.xml:
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/biojava3-structure/src/test/resources/describeMol/empty.xml:
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/biojava3-structure/src/test/resources/describeMol/same_ecs.xml:
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1 |
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/biojava3-ws/pom.xml:
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1 |
2 | 4.0.0
3 |
4 | biojava
5 | org.biojava
6 | 3.0.6-SNAPSHOT
7 |
8 | biojava3-ws
9 | biojava3-ws
10 | This module deals with bioinformatics web services that could be used to process Biojava objects in a useful manner.
11 |
12 |
13 | org.biojava
14 | biojava3-core
15 | 3.0.6-SNAPSHOT
16 | compile
17 |
18 |
19 | junit
20 | junit
21 | test
22 |
23 |
24 | net.sf.json-lib
25 | json-lib
26 | 2.3
27 | jdk15
28 |
29 |
30 |
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/biojava3-ws/src/main/java/org/biojava3/ws/alignment/package.html:
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1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 | This package contains the interfaces that need to be implemented by discrete alignment services.
9 | The development philosophy is to separate actual submission of alignment requests from getting the
10 | corresponding results in any format supported by the service.
11 |
12 |
13 |
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/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/BlastMatrixEnum.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on 2011-12-25
21 | *
22 | */
23 |
24 | package org.biojava3.ws.alignment.qblast;
25 |
26 | /**
27 | * Enum representing matrices supported by QBlast
28 | *
29 | * @author Gediminas Rimsa
30 | */
31 | public enum BlastMatrixEnum {
32 |
33 | BLOSUM45,
34 | BLOSUM50,
35 | BLOSUM62,
36 | BLOSUM80,
37 | BLOSUM90,
38 | PAM250,
39 | PAM30,
40 | PAM70
41 |
42 | }
43 |
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/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on 2011-11-20
21 | *
22 | */
23 |
24 | package org.biojava3.ws.alignment.qblast;
25 |
26 | /**
27 | * Enum representing available output alignment types.
28 | *
29 | * Values as used in QBlast URL API.
30 | *
31 | * @author Gediminas Rimsa
32 | */
33 | public enum BlastOutputAlignmentFormatEnum {
34 |
35 | Pairwise,
36 | QueryAnchored,
37 | QueryAnchoredNoIdentities,
38 | FlatQueryAnchored,
39 | FlatQueryAnchoredNoIdentities,
40 | Tabular
41 |
42 | }
43 |
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/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/BlastOutputFormatEnum.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on 2011-11-20
21 | *
22 | */
23 |
24 | package org.biojava3.ws.alignment.qblast;
25 |
26 | /**
27 | * Enum representing available output formats.
28 | *
29 | * Values are as used by QBlast URL API.
30 | *
31 | * @author Gediminas Rimsa
32 | */
33 | public enum BlastOutputFormatEnum {
34 |
35 | Text,
36 | XML,
37 | HTML
38 |
39 | }
40 |
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/biojava3-ws/src/main/java/org/biojava3/ws/alignment/qblast/BlastProgramEnum.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BioJava development code
3 | *
4 | * This code may be freely distributed and modified under the
5 | * terms of the GNU Lesser General Public Licence. This should
6 | * be distributed with the code. If you do not have a copy,
7 | * see:
8 | *
9 | * http://www.gnu.org/copyleft/lesser.html
10 | *
11 | * Copyright for this code is held jointly by the individual
12 | * authors. These should be listed in @author doc comments.
13 | *
14 | * For more information on the BioJava project and its aims,
15 | * or to join the biojava-l mailing list, visit the home page
16 | * at:
17 | *
18 | * http://www.biojava.org/
19 | *
20 | * Created on 2011-11-20
21 | *
22 | */
23 |
24 | package org.biojava3.ws.alignment.qblast;
25 |
26 | /**
27 | * Enum representing available blast programs.
28 | *
29 | * Values are as used by QBlast URL API.
30 | *
31 | * @author Gediminas Rimsa
32 | */
33 | public enum BlastProgramEnum {
34 |
35 | blastn,
36 | blastp,
37 | blastx,
38 | megablast,
39 | tblastn,
40 | tblastx
41 |
42 | }
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/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/HmmerScan.java:
--------------------------------------------------------------------------------
1 | package org.biojava3.ws.hmmer;
2 |
3 | import java.io.IOException;
4 |
5 | import java.util.SortedSet;
6 |
7 | import org.biojava3.core.sequence.ProteinSequence;
8 |
9 | /** Interface for performing Hmmscans on sequences.
10 | *
11 | * @author Andreas Prlic
12 | * @since 3.0.3
13 | */
14 | public interface HmmerScan {
15 |
16 | public SortedSet scan(ProteinSequence sequence) throws IOException;
17 |
18 | }
19 |
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/ignore.txt:
--------------------------------------------------------------------------------
1 | target
2 | .settings
3 | .classpath
4 | .profile
5 | .project
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/integrationtest/src/test/java/org/biojava/bio/structure/HeaderOnlyTest.java:
--------------------------------------------------------------------------------
1 | package org.biojava.bio.structure;
2 |
3 | public class HeaderOnlyTest extends MMcifTest {
4 |
5 | public HeaderOnlyTest(){
6 | super();
7 | setHeaderOnly(true);
8 | }
9 |
10 |
11 | }
12 |
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/integrationtest/src/test/java/org/integrationtest/AppTest.java:
--------------------------------------------------------------------------------
1 | package org.integrationtest;
2 |
3 | import junit.framework.Test;
4 | import junit.framework.TestCase;
5 | import junit.framework.TestSuite;
6 |
7 | /**
8 | * Unit test for simple App.
9 | */
10 | public class AppTest
11 | extends TestCase
12 | {
13 | /**
14 | * Create the test case
15 | *
16 | * @param testName name of the test case
17 | */
18 | public AppTest( String testName )
19 | {
20 | super( testName );
21 | }
22 |
23 | /**
24 | * @return the suite of tests being tested
25 | */
26 | public static Test suite()
27 | {
28 | return new TestSuite( AppTest.class );
29 | }
30 |
31 | /**
32 | * Rigourous Test :-)
33 | */
34 | public void testApp()
35 | {
36 | assertTrue( true );
37 | }
38 | }
39 |
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/protein-comparison-tool/src/main/assembly/db.out:
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1 | #Legend:
2 | # name1 name2 score z-score rmsd len1 len2 sim1 sim2
3 | 4hhb.C 4hhb.D 309.61 6.47 1.41 141 146 99 95 0.43 null
4 | 4hhb:0 4hhb:1 366.29 6.47 1.49 141 146 99 95 0.43 null
5 | 1cdg.A 1tim.B 512.44 5.04 4.66 686 247 24 67 0.09 null
6 | 1hiv.A 1a4w.H 229.12 2.58 4.14 100 249 69 28 0.10 null
7 | 1RLW 1BYN 134.17 5.86 2.01 126 128 83 81 0.22 null
8 | 2sim 1nsb 571.50 5.86 2.99 381 780 72 35 0.10 null
9 | 1CEW 1mol 127.71 3.70 3.05 108 188 74 43 0.04 null
10 | 1TEN 3HHR 133.27 4.58 1.87 89 573 98 15 0.18 null
11 | 4hhb:(A:10-40,B:10-40) 4hhb:(C:10-40,D:10-40) 170.65 5.33 0.27 62 62 100 100 1.00 null
12 |
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/protein-comparison-tool/src/main/assembly/example.lst:
--------------------------------------------------------------------------------
1 | # an example input for a DB search
2 | 4hhb.C 4hhb.D
3 | 4hhb:0 4hhb:1
4 | 1cdg.A 1tim.B
5 | 1hiv.A 1a4w.H
6 | 1RLW 1BYN
7 | 2sim 1nsb
8 | 1CEW 1mol
9 | 1TEN 3HHR
10 | 4hhb:(A:10-40,B:10-40) 4hhb:(C:10-40,D:10-40)
11 |
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/protein-comparison-tool/src/main/assembly/runFATCAT.sh:
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1 | #!/bin/bash
2 |
3 | # examples:
4 |
5 | # bash runFATCAT.sh -pdb1 4hhb.A -pdb2 4hhb.B -pdbFilePath /tmp/ -autoFetch -show3d
6 | # bash runFATCAT.sh -pdb1 4hhb.A -pdb2 4hhb.B -pdbFilePath /tmp/ -printXML
7 | # bash runFATCAT.sh -pdb1 4hhb.A -pdb2 4hhb.B -pdbFilePath /tmp/ -printFatCat
8 | #
9 | # run a flexible alignment:
10 | # bash runFATCAT.sh -pdb1 4hhb.A -pdb2 4hhb.B -pdbFilePath /tmp/ -printFatCat -flexible
11 | #
12 | # for more examples see runCE.sh
13 | # jCE works almost exactly the same...
14 |
15 | # send the arguments to the java app
16 | args="$*"
17 |
18 | java -Xmx500M -cp "$PWD/jars/*" org.biojava.bio.structure.align.fatcat.FatCat $args
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/protein-comparison-tool/src/main/assembly/startFarmJob.sh:
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1 | #!/bin/bash
2 |
3 | # example:
4 | # startFarmJob.sh -pdbFilePath /Users/ap3/WORK/PDB -nrAlignments 10
5 |
6 | # send the arguments to the java app
7 | # allows to specify a different config file
8 | args="$*"
9 |
10 | if [ -f $OSG_APP/engage/jdk1.6.0_16/bin/java ]; then
11 | $OSG_APP/engage/jdk1.6.0_16/bin/java -Xmx1G -cp "$PWD/jars/*" org.biojava.bio.structure.align.FarmJob $args
12 | else
13 | if [ -f /osg/osg-app/engage/jdk1.6.0_03/bin/java ]; then
14 | /osg/osg-app/engage/jdk1.6.0_03/bin/java -Xmx1G -cp "$PWD/jars/*" org.biojava.bio.structure.align.FarmJob $args
15 | else
16 | which java
17 | java -version
18 | java -Xmx1G -cp "$PWD/jars/*" org.biojava.bio.structure.align.FarmJob $args
19 | fi
20 | fi
21 |
22 | exit $?
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/readme.txt:
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1 | Welcome to BioJava v.3
2 |
3 | BioJava is an open-source project dedicated to providing a Java framework for processing biological data. Please visit our homepage:
4 |
5 | http://www.biojava.org/
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