├── .gitignore ├── .gitmodules ├── .travis.yml ├── CMakeLists.txt ├── LICENSE.txt ├── README.md ├── crispr_repression2.png ├── example ├── BiosystemDesignExample.cpp ├── CMakeLists.txt ├── CRISPRRepressionExample.cpp ├── CRISPR_example.xml ├── README.md ├── SequenceAssemblyExample.cpp └── Xcode │ ├── example.xcodeproj │ ├── project.pbxproj │ └── project.xcworkspace │ │ └── contents.xcworkspacedata │ └── example │ └── main.cpp ├── gene_cassette.png ├── installer ├── Win32_installer.iss └── Win64_installer.iss ├── logo.jpg ├── manual ├── CMakeLists.txt ├── CRISPRTemplate.png ├── CRISPRTumorKiller.png ├── Doxyfile ├── Doxyfile.bak ├── Doxyfile.in ├── DoxygenLayout.xml ├── FindDoxygen.cmake ├── Makefile ├── SBOLlogo2_high_res.jpg ├── cmake_install.cmake ├── cmakescreen.png ├── component_definition_uml.png ├── crispr_repression2.png ├── customclasspage.bak ├── developerspage.bak ├── doxy2swig.py ├── gene_cassette.png ├── getting_started.dox ├── installation.dox ├── mainpage.dox ├── modules.dox └── sequences.dox ├── source ├── CMakeLists.txt ├── PtrWrapper.hh ├── RasqalDataGraph.cc ├── RasqalDataGraph.hh ├── RasqalQueryResults.cc ├── RasqalQueryResults.hh ├── SharedPtrWrapper.hh ├── a.txt ├── assembly.cpp ├── assembly.h ├── attachment.h ├── collection.h ├── combinatorialderivation.h ├── component.h ├── componentdefinition.h ├── config.cpp ├── config.h ├── constants.h ├── dbtl.cpp ├── dbtl.h ├── document.cpp ├── document.h ├── experiment.h ├── identified.h ├── implementation.h ├── interaction.h ├── libxml2 │ ├── AUTHORS │ ├── CMakeLists.txt │ ├── COPYING │ ├── ChangeLog │ ├── Copyright │ ├── DOCBparser.c │ ├── HTMLparser.c │ ├── HTMLtree.c │ ├── NEWS │ ├── README.libxml2 │ ├── README.md │ ├── SAX.c │ ├── SAX2.c │ ├── THIS_VERSION_IS_2.9.4 │ ├── TODO │ ├── TODO_SCHEMAS │ ├── buf.c │ ├── buf.h │ ├── c14n.c │ ├── catalog.c │ ├── chvalid.c │ ├── debugXML.c │ ├── dict.c │ ├── elfgcchack.h │ ├── enc.h │ ├── encoding.c │ ├── entities.c │ ├── error.c │ ├── globals.c │ ├── hash.c │ ├── include │ │ ├── libxml │ │ │ ├── DOCBparser.h │ │ │ ├── HTMLparser.h │ │ │ ├── HTMLtree.h │ │ │ ├── SAX.h │ │ │ ├── SAX2.h │ │ │ ├── c14n.h │ │ │ ├── catalog.h │ │ │ ├── chvalid.h │ │ │ ├── debugXML.h │ │ │ ├── dict.h │ │ │ ├── encoding.h │ │ │ ├── entities.h │ │ │ ├── globals.h │ │ │ ├── hash.h │ │ │ ├── list.h │ │ │ ├── nanoftp.h │ │ │ ├── nanohttp.h │ │ │ ├── parser.h │ │ │ ├── parserInternals.h │ │ │ ├── pattern.h │ │ │ ├── relaxng.h │ │ │ ├── schemasInternals.h │ │ │ ├── schematron.h │ │ │ ├── threads.h │ │ │ ├── tree.h │ │ │ ├── uri.h │ │ │ ├── valid.h │ │ │ ├── xinclude.h │ │ │ ├── xlink.h │ │ │ ├── xmlIO.h │ │ │ ├── xmlautomata.h │ │ │ ├── xmlerror.h │ │ │ ├── xmlexports.h │ │ │ ├── xmlmemory.h │ │ │ ├── xmlmodule.h │ │ │ ├── xmlreader.h │ │ │ ├── xmlregexp.h │ │ │ ├── xmlsave.h │ │ │ ├── xmlschemas.h │ │ │ ├── xmlschemastypes.h │ │ │ ├── xmlstring.h │ │ │ ├── xmlunicode.h │ │ │ ├── xmlversion.h │ │ │ ├── xmlwriter.h │ │ │ ├── xpath.h │ │ │ ├── xpathInternals.h │ │ │ └── xpointer.h │ │ └── wsockcompat.h │ ├── legacy.c │ ├── libxml.h │ ├── list.c │ ├── nanoftp.c │ ├── nanohttp.c │ ├── parser.c │ ├── parserInternals.c │ ├── pattern.c │ ├── relaxng.c │ ├── runsuite.c │ ├── runtest.c │ ├── runxmlconf.c │ ├── save.h │ ├── schematron.c │ ├── testAutomata.c │ ├── testC14N.c │ ├── testHTML.c │ ├── testModule.c │ ├── testReader.c │ ├── testRegexp.c │ ├── testRelax.c │ ├── testSAX.c │ ├── testSchemas.c │ ├── testThreads.c │ ├── testThreadsWin32.c │ ├── testURI.c │ ├── testXPath.c │ ├── testapi.c │ ├── testchar.c │ ├── testdict.c │ ├── testdso.c │ ├── testlimits.c │ ├── testrecurse.c │ ├── threads.c │ ├── timsort.h │ ├── tree.c │ ├── trio.c │ ├── trio.h │ ├── triodef.h │ ├── trionan.c │ ├── trionan.h │ ├── triop.h │ ├── triostr.c │ ├── triostr.h │ ├── uri.c │ ├── valid.c │ ├── win32 │ │ └── config.h │ ├── xinclude.c │ ├── xlink.c │ ├── xmlIO.c │ ├── xmlcatalog.c │ ├── xmllint.c │ ├── xmlmemory.c │ ├── xmlmodule.c │ ├── xmlreader.c │ ├── xmlregexp.c │ ├── xmlsave.c │ ├── xmlschemas.c │ ├── xmlschemastypes.c │ ├── xmlstring.c │ ├── xmlunicode.c │ ├── xmlwriter.c │ ├── xpath.c │ ├── xpointer.c │ ├── xzlib.c │ └── xzlib.h ├── location.h ├── mapsto.h ├── measurement.h ├── mergestaticlibs.cmake ├── model.h ├── module.h ├── moduledefinition.h ├── object.cpp ├── object.h ├── participation.h ├── partshop.cpp ├── partshop.h ├── properties.cpp ├── properties.cpp~ ├── properties.h ├── properties.h~ ├── property.h ├── provo.h ├── raptor │ ├── CMakeFiles │ │ └── progress.marks │ ├── CMakeLists.txt │ ├── FindCURL.bak │ ├── FindCURL.cmake │ ├── FindJsonCpp.cmake │ ├── FindLibXslt.bak │ ├── FindLibXslt.cmake │ ├── FindPythonLibs.cmake │ ├── FindRAPTOR.bak │ ├── FindRAPTOR.cmake │ ├── FindRASQAL.cmake │ ├── include │ │ ├── curl │ │ │ ├── curl.h │ │ │ ├── curlbuild.h │ │ │ ├── curlrules.h │ │ │ ├── curlver.h │ │ │ ├── easy.h │ │ │ ├── mprintf.h │ │ │ ├── multi.h │ │ │ ├── stdcheaders.h │ │ │ └── typecheck-gcc.h │ │ ├── json │ │ │ ├── allocator.h │ │ │ ├── assertions.h │ │ │ ├── autolink.h │ │ │ ├── config.h │ │ │ ├── features.h │ │ │ ├── forwards.h │ │ │ ├── json.h │ │ │ ├── reader.h │ │ │ ├── value.h │ │ │ ├── version.h │ │ │ └── writer.h │ │ └── raptor2 │ │ │ ├── raptor.h │ │ │ ├── raptor2.h │ │ │ └── raptor_internal.h │ ├── lib │ │ ├── cmake │ │ │ ├── Raptor2Config-debug.cmake │ │ │ ├── Raptor2Config-release.cmake │ │ │ └── Raptor2Config.cmake │ │ ├── pkgconfig │ │ │ └── raptor2.pc │ │ ├── x64 │ │ │ ├── jsoncpp.lib │ │ │ ├── libcurl.lib │ │ │ ├── libiconv.lib │ │ │ ├── libxml2.lib │ │ │ ├── libz.lib │ │ │ └── raptor2.lib │ │ └── x86 │ │ │ ├── jsoncpp.lib │ │ │ ├── libcurl.lib │ │ │ ├── libiconv.lib │ │ │ ├── libxml2.lib │ │ │ ├── libz.lib │ │ │ └── raptor2.lib │ └── share │ │ └── man │ │ └── man1 │ │ └── rapper.1 ├── sbol.h ├── sbolerror.cpp ├── sbolerror.h ├── sequence.h ├── sequenceannotation.h ├── sequenceconstraint.h ├── toplevel.h ├── validation.cpp └── validation.h ├── test ├── 1-s2.pdf ├── CMakeLists.txt ├── dirent.c ├── dirent.h ├── log.txt └── test.cpp ├── tutorial ├── buildCRISPR.tex ├── figures │ ├── addCrisprModel1.png │ ├── addCrisprModel2.png │ ├── addMavenDependency1.png │ ├── addMavenDependency2.png │ ├── addMavenDependency3.png │ ├── createNewMavenProject1.png │ ├── createNewMavenProject10.png │ ├── createNewMavenProject1_backup.png │ ├── createNewMavenProject1_backup1.png │ ├── createNewMavenProject2.png │ ├── createNewMavenProject3.png │ ├── createNewMavenProject4.png │ ├── createNewMavenProject5.png │ ├── createNewMavenProject6.png │ ├── createNewMavenProject7.png │ ├── createNewMavenProject8.png │ ├── createNewMavenProject9.png │ └── crispr_repression2.png ├── otherMethodsInAPI.tex ├── pom.xml ├── setupMavenPrj.tex ├── top.aux ├── top.bbl ├── top.bib ├── top.blg ├── top.fdb_latexmk ├── top.fls ├── top.log ├── top.out ├── top.pdf ├── top.synctex.gz └── top.tex └── wrapper ├── CMakeLists.txt ├── CRISPR_example.py ├── FindSWIG.cmake ├── __init__.py ├── assembly_example.py ├── 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