X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftest%2FTest.java;h=5961561660b4fdda2eef7eda8fa3658ef5f1184e;hb=bb89b28b9d81346c08a918a2fe673a418ef8e20a;hp=f38023925b3c5cd075cf3e1eacfa0029a7e82024;hpb=b17e87d9cb4185a396c2021d32d005c5769b6995;p=jalview.git diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index f380239..5961561 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -54,9 +54,11 @@ import org.forester.io.parsers.nhx.NHXParser; import org.forester.io.parsers.phyloxml.PhyloXmlParser; import org.forester.io.parsers.tol.TolParser; import org.forester.io.writers.PhylogenyWriter; +import org.forester.msa.BasicMsa; import org.forester.msa.Mafft; import org.forester.msa.Msa; import org.forester.msa.MsaInferrer; +import org.forester.msa.MsaMethods; import org.forester.pccx.TestPccx; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyBranch; @@ -81,14 +83,13 @@ import org.forester.phylogeny.data.Taxonomy; import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; +import org.forester.protein.Protein; import org.forester.sdi.SDI; import org.forester.sdi.SDIR; import org.forester.sdi.SDIse; -import org.forester.sdi.TaxonomyAssigner; import org.forester.sdi.TestGSDI; import org.forester.sequence.BasicSequence; import org.forester.sequence.Sequence; -import org.forester.surfacing.Protein; import org.forester.surfacing.TestSurfacing; import org.forester.tools.ConfidenceAssessor; import org.forester.tools.SupportCount; @@ -101,10 +102,10 @@ import org.forester.util.DescriptiveStatistics; import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; import org.forester.util.GeneralTable; -import org.forester.ws.uniprot.DatabaseTools; -import org.forester.ws.uniprot.SequenceDatabaseEntry; -import org.forester.ws.uniprot.UniProtTaxonomy; -import org.forester.ws.uniprot.UniProtWsTools; +import org.forester.util.SequenceIdParser; +import org.forester.ws.seqdb.SequenceDatabaseEntry; +import org.forester.ws.seqdb.SequenceDbWsTools; +import org.forester.ws.seqdb.UniProtTaxonomy; import org.forester.ws.wabi.TxSearch; import org.forester.ws.wabi.TxSearch.RANKS; import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS; @@ -169,6 +170,16 @@ public final class Test { System.exit( -1 ); } final long start_time = new Date().getTime(); + System.out.print( "Sequence id parsing: " ); + if ( testSequenceIdParsing() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + System.exit( -1 ); //TODO FIXME remove me!! ~ + failed++; + } System.out.print( "Hmmscan output parser: " ); if ( testHmmscanOutputParser() ) { System.out.println( "OK." ); @@ -484,15 +495,6 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "Taxonomy assigner: " ); - if ( Test.testTaxonomyAssigner() ) { - System.out.println( "OK." ); - succeeded++; - } - else { - System.out.println( "failed." ); - failed++; - } System.out.print( "SDIunrooted: " ); if ( Test.testSDIunrooted() ) { System.out.println( "OK." ); @@ -685,9 +687,27 @@ public final class Test { System.out.println( "failed." ); failed++; } - if ( Mafft.isInstalled() ) { + //---- + String path = ""; + final String os = ForesterUtil.OS_NAME.toLowerCase(); + if ( ( os.indexOf( "mac" ) >= 0 ) && ( os.indexOf( "os" ) > 0 ) ) { + path = "/usr/local/bin/mafft"; + } + else if ( os.indexOf( "win" ) >= 0 ) { + path = "C:\\Program Files\\mafft-win\\mafft.bat"; + } + else { + path = "/home/czmasek/bin/mafft"; + } + if ( !Mafft.isInstalled( path ) ) { + path = "mafft"; + } + if ( !Mafft.isInstalled( path ) ) { + path = "/usr/local/bin/mafft"; + } + if ( Mafft.isInstalled( path ) ) { System.out.print( "MAFFT (external program): " ); - if ( Test.testMafft() ) { + if ( Test.testMafft( path ) ) { System.out.println( "OK." ); succeeded++; } @@ -695,6 +715,7 @@ public final class Test { System.out.println( "failed [will not count towards failed tests]" ); } } + //---- System.out.print( "Next nodes with collapsed: " ); if ( Test.testNextNodeWithCollapsing() ) { System.out.println( "OK." ); @@ -704,6 +725,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "Simple MSA quality: " ); + if ( Test.testMsaQualityMethod() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } // System.out.print( "WABI TxSearch: " ); // if ( Test.testWabiTxSearch() ) { // System.out.println( "OK." ); @@ -1703,6 +1733,7 @@ public final class Test { final List> tl = BasicTableParser.parse( source2.toString(), ";", false, + false, "comment:", false ); if ( tl.size() != 2 ) { @@ -1903,26 +1934,6 @@ public final class Test { return false; } final PhylogenyNode n = t3.getNode( "ABC" ); - PhylogenyNodeIterator it; - for( it = n.iterateChildNodesForward(); it.hasNext(); ) { - it.next(); - } - for( it.reset(); it.hasNext(); ) { - it.next(); - } - final PhylogenyNodeIterator it2 = n.iterateChildNodesForward(); - if ( !it2.next().getName().equals( "A" ) ) { - return false; - } - if ( !it2.next().getName().equals( "B" ) ) { - return false; - } - if ( !it2.next().getName().equals( "C" ) ) { - return false; - } - if ( it2.hasNext() ) { - return false; - } final Phylogeny t4 = factory.create( "((A:1,B:2,C:10)ABC:1,(D:3,E:5)DE:3,(F,G,H,I))", new NHXParser() )[ 0 ]; if ( t4.getNumberOfExternalNodes() != 9 ) { return false; @@ -2122,7 +2133,7 @@ public final class Test { return false; } t2.setIdentifier( new Identifier( "ecoli" ) ); - t2.setTaxonomyCode( "other" ); + t2.setTaxonomyCode( "OTHER" ); t2.setScientificName( "what" ); t2.setCommonName( "something" ); if ( !t1.isEqual( t2 ) ) { @@ -2850,7 +2861,7 @@ public final class Test { dss3.addValue( 10 ); final AsciiHistogram histo = new AsciiHistogram( dss3 ); histo.toStringBuffer( 10, '=', 40, 5 ); - histo.toStringBuffer( 3, 8, 10, '=', 40, 5 ); + histo.toStringBuffer( 3, 8, 10, '=', 40, 5, null ); } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -3200,200 +3211,199 @@ public final class Test { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); final Phylogeny p1 = factory.create( "((((((A,B)ab,C)abc,D)abcd,E)abcde,F)abcdef,(G,H)gh)abcdefgh", new NHXParser() )[ 0 ]; - final PhylogenyMethods pm = PhylogenyMethods.getInstance(); - final PhylogenyNode A = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) ); + final PhylogenyNode A = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "A" ) ); if ( !A.getName().equals( "A" ) ) { return false; } - final PhylogenyNode gh = pm.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) ); + final PhylogenyNode gh = PhylogenyMethods.obtainLCA( p1.getNode( "gh" ), p1.getNode( "gh" ) ); if ( !gh.getName().equals( "gh" ) ) { return false; } - final PhylogenyNode ab = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) ); + final PhylogenyNode ab = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "B" ) ); if ( !ab.getName().equals( "ab" ) ) { return false; } - final PhylogenyNode ab2 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) ); + final PhylogenyNode ab2 = PhylogenyMethods.obtainLCA( p1.getNode( "B" ), p1.getNode( "A" ) ); if ( !ab2.getName().equals( "ab" ) ) { return false; } - final PhylogenyNode gh2 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) ); + final PhylogenyNode gh2 = PhylogenyMethods.obtainLCA( p1.getNode( "H" ), p1.getNode( "G" ) ); if ( !gh2.getName().equals( "gh" ) ) { return false; } - final PhylogenyNode gh3 = pm.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) ); + final PhylogenyNode gh3 = PhylogenyMethods.obtainLCA( p1.getNode( "G" ), p1.getNode( "H" ) ); if ( !gh3.getName().equals( "gh" ) ) { return false; } - final PhylogenyNode abc = pm.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) ); + final PhylogenyNode abc = PhylogenyMethods.obtainLCA( p1.getNode( "C" ), p1.getNode( "A" ) ); if ( !abc.getName().equals( "abc" ) ) { return false; } - final PhylogenyNode abc2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) ); + final PhylogenyNode abc2 = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "C" ) ); if ( !abc2.getName().equals( "abc" ) ) { return false; } - final PhylogenyNode abcd = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) ); + final PhylogenyNode abcd = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "D" ) ); if ( !abcd.getName().equals( "abcd" ) ) { return false; } - final PhylogenyNode abcd2 = pm.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) ); + final PhylogenyNode abcd2 = PhylogenyMethods.obtainLCA( p1.getNode( "D" ), p1.getNode( "A" ) ); if ( !abcd2.getName().equals( "abcd" ) ) { return false; } - final PhylogenyNode abcdef = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) ); + final PhylogenyNode abcdef = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "F" ) ); if ( !abcdef.getName().equals( "abcdef" ) ) { return false; } - final PhylogenyNode abcdef2 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) ); + final PhylogenyNode abcdef2 = PhylogenyMethods.obtainLCA( p1.getNode( "F" ), p1.getNode( "A" ) ); if ( !abcdef2.getName().equals( "abcdef" ) ) { return false; } - final PhylogenyNode abcdef3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) ); + final PhylogenyNode abcdef3 = PhylogenyMethods.obtainLCA( p1.getNode( "ab" ), p1.getNode( "F" ) ); if ( !abcdef3.getName().equals( "abcdef" ) ) { return false; } - final PhylogenyNode abcdef4 = pm.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) ); + final PhylogenyNode abcdef4 = PhylogenyMethods.obtainLCA( p1.getNode( "F" ), p1.getNode( "ab" ) ); if ( !abcdef4.getName().equals( "abcdef" ) ) { return false; } - final PhylogenyNode abcde = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) ); + final PhylogenyNode abcde = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "E" ) ); if ( !abcde.getName().equals( "abcde" ) ) { return false; } - final PhylogenyNode abcde2 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) ); + final PhylogenyNode abcde2 = PhylogenyMethods.obtainLCA( p1.getNode( "E" ), p1.getNode( "A" ) ); if ( !abcde2.getName().equals( "abcde" ) ) { return false; } - final PhylogenyNode r = pm.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) ); + final PhylogenyNode r = PhylogenyMethods.obtainLCA( p1.getNode( "abcdefgh" ), p1.getNode( "abcdefgh" ) ); if ( !r.getName().equals( "abcdefgh" ) ) { return false; } - final PhylogenyNode r2 = pm.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) ); + final PhylogenyNode r2 = PhylogenyMethods.obtainLCA( p1.getNode( "A" ), p1.getNode( "H" ) ); if ( !r2.getName().equals( "abcdefgh" ) ) { return false; } - final PhylogenyNode r3 = pm.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) ); + final PhylogenyNode r3 = PhylogenyMethods.obtainLCA( p1.getNode( "H" ), p1.getNode( "A" ) ); if ( !r3.getName().equals( "abcdefgh" ) ) { return false; } - final PhylogenyNode abcde3 = pm.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) ); + final PhylogenyNode abcde3 = PhylogenyMethods.obtainLCA( p1.getNode( "E" ), p1.getNode( "abcde" ) ); if ( !abcde3.getName().equals( "abcde" ) ) { return false; } - final PhylogenyNode abcde4 = pm.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) ); + final PhylogenyNode abcde4 = PhylogenyMethods.obtainLCA( p1.getNode( "abcde" ), p1.getNode( "E" ) ); if ( !abcde4.getName().equals( "abcde" ) ) { return false; } - final PhylogenyNode ab3 = pm.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) ); + final PhylogenyNode ab3 = PhylogenyMethods.obtainLCA( p1.getNode( "ab" ), p1.getNode( "B" ) ); if ( !ab3.getName().equals( "ab" ) ) { return false; } - final PhylogenyNode ab4 = pm.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) ); + final PhylogenyNode ab4 = PhylogenyMethods.obtainLCA( p1.getNode( "B" ), p1.getNode( "ab" ) ); if ( !ab4.getName().equals( "ab" ) ) { return false; } final Phylogeny p2 = factory.create( "(a,b,(((c,d)cd,e)cde,f)cdef)r", new NHXParser() )[ 0 ]; - final PhylogenyNode cd = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) ); + final PhylogenyNode cd = PhylogenyMethods.obtainLCA( p2.getNode( "c" ), p2.getNode( "d" ) ); if ( !cd.getName().equals( "cd" ) ) { return false; } - final PhylogenyNode cd2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) ); + final PhylogenyNode cd2 = PhylogenyMethods.obtainLCA( p2.getNode( "d" ), p2.getNode( "c" ) ); if ( !cd2.getName().equals( "cd" ) ) { return false; } - final PhylogenyNode cde = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) ); + final PhylogenyNode cde = PhylogenyMethods.obtainLCA( p2.getNode( "c" ), p2.getNode( "e" ) ); if ( !cde.getName().equals( "cde" ) ) { return false; } - final PhylogenyNode cde2 = pm.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) ); + final PhylogenyNode cde2 = PhylogenyMethods.obtainLCA( p2.getNode( "e" ), p2.getNode( "c" ) ); if ( !cde2.getName().equals( "cde" ) ) { return false; } - final PhylogenyNode cdef = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) ); + final PhylogenyNode cdef = PhylogenyMethods.obtainLCA( p2.getNode( "c" ), p2.getNode( "f" ) ); if ( !cdef.getName().equals( "cdef" ) ) { return false; } - final PhylogenyNode cdef2 = pm.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) ); + final PhylogenyNode cdef2 = PhylogenyMethods.obtainLCA( p2.getNode( "d" ), p2.getNode( "f" ) ); if ( !cdef2.getName().equals( "cdef" ) ) { return false; } - final PhylogenyNode cdef3 = pm.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) ); + final PhylogenyNode cdef3 = PhylogenyMethods.obtainLCA( p2.getNode( "f" ), p2.getNode( "d" ) ); if ( !cdef3.getName().equals( "cdef" ) ) { return false; } - final PhylogenyNode rt = pm.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) ); + final PhylogenyNode rt = PhylogenyMethods.obtainLCA( p2.getNode( "c" ), p2.getNode( "a" ) ); if ( !rt.getName().equals( "r" ) ) { return false; } final Phylogeny p3 = factory .create( "((((a,(b,c)bc)abc,(d,e)de)abcde,f)abcdef,(((g,h)gh,(i,j)ij)ghij,k)ghijk,l)", new NHXParser() )[ 0 ]; - final PhylogenyNode bc_3 = pm.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) ); + final PhylogenyNode bc_3 = PhylogenyMethods.obtainLCA( p3.getNode( "b" ), p3.getNode( "c" ) ); if ( !bc_3.getName().equals( "bc" ) ) { return false; } - final PhylogenyNode ac_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) ); + final PhylogenyNode ac_3 = PhylogenyMethods.obtainLCA( p3.getNode( "a" ), p3.getNode( "c" ) ); if ( !ac_3.getName().equals( "abc" ) ) { return false; } - final PhylogenyNode ad_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) ); + final PhylogenyNode ad_3 = PhylogenyMethods.obtainLCA( p3.getNode( "a" ), p3.getNode( "d" ) ); if ( !ad_3.getName().equals( "abcde" ) ) { return false; } - final PhylogenyNode af_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) ); + final PhylogenyNode af_3 = PhylogenyMethods.obtainLCA( p3.getNode( "a" ), p3.getNode( "f" ) ); if ( !af_3.getName().equals( "abcdef" ) ) { return false; } - final PhylogenyNode ag_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) ); + final PhylogenyNode ag_3 = PhylogenyMethods.obtainLCA( p3.getNode( "a" ), p3.getNode( "g" ) ); if ( !ag_3.getName().equals( "" ) ) { return false; } if ( !ag_3.isRoot() ) { return false; } - final PhylogenyNode al_3 = pm.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) ); + final PhylogenyNode al_3 = PhylogenyMethods.obtainLCA( p3.getNode( "a" ), p3.getNode( "l" ) ); if ( !al_3.getName().equals( "" ) ) { return false; } if ( !al_3.isRoot() ) { return false; } - final PhylogenyNode kl_3 = pm.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) ); + final PhylogenyNode kl_3 = PhylogenyMethods.obtainLCA( p3.getNode( "k" ), p3.getNode( "l" ) ); if ( !kl_3.getName().equals( "" ) ) { return false; } if ( !kl_3.isRoot() ) { return false; } - final PhylogenyNode fl_3 = pm.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) ); + final PhylogenyNode fl_3 = PhylogenyMethods.obtainLCA( p3.getNode( "f" ), p3.getNode( "l" ) ); if ( !fl_3.getName().equals( "" ) ) { return false; } if ( !fl_3.isRoot() ) { return false; } - final PhylogenyNode gk_3 = pm.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) ); + final PhylogenyNode gk_3 = PhylogenyMethods.obtainLCA( p3.getNode( "g" ), p3.getNode( "k" ) ); if ( !gk_3.getName().equals( "ghijk" ) ) { return false; } final Phylogeny p4 = factory.create( "(a,b,c)r", new NHXParser() )[ 0 ]; - final PhylogenyNode r_4 = pm.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) ); + final PhylogenyNode r_4 = PhylogenyMethods.obtainLCA( p4.getNode( "b" ), p4.getNode( "c" ) ); if ( !r_4.getName().equals( "r" ) ) { return false; } final Phylogeny p5 = factory.create( "((a,b),c,d)root", new NHXParser() )[ 0 ]; - final PhylogenyNode r_5 = pm.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) ); + final PhylogenyNode r_5 = PhylogenyMethods.obtainLCA( p5.getNode( "a" ), p5.getNode( "c" ) ); if ( !r_5.getName().equals( "root" ) ) { return false; } final Phylogeny p6 = factory.create( "((a,b),c,d)rot", new NHXParser() )[ 0 ]; - final PhylogenyNode r_6 = pm.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) ); + final PhylogenyNode r_6 = PhylogenyMethods.obtainLCA( p6.getNode( "c" ), p6.getNode( "a" ) ); if ( !r_6.getName().equals( "rot" ) ) { return false; } final Phylogeny p7 = factory.create( "(((a,b)x,c)x,d,e)rott", new NHXParser() )[ 0 ]; - final PhylogenyNode r_7 = pm.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) ); + final PhylogenyNode r_7 = PhylogenyMethods.obtainLCA( p7.getNode( "a" ), p7.getNode( "e" ) ); if ( !r_7.getName().equals( "rott" ) ) { return false; } @@ -3433,10 +3443,16 @@ public final class Test { if ( p1.getNumberOfProteinDomains() != 15 ) { return false; } + if ( p1.getLength() != 850 ) { + return false; + } final Protein p2 = proteins.get( 1 ); if ( p2.getNumberOfProteinDomains() != 51 ) { return false; } + if ( p2.getLength() != 1291 ) { + return false; + } final Protein p3 = proteins.get( 2 ); if ( p3.getNumberOfProteinDomains() != 2 ) { return false; @@ -4699,51 +4715,81 @@ public final class Test { if ( PhylogenyMethods.getSpecies( n23 ).length() > 0 ) { return false; } - if ( NHXParser.LIMIT_SPECIES_NAMES_TO_FIVE_CHARS ) { - final PhylogenyNode a = PhylogenyNode - .createInstanceFromNhxString( "n10_ECOLI/1-2", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) { - return false; - } - if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) { - return false; - } - final PhylogenyNode b = PhylogenyNode - .createInstanceFromNhxString( "n10_ECOLI1/1-2", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) { - return false; - } - if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) { - return false; - } - final PhylogenyNode c = PhylogenyNode - .createInstanceFromNhxString( "n10_RATAF12/1000-2000", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) { - return false; - } - if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) { - return false; - } - final PhylogenyNode d = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT1/1-2", - PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !d.getName().equals( "n10_RAT1/1-2" ) ) { - return false; - } - if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) { - return false; - } - final PhylogenyNode e = PhylogenyNode - .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); - if ( !e.getName().equals( "n10_RAT1" ) ) { - return false; - } - if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) { - return false; - } + final PhylogenyNode a = PhylogenyNode + .createInstanceFromNhxString( "n10_ECOLI/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + if ( !a.getName().equals( "n10_ECOLI/1-2" ) ) { + return false; + } + if ( !PhylogenyMethods.getSpecies( a ).equals( "ECOLI" ) ) { + return false; + } + final PhylogenyNode b = PhylogenyNode + .createInstanceFromNhxString( "n10_ECOLI1/1-2", + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + if ( !b.getName().equals( "n10_ECOLI1/1-2" ) ) { + return false; + } + if ( !PhylogenyMethods.getSpecies( b ).equals( "ECOLI" ) ) { + return false; + } + final PhylogenyNode c = PhylogenyNode + .createInstanceFromNhxString( "n10_RATAF12/1000-2000", + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + if ( !c.getName().equals( "n10_RATAF12/1000-2000" ) ) { + return false; + } + if ( !PhylogenyMethods.getSpecies( c ).equals( "RATAF" ) ) { + return false; + } + final PhylogenyNode c1 = PhylogenyNode + .createInstanceFromNhxString( "n10_BOVIN_1/1000-2000", + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + if ( !c1.getName().equals( "n10_BOVIN_1/1000-2000" ) ) { + return false; + } + if ( !PhylogenyMethods.getSpecies( c1 ).equals( "BOVIN" ) ) { + return false; + } + final PhylogenyNode c2 = PhylogenyNode + .createInstanceFromNhxString( "n10_Bovin_1/1000-2000", + PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + if ( !c2.getName().equals( "n10_Bovin_1/1000-2000" ) ) { + return false; + } + if ( !PhylogenyMethods.getSpecies( c2 ).equals( "" ) ) { + return false; + } + final PhylogenyNode d = PhylogenyNode + .createInstanceFromNhxString( "n10_RAT1/1-2", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + if ( !d.getName().equals( "n10_RAT1/1-2" ) ) { + return false; + } + if ( !PhylogenyMethods.getSpecies( d ).equals( "RAT" ) ) { + return false; + } + final PhylogenyNode e = PhylogenyNode + .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + if ( !e.getName().equals( "n10_RAT1" ) ) { + return false; + } + if ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( e ) ) ) { + return false; + } + final PhylogenyNode e2 = PhylogenyNode + .createInstanceFromNhxString( "n10_RAT1", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); + if ( !e2.getName().equals( "n10_RAT1" ) ) { + return false; + } + if ( !PhylogenyMethods.getSpecies( e2 ).equals( "RAT" ) ) { + return false; + } + final PhylogenyNode e3 = PhylogenyNode + .createInstanceFromNhxString( "n10_RAT~", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); + if ( !e3.getName().equals( "n10_RAT~" ) ) { + return false; + } + if ( !PhylogenyMethods.getSpecies( e3 ).equals( "RAT" ) ) { + return false; } final PhylogenyNode n11 = PhylogenyNode .createInstanceFromNhxString( "n111111_ECOLI/jdj:0.4", @@ -4769,6 +4815,22 @@ public final class Test { if ( PhylogenyMethods.getSpecies( n12 ).length() > 0 ) { return false; } + final PhylogenyNode m = PhylogenyNode + .createInstanceFromNhxString( "n10_MOUSEa", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); + if ( !m.getName().equals( "n10_MOUSEa" ) ) { + return false; + } + if ( !PhylogenyMethods.getSpecies( m ).equals( "MOUSE" ) ) { + return false; + } + final PhylogenyNode o = PhylogenyNode + .createInstanceFromNhxString( "n10_MOUSE_", PhylogenyMethods.TAXONOMY_EXTRACTION.YES ); + if ( !o.getName().equals( "n10_MOUSE_" ) ) { + return false; + } + if ( !PhylogenyMethods.getSpecies( o ).equals( "MOUSE" ) ) { + return false; + } final Property tvu1 = n5.getNodeData().getProperties().getProperty( "tag1" ); final Property tvu3 = n5.getNodeData().getProperties().getProperty( "tag3" ); if ( !tvu1.getRef().equals( "tag1" ) ) { @@ -4853,7 +4915,7 @@ public final class Test { if ( !n13.getName().equals( "blah_12345/1-2" ) ) { return false; } - if ( !PhylogenyMethods.getSpecies( n13 ).equals( "" ) ) { + if ( !PhylogenyMethods.getSpecies( n13 ).equals( "12345" ) ) { return false; } final PhylogenyNode n14 = PhylogenyNode @@ -7444,365 +7506,10 @@ public final class Test { return true; } - private static boolean testTaxonomyAssigner() { - try { - String s0_str = "(((([&&NHX:S=A],[&&NHX:S=B])[&&NHX:S=AB],[&&NHX:S=C])[&&NHX:S=ABC],[&&NHX:S=D])[&&NHX:S=ABCD],[&&NHX:S=E])[&&NHX:S=ABCDE]"; - String g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=B])b,[&&NHX:S=C])c"; - Phylogeny s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ]; - Phylogeny g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - s0.setRooted( true ); - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) { - return false; - } - g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) { - return false; - } - g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=A])b,[&&NHX:S=A])c"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) { - return false; - } - g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=A])c"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) { - return false; - } - g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=C])b,[&&NHX:S=D])c"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "AB" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABC" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=C])b,[&&NHX:S=D])c"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) { - return false; - } - g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=E])a,[&&NHX:S=A])b,[&&NHX:S=A])c"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCDE" ) ) { - return false; - } - s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])[&&NHX:S=ABCD]," - + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])[&&NHX:S=EFGH]," - + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])[&&NHX:S=IJKL], " - + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])[&&NHX:S=MNOP])[&&NHX:S=ROOT]"; - s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ]; - s0.setRooted( true ); - g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a," - + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])b," - + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L])c, " - + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P])d)r"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) { - return false; - } - if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) { - return false; - } - if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) { - return false; - } - g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a," - + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b," - + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=I])c, " - + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=O])d)r"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "IJKL" ) ) { - return false; - } - if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "MNOP" ) ) { - return false; - } - if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) { - return false; - } - g0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=A],[&&NHX:S=B])a," - + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=F],[&&NHX:S=F])b," - + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, " - + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=A],[&&NHX:S=O])d)r"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "EFGH" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) { - return false; - } - if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) { - return false; - } - if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) { - return false; - } - g0_str = "(([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])a," - + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])b," - + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c, " - + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) { - return false; - } - if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) { - return false; - } - if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) { - return false; - } - g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])a,[&&NHX:S=A])b,[&&NHX:S=A])c"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) { - return false; - } - g0_str = "((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=B])a,[&&NHX:S=I])b,[&&NHX:S=J])c"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) { - return false; - } - g0_str = "(((([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])a," - + "([&&NHX:S=D],[&&NHX:S=C],[&&NHX:S=B],[&&NHX:S=A])b)ab," - + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, " - + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) { - return false; - } - if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) { - return false; - } - if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) { - return false; - } - if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) { - return false; - } - g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a," - + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab," - + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, " - + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])d)r"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) { - return false; - } - if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) { - return false; - } - if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) { - return false; - } - if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) { - return false; - } - g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a," - + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab," - + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L])c)abc, " - + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "L" ) ) { - return false; - } - if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) { - return false; - } - if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) { - return false; - } - if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) { - return false; - } - g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a," - + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab," - + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, " - + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( !g0.getNode( "a" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "b" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "ab" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) { - return false; - } - if ( !g0.getNode( "abc" ).getNodeData().getTaxonomy().getScientificName().equals( "ABCD" ) ) { - return false; - } - if ( !g0.getNode( "d" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) { - return false; - } - if ( !g0.getNode( "r" ).getNodeData().getTaxonomy().getScientificName().equals( "ROOT" ) ) { - return false; - } - s0_str = "(([&&NHX:S=A],[&&NHX:S=B],[&&NHX:S=C],[&&NHX:S=D])," - + "([&&NHX:S=E],[&&NHX:S=F],[&&NHX:S=G],[&&NHX:S=H])," - + "([&&NHX:S=I],[&&NHX:S=J],[&&NHX:S=K],[&&NHX:S=L]), " - + "([&&NHX:S=M],[&&NHX:S=N],[&&NHX:S=O],[&&NHX:S=P]))"; - s0 = ParserBasedPhylogenyFactory.getInstance().create( s0_str, new NHXParser() )[ 0 ]; - s0.setRooted( true ); - g0_str = "(((([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=C],[&&NHX:S=D])a," - + "([&&NHX:S=D],[&&NHX:S=D],[&&NHX:S=B],[&&NHX:S=A])b)ab," - + "([&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A],[&&NHX:S=A])c)abc, " - + "([&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=L],[&&NHX:S=A])d)r"; - g0 = ParserBasedPhylogenyFactory.getInstance().create( g0_str, new NHXParser() )[ 0 ]; - g0.setRooted( true ); - TaxonomyAssigner.execute( g0, s0 ); - if ( g0.getNode( "a" ).getNodeData().isHasTaxonomy() ) { - return false; - } - if ( !g0.getNode( "c" ).getNodeData().getTaxonomy().getScientificName().equals( "A" ) ) { - return false; - } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - private static boolean testUniprotTaxonomySearch() { try { - List results = UniProtWsTools - .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 ); + List results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone", + 10 ); if ( results.size() != 1 ) { return false; } @@ -7822,7 +7529,7 @@ public final class Test { return false; } results = null; - results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 ); + results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 ); if ( results.size() != 1 ) { return false; } @@ -7842,7 +7549,7 @@ public final class Test { return false; } results = null; - results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 ); + results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 ); if ( results.size() != 1 ) { return false; } @@ -7862,7 +7569,7 @@ public final class Test { return false; } results = null; - results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 ); + results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 ); if ( results.size() != 1 ) { return false; } @@ -7910,90 +7617,90 @@ public final class Test { //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals //Protein: 3 letters + 5 numerals //http://www.ncbi.nlm.nih.gov/Sequin/acc.html - if ( !DatabaseTools.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) { + if ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) { return false; } - if ( !DatabaseTools.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) { + if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861." ).equals( "AY423861" ) ) { return false; } - if ( DatabaseTools.parseGenbankAccessor( "AAY423861" ) != null ) { + if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) { return false; } - if ( DatabaseTools.parseGenbankAccessor( "AY4238612" ) != null ) { + if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) { return false; } - if ( DatabaseTools.parseGenbankAccessor( "AAY4238612" ) != null ) { + if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) { return false; } - if ( DatabaseTools.parseGenbankAccessor( "Y423861" ) != null ) { + if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) { return false; } - if ( !DatabaseTools.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) { + if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) { return false; } - if ( !DatabaseTools.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) { + if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) { return false; } - if ( DatabaseTools.parseGenbankAccessor( "|S123456" ) != null ) { + if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) { return false; } - if ( DatabaseTools.parseGenbankAccessor( "ABC123456" ) != null ) { + if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) { return false; } - if ( !DatabaseTools.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) { + if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) { return false; } - if ( !DatabaseTools.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) { + if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) { return false; } - if ( DatabaseTools.parseGenbankAccessor( "ABCD12345" ) != null ) { + if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) { return false; } return true; } private static boolean testUniprotEntryRetrieval() { - if ( !UniProtWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) { + if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) { return false; } - if ( UniProtWsTools.parseUniProtAccessor( "EP12345" ) != null ) { + if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) { return false; } - if ( UniProtWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) { + if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) { return false; } - if ( UniProtWsTools.parseUniProtAccessor( "P12345E" ) != null ) { + if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) { return false; } - if ( UniProtWsTools.parseUniProtAccessor( "P123455" ) != null ) { + if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) { return false; } - if ( UniProtWsTools.parseUniProtAccessor( "EP12345E" ) != null ) { + if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) { return false; } - if ( UniProtWsTools.parseUniProtAccessor( "AY423861" ) != null ) { + if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) { return false; } - if ( !UniProtWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) { + if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) { return false; } - if ( UniProtWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) { + if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) { return false; } - if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) { + if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) { return false; } - if ( !UniProtWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) { + if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) { return false; } - if ( !UniProtWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) { + if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) { return false; } - if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) { + if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) { return false; } try { - final SequenceDatabaseEntry entry = UniProtWsTools.obtainUniProtEntry( "P12345", 200 ); + final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 ); if ( !entry.getAccession().equals( "P12345" ) ) { return false; } @@ -8176,12 +7883,48 @@ public final class Test { try { final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n"; final Msa msa_0 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_0.getBytes() ) ); - final String msa_str_1 = "seq_1 abc\nseq2 ghi\nseq_1 def\nseq2 jkm\n"; + final String msa_str_1 = "seq1 abc\nseq2 ghi\nseq1 def\nseq2 jkm\n"; final Msa msa_1 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_1.getBytes() ) ); final String msa_str_2 = "seq1 abc\nseq2 ghi\n\ndef\njkm\n"; final Msa msa_2 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_2.getBytes() ) ); final String msa_str_3 = "seq1 abc\n def\nseq2 ghi\n jkm\n"; final Msa msa_3 = GeneralMsaParser.parse( new ByteArrayInputStream( msa_str_3.getBytes() ) ); + if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { + return false; + } + if ( !msa_1.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { + return false; + } + if ( !msa_1.getIdentifier( 0 ).toString().equals( "seq1" ) ) { + return false; + } + if ( !msa_1.getIdentifier( 1 ).toString().equals( "seq2" ) ) { + return false; + } + if ( !msa_2.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { + return false; + } + if ( !msa_2.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { + return false; + } + if ( !msa_2.getIdentifier( 0 ).toString().equals( "seq1" ) ) { + return false; + } + if ( !msa_2.getIdentifier( 1 ).toString().equals( "seq2" ) ) { + return false; + } + if ( !msa_3.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) { + return false; + } + if ( !msa_3.getSequenceAsString( 1 ).toString().equalsIgnoreCase( "ghixkm" ) ) { + return false; + } + if ( !msa_3.getIdentifier( 0 ).toString().equals( "seq1" ) ) { + return false; + } + if ( !msa_3.getIdentifier( 1 ).toString().equals( "seq2" ) ) { + return false; + } final Msa msa_4 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) ); if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) { return false; @@ -8220,7 +7963,7 @@ public final class Test { return true; } - private static boolean testMafft() { + private static boolean testMafft( final String path ) { try { final List opts = new ArrayList(); opts.add( "--maxiterate" ); @@ -8228,9 +7971,12 @@ public final class Test { opts.add( "--localpair" ); opts.add( "--quiet" ); Msa msa = null; - final MsaInferrer mafft = Mafft.createInstance(); - msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi.fasta" ), opts ); - if ( ( msa == null ) || ( msa.getLength() < 10 ) || ( msa.getNumberOfSequences() != 19 ) ) { + final MsaInferrer mafft = Mafft.createInstance( path ); + msa = mafft.infer( new File( PATH_TO_TEST_DATA + "ncbi_sn.fasta" ), opts ); + if ( ( msa == null ) || ( msa.getLength() < 20 ) || ( msa.getNumberOfSequences() != 19 ) ) { + return false; + } + if ( !msa.getIdentifier( 0 ).toString().equals( "a" ) ) { return false; } } @@ -8801,4 +8547,141 @@ public final class Test { } return true; } + + private static boolean testMsaQualityMethod() { + try { + final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" ); + final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" ); + final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" ); + final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" ); + final List l = new ArrayList(); + l.add( s0 ); + l.add( s1 ); + l.add( s2 ); + l.add( s3 ); + final Msa msa = BasicMsa.createInstance( l ); + if ( !isEqual( 1, MsaMethods.calculateIdentityRatio( msa, 0 ) ) ) { + return false; + } + if ( !isEqual( 0.5, MsaMethods.calculateIdentityRatio( msa, 1 ) ) ) { + return false; + } + if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 2 ) ) ) { + return false; + } + if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testSequenceIdParsing() { + try { + Identifier id = SequenceIdParser.parse( "gb_ADF31344_segmented_worms_" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) + || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getProvider() ); + } + return false; + } + // + id = SequenceIdParser.parse( "segmented worms|gb_ADF31344" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) + || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getProvider() ); + } + return false; + } + // + id = SequenceIdParser.parse( "segmented worms gb_ADF31344 and more" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) + || !id.getValue().equals( "ADF31344" ) || !id.getProvider().equals( "ncbi" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getProvider() ); + } + return false; + } + // + id = SequenceIdParser.parse( "gb_AAA96518_1" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) + || !id.getValue().equals( "AAA96518" ) || !id.getProvider().equals( "ncbi" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getProvider() ); + } + return false; + } + // + id = SequenceIdParser.parse( "gb_EHB07727_1_rodents_" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) + || !id.getValue().equals( "EHB07727" ) || !id.getProvider().equals( "ncbi" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getProvider() ); + } + return false; + } + // + id = SequenceIdParser.parse( "dbj_BAF37827_1_turtles_" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) + || !id.getValue().equals( "BAF37827" ) || !id.getProvider().equals( "ncbi" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getProvider() ); + } + return false; + } + // + id = SequenceIdParser.parse( "emb_CAA73223_1_primates_" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) + || !id.getValue().equals( "CAA73223" ) || !id.getProvider().equals( "ncbi" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getProvider() ); + } + return false; + } + // + id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) + || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getProvider() ); + } + return false; + } + // + id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" ); + if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() ) + || !id.getValue().equals( "XP_002434188" ) || !id.getProvider().equals( "refseq" ) ) { + if ( id != null ) { + System.out.println( "value =" + id.getValue() ); + System.out.println( "provider=" + id.getProvider() ); + } + return false; + } + // + id = SequenceIdParser.parse( "XP_12345" ); + if ( id != null ) { + return false; + } + // lcl_91970_unknown_ + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } }