X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftest%2FTest.java;h=3efa3540f5a216bee1b3432b249861e31c520cd3;hb=fea4064e24c6cb362b0e033cf7047afd20f5f53f;hp=94798ae9301bfb4431b8ea2f9d3f00909683214b;hpb=baf4db894c841b22eabbd31a03dd552167d43c60;p=jalview.git diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index 94798ae..3efa354 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -40,6 +40,9 @@ import java.util.Locale; import java.util.Set; import java.util.SortedSet; +import javax.net.ssl.HttpsURLConnection; +import javax.net.ssl.SSLContext; + import org.forester.application.support_transfer; import org.forester.archaeopteryx.AptxUtil; import org.forester.archaeopteryx.TreePanelUtil; @@ -125,10 +128,7 @@ import org.forester.util.SequenceAccessionTools; 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; -import org.forester.ws.wabi.TxSearch.TAX_RANK; + @SuppressWarnings( "unused") public final class Test { @@ -150,7 +150,7 @@ public final class Test { private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true; private final static double ZERO_DIFF = 1.0E-9; - public static boolean isEqual( final double a, final double b ) { + private static boolean isEqual( final double a, final double b ) { return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF ); } @@ -181,15 +181,7 @@ public final class Test { System.exit( -1 ); } final long start_time = new Date().getTime(); - System.out.print( "MSA entropy: " ); - if ( Test.testMsaEntropy() ) { - System.out.println( "OK." ); - succeeded++; - } - else { - System.out.println( "failed." ); - failed++; - } + System.out.print( "Basic node methods: " ); if ( Test.testBasicNodeMethods() ) { System.out.println( "OK." ); @@ -931,6 +923,15 @@ public final class Test { System.out.println( "failed." ); failed++; } + System.out.print( "MSA entropy: " ); + if ( Test.testMsaEntropy() ) { + System.out.println( "OK." ); + succeeded++; + } + else { + System.out.println( "failed." ); + failed++; + } if ( PERFORM_DB_TESTS ) { System.out.print( "Uniprot Entry Retrieval: " ); if ( Test.testUniprotEntryRetrieval() ) { @@ -971,8 +972,8 @@ public final class Test { } } if ( PERFORM_WEB_TREE_ACCESS ) { - System.out.print( "NHX parsing from URL: " ); - if ( Test.testNHXparsingFromURL() ) { + System.out.print( "TreeBase acccess: " ); + if ( Test.testTreeBaseReading() ) { System.out.println( "OK." ); succeeded++; } @@ -980,8 +981,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "NHX parsing from URL 2: " ); - if ( Test.testNHXparsingFromURL2() ) { + System.out.print( "ToL access: " ); + if ( Test.testToLReading() ) { System.out.println( "OK." ); succeeded++; } @@ -989,8 +990,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "phyloXML parsing from URL: " ); - if ( Test.testPhyloXMLparsingFromURL() ) { + System.out.print( "NHX parsing from URL: " ); + if ( Test.testNHXparsingFromURL() ) { System.out.println( "OK." ); succeeded++; } @@ -998,8 +999,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - System.out.print( "TreeBase acccess: " ); - if ( Test.testTreeBaseReading() ) { + System.out.print( "NHX parsing from URL 2: " ); + if ( Test.testNHXparsingFromURL2() ) { System.out.println( "OK." ); succeeded++; } @@ -1007,9 +1008,8 @@ public final class Test { System.out.println( "failed." ); failed++; } - // - System.out.print( "ToL access: " ); - if ( Test.testToLReading() ) { + System.out.print( "phyloXML parsing from URL: " ); + if ( Test.testPhyloXMLparsingFromURL() ) { System.out.println( "OK." ); succeeded++; } @@ -1017,7 +1017,6 @@ public final class Test { System.out.println( "failed." ); failed++; } - // System.out.print( "TreeFam access: " ); if ( Test.testTreeFamReading() ) { System.out.println( "OK." ); @@ -1027,8 +1026,6 @@ public final class Test { System.out.println( "failed." ); failed++; } - // - // System.out.print( "Pfam tree access: " ); if ( Test.testPfamTreeReading() ) { System.out.println( "OK." ); @@ -1057,7 +1054,7 @@ public final class Test { } } - public static boolean testEngulfingOverlapRemoval() { + private static boolean testEngulfingOverlapRemoval() { try { final Domain d0 = new BasicDomain( "d0", 0, 8, ( short ) 1, ( short ) 1, 0.1, 1 ); final Domain d1 = new BasicDomain( "d1", 0, 1, ( short ) 1, ( short ) 1, 0.1, 1 ); @@ -1156,7 +1153,7 @@ public final class Test { return true; } - public static final boolean testNHXparsingFromURL2() { + private static final boolean testNHXparsingFromURL2() { try { final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh"; final Phylogeny phys[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ), @@ -1223,7 +1220,7 @@ public final class Test { return true; } - public static final boolean testNHXparsingFromURL() { + private static final boolean testNHXparsingFromURL() { try { final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh"; final URL u = new URL( s ); @@ -1291,7 +1288,7 @@ public final class Test { return true; } - public static boolean testOverlapRemoval() { + private static boolean testOverlapRemoval() { try { final Domain d0 = new BasicDomain( "d0", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 0.1, 1 ); final Domain d1 = new BasicDomain( "d1", ( short ) 7, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 ); @@ -1445,49 +1442,61 @@ public final class Test { return true; } - public static final boolean testPfamTreeReading() { + private static final boolean testPfamTreeReading() { try { final URL u = new URL( WebserviceUtil.PFAM_SERVER + "/family/PF" + "01849" + "/tree/download" ); final NHXParser parser = new NHXParser(); parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); parser.setReplaceUnderscores( false ); parser.setGuessRootedness( true ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys = factory.create( u.openStream(), parser ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser); if ( ( phys == null ) || ( phys.length != 1 ) ) { return false; } if ( phys[ 0 ].getNumberOfExternalNodes() < 10 ) { return false; } + final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u, parser); + if ( ( phys2 == null ) || ( phys2.length != 1 ) ) { + return false; + } + if ( phys2[ 0 ].getNumberOfExternalNodes() != phys[ 0 ].getNumberOfExternalNodes() ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace(); + return false; } return true; } - public static final boolean testPhyloXMLparsingFromURL() { + private static final boolean testPhyloXMLparsingFromURL() { try { final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/archaeopteryx_a/apaf_bcl2.xml"; final URL u = new URL( s ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys = factory.create( u.openStream(), PhyloXmlParser.createPhyloXmlParser() ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, PhyloXmlParser.createPhyloXmlParser() ); + if ( ( phys == null ) || ( phys.length != 2 ) ) { return false; } + final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u, PhyloXmlParser.createPhyloXmlParser() ); + + if ( ( phys2 == null ) || ( phys2.length != 2 ) ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace(); + return false; } return true; } - public static final boolean testToLReading() { + private static final boolean testToLReading() { try { final URL u = new URL( WebserviceUtil.TOL_URL_BASE + "15079" ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys = factory.create( u.openStream(), new TolParser() ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, new TolParser() ); if ( ( phys == null ) || ( phys.length != 1 ) ) { return false; } @@ -1500,47 +1509,138 @@ public final class Test { if ( phys[ 0 ].getNumberOfExternalNodes() < 5 ) { return false; } + // + final URL u2 = new URL( WebserviceUtil.TOL_URL_BASE + "17706" ); + final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u2, new TolParser() ); + if ( ( phys2 == null ) || ( phys2.length != 1 ) ) { + return false; + } + if ( !phys2[ 0 ].getRoot().getNodeData().getTaxonomy().getIdentifier().getValue().equals( "17706" ) ) { + return false; + } + if ( phys2[ 0 ].getNumberOfExternalNodes() < 5 ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace(); + return false; } return true; } - public static final boolean testTreeBaseReading() { + private static final boolean testTreeBaseReading() { try { - final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" ); + final URL u = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "72557?format=nexus" ); final NexusPhylogeniesParser parser = new NexusPhylogeniesParser(); parser.setReplaceUnderscores( true ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys = factory.create( u.openStream(), parser ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser ); if ( ( phys == null ) || ( phys.length != 1 ) ) { return false; } + final URL u_1 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "2406?format=nexus" ); + final NexusPhylogeniesParser parser_1 = new NexusPhylogeniesParser(); + final Phylogeny[] phys_1 = ForesterUtil.readPhylogeniesFromUrl( u_1, parser_1 ); + if ( ( phys_1 == null ) || ( phys_1.length != 1 ) ) { + return false; + } + final URL u_2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "422?format=nexus" ); + final NexusPhylogeniesParser parser_2 = new NexusPhylogeniesParser(); + final Phylogeny[] phys_2 = ForesterUtil.readPhylogeniesFromUrl( u_2, parser_2 ); + if ( ( phys_2 == null ) || ( phys_2.length != 1 ) ) { + return false; + } + final URL u_3 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "2654?format=nexus" ); + final NexusPhylogeniesParser parser_3 = new NexusPhylogeniesParser(); + final Phylogeny[] phys_3 = ForesterUtil.readPhylogeniesFromUrl( u_3, parser_3 ); + if ( ( phys_3 == null ) || ( phys_3.length != 1 ) ) { + return false; + } + final URL u_4 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_TREE_URL_BASE + "825?format=nexus" ); + final NexusPhylogeniesParser parser_4 = new NexusPhylogeniesParser(); + final Phylogeny[] phys_4 = ForesterUtil.readPhylogeniesFromUrl( u_4, parser_4 ); + if ( ( phys_4 == null ) || ( phys_4.length != 1 ) ) { + return false; + } final URL u2 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15613?format=nexus" ); final NexusPhylogeniesParser parser2 = new NexusPhylogeniesParser(); parser2.setReplaceUnderscores( true ); - final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys2 = factory2.create( u2.openStream(), parser2 ); + final Phylogeny[] phys2 = ForesterUtil.readPhylogeniesFromUrl( u2, parser2 ); if ( ( phys2 == null ) || ( phys2.length != 9 ) ) { return false; } + final URL u3 = new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "14909?format=nexus" ); + final NexusPhylogeniesParser parser3 = new NexusPhylogeniesParser(); + final Phylogeny[] phys3 = ForesterUtil.readPhylogeniesFromUrl( u3, parser3 ); + if ( ( phys3 == null ) || ( phys3.length != 2 ) ) { + return false; + } + final Phylogeny[] phys4 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "14525?format=nexus" ), + new NexusPhylogeniesParser() ); + if ( ( phys4 == null ) || ( phys4.length != 1 ) ) { + return false; + } + final Phylogeny[] phys5 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "15632?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys5 == null ) || ( phys5.length != 1 ) ) { + return false; + } + final Phylogeny[] phys6 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "10190?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys6 == null ) || ( phys6.length != 1 ) ) { + return false; + } + final Phylogeny[] phys7 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "13246?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys7 == null ) || ( phys7.length != 2 ) ) { + return false; + } + final Phylogeny[] phys8 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "11662?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys8 == null ) || ( phys8.length != 2 ) ) { + return false; + } + final Phylogeny[] phys9 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "562?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys9 == null ) || ( phys9.length != 4 ) ) { + return false; + } + final Phylogeny[] phys16424 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "16424?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys16424 == null ) || ( phys16424.length != 1 ) ) { + return false; + } + final Phylogeny[] phys17878 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "17878?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys17878 == null ) || ( phys17878.length != 17 ) ) { + return false; + } + final Phylogeny[] phys18804 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "18804?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys18804 == null ) || ( phys18804.length != 2 ) ) { + return false; + } + final Phylogeny[] phys346 = ForesterUtil.readPhylogeniesFromUrl( new URL( WebserviceUtil.TREEBASE_PHYLOWS_STUDY_URL_BASE + "346?format=nexus" ) , + new NexusPhylogeniesParser() ); + if ( ( phys346 == null ) || ( phys346.length != 1 ) ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace(); + return false; } return true; } - public static final boolean testTreeFamReading() { + private static final boolean testTreeFamReading() { try { final URL u = new URL( WebserviceUtil.TREE_FAM_URL_BASE + "101004" + "/tree/newick" ); final NHXParser parser = new NHXParser(); parser.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO ); parser.setReplaceUnderscores( false ); parser.setGuessRootedness( true ); - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - final Phylogeny[] phys = factory.create( u.openStream(), parser ); + final Phylogeny[] phys = ForesterUtil.readPhylogeniesFromUrl( u, parser ); if ( ( phys == null ) || ( phys.length != 1 ) ) { return false; } @@ -1550,6 +1650,7 @@ public final class Test { } catch ( final Exception e ) { e.printStackTrace(); + return false; } return true; } @@ -1776,6 +1877,21 @@ public final class Test { if ( !t3.getIdentifier().getProvider().equals( "treebank" ) ) { return false; } + if ( !t3.getNode( "root node" ).isDuplication() ) { + return false; + } + if ( !t3.getNode( "node a" ).isDuplication() ) { + return false; + } + if ( t3.getNode( "node a" ).isSpeciation() ) { + return false; + } + if ( t3.getNode( "node bc" ).isDuplication() ) { + return false; + } + if ( !t3.getNode( "node bc" ).isSpeciation() ) { + return false; + } if ( !t3.getNode( "root node" ).getNodeData().getSequence().getType().equals( "protein" ) ) { return false; } @@ -2103,7 +2219,7 @@ public final class Test { return false; } if ( t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ) - .getConfidence() != 2144 ) { + .getConfidence() != 0 ) { return false; } if ( !t3_rt.getNode( "node bc" ).getNodeData().getSequence().getDomainArchitecture().getDomain( 0 ).getId() @@ -4016,7 +4132,7 @@ public final class Test { System.out.println( entry.getAnnotations().first().getRefSource() ); return false; } - if ( entry.getCrossReferences().size() != 5 ) { + if ( entry.getCrossReferences().size() < 1 ) { return false; } final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" ); @@ -4039,7 +4155,7 @@ public final class Test { System.out.println( entry1.getGeneName() ); return false; } - if ( entry1.getCrossReferences().size() != 6 ) { + if ( entry1.getCrossReferences().size() < 1 ) { return false; } final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" ); @@ -4063,10 +4179,15 @@ public final class Test { System.out.println( entry2.getGeneName() ); return false; } - if ( entry2.getCrossReferences().size() != 3 ) { + if ( entry2.getCrossReferences().size() < 1 ) { + return false; + } + if ( !entry2.getChromosome().equals( "20" ) ) { + return false; + } + if ( !entry2.getMap().equals( "20q11.22" ) ) { return false; } - // final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" ); if ( !entry3.getAccession().equals( "HM043801" ) ) { return false; @@ -4090,7 +4211,7 @@ public final class Test { if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) { return false; } - if ( entry3.getCrossReferences().size() < 7 ) { + if ( entry3.getCrossReferences().size() < 1 ) { return false; } final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" ); @@ -4113,21 +4234,6 @@ public final class Test { System.out.println( entry4.getGeneName() ); return false; } - // if ( !entry4.getChromosome().equals( "ras" ) ) { - // System.out.println( entry4.getChromosome() ); - // return false; - // } - // if ( !entry4.getMap().equals( "ras" ) ) { - // System.out.println( entry4.getMap() ); - // return false; - // } - //TODO FIXME gi... - // - //TODO fails: - // final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "M30539" ); - // if ( !entry5.getAccession().equals( "HM043801" ) ) { - // return false; - // } final SequenceDatabaseEntry entry5 = SequenceDbWsTools.obtainEntry( "AAZ45343.1" ); if ( !entry5.getAccession().equals( "AAZ45343" ) ) { return false; @@ -4144,6 +4250,25 @@ public final class Test { System.out.println( entry5.getTaxonomyIdentifier() ); return false; } + final SequenceDatabaseEntry entry6 = SequenceDbWsTools.obtainEntry( "M30539" ); + if ( !entry6.getAccession().equals( "M30539" ) ) { + return false; + } + if ( !entry6.getGeneName().equals( "ras" ) ) { + return false; + } + if ( !entry6.getSequenceName().equals( "Human SK2 c-Ha-ras-1 oncogene-encoded protein gene, exon 1" ) ) { + return false; + } + if ( !entry6.getTaxonomyIdentifier().equals( "9606" ) ) { + return false; + } + if ( !entry6.getTaxonomyScientificName().equals( "Homo sapiens" ) ) { + return false; + } + if ( entry6.getCrossReferences().size() < 1 ) { + return false; + } } catch ( final IOException e ) { System.out.println(); @@ -4870,12 +4995,22 @@ public final class Test { private static boolean testFastaParser() { try { - if ( !FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ) ) { + FileInputStream fis1 = new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ); + if ( !FastaParser.isLikelyFasta( fis1 ) ) { + fis1.close(); return false; } - if ( FastaParser.isLikelyFasta( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) ) ) { + else { + fis1.close(); + } + FileInputStream fis2 = new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ); + if ( FastaParser.isLikelyFasta( fis2 ) ) { + fis2.close(); return false; } + else { + fis2.close(); + } final Msa msa_0 = FastaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "fasta_0.fasta" ) ); if ( !msa_0.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "ACGTGKXFMFDMXEXXXSFMFMF" ) ) { return false; @@ -6225,21 +6360,23 @@ public final class Test { l.add( s2 ); l.add( s3 ); final Msa msa = BasicMsa.createInstance( l ); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 0 ) ); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 1 ) ); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 2 ) ); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 3 ) ); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 4 ) ); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 5 ) ); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 6 ) ); - System.out.println(); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 0 ) ); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 1 ) ); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 2 ) ); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 3 ) ); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 4 ) ); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 5 ) ); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 6 ) ); + //TODO need to DO the tests!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + //FIXME + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 0 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 1 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 2 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 3 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 4 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 5 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa, 6 ) ); + // System.out.println(); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 0 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 1 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 2 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 3 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 4 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 5 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 6, msa, 6 ) ); final List l2 = new ArrayList(); l2.add( BasicSequence.createAaSequence( "1", "AAAAAAA" ) ); l2.add( BasicSequence.createAaSequence( "2", "AAAIACC" ) ); @@ -6264,10 +6401,10 @@ public final class Test { l2.add( BasicSequence.createAaSequence( "21", "AAIIIIF" ) ); l2.add( BasicSequence.createAaSequence( "22", "AIIIVVW" ) ); final Msa msa2 = BasicMsa.createInstance( l2 ); - System.out.println(); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 0 ) ); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 1 ) ); - System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 2 ) ); + // System.out.println(); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 0 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 1 ) ); + // System.out.println( MsaMethods.calcNormalizedShannonsEntropy( 20, msa2, 2 ) ); } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -9450,14 +9587,11 @@ public final class Test { if ( !p11.toNewHampshireX().equals( "(('A: \"':0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) { return false; } - final Phylogeny p12 = factory - .create( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]", - new NHXParser() )[ 0 ]; + final Phylogeny p12 = factory.create( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]", + new NHXParser() )[ 0 ]; if ( !p12.toNewHampshireX().equals( "((A:0.2,B:0.3):0.5[&&NHX:B=91],C:0.1)root:0.1[&&NHX:B=100]" ) ) { return false; } - - } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -12663,7 +12797,7 @@ public final class Test { private static boolean testUniprotEntryRetrieval() { try { - final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 ); + final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 5000 ); if ( !entry.getAccession().equals( "P12345" ) ) { return false; } @@ -12682,12 +12816,16 @@ public final class Test { if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) { return false; } + if ( entry.getMolecularSequence() == null ) { + return false; + } if ( !entry .getMolecularSequence() .getMolecularSequenceAsString() .startsWith( "MALLHSARVLSGVASAFHPGLAAAASARASSWWAHVEMGPPDPILGVTEAYKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKGLDKEYLPIGGLAEFCRASAELALGENSEV" ) || !entry.getMolecularSequence().getMolecularSequenceAsString().endsWith( "LAHAIHQVTK" ) ) { - System.out.println( entry.getMolecularSequence().getMolecularSequenceAsString() ); + System.out.println( "got: " + entry.getMolecularSequence().getMolecularSequenceAsString() ); + System.out.println( "expected something else." ); return false; } } @@ -12697,6 +12835,10 @@ public final class Test { e.printStackTrace( System.out ); return true; } + catch ( final NullPointerException f ) { + f.printStackTrace( System.out ); + return false; + } catch ( final Exception e ) { return false; } @@ -12886,60 +13028,6 @@ public final class Test { } return true; } - - private static boolean testWabiTxSearch() { - try { - String result = ""; - result = TxSearch.searchSimple( "nematostella" ); - result = TxSearch.getTxId( "nematostella" ); - if ( !result.equals( "45350" ) ) { - return false; - } - result = TxSearch.getTxName( "45350" ); - if ( !result.equals( "Nematostella" ) ) { - return false; - } - result = TxSearch.getTxId( "nematostella vectensis" ); - if ( !result.equals( "45351" ) ) { - return false; - } - result = TxSearch.getTxName( "45351" ); - if ( !result.equals( "Nematostella vectensis" ) ) { - return false; - } - result = TxSearch.getTxId( "Bacillus subtilis subsp. subtilis str. N170" ); - if ( !result.equals( "536089" ) ) { - return false; - } - result = TxSearch.getTxName( "536089" ); - if ( !result.equals( "Bacillus subtilis subsp. subtilis str. N170" ) ) { - return false; - } - final List queries = new ArrayList(); - queries.add( "Campylobacter coli" ); - queries.add( "Escherichia coli" ); - queries.add( "Arabidopsis" ); - queries.add( "Trichoplax" ); - queries.add( "Samanea saman" ); - queries.add( "Kluyveromyces marxianus" ); - queries.add( "Bacillus subtilis subsp. subtilis str. N170" ); - queries.add( "Bornavirus parrot/PDD/2008" ); - final List ranks = new ArrayList(); - ranks.add( RANKS.SUPERKINGDOM ); - ranks.add( RANKS.KINGDOM ); - ranks.add( RANKS.FAMILY ); - ranks.add( RANKS.GENUS ); - ranks.add( RANKS.TRIBE ); - result = TxSearch.searchLineage( queries, ranks ); - result = TxSearch.searchParam( "Homo sapiens", TAX_NAME_CLASS.ALL, TAX_RANK.SPECIES, 10, true ); - result = TxSearch.searchParam( "Samanea saman", TAX_NAME_CLASS.SCIENTIFIC_NAME, TAX_RANK.ALL, 10, true ); - } - catch ( final Exception e ) { - System.out.println(); - System.out.println( "the following might be due to absence internet connection:" ); - e.printStackTrace( System.out ); - return false; - } - return true; - } + + }