import org.forester.archaeopteryx.AptxUtil;
import org.forester.archaeopteryx.TreePanelUtil;
import org.forester.archaeopteryx.webservices.WebserviceUtil;
+import org.forester.clade_analysis.CladeAnalysisTest;
import org.forester.development.DevelopmentTools;
import org.forester.evoinference.TestPhylogenyReconstruction;
import org.forester.evoinference.matrix.character.CharacterStateMatrix;
succeeded++;
}
System.out.println( "OK." );
+ System.out.print( "Common prefix: " );
+ if ( !testCommonPrefix() ) {
+ System.out.println( "failed." );
+ failed++;
+ }
+ else {
+ succeeded++;
+ }
+ System.out.println( "OK." );
+ System.out.print( "Common prefix sep: " );
+ if ( !testCommonPrefixSep() ) {
+ System.out.println( "failed." );
+ failed++;
+ }
+ else {
+ succeeded++;
+ }
+ System.out.println( "OK." );
+ System.out.print( "Contains prefix: " );
+ if ( !testContainsPrefix() ) {
+ System.out.println( "failed." );
+ failed++;
+ }
+ else {
+ succeeded++;
+ }
+ System.out.println( "OK." );
System.out.print( "Sequence writer: " );
if ( testSequenceWriter() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "Phylogeny methods:" );
+ if ( Test.testPhylogenyMethods() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Postorder Iterator: " );
if ( Test.testPostOrderIterator() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "Clade analyis: " );
+ if ( CladeAnalysisTest.test() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Phylogeny reconstruction:" );
System.out.println();
if ( TestPhylogenyReconstruction.test( new File( PATH_TO_TEST_DATA ) ) ) {
return true;
}
+ private static boolean testCommonPrefix() {
+ final List<String> l0 = new ArrayList<String>();
+ l0.add( "abc" );
+ if ( !ForesterUtil.greatestCommonPrefix( l0 ).equals( "abc" ) ) {
+ return false;
+ }
+ final List<String> l1 = new ArrayList<String>();
+ l1.add( "abc" );
+ l1.add( "abX" );
+ if ( !ForesterUtil.greatestCommonPrefix( l1 ).equals( "ab" ) ) {
+ return false;
+ }
+ final List<String> l2 = new ArrayList<String>();
+ l2.add( "abc" );
+ l2.add( "abX" );
+ l2.add( "axy" );
+ if ( !ForesterUtil.greatestCommonPrefix( l2 ).equals( "a" ) ) {
+ return false;
+ }
+ final List<String> l3 = new ArrayList<String>();
+ l3.add( "abXsdfsdfsdfsdfsdfsd" );
+ l3.add( "abXsdfsdfsdfsdfsdfsd" );
+ l3.add( "abc" );
+ l3.add( "abXsdfsdfsdfsdfsdfsd" );
+ l3.add( "ab" );
+ l3.add( "abc" );
+ l3.add( "ab" );
+ if ( !ForesterUtil.greatestCommonPrefix( l3 ).equals( "ab" ) ) {
+ return false;
+ }
+ final List<String> l4 = new ArrayList<String>();
+ l4.add( "abXsdfsdfsdfsdfsdfsd" );
+ l4.add( "abXsdfsdfsdfsdfsdfsd" );
+ l4.add( "abc" );
+ l4.add( "Xsdfsdfsdfsdfsdfsd" );
+ l4.add( "ab" );
+ l4.add( "abc" );
+ if ( !ForesterUtil.greatestCommonPrefix( l4 ).equals( "" ) ) {
+ return false;
+ }
+ final List<String> l5 = new ArrayList<String>();
+ l5.add( "" );
+ if ( !ForesterUtil.greatestCommonPrefix( l5 ).equals( "" ) ) {
+ return false;
+ }
+ final List<String> l6 = new ArrayList<String>();
+ l6.add( "abc" );
+ l6.add( "abX" );
+ l6.add( "" );
+ if ( !ForesterUtil.greatestCommonPrefix( l6 ).equals( "" ) ) {
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testCommonPrefixSep() {
+ final List<String> l0 = new ArrayList<String>();
+ l0.add( "a.b.c" );
+ if ( !ForesterUtil.greatestCommonPrefix( l0, "." ).equals( "a.b.c" ) ) {
+ return false;
+ }
+ final List<String> l1 = new ArrayList<String>();
+ l1.add( "a.b.c" );
+ l1.add( "a.b.X" );
+ if ( !ForesterUtil.greatestCommonPrefix( l1, "." ).equals( "a.b" ) ) {
+ return false;
+ }
+ final List<String> l2 = new ArrayList<String>();
+ l2.add( "a.b.c." );
+ l2.add( "a.b.X." );
+ l2.add( "a.x.y." );
+ if ( !ForesterUtil.greatestCommonPrefix( l2, "." ).equals( "a" ) ) {
+ return false;
+ }
+ final List<String> l3 = new ArrayList<String>();
+ l3.add( "a/b/X/s/d/f/s/d/f/s/d/f/s/d/f/s/d/f/s/d/" );
+ l3.add( "a/b/X/s/d/f/s/d/f/s/d/f/s/d/f/s/d/f/s/d" );
+ l3.add( "a/b/c" );
+ l3.add( "a/b/X/s/d/f/s/d/f/s/d/f/s/d/f/s/d/f/s/d/" );
+ l3.add( "a/b/" );
+ l3.add( "a/b/c/" );
+ l3.add( "a/b////////" );
+ if ( !ForesterUtil.greatestCommonPrefix( l3, "/" ).equals( "a/b" ) ) {
+ return false;
+ }
+ final List<String> l4 = new ArrayList<String>();
+ l4.add( "a.b.X.s.d.f.s.d.f.s.d.f.s.d.f.s.d.f.s.d" );
+ l4.add( "a.b.X.s.d.f.s.d.f.s.d.f.s.d.f.s.d.f.s.d" );
+ l4.add( "a.b.c" );
+ l4.add( "X.s.d.f.s.d.f.s.d.f.s.d.f.s.d.f.s.d..." );
+ l4.add( "a.b" );
+ l4.add( "a.b.c" );
+ if ( !ForesterUtil.greatestCommonPrefix( l4, "." ).equals( "" ) ) {
+ return false;
+ }
+ final List<String> l5 = new ArrayList<String>();
+ l5.add( "" );
+ if ( !ForesterUtil.greatestCommonPrefix( l5, "_" ).equals( "" ) ) {
+ return false;
+ }
+ final List<String> l6 = new ArrayList<String>();
+ l6.add( "_" );
+ l6.add( "__" );
+ if ( !ForesterUtil.greatestCommonPrefix( l6, "_" ).equals( "" ) ) {
+ return false;
+ }
+ final List<String> l7 = new ArrayList<String>();
+ l7.add( "a,b,c" );
+ l7.add( "a,b,X" );
+ l7.add( "" );
+ l7.add( ",,,,,,,,,," );
+ if ( !ForesterUtil.greatestCommonPrefix( l7, "," ).equals( "" ) ) {
+ return false;
+ }
+ final List<String> l8 = new ArrayList<String>();
+ l8.add( "123.304.403.04" );
+ l8.add( "123.304.403.04.02" );
+ l8.add( "123.304.403.03.03" );
+ if ( !ForesterUtil.greatestCommonPrefix( l8, "." ).equals( "123.304.403" ) ) {
+ return false;
+ }
+ final List<String> l9 = new ArrayList<String>();
+ l9.add( "123.304.403.04" );
+ l9.add( "123.304.403.04.02" );
+ l9.add( "123.304.402.03.03" );
+ if ( !ForesterUtil.greatestCommonPrefix( l9, "." ).equals( "123.304" ) ) {
+ return false;
+ }
+ final List<String> l10 = new ArrayList<String>();
+ l10.add( "abcde" );
+ l10.add( "adc" );
+ if ( !ForesterUtil.greatestCommonPrefix( l10, "." ).equals( "" ) ) {
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testContainsPrefix() {
+ if ( !ForesterUtil.isContainsPrefix( "a.b", "a", "." ) ) {
+ return false;
+ }
+ if ( !ForesterUtil.isContainsPrefix( "a.b.c", "a", "." ) ) {
+ return false;
+ }
+ if ( !ForesterUtil.isContainsPrefix( "a.b.c", "a.b", "." ) ) {
+ return false;
+ }
+ if ( !ForesterUtil.isContainsPrefix( "a.b", "a.b", "." ) ) {
+ return false;
+ }
+ if ( !ForesterUtil.isContainsPrefix( "a", "a", "." ) ) {
+ return false;
+ }
+ if ( !ForesterUtil.isContainsPrefix( ".a.b", ".a", "." ) ) {
+ return false;
+ }
+ if ( !ForesterUtil.isContainsPrefix( ".a.b.", ".a", "." ) ) {
+ return false;
+ }
+ if ( !ForesterUtil.isContainsPrefix( ".a.b.", ".a.", "." ) ) {
+ return false;
+ }
+ if ( !ForesterUtil.isContainsPrefix( "a..b.", "a", "." ) ) {
+ return false;
+ }
+ if ( !ForesterUtil.isContainsPrefix( "a..b.", "a..", "." ) ) {
+ return false;
+ }
+ if ( ForesterUtil.isContainsPrefix( "a", "a.b", "." ) ) {
+ return false;
+ }
+ if ( ForesterUtil.isContainsPrefix( "a_b", "a", "." ) ) {
+ return false;
+ }
+ if ( ForesterUtil.isContainsPrefix( ".a.", ".a.b.", "." ) ) {
+ return false;
+ }
+ if ( ForesterUtil.isContainsPrefix( "a.b.c", "a.x", "." ) ) {
+ return false;
+ }
+ return true;
+ }
+
private static boolean testUTF8ParsingFromFile() {
try {
final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
.equals( "ECOLI" ) ) {
return false;
}
- if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blag_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE )
+ if ( !ParserUtils.extractTaxonomyCodeFromNodeName( "blagg_9YX45-blag", TAXONOMY_EXTRACTION.AGGRESSIVE )
.equals( "9YX45" ) ) {
return false;
}
private static boolean testGeneralMsaParser() {
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 Msa msa_0 = GeneralMsaParser.parseMsa( new ByteArrayInputStream( msa_str_0.getBytes() ) );
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 Msa msa_1 = GeneralMsaParser.parseMsa( 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 Msa msa_2 = GeneralMsaParser.parseMsa( 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() ) );
+ final Msa msa_3 = GeneralMsaParser.parseMsa( new ByteArrayInputStream( msa_str_3.getBytes() ) );
if ( !msa_1.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdef" ) ) {
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" ) );
+ final Msa msa_4 = GeneralMsaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "msa_1.txt" ) );
if ( !msa_4.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
return false;
}
if ( !msa_4.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxphhhhhhhhzz" ) ) {
return false;
}
- final Msa msa_5 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
+ final Msa msa_5 = GeneralMsaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "msa_2.txt" ) );
if ( !msa_5.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefxx" ) ) {
return false;
}
if ( !msa_5.getSequenceAsString( 2 ).toString().equalsIgnoreCase( "klmnxpzz" ) ) {
return false;
}
- final Msa msa_6 = GeneralMsaParser.parse( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
+ final Msa msa_6 = GeneralMsaParser.parseMsa( new FileInputStream( PATH_TO_TEST_DATA + "msa_3.txt" ) );
if ( !msa_6.getSequenceAsString( 0 ).toString().equalsIgnoreCase( "abcdefeeeeeeeexx" ) ) {
return false;
}
if ( s0.match( query_nodes ) ) {
return false;
}
- /////////
- // query_nodes = new HashSet<PhylogenyNode>();
- // query_nodes.add( new PhylogenyNode( "X" ) );
- // query_nodes.add( new PhylogenyNode( "Y" ) );
- // query_nodes.add( new PhylogenyNode( "A" ) );
- // query_nodes.add( new PhylogenyNode( "B" ) );
- // query_nodes.add( new PhylogenyNode( "C" ) );
- // query_nodes.add( new PhylogenyNode( "D" ) );
- // query_nodes.add( new PhylogenyNode( "E" ) );
- // query_nodes.add( new PhylogenyNode( "F" ) );
- // query_nodes.add( new PhylogenyNode( "G" ) );
- // if ( !s0.match( query_nodes ) ) {
- // return false;
- // }
- // query_nodes = new HashSet<PhylogenyNode>();
- // query_nodes.add( new PhylogenyNode( "X" ) );
- // query_nodes.add( new PhylogenyNode( "Y" ) );
- // query_nodes.add( new PhylogenyNode( "A" ) );
- // query_nodes.add( new PhylogenyNode( "B" ) );
- // query_nodes.add( new PhylogenyNode( "C" ) );
- // if ( !s0.match( query_nodes ) ) {
- // return false;
- // }
- // //
- // query_nodes = new HashSet<PhylogenyNode>();
- // query_nodes.add( new PhylogenyNode( "X" ) );
- // query_nodes.add( new PhylogenyNode( "Y" ) );
- // query_nodes.add( new PhylogenyNode( "D" ) );
- // query_nodes.add( new PhylogenyNode( "E" ) );
- // query_nodes.add( new PhylogenyNode( "F" ) );
- // query_nodes.add( new PhylogenyNode( "G" ) );
- // if ( !s0.match( query_nodes ) ) {
- // return false;
- // }
- // //
- // query_nodes = new HashSet<PhylogenyNode>();
- // query_nodes.add( new PhylogenyNode( "X" ) );
- // query_nodes.add( new PhylogenyNode( "Y" ) );
- // query_nodes.add( new PhylogenyNode( "A" ) );
- // query_nodes.add( new PhylogenyNode( "B" ) );
- // query_nodes.add( new PhylogenyNode( "C" ) );
- // query_nodes.add( new PhylogenyNode( "D" ) );
- // if ( !s0.match( query_nodes ) ) {
- // return false;
- // }
- // //
- // query_nodes = new HashSet<PhylogenyNode>();
- // query_nodes.add( new PhylogenyNode( "X" ) );
- // query_nodes.add( new PhylogenyNode( "Y" ) );
- // query_nodes.add( new PhylogenyNode( "E" ) );
- // query_nodes.add( new PhylogenyNode( "F" ) );
- // query_nodes.add( new PhylogenyNode( "G" ) );
- // if ( !s0.match( query_nodes ) ) {
- // return false;
- // }
- // //
- // query_nodes = new HashSet<PhylogenyNode>();
- // query_nodes.add( new PhylogenyNode( "X" ) );
- // query_nodes.add( new PhylogenyNode( "Y" ) );
- // query_nodes.add( new PhylogenyNode( "F" ) );
- // query_nodes.add( new PhylogenyNode( "G" ) );
- // if ( !s0.match( query_nodes ) ) {
- // return false;
- // }
- //
+
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
if ( s0.match( query_nodes ) ) {
return false;
}
- ///////////////////////////
- //
+
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "X" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "Y" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
if ( !s0.match( query_nodes ) ) {
return false;
}
- //
query_nodes = new HashSet<PhylogenyNode>();
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "F" ) );
query_nodes.add( PhylogenyNode.createInstanceFromNhxString( "G" ) );
return false;
}
final PhylogenyNode n3 = PhylogenyNode
- .createInstanceFromNhxString( "BLAG_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BLAGG_12345", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n3.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
System.out.println( n3.toString() );
return false;
return false;
}
final PhylogenyNode n6 = PhylogenyNode
- .createInstanceFromNhxString( "BLAG-12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BLAGG-12345-blag",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n6.getNodeData().isHasTaxonomy() ) {
System.out.println( n6.toString() );
return false;
}
final PhylogenyNode n7 = PhylogenyNode
- .createInstanceFromNhxString( "BLAG-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BL-12345_blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n7.getNodeData().isHasTaxonomy() ) {
System.out.println( n7.toString() );
return false;
}
final PhylogenyNode n8 = PhylogenyNode
- .createInstanceFromNhxString( "BLAG_12345-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BLAGG_12345-blag",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n8.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
System.out.println( n8.toString() );
return false;
}
final PhylogenyNode n9 = PhylogenyNode
- .createInstanceFromNhxString( "BLAG_12345/blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BLAGG_12345/blag",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n9.getNodeData().getTaxonomy().getIdentifier().getValue().equals( "12345" ) ) {
System.out.println( n9.toString() );
return false;
}
final PhylogenyNode n10x = PhylogenyNode
- .createInstanceFromNhxString( "BLAG_12X45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BLAG!_12X45-blag",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n10x.getNodeData().isHasTaxonomy() ) {
System.out.println( n10x.toString() );
return false;
}
final PhylogenyNode n10xx = PhylogenyNode
- .createInstanceFromNhxString( "BLAG_1YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BLAG!_1YX45-blag",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( n10xx.getNodeData().isHasTaxonomy() ) {
System.out.println( n10xx.toString() );
return false;
}
final PhylogenyNode n10 = PhylogenyNode
- .createInstanceFromNhxString( "BLAG_9YX45-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ .createInstanceFromNhxString( "BLAGG_9YX45-blag",
+ NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
if ( !n10.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9YX45" ) ) {
System.out.println( n10.toString() );
return false;
}
+ final PhylogenyNode n10v = PhylogenyNode
+ .createInstanceFromNhxString( "BLAGG_BPM1-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n10v.getNodeData().getTaxonomy().getTaxonomyCode().equals( "BPM1" ) ) {
+ System.out.println( n10v.toString() );
+ return false;
+ }
+ final PhylogenyNode n10v2 = PhylogenyNode
+ .createInstanceFromNhxString( "BLAGG_ABV-blag", NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ if ( !n10v2.getNodeData().getTaxonomy().getTaxonomyCode().equals( "ABV" ) ) {
+ System.out.println( n10v2.toString() );
+ return false;
+ }
final PhylogenyNode n11 = PhylogenyNode
- .createInstanceFromNhxString( "BLAG_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ .createInstanceFromNhxString( "BLAG@_Mus_musculus", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
if ( !n11.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus" ) ) {
System.out.println( n11.toString() );
return false;
}
final PhylogenyNode n12 = PhylogenyNode
- .createInstanceFromNhxString( "BLAG_Mus_musculus_musculus",
+ .createInstanceFromNhxString( "BLA_G_Mus_musculus_musculus",
NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
if ( !n12.getNodeData().getTaxonomy().getScientificName().equals( "Mus musculus musculus" ) ) {
System.out.println( n12.toString() );
return false;
}
final PhylogenyNode n13 = PhylogenyNode
- .createInstanceFromNhxString( "BLAG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ .createInstanceFromNhxString( "BLAaG_Mus_musculus1", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
if ( n13.getNodeData().isHasTaxonomy() ) {
System.out.println( n13.toString() );
return false;
return true;
}
+ private static boolean testPhylogenyMethods() {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)r", new NHXParser() )[ 0 ];
+ if ( PhylogenyMethods.calculateLevel( t0.getNode( "A" ) ) != 0 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.calculateLevel( t0.getNode( "B" ) ) != 0 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.calculateLevel( t0.getNode( "ab" ) ) != 1 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.calculateLevel( t0.getNode( "C" ) ) != 0 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.calculateLevel( t0.getNode( "abc" ) ) != 2 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.calculateLevel( t0.getNode( "D" ) ) != 0 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.calculateLevel( t0.getNode( "abcd" ) ) != 3 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.calculateLevel( t0.getNode( "E" ) ) != 0 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.calculateLevel( t0.getNode( "r" ) ) != 4 ) {
+ return false;
+ }
+ final Phylogeny t1 = factory.create( "((((A,B)ab,C)abc,D)abcd,E,((((((X)1)2)3)4)5)6)r",
+ new NHXParser() )[ 0 ];
+ if ( PhylogenyMethods.calculateLevel( t1.getNode( "r" ) ) != 7 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.calculateLevel( t1.getNode( "X" ) ) != 0 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.calculateLevel( t1.getNode( "6" ) ) != 6 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.calculateLevel( t1.getNode( "5" ) ) != 5 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.calculateLevel( t1.getNode( "4" ) ) != 4 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.calculateLevel( t1.getNode( "3" ) ) != 3 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.calculateLevel( t1.getNode( "2" ) ) != 2 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.calculateLevel( t1.getNode( "1" ) ) != 1 ) {
+ return false;
+ }
+ if ( PhylogenyMethods.calculateLevel( t1.getNode( "abcd" ) ) != 3 ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
private static boolean testUniprotEntryRetrieval() {
try {
final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 5000 );
git://source.jalview.org / jalview.git / blobdiff