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.util.ForesterUtil;
import org.forester.util.GeneralTable;
import org.forester.util.SequenceIdParser;
-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.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;
System.exit( -1 );
}
final long start_time = new Date().getTime();
-
-
-
System.out.print( "Sequence id parsing: " );
- if ( testSequenceIdParsing() ) {
+ if ( testSequenceIdParsing() ) {
System.out.println( "OK." );
succeeded++;
}
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." );
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;
return false;
}
t2.setIdentifier( new Identifier( "ecoli" ) );
- t2.setTaxonomyCode( "other" );
+ t2.setTaxonomyCode( "OTHER" );
t2.setScientificName( "what" );
t2.setCommonName( "something" );
if ( !t1.isEqual( t2 ) ) {
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( "" ) ) {
- 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( "" ) ) {
- 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 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",
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" ) ) {
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
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<UniProtTaxonomy> results = UniProtWsTools
- .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 );
+ List<UniProtTaxonomy> results = SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( "starlet sea anemone",
+ 10 );
if ( results.size() != 1 ) {
return false;
}
return false;
}
results = null;
- results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
+ results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
if ( results.size() != 1 ) {
return false;
}
return false;
}
results = null;
- results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 );
+ results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
if ( results.size() != 1 ) {
return false;
}
return false;
}
results = null;
- results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
+ results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
if ( results.size() != 1 ) {
return false;
}
}
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;
}
}
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 ) || 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() );
}
//
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 ) || 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() );
}
//
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 ) || 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 ) || 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() );
}
//
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 ) || 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() );
}
//
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 ) || 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() );
}
//
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 ) || 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() );
}
//
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( "ncbi" ) ) {
+ 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() );
}
//
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( "ncbi" ) ) {
+ 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() );
if ( id != null ) {
return false;
}
-
// lcl_91970_unknown_
}
catch ( final Exception e ) {