// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// Copyright (C) 2014 Christian M. Zmasek
+// Copyright (C) 2014 Sanford-Burnham Medical Research Institute
// All rights reserved
//
// This library is free software; you can redistribute it and/or
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
-// Contact: phylosoft @ gmail . com
// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.test;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
+import java.io.StringWriter;
+import java.io.Writer;
import java.net.URL;
import java.util.ArrayList;
import java.util.Date;
import java.util.SortedSet;
import org.forester.application.support_transfer;
+import org.forester.archaeopteryx.AptxUtil;
import org.forester.archaeopteryx.TreePanelUtil;
import org.forester.archaeopteryx.webservices.WebserviceUtil;
import org.forester.development.DevelopmentTools;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.io.writers.SequenceWriter;
import org.forester.msa.BasicMsa;
+import org.forester.msa.DeleteableMsa;
import org.forester.msa.Mafft;
import org.forester.msa.Msa;
+import org.forester.msa.Msa.MSA_FORMAT;
import org.forester.msa.MsaInferrer;
import org.forester.msa.MsaMethods;
import org.forester.pccx.TestPccx;
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." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "Deleteable MSA: " );
+ if ( Test.testDeleteableMsa() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
if ( PERFORM_DB_TESTS ) {
System.out.print( "Uniprot Entry Retrieval: " );
if ( Test.testUniprotEntryRetrieval() ) {
System.out.println( "failed." );
failed++;
}
+ System.out.print( "NHX parsing from URL 2: " );
+ if ( Test.testNHXparsingFromURL2() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "phyloXML parsing from URL: " );
if ( Test.testPhyloXMLparsingFromURL() ) {
System.out.println( "OK." );
return true;
}
+ public 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 ),
+ false,
+ false,
+ false,
+ TAXONOMY_EXTRACTION.NO,
+ false );
+ if ( ( phys == null ) || ( phys.length != 5 ) ) {
+ return false;
+ }
+ if ( !phys[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
+ System.out.println( phys[ 0 ].toNewHampshire() );
+ return false;
+ }
+ if ( !phys[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
+ System.out.println( phys[ 1 ].toNewHampshire() );
+ return false;
+ }
+ final Phylogeny phys2[] = AptxUtil.readPhylogeniesFromUrl( new URL( s ),
+ false,
+ false,
+ false,
+ TAXONOMY_EXTRACTION.NO,
+ false );
+ if ( ( phys2 == null ) || ( phys2.length != 5 ) ) {
+ return false;
+ }
+ if ( !phys2[ 0 ].toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
+ System.out.println( phys2[ 0 ].toNewHampshire() );
+ return false;
+ }
+ if ( !phys2[ 1 ].toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
+ System.out.println( phys2[ 1 ].toNewHampshire() );
+ return false;
+ }
+ final Phylogeny phys3[] = AptxUtil.readPhylogeniesFromUrl( new URL( "http://swisstree.vital-it.ch:80/"
+ + "SwissTree/ST001/consensus_tree.nhx" ), false, false, false, TAXONOMY_EXTRACTION.NO, false );
+ if ( ( phys3 == null ) || ( phys3.length != 1 ) ) {
+ return false;
+ }
+ if ( !phys3[ 0 ]
+ .toNewHampshire()
+ .equals( "((((POP23a_CIOIN_ENSCING00000016202,POP23b_CIOIN_ENSCING00000016169),POP23_CIOSA_ENSCSAVG00000000248),((POP23a_BRAFL_C3ZMF1,POP23b_BRAFL_121417),(((POP3_ORYLA_ENSORLG00000019669,POP3_GASAC_ENSGACG00000014023,POP3_DANRE_Q6JWW1),(POP3_XENTR_B1H1F6,(POP3_CHICK_Q9DG25,(POP3_ORNAN_ENSOANG00000004179,POP3_MONDO_ENSMODG00000018033,((POP3_MOUSE_Q9ES81,POP3_RAT_Q3BCU3),POP3_RABIT_ENSOCUG00000025973,POP3_MACMU_ENSMMUG00000014473,POP3_HUMAN_Q9HBV1))))),(((POP2_GASAC_ENSGACG00000001420,POP2_ORYLA_ENSORLG00000008627,POP2_TAKRU_ENSTRUG00000015933),POP2_DANRE_ENSDARG00000069922),POP2_XENTR_ENSXETG00000018064,(((POP2_TAEGU_ENSTGUG00000013383,POP2_CHICK_Q6T9Z5),POP2_ANOCA_ENSACAG00000003557),((POP2_MACEU_ENSMEUG00000015825,POP2_MONDO_ENSMODG00000018205),((POP2_RABIT_ENSOCUG00000009515,(POP2_RAT_Q6P722,POP2_MOUSE_Q9ES82)),(POP2_MACMU_ENSMMUG00000000905,POP2_HUMAN_Q9HBU9)))))))),((POP1_CIOSA_ENSCSAVG00000000247,POP1_CIOIN_ENSCING00000000496),((POP1_DANRE_Q5PQZ7,(POP1_ORYLA_ENSORLG00000019663,POP1_GASAC_ENSGACG00000014015,POP1_TAKRU_ENSORLG00000019663)),(POP1_XENTR_B1H1G2,(POP1_ANOCA_ENSACAG00000003910,(POP1_TAEGU_ENSTGUG00000012218,POP1_CHICK_Q9DG23)),POP1_ORNAN_ENSOANG00000004180,POP1_MONDO_ENSMODG00000018034,(POP1_RABIT_ENSOCUG00000016944,(POP1_RAT_Q3BCU4,POP1_MOUSE_Q9ES83),(POP1_HUMAN_Q8NE79,POP1_MACMU_ENSMMUG00000014471))))));" ) ) {
+ System.out.println( phys3[ 0 ].toNewHampshire() );
+ return false;
+ }
+ final Phylogeny phys4[] = AptxUtil.readPhylogeniesFromUrl( new URL( "http://swisstree.vital-it.ch:80/"
+ + "SwissTree/ST001/consensus_tree.nhx" ), false, false, false, TAXONOMY_EXTRACTION.NO, false );
+ if ( ( phys4 == null ) || ( phys4.length != 1 ) ) {
+ return false;
+ }
+ if ( !phys4[ 0 ]
+ .toNewHampshire()
+ .equals( "((((POP23a_CIOIN_ENSCING00000016202,POP23b_CIOIN_ENSCING00000016169),POP23_CIOSA_ENSCSAVG00000000248),((POP23a_BRAFL_C3ZMF1,POP23b_BRAFL_121417),(((POP3_ORYLA_ENSORLG00000019669,POP3_GASAC_ENSGACG00000014023,POP3_DANRE_Q6JWW1),(POP3_XENTR_B1H1F6,(POP3_CHICK_Q9DG25,(POP3_ORNAN_ENSOANG00000004179,POP3_MONDO_ENSMODG00000018033,((POP3_MOUSE_Q9ES81,POP3_RAT_Q3BCU3),POP3_RABIT_ENSOCUG00000025973,POP3_MACMU_ENSMMUG00000014473,POP3_HUMAN_Q9HBV1))))),(((POP2_GASAC_ENSGACG00000001420,POP2_ORYLA_ENSORLG00000008627,POP2_TAKRU_ENSTRUG00000015933),POP2_DANRE_ENSDARG00000069922),POP2_XENTR_ENSXETG00000018064,(((POP2_TAEGU_ENSTGUG00000013383,POP2_CHICK_Q6T9Z5),POP2_ANOCA_ENSACAG00000003557),((POP2_MACEU_ENSMEUG00000015825,POP2_MONDO_ENSMODG00000018205),((POP2_RABIT_ENSOCUG00000009515,(POP2_RAT_Q6P722,POP2_MOUSE_Q9ES82)),(POP2_MACMU_ENSMMUG00000000905,POP2_HUMAN_Q9HBU9)))))))),((POP1_CIOSA_ENSCSAVG00000000247,POP1_CIOIN_ENSCING00000000496),((POP1_DANRE_Q5PQZ7,(POP1_ORYLA_ENSORLG00000019663,POP1_GASAC_ENSGACG00000014015,POP1_TAKRU_ENSORLG00000019663)),(POP1_XENTR_B1H1G2,(POP1_ANOCA_ENSACAG00000003910,(POP1_TAEGU_ENSTGUG00000012218,POP1_CHICK_Q9DG23)),POP1_ORNAN_ENSOANG00000004180,POP1_MONDO_ENSMODG00000018034,(POP1_RABIT_ENSOCUG00000016944,(POP1_RAT_Q3BCU4,POP1_MOUSE_Q9ES83),(POP1_HUMAN_Q8NE79,POP1_MACMU_ENSMMUG00000014471))))));" ) ) {
+ System.out.println( phys4[ 0 ].toNewHampshire() );
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ return true;
+ }
+
public static final boolean testNHXparsingFromURL() {
try {
final String s = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/examples/simple/simple_1.nh";
.equals( "Escherichia coli str. K-12 substr. MG1655star" ) ) {
return false;
}
- //
if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp." ).equals( "Macrocera sp." ) ) {
return false;
}
if ( !ParserUtils.extractScientificNameFromNodeName( "Macrocera sp" ).equals( "Macrocera sp." ) ) {
return false;
}
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp merenskyanum 07 48" )
+ .equals( "Sesamum rigidum subsp. merenskyanum" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum ssp. merenskyanum" )
+ .equals( "Sesamum rigidum subsp. merenskyanum" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum (ssp. merenskyanum)" )
+ .equals( "Sesamum rigidum (subsp. merenskyanum)" ) ) {
+ return false;
+ }
+ if ( !ParserUtils.extractScientificNameFromNodeName( "Sesamum rigidum (ssp merenskyanum)" )
+ .equals( "Sesamum rigidum (subsp. merenskyanum)" ) ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
return true;
}
+ private static boolean testMsaEntropy() {
+ try {
+ final Sequence s0 = BasicSequence.createAaSequence( "a", "AAAAAAA" );
+ final Sequence s1 = BasicSequence.createAaSequence( "b", "AAAIACC" );
+ final Sequence s2 = BasicSequence.createAaSequence( "c", "AAIIIIF" );
+ final Sequence s3 = BasicSequence.createAaSequence( "d", "AIIIVVW" );
+ final List<Sequence> l = new ArrayList<Sequence>();
+ l.add( s0 );
+ l.add( s1 );
+ 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 ) );
+ final List<Sequence> l2 = new ArrayList<Sequence>();
+ l2.add( BasicSequence.createAaSequence( "1", "AAAAAAA" ) );
+ l2.add( BasicSequence.createAaSequence( "2", "AAAIACC" ) );
+ l2.add( BasicSequence.createAaSequence( "3", "AAIIIIF" ) );
+ l2.add( BasicSequence.createAaSequence( "4", "AIIIVVW" ) );
+ l2.add( BasicSequence.createAaSequence( "5", "AAAAAAA" ) );
+ l2.add( BasicSequence.createAaSequence( "6", "AAAIACC" ) );
+ l2.add( BasicSequence.createAaSequence( "7", "AAIIIIF" ) );
+ l2.add( BasicSequence.createAaSequence( "8", "AIIIVVW" ) );
+ l2.add( BasicSequence.createAaSequence( "9", "AAAAAAA" ) );
+ l2.add( BasicSequence.createAaSequence( "10", "AAAIACC" ) );
+ l2.add( BasicSequence.createAaSequence( "11", "AAIIIIF" ) );
+ l2.add( BasicSequence.createAaSequence( "12", "AIIIVVW" ) );
+ l2.add( BasicSequence.createAaSequence( "13", "AAIIIIF" ) );
+ l2.add( BasicSequence.createAaSequence( "14", "AIIIVVW" ) );
+ l2.add( BasicSequence.createAaSequence( "15", "AAAAAAA" ) );
+ l2.add( BasicSequence.createAaSequence( "16", "AAAIACC" ) );
+ l2.add( BasicSequence.createAaSequence( "17", "AAIIIIF" ) );
+ l2.add( BasicSequence.createAaSequence( "18", "AIIIVVW" ) );
+ l2.add( BasicSequence.createAaSequence( "19", "AAAAAAA" ) );
+ l2.add( BasicSequence.createAaSequence( "20", "AAAIACC" ) );
+ 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 ) );
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testDeleteableMsa() {
+ try {
+ final Sequence s0 = BasicSequence.createAaSequence( "a", "AAAA" );
+ final Sequence s1 = BasicSequence.createAaSequence( "b", "BAAA" );
+ final Sequence s2 = BasicSequence.createAaSequence( "c", "CAAA" );
+ final Sequence s3 = BasicSequence.createAaSequence( "d", "DAAA" );
+ final Sequence s4 = BasicSequence.createAaSequence( "e", "EAAA" );
+ final Sequence s5 = BasicSequence.createAaSequence( "f", "FAAA" );
+ final List<Sequence> l0 = new ArrayList<Sequence>();
+ l0.add( s0 );
+ l0.add( s1 );
+ l0.add( s2 );
+ l0.add( s3 );
+ l0.add( s4 );
+ l0.add( s5 );
+ final DeleteableMsa dmsa0 = DeleteableMsa.createInstance( l0 );
+ dmsa0.deleteRow( "b", false );
+ if ( !dmsa0.getIdentifier( 1 ).equals( "c" ) ) {
+ return false;
+ }
+ dmsa0.deleteRow( "e", false );
+ dmsa0.deleteRow( "a", false );
+ dmsa0.deleteRow( "f", false );
+ if ( dmsa0.getLength() != 4 ) {
+ return false;
+ }
+ if ( dmsa0.getNumberOfSequences() != 2 ) {
+ return false;
+ }
+ if ( !dmsa0.getIdentifier( 0 ).equals( "c" ) ) {
+ return false;
+ }
+ if ( !dmsa0.getIdentifier( 1 ).equals( "d" ) ) {
+ return false;
+ }
+ if ( dmsa0.getResidueAt( 0, 0 ) != 'C' ) {
+ return false;
+ }
+ if ( !dmsa0.getSequenceAsString( 0 ).toString().equals( "CAAA" ) ) {
+ return false;
+ }
+ if ( dmsa0.getColumnAt( 0 ).size() != 2 ) {
+ return false;
+ }
+ dmsa0.deleteRow( "c", false );
+ dmsa0.deleteRow( "d", false );
+ if ( dmsa0.getNumberOfSequences() != 0 ) {
+ return false;
+ }
+ //
+ final Sequence s_0 = BasicSequence.createAaSequence( "a", "--A---B-C--X----" );
+ final Sequence s_1 = BasicSequence.createAaSequence( "b", "--B-----C-------" );
+ final Sequence s_2 = BasicSequence.createAaSequence( "c", "--C--AB-C------Z" );
+ final Sequence s_3 = BasicSequence.createAaSequence( "d", "--D--AA-C-------" );
+ final Sequence s_4 = BasicSequence.createAaSequence( "e", "--E--AA-C-------" );
+ final Sequence s_5 = BasicSequence.createAaSequence( "f", "--F--AB-CD--Y---" );
+ final List<Sequence> l1 = new ArrayList<Sequence>();
+ l1.add( s_0 );
+ l1.add( s_1 );
+ l1.add( s_2 );
+ l1.add( s_3 );
+ l1.add( s_4 );
+ l1.add( s_5 );
+ final DeleteableMsa dmsa1 = DeleteableMsa.createInstance( l1 );
+ dmsa1.deleteGapOnlyColumns();
+ dmsa1.deleteRow( "a", false );
+ dmsa1.deleteRow( "f", false );
+ dmsa1.deleteRow( "d", false );
+ dmsa1.deleteGapOnlyColumns();
+ if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C-" ) ) {
+ return false;
+ }
+ if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "CABCZ" ) ) {
+ return false;
+ }
+ if ( !dmsa1.getSequenceAsString( 2 ).toString().equals( "EAAC-" ) ) {
+ return false;
+ }
+ dmsa1.deleteRow( "c", false );
+ dmsa1.deleteGapOnlyColumns();
+ final Writer w0 = new StringWriter();
+ dmsa1.write( w0, MSA_FORMAT.FASTA );
+ final Writer w1 = new StringWriter();
+ dmsa1.write( w1, MSA_FORMAT.PHYLIP );
+ if ( !dmsa1.getSequenceAsString( 0 ).toString().equals( "B--C" ) ) {
+ return false;
+ }
+ if ( !dmsa1.getSequenceAsString( 1 ).toString().equals( "EAAC" ) ) {
+ return false;
+ }
+ //
+ final Sequence s__0 = BasicSequence.createAaSequence( "a", "A------" );
+ final Sequence s__1 = BasicSequence.createAaSequence( "b", "BB-----" );
+ final Sequence s__2 = BasicSequence.createAaSequence( "c", "CCC----" );
+ final Sequence s__3 = BasicSequence.createAaSequence( "d", "DDDD---" );
+ final Sequence s__4 = BasicSequence.createAaSequence( "e", "EEEEE--" );
+ final Sequence s__5 = BasicSequence.createAaSequence( "f", "FFFFFF-" );
+ final List<Sequence> l2 = new ArrayList<Sequence>();
+ l2.add( s__0 );
+ l2.add( s__1 );
+ l2.add( s__2 );
+ l2.add( s__3 );
+ l2.add( s__4 );
+ l2.add( s__5 );
+ final DeleteableMsa dmsa2 = DeleteableMsa.createInstance( l2 );
+ dmsa2.deleteGapColumns( 0.5 );
+ if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A---" ) ) {
+ return false;
+ }
+ if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB--" ) ) {
+ return false;
+ }
+ if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CCC-" ) ) {
+ return false;
+ }
+ dmsa2.deleteGapColumns( 0.2 );
+ if ( !dmsa2.getSequenceAsString( 0 ).toString().equals( "A-" ) ) {
+ return false;
+ }
+ if ( !dmsa2.getSequenceAsString( 1 ).toString().equals( "BB" ) ) {
+ return false;
+ }
+ if ( !dmsa2.getSequenceAsString( 2 ).toString().equals( "CC" ) ) {
+ return false;
+ }
+ dmsa2.deleteGapColumns( 0 );
+ dmsa2.deleteRow( "a", false );
+ dmsa2.deleteRow( "b", false );
+ dmsa2.deleteRow( "f", false );
+ dmsa2.deleteRow( "e", false );
+ dmsa2.setIdentifier( 0, "new_c" );
+ dmsa2.setIdentifier( 1, "new_d" );
+ dmsa2.setResidueAt( 0, 0, 'x' );
+ final Sequence s = dmsa2.deleteRow( "new_d", true );
+ if ( !s.getMolecularSequenceAsString().equals( "D" ) ) {
+ return false;
+ }
+ final Writer w = new StringWriter();
+ dmsa2.write( w, MSA_FORMAT.PHYLIP );
+ final String phylip = w.toString();
+ if ( !phylip.equals( "1 1" + ForesterUtil.LINE_SEPARATOR + "new_c x" + ForesterUtil.LINE_SEPARATOR ) ) {
+ System.out.println( phylip );
+ return false;
+ }
+ final Writer w2 = new StringWriter();
+ dmsa2.write( w2, MSA_FORMAT.FASTA );
+ final String fasta = w2.toString();
+ if ( !fasta.equals( ">new_c" + ForesterUtil.LINE_SEPARATOR + "x" + ForesterUtil.LINE_SEPARATOR ) ) {
+ System.out.println( fasta );
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
private static boolean testNextNodeWithCollapsing() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
}
return false;
}
- //
id = SequenceAccessionTools.parseAccessorFromString( "segmented worms|gb_ADF31344" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
}
return false;
}
- //
id = SequenceAccessionTools.parseAccessorFromString( "segmented worms gb_ADF31344 and more" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
}
return false;
}
- //
id = SequenceAccessionTools.parseAccessorFromString( "gb_AAA96518_1" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "AAA96518" ) || !id.getSource().equals( "ncbi" ) ) {
}
return false;
}
- //
id = SequenceAccessionTools.parseAccessorFromString( "gb_EHB07727_1_rodents_" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "EHB07727" ) || !id.getSource().equals( "ncbi" ) ) {
}
return false;
}
- //
id = SequenceAccessionTools.parseAccessorFromString( "dbj_BAF37827_1_turtles_" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "BAF37827" ) || !id.getSource().equals( "ncbi" ) ) {
}
return false;
}
- //
id = SequenceAccessionTools.parseAccessorFromString( "emb_CAA73223_1_primates_" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "CAA73223" ) || !id.getSource().equals( "ncbi" ) ) {
}
return false;
}
- //
id = SequenceAccessionTools.parseAccessorFromString( "mites|ref_XP_002434188_1" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
}
return false;
}
- //
id = SequenceAccessionTools.parseAccessorFromString( "mites_ref_XP_002434188_1_bla_XP_12345" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "XP_002434188" ) || !id.getSource().equals( "refseq" ) ) {
}
return false;
}
- //
id = SequenceAccessionTools.parseAccessorFromString( "P4A123" );
if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
|| !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "uniprot" ) ) {
System.out.println( "provider=" + id.getSource() );
return false;
}
+ //
+ id = SequenceAccessionTools.parseAccessorFromString( "N3B004Z009" );
+ if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+ || !id.getValue().equals( "N3B004Z009" ) || !id.getSource().equals( "uniprot" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getSource() );
+ }
+ return false;
+ }
+ id = SequenceAccessionTools.parseAccessorFromString( "A4CAA4ZBB9" );
+ if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+ || !id.getValue().equals( "A4CAA4ZBB9" ) || !id.getSource().equals( "uniprot" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getSource() );
+ }
+ return false;
+ }
+ id = SequenceAccessionTools.parseAccessorFromString( "ecoli_A4CAA4ZBB9_rt" );
+ if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+ || !id.getValue().equals( "A4CAA4ZBB9" ) || !id.getSource().equals( "uniprot" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getSource() );
+ }
+ return false;
+ }
+ id = SequenceAccessionTools.parseAccessorFromString( "Q4CAA4ZBB9" );
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getSource() );
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
System.out.println( n21.toString() );
return false;
}
+ final PhylogenyNode n22 = PhylogenyNode
+ .createInstanceFromNhxString( "NEMVE_Nematostella_vectensis",
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n22.getNodeData().getTaxonomy().getTaxonomyCode().equals( "NEMVE" ) ) {
+ System.out.println( n22.toString() );
+ return false;
+ }
+ final PhylogenyNode n23 = PhylogenyNode
+ .createInstanceFromNhxString( "9EMVE_Nematostella_vectensis",
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n23.getNodeData().getTaxonomy().getScientificName().equals( "Nematostella vectensis" ) ) {
+ System.out.println( n23.toString() );
+ return false;
+ }
+ final PhylogenyNode n24 = PhylogenyNode
+ .createInstanceFromNhxString( "9EMVE_Nematostella", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n24.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9EMVE" ) ) {
+ System.out.println( n24.toString() );
+ return false;
+ }
+ //
+ final PhylogenyNode n25 = PhylogenyNode
+ .createInstanceFromNhxString( "Nematostella_vectensis_NEMVE",
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n25.getNodeData().getTaxonomy().getTaxonomyCode().equals( "NEMVE" ) ) {
+ System.out.println( n25.toString() );
+ return false;
+ }
+ final PhylogenyNode n26 = PhylogenyNode
+ .createInstanceFromNhxString( "Nematostella_vectensis_9EMVE",
+ NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n26.getNodeData().getTaxonomy().getScientificName().equals( "Nematostella vectensis" ) ) {
+ System.out.println( n26.toString() );
+ return false;
+ }
+ final PhylogenyNode n27 = PhylogenyNode
+ .createInstanceFromNhxString( "Nematostella_9EMVE", NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+ if ( !n27.getNodeData().getTaxonomy().getTaxonomyCode().equals( "9EMVE" ) ) {
+ System.out.println( n27.toString() );
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
git://source.jalview.org / jalview.git / blobdiff