import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
+import java.net.URL;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashSet;
@SuppressWarnings( "unused")
public final class Test {
- private final static boolean PERFORM_DB_TESTS = true;
- private final static double ZERO_DIFF = 1.0E-9;
- private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
- + ForesterUtil.getFileSeparator() + "test_data"
- + ForesterUtil.getFileSeparator();
private final static String PATH_TO_RESOURCES = System.getProperty( "user.dir" )
+ ForesterUtil.getFileSeparator() + "resources"
+ ForesterUtil.getFileSeparator();
- private final static boolean USE_LOCAL_PHYLOXML_SCHEMA = true;
- private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
+ private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
+ + ForesterUtil.getFileSeparator() + "test_data"
+ + ForesterUtil.getFileSeparator();
+ private final static boolean PERFORM_DB_TESTS = false;
+ private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
+ ForesterConstants.PHYLO_XML_VERSION + "/"
+ ForesterConstants.PHYLO_XML_XSD;
- private static final String PHYLOXML_LOCAL_XSD = PATH_TO_RESOURCES + "phyloxml_schema/"
+ private static final String PHYLOXML_REMOTE_XSD = ForesterConstants.PHYLO_XML_LOCATION + "/"
+ ForesterConstants.PHYLO_XML_VERSION + "/"
+ ForesterConstants.PHYLO_XML_XSD;
+ 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 ) {
return ( ( Math.abs( a - b ) ) < Test.ZERO_DIFF );
System.out.println( "failed." );
failed++;
}
- if ( PERFORM_DB_TESTS ) {
- System.out.print( "Ebi Entry Retrieval: " );
- if ( Test.testEbiEntryRetrieval() ) {
- System.out.println( "OK." );
- succeeded++;
- }
- else {
- System.out.println( "failed." );
- failed++;
- }
- }
- System.exit( 0 );
System.out.print( "UniProtKB id extraction: " );
if ( Test.testExtractUniProtKbProteinSeqIdentifier() ) {
System.out.println( "OK." );
failed++;
}
if ( PERFORM_DB_TESTS ) {
+ System.out.print( "Ebi Entry Retrieval: " );
+ if ( Test.testEbiEntryRetrieval() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
+ }
+ // System.exit( 0 );
+ if ( PERFORM_DB_TESTS ) {
System.out.print( "Sequence DB tools 2: " );
if ( testSequenceDbWsTools2() ) {
System.out.println( "OK." );
System.exit( -1 );
}
}
+ // System.exit( 0 );
System.out.print( "Hmmscan output parser: " );
if ( testHmmscanOutputParser() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ //
+ System.out.print( "Overlap removal: " );
+ if ( !org.forester.test.Test.testOverlapRemoval() ) {
+ System.out.println( "failed." );
+ failed++;
+ }
+ else {
+ succeeded++;
+ }
+ System.out.println( "OK." );
+ System.out.print( "Engulfing overlap removal: " );
+ if ( !Test.testEngulfingOverlapRemoval() ) {
+ System.out.println( "failed." );
+ failed++;
+ }
+ else {
+ succeeded++;
+ }
+ System.out.println( "OK." );
+ //
System.out.print( "Taxonomy code extraction: " );
if ( Test.testExtractTaxonomyCodeFromNodeName() ) {
System.out.println( "OK." );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "Tree copy: " );
+ if ( Test.testTreeCopy() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.print( "Basic tree methods: " );
if ( Test.testBasicTreeMethods() ) {
System.out.println( "OK." );
path = "C:\\Program Files\\mafft-win\\mafft.bat";
}
else {
- path = "/home/czmasek/bin/mafft";
- }
- if ( !MsaInferrer.isInstalled( path ) ) {
path = "mafft";
- }
- if ( !MsaInferrer.isInstalled( path ) ) {
- path = "/usr/local/bin/mafft";
+ if ( !MsaInferrer.isInstalled( path ) ) {
+ path = "/usr/bin/mafft";
+ }
+ if ( !MsaInferrer.isInstalled( path ) ) {
+ path = "/usr/local/bin/mafft";
+ }
}
if ( MsaInferrer.isInstalled( path ) ) {
System.out.print( "MAFFT (external program): " );
System.out.println( "failed." );
failed++;
}
+ System.out.print( "NHX parsing from URL: " );
+ if ( Test.testNHXparsingFromURL() ) {
+ 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." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
System.out.println();
final Runtime rt = java.lang.Runtime.getRuntime();
final long free_memory = rt.freeMemory() / 1000000;
}
}
+ public 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 );
+ final Domain d2 = new BasicDomain( "d2", 0, 2, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain d3 = new BasicDomain( "d3", 7, 8, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain d4 = new BasicDomain( "d4", 7, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain d5 = new BasicDomain( "d4", 0, 9, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain d6 = new BasicDomain( "d4", 4, 5, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final List<Boolean> covered = new ArrayList<Boolean>();
+ covered.add( true ); // 0
+ covered.add( false ); // 1
+ covered.add( true ); // 2
+ covered.add( false ); // 3
+ covered.add( true ); // 4
+ covered.add( true ); // 5
+ covered.add( false ); // 6
+ covered.add( true ); // 7
+ covered.add( true ); // 8
+ if ( ForesterUtil.isEngulfed( d0, covered ) ) {
+ return false;
+ }
+ if ( ForesterUtil.isEngulfed( d1, covered ) ) {
+ return false;
+ }
+ if ( ForesterUtil.isEngulfed( d2, covered ) ) {
+ return false;
+ }
+ if ( !ForesterUtil.isEngulfed( d3, covered ) ) {
+ return false;
+ }
+ if ( ForesterUtil.isEngulfed( d4, covered ) ) {
+ return false;
+ }
+ if ( ForesterUtil.isEngulfed( d5, covered ) ) {
+ return false;
+ }
+ if ( !ForesterUtil.isEngulfed( d6, covered ) ) {
+ return false;
+ }
+ final Domain a = new BasicDomain( "a", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain b = new BasicDomain( "b", 8, 20, ( short ) 1, ( short ) 1, 0.2, 1 );
+ final Domain c = new BasicDomain( "c", 15, 16, ( short ) 1, ( short ) 1, 0.3, 1 );
+ final Protein abc = new BasicProtein( "abc", "nemve", 0 );
+ abc.addProteinDomain( a );
+ abc.addProteinDomain( b );
+ abc.addProteinDomain( c );
+ final Protein abc_r1 = ForesterUtil.removeOverlappingDomains( 3, false, abc );
+ final Protein abc_r2 = ForesterUtil.removeOverlappingDomains( 3, true, abc );
+ if ( abc.getNumberOfProteinDomains() != 3 ) {
+ return false;
+ }
+ if ( abc_r1.getNumberOfProteinDomains() != 3 ) {
+ return false;
+ }
+ if ( abc_r2.getNumberOfProteinDomains() != 2 ) {
+ return false;
+ }
+ if ( !abc_r2.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
+ return false;
+ }
+ if ( !abc_r2.getProteinDomain( 1 ).getDomainId().equals( "b" ) ) {
+ return false;
+ }
+ final Domain d = new BasicDomain( "d", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain e = new BasicDomain( "e", 8, 20, ( short ) 1, ( short ) 1, 0.3, 1 );
+ final Domain f = new BasicDomain( "f", 15, 16, ( short ) 1, ( short ) 1, 0.2, 1 );
+ final Protein def = new BasicProtein( "def", "nemve", 0 );
+ def.addProteinDomain( d );
+ def.addProteinDomain( e );
+ def.addProteinDomain( f );
+ final Protein def_r1 = ForesterUtil.removeOverlappingDomains( 5, false, def );
+ final Protein def_r2 = ForesterUtil.removeOverlappingDomains( 5, true, def );
+ if ( def.getNumberOfProteinDomains() != 3 ) {
+ return false;
+ }
+ if ( def_r1.getNumberOfProteinDomains() != 3 ) {
+ return false;
+ }
+ if ( def_r2.getNumberOfProteinDomains() != 3 ) {
+ return false;
+ }
+ if ( !def_r2.getProteinDomain( 0 ).getDomainId().equals( "d" ) ) {
+ return false;
+ }
+ if ( !def_r2.getProteinDomain( 1 ).getDomainId().equals( "f" ) ) {
+ return false;
+ }
+ if ( !def_r2.getProteinDomain( 2 ).getDomainId().equals( "e" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ public 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() );
+ if ( ( phys == null ) || ( phys.length != 2 ) ) {
+ 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";
+ final URL u = new URL( s );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny[] phys = factory.create( u, new NHXParser() );
+ 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 = factory.create( u.openStream(), new NHXParser() );
+ 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;
+ }
+ final PhylogenyFactory factory2 = ParserBasedPhylogenyFactory.getInstance();
+ final NHXParser p = new NHXParser();
+ final URL u2 = new URL( s );
+ p.setSource( u2 );
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
+ return false;
+ }
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
+ return false;
+ }
+ if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
+ return false;
+ }
+ p.reset();
+ if ( !p.hasNext() ) {
+ return false;
+ }
+ if ( !p.next().toNewHampshire().equals( "((((A,B),C),D),(E,F));" ) ) {
+ return false;
+ }
+ if ( !p.next().toNewHampshire().equals( "((1,2,3),(4,5,6),(7,8,9));" ) ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ return true;
+ }
+
+ public 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 );
+ final Domain d2 = new BasicDomain( "d2", ( short ) 0, ( short ) 20, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain d3 = new BasicDomain( "d3", ( short ) 9, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final Domain d4 = new BasicDomain( "d4", ( short ) 7, ( short ) 8, ( short ) 1, ( short ) 1, 0.1, 1 );
+ final List<Boolean> covered = new ArrayList<Boolean>();
+ covered.add( true ); // 0
+ covered.add( false ); // 1
+ covered.add( true ); // 2
+ covered.add( false ); // 3
+ covered.add( true ); // 4
+ covered.add( true ); // 5
+ covered.add( false ); // 6
+ covered.add( true ); // 7
+ covered.add( true ); // 8
+ if ( ForesterUtil.calculateOverlap( d0, covered ) != 3 ) {
+ return false;
+ }
+ if ( ForesterUtil.calculateOverlap( d1, covered ) != 2 ) {
+ return false;
+ }
+ if ( ForesterUtil.calculateOverlap( d2, covered ) != 6 ) {
+ return false;
+ }
+ if ( ForesterUtil.calculateOverlap( d3, covered ) != 0 ) {
+ return false;
+ }
+ if ( ForesterUtil.calculateOverlap( d4, covered ) != 2 ) {
+ return false;
+ }
+ final Domain a = new BasicDomain( "a", ( short ) 2, ( short ) 5, ( short ) 1, ( short ) 1, 1, -1 );
+ final Domain b = new BasicDomain( "b", ( short ) 2, ( short ) 10, ( short ) 1, ( short ) 1, 0.1, -1 );
+ final Protein ab = new BasicProtein( "ab", "varanus", 0 );
+ ab.addProteinDomain( a );
+ ab.addProteinDomain( b );
+ final Protein ab_s0 = ForesterUtil.removeOverlappingDomains( 3, false, ab );
+ if ( ab.getNumberOfProteinDomains() != 2 ) {
+ return false;
+ }
+ if ( ab_s0.getNumberOfProteinDomains() != 1 ) {
+ return false;
+ }
+ if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "b" ) ) {
+ return false;
+ }
+ final Protein ab_s1 = ForesterUtil.removeOverlappingDomains( 4, false, ab );
+ if ( ab.getNumberOfProteinDomains() != 2 ) {
+ return false;
+ }
+ if ( ab_s1.getNumberOfProteinDomains() != 2 ) {
+ return false;
+ }
+ final Domain c = new BasicDomain( "c", ( short ) 20000, ( short ) 20500, ( short ) 1, ( short ) 1, 10, 1 );
+ final Domain d = new BasicDomain( "d",
+ ( short ) 10000,
+ ( short ) 10500,
+ ( short ) 1,
+ ( short ) 1,
+ 0.0000001,
+ 1 );
+ final Domain e = new BasicDomain( "e", ( short ) 5000, ( short ) 5500, ( short ) 1, ( short ) 1, 0.0001, 1 );
+ final Protein cde = new BasicProtein( "cde", "varanus", 0 );
+ cde.addProteinDomain( c );
+ cde.addProteinDomain( d );
+ cde.addProteinDomain( e );
+ final Protein cde_s0 = ForesterUtil.removeOverlappingDomains( 0, false, cde );
+ if ( cde.getNumberOfProteinDomains() != 3 ) {
+ return false;
+ }
+ if ( cde_s0.getNumberOfProteinDomains() != 3 ) {
+ return false;
+ }
+ final Domain f = new BasicDomain( "f", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
+ final Domain g = new BasicDomain( "g", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
+ final Domain h = new BasicDomain( "h", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
+ final Domain i = new BasicDomain( "i", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.5, 1 );
+ final Domain i2 = new BasicDomain( "i", ( short ) 5, ( short ) 30, ( short ) 1, ( short ) 1, 0.5, 10 );
+ final Protein fghi = new BasicProtein( "fghi", "varanus", 0 );
+ fghi.addProteinDomain( f );
+ fghi.addProteinDomain( g );
+ fghi.addProteinDomain( h );
+ fghi.addProteinDomain( i );
+ fghi.addProteinDomain( i );
+ fghi.addProteinDomain( i );
+ fghi.addProteinDomain( i2 );
+ final Protein fghi_s0 = ForesterUtil.removeOverlappingDomains( 10, false, fghi );
+ if ( fghi.getNumberOfProteinDomains() != 7 ) {
+ return false;
+ }
+ if ( fghi_s0.getNumberOfProteinDomains() != 1 ) {
+ return false;
+ }
+ if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().equals( "h" ) ) {
+ return false;
+ }
+ final Protein fghi_s1 = ForesterUtil.removeOverlappingDomains( 11, false, fghi );
+ if ( fghi.getNumberOfProteinDomains() != 7 ) {
+ return false;
+ }
+ if ( fghi_s1.getNumberOfProteinDomains() != 7 ) {
+ return false;
+ }
+ final Domain j = new BasicDomain( "j", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 10, 1 );
+ final Domain k = new BasicDomain( "k", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.01, 1 );
+ final Domain l = new BasicDomain( "l", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 1, 0.0001, 1 );
+ final Domain m = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 1, ( short ) 4, 0.5, 1 );
+ final Domain m0 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 2, ( short ) 4, 0.5, 1 );
+ final Domain m1 = new BasicDomain( "m", ( short ) 10, ( short ) 20, ( short ) 3, ( short ) 4, 0.5, 1 );
+ final Domain m2 = new BasicDomain( "m", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
+ final Protein jklm = new BasicProtein( "jklm", "varanus", 0 );
+ jklm.addProteinDomain( j );
+ jklm.addProteinDomain( k );
+ jklm.addProteinDomain( l );
+ jklm.addProteinDomain( m );
+ jklm.addProteinDomain( m0 );
+ jklm.addProteinDomain( m1 );
+ jklm.addProteinDomain( m2 );
+ final Protein jklm_s0 = ForesterUtil.removeOverlappingDomains( 10, false, jklm );
+ if ( jklm.getNumberOfProteinDomains() != 7 ) {
+ return false;
+ }
+ if ( jklm_s0.getNumberOfProteinDomains() != 1 ) {
+ return false;
+ }
+ if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().equals( "l" ) ) {
+ return false;
+ }
+ final Protein jklm_s1 = ForesterUtil.removeOverlappingDomains( 11, false, jklm );
+ if ( jklm.getNumberOfProteinDomains() != 7 ) {
+ return false;
+ }
+ if ( jklm_s1.getNumberOfProteinDomains() != 7 ) {
+ return false;
+ }
+ final Domain only = new BasicDomain( "only", ( short ) 5, ( short ) 30, ( short ) 4, ( short ) 4, 0.5, 10 );
+ final Protein od = new BasicProtein( "od", "varanus", 0 );
+ od.addProteinDomain( only );
+ final Protein od_s0 = ForesterUtil.removeOverlappingDomains( 0, false, od );
+ if ( od.getNumberOfProteinDomains() != 1 ) {
+ return false;
+ }
+ if ( od_s0.getNumberOfProteinDomains() != 1 ) {
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
private final static Phylogeny createPhylogeny( final String nhx ) throws IOException {
final Phylogeny p = ParserBasedPhylogenyFactory.getInstance().create( nhx, new NHXParser() )[ 0 ];
return p;
private static boolean testBasicPhyloXMLparsing() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhyloXmlParser xml_parser = new PhyloXmlParser();
+ final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
final Phylogeny[] phylogenies_0 = factory.create( Test.PATH_TO_TEST_DATA + "phyloxml_test_t1.xml",
xml_parser );
if ( xml_parser.getErrorCount() > 0 ) {
private static boolean testBasicPhyloXMLparsingRoundtrip() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhyloXmlParser xml_parser = new PhyloXmlParser();
+ final PhyloXmlParser xml_parser = PhyloXmlParser.createPhyloXmlParser();
if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
}
// Do nothing -- means were not running from jar.
}
if ( xml_parser == null ) {
- xml_parser = new PhyloXmlParser();
+ xml_parser = PhyloXmlParser.createPhyloXmlParser();
if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
}
private static boolean testBasicTreeMethods() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny t1 = factory.create();
- if ( !t1.isEmpty() ) {
- return false;
- }
final Phylogeny t2 = factory.create( "((A:1,B:2)AB:1,(C:3,D:5)CD:3)ABCD:0.5", new NHXParser() )[ 0 ];
if ( t2.getNumberOfExternalNodes() != 4 ) {
return false;
return true;
}
- private static boolean testGenbankAccessorParsing() {
- //The format for GenBank Accession numbers are:
- //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
- //Protein: 3 letters + 5 numerals
- //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
- if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "AY423861" ).equals( "AY423861" ) ) {
- return false;
- }
- if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) {
- return false;
- }
- if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
- return false;
- }
- if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) {
- return false;
- }
- if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AY4238612" ) != null ) {
- return false;
- }
- if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY4238612" ) != null ) {
- return false;
- }
- if ( SequenceAccessionTools.parseGenbankAccessorFromString( "Y423861" ) != null ) {
- return false;
- }
- if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "S12345" ).equals( "S12345" ) ) {
- return false;
- }
- if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "|S12345|" ).equals( "S12345" ) ) {
- return false;
- }
- if ( SequenceAccessionTools.parseGenbankAccessorFromString( "|S123456" ) != null ) {
- return false;
- }
- if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABC123456" ) != null ) {
- return false;
- }
- if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "ABC12345" ).equals( "ABC12345" ) ) {
- return false;
+ private static boolean testEbiEntryRetrieval() {
+ try {
+ final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainEntry( "AAK41263" );
+ if ( !entry.getAccession().equals( "AAK41263" ) ) {
+ System.out.println( entry.getAccession() );
+ return false;
+ }
+ if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) {
+ System.out.println( entry.getTaxonomyScientificName() );
+ return false;
+ }
+ if ( !entry.getSequenceName()
+ .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) {
+ System.out.println( entry.getSequenceName() );
+ return false;
+ }
+ // if ( !entry.getSequenceSymbol().equals( "" ) ) {
+ // System.out.println( entry.getSequenceSymbol() );
+ // return false;
+ // }
+ if ( !entry.getGeneName().equals( "treX-like" ) ) {
+ System.out.println( entry.getGeneName() );
+ return false;
+ }
+ if ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) {
+ System.out.println( entry.getTaxonomyIdentifier() );
+ return false;
+ }
+ if ( !entry.getAnnotations().first().getRefValue().equals( "3.2.1.33" ) ) {
+ System.out.println( entry.getAnnotations().first().getRefValue() );
+ return false;
+ }
+ if ( !entry.getAnnotations().first().getRefSource().equals( "EC" ) ) {
+ System.out.println( entry.getAnnotations().first().getRefSource() );
+ return false;
+ }
+ if ( entry.getCrossReferences().size() != 5 ) {
+ return false;
+ }
+ //
+ final SequenceDatabaseEntry entry1 = SequenceDbWsTools.obtainEntry( "ABJ16409" );
+ if ( !entry1.getAccession().equals( "ABJ16409" ) ) {
+ return false;
+ }
+ if ( !entry1.getTaxonomyScientificName().equals( "Felis catus" ) ) {
+ System.out.println( entry1.getTaxonomyScientificName() );
+ return false;
+ }
+ if ( !entry1.getSequenceName().equals( "Felis catus (domestic cat) partial BCL2" ) ) {
+ System.out.println( entry1.getSequenceName() );
+ return false;
+ }
+ if ( !entry1.getTaxonomyIdentifier().equals( "9685" ) ) {
+ System.out.println( entry1.getTaxonomyIdentifier() );
+ return false;
+ }
+ if ( !entry1.getGeneName().equals( "BCL2" ) ) {
+ System.out.println( entry1.getGeneName() );
+ return false;
+ }
+ if ( entry1.getCrossReferences().size() != 6 ) {
+ return false;
+ }
+ //
+ final SequenceDatabaseEntry entry2 = SequenceDbWsTools.obtainEntry( "NM_184234" );
+ if ( !entry2.getAccession().equals( "NM_184234" ) ) {
+ return false;
+ }
+ if ( !entry2.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
+ System.out.println( entry2.getTaxonomyScientificName() );
+ return false;
+ }
+ if ( !entry2.getSequenceName()
+ .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
+ System.out.println( entry2.getSequenceName() );
+ return false;
+ }
+ if ( !entry2.getTaxonomyIdentifier().equals( "9606" ) ) {
+ System.out.println( entry2.getTaxonomyIdentifier() );
+ return false;
+ }
+ if ( !entry2.getGeneName().equals( "RBM39" ) ) {
+ System.out.println( entry2.getGeneName() );
+ return false;
+ }
+ if ( entry2.getCrossReferences().size() != 3 ) {
+ return false;
+ }
+ //
+ final SequenceDatabaseEntry entry3 = SequenceDbWsTools.obtainEntry( "HM043801" );
+ if ( !entry3.getAccession().equals( "HM043801" ) ) {
+ return false;
+ }
+ if ( !entry3.getTaxonomyScientificName().equals( "Bursaphelenchus xylophilus" ) ) {
+ System.out.println( entry3.getTaxonomyScientificName() );
+ return false;
+ }
+ if ( !entry3.getSequenceName().equals( "Bursaphelenchus xylophilus RAF gene, complete cds" ) ) {
+ System.out.println( entry3.getSequenceName() );
+ return false;
+ }
+ if ( !entry3.getTaxonomyIdentifier().equals( "6326" ) ) {
+ System.out.println( entry3.getTaxonomyIdentifier() );
+ return false;
+ }
+ if ( !entry3.getSequenceSymbol().equals( "RAF" ) ) {
+ System.out.println( entry3.getSequenceSymbol() );
+ return false;
+ }
+ if ( !ForesterUtil.isEmpty( entry3.getGeneName() ) ) {
+ return false;
+ }
+ if ( entry3.getCrossReferences().size() != 8 ) {
+ return false;
+ }
+ //
+ //
+ final SequenceDatabaseEntry entry4 = SequenceDbWsTools.obtainEntry( "AAA36557.1" );
+ if ( !entry4.getAccession().equals( "AAA36557" ) ) {
+ return false;
+ }
+ if ( !entry4.getTaxonomyScientificName().equals( "Homo sapiens" ) ) {
+ System.out.println( entry4.getTaxonomyScientificName() );
+ return false;
+ }
+ if ( !entry4.getSequenceName().equals( "Homo sapiens (human) ras protein" ) ) {
+ System.out.println( entry4.getSequenceName() );
+ return false;
+ }
+ if ( !entry4.getTaxonomyIdentifier().equals( "9606" ) ) {
+ System.out.println( entry4.getTaxonomyIdentifier() );
+ return false;
+ }
+ if ( !entry4.getGeneName().equals( "ras" ) ) {
+ 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;
+ }
+ if ( !entry5.getTaxonomyScientificName().equals( "Dechloromonas aromatica RCB" ) ) {
+ System.out.println( entry5.getTaxonomyScientificName() );
+ return false;
+ }
+ if ( !entry5.getSequenceName().equals( "Dechloromonas aromatica RCB 1,4-alpha-glucan branching enzyme" ) ) {
+ System.out.println( entry5.getSequenceName() );
+ return false;
+ }
+ if ( !entry5.getTaxonomyIdentifier().equals( "159087" ) ) {
+ System.out.println( entry5.getTaxonomyIdentifier() );
+ return false;
+ }
}
- if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "&ABC12345&" ).equals( "ABC12345" ) ) {
- return false;
+ catch ( final IOException e ) {
+ System.out.println();
+ System.out.println( "the following might be due to absence internet connection:" );
+ e.printStackTrace( System.out );
+ return true;
}
- if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABCD12345" ) != null ) {
+ catch ( final Exception e ) {
+ e.printStackTrace();
return false;
}
return true;
return true;
}
+ private static boolean testGenbankAccessorParsing() {
+ //The format for GenBank Accession numbers are:
+ //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals
+ //Protein: 3 letters + 5 numerals
+ //http://www.ncbi.nlm.nih.gov/Sequin/acc.html
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "AY423861" ).equals( "AY423861" ) ) {
+ return false;
+ }
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) {
+ return false;
+ }
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
+ return false;
+ }
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) {
+ return false;
+ }
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AY4238612" ) != null ) {
+ return false;
+ }
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY4238612" ) != null ) {
+ return false;
+ }
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "Y423861" ) != null ) {
+ return false;
+ }
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "S12345" ).equals( "S12345" ) ) {
+ return false;
+ }
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "|S12345|" ).equals( "S12345" ) ) {
+ return false;
+ }
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "|S123456" ) != null ) {
+ return false;
+ }
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABC123456" ) != null ) {
+ return false;
+ }
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "ABC12345" ).equals( "ABC12345" ) ) {
+ return false;
+ }
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "&ABC12345&" ).equals( "ABC12345" ) ) {
+ return false;
+ }
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABCD12345" ) != null ) {
+ return false;
+ }
+ return true;
+ }
+
private static boolean testGeneralMsaParser() {
try {
final String msa_str_0 = "seq1 abcd\n\nseq2 efgh\n";
private static boolean testGetLCA2() {
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
+ // final Phylogeny p_a = factory.create( "(a)", new NHXParser() )[ 0 ];
+ final Phylogeny p_a = NHXParser.parse( "(a)" )[ 0 ];
PhylogenyMethods.preOrderReId( p_a );
final PhylogenyNode p_a_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_a.getNode( "a" ),
p_a.getNode( "a" ) );
if ( !p_a_1.getName().equals( "a" ) ) {
return false;
}
- final Phylogeny p_b = factory.create( "((a)b)", new NHXParser() )[ 0 ];
+ final Phylogeny p_b = NHXParser.parse( "((a)b)" )[ 0 ];
PhylogenyMethods.preOrderReId( p_b );
final PhylogenyNode p_b_1 = PhylogenyMethods.calculateLCAonTreeWithIdsInPreOrder( p_b.getNode( "b" ),
p_b.getNode( "a" ) );
if ( parser2.getDomainsIgnoredDueToDuf() != 0 ) {
return false;
}
- if ( parser2.getDomainsIgnoredDueToEval() != 0 ) {
+ if ( parser2.getDomainsIgnoredDueToFsEval() != 0 ) {
+ return false;
+ }
+ if ( parser2.getDomainsIgnoredDueToIEval() != 0 ) {
return false;
}
final Protein p1 = proteins.get( 0 );
if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerDomainScore(), 135.7 ) ) {
return false;
}
- if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceEvalue(), 8.3e-40 ) ) {
- return false;
- }
- if ( !Test.isEqual( p4.getProteinDomain( 0 ).getPerSequenceScore(), 136.3 ) ) {
- return false;
- }
if ( !Test.isEqual( p4.getProteinDomain( 0 ).getNumber(), 1 ) ) {
return false;
}
private static boolean testMsaQualityMethod() {
try {
- final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJ" );
- final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJ" );
- final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJ" );
- final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ" );
+ final Sequence s0 = BasicSequence.createAaSequence( "a", "ABAXEFGHIJJE-" );
+ final Sequence s1 = BasicSequence.createAaSequence( "b", "ABBXEFGHIJJBB" );
+ final Sequence s2 = BasicSequence.createAaSequence( "c", "AXCXEFGHIJJ--" );
+ final Sequence s3 = BasicSequence.createAaSequence( "d", "AXDDEFGHIJ---" );
final List<Sequence> l = new ArrayList<Sequence>();
l.add( s0 );
l.add( s1 );
if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 3 ) ) ) {
return false;
}
+ if ( !isEqual( 0.75, MsaMethods.calculateIdentityRatio( msa, 10 ) ) ) {
+ return false;
+ }
+ if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 11 ) ) ) {
+ return false;
+ }
+ if ( !isEqual( 0.25, MsaMethods.calculateIdentityRatio( msa, 12 ) ) ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
if ( p.next() != null ) {
return false;
}
+ //
+ final String p30_str = "(A,B);(C,D)";
+ final NHXParser p30 = new NHXParser();
+ p30.setSource( p30_str );
+ if ( !p30.hasNext() ) {
+ return false;
+ }
+ Phylogeny phy30 = p30.next();
+ if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
+ System.out.println( phy30.toNewHampshire() );
+ return false;
+ }
+ if ( !p30.hasNext() ) {
+ return false;
+ }
+ Phylogeny phy301 = p30.next();
+ if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
+ System.out.println( phy301.toNewHampshire() );
+ return false;
+ }
+ if ( p30.hasNext() ) {
+ return false;
+ }
+ if ( p30.hasNext() ) {
+ return false;
+ }
+ if ( p30.next() != null ) {
+ return false;
+ }
+ if ( p30.next() != null ) {
+ return false;
+ }
+ p30.reset();
+ if ( !p30.hasNext() ) {
+ return false;
+ }
+ phy30 = p30.next();
+ if ( !phy30.toNewHampshire().equals( "(A,B);" ) ) {
+ System.out.println( phy30.toNewHampshire() );
+ return false;
+ }
+ if ( !p30.hasNext() ) {
+ return false;
+ }
+ phy301 = p30.next();
+ if ( !phy301.toNewHampshire().equals( "(C,D);" ) ) {
+ System.out.println( phy301.toNewHampshire() );
+ return false;
+ }
+ if ( p30.hasNext() ) {
+ return false;
+ }
+ if ( p30.hasNext() ) {
+ return false;
+ }
+ if ( p30.next() != null ) {
+ return false;
+ }
+ if ( p30.next() != null ) {
+ return false;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
// Do nothing -- means were not running from jar.
}
if ( xml_parser == null ) {
- xml_parser = new PhyloXmlParser();
+ xml_parser = PhyloXmlParser.createPhyloXmlParser();
if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
}
return true;
}
- private static boolean testSequenceIdParsing() {
+ private static boolean testSequenceDbWsTools1() {
try {
- Accession id = SequenceAccessionTools.parseAccessorFromString( "gb_ADF31344_segmented_worms_" );
- if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
- || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
- if ( id != null ) {
- System.out.println( "value =" + id.getValue() );
- System.out.println( "provider=" + id.getSource() );
- }
+ final PhylogenyNode n = new PhylogenyNode();
+ n.setName( "NP_001025424" );
+ Accession acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
+ || !acc.getValue().equals( "NP_001025424" ) ) {
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" ) ) {
- if ( id != null ) {
- System.out.println( "value =" + id.getValue() );
- System.out.println( "provider=" + id.getSource() );
- }
+ n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" );
+ acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
+ || !acc.getValue().equals( "NP_001025424" ) ) {
return false;
}
- //
- id = SequenceAccessionTools.parseAccessorFromString( "segmented worms gb_ADF31344 and more" );
- if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+ n.setName( "NP_001025424.1" );
+ acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
+ || !acc.getValue().equals( "NP_001025424" ) ) {
+ return false;
+ }
+ n.setName( "NM_001030253" );
+ acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
+ || !acc.getValue().equals( "NM_001030253" ) ) {
+ return false;
+ }
+ n.setName( "BCL2_HUMAN" );
+ acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
+ || !acc.getValue().equals( "BCL2_HUMAN" ) ) {
+ System.out.println( acc.toString() );
+ return false;
+ }
+ n.setName( "P10415" );
+ acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
+ || !acc.getValue().equals( "P10415" ) ) {
+ System.out.println( acc.toString() );
+ return false;
+ }
+ n.setName( " P10415 " );
+ acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
+ || !acc.getValue().equals( "P10415" ) ) {
+ System.out.println( acc.toString() );
+ return false;
+ }
+ n.setName( "_P10415|" );
+ acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
+ || !acc.getValue().equals( "P10415" ) ) {
+ System.out.println( acc.toString() );
+ return false;
+ }
+ n.setName( "AY695820" );
+ acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
+ || !acc.getValue().equals( "AY695820" ) ) {
+ System.out.println( acc.toString() );
+ return false;
+ }
+ n.setName( "_AY695820_" );
+ acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
+ || !acc.getValue().equals( "AY695820" ) ) {
+ System.out.println( acc.toString() );
+ return false;
+ }
+ n.setName( "AAA59452" );
+ acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
+ || !acc.getValue().equals( "AAA59452" ) ) {
+ System.out.println( acc.toString() );
+ return false;
+ }
+ n.setName( "_AAA59452_" );
+ acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
+ || !acc.getValue().equals( "AAA59452" ) ) {
+ System.out.println( acc.toString() );
+ return false;
+ }
+ n.setName( "AAA59452.1" );
+ acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
+ || !acc.getValue().equals( "AAA59452.1" ) ) {
+ System.out.println( acc.toString() );
+ return false;
+ }
+ n.setName( "_AAA59452.1_" );
+ acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
+ || !acc.getValue().equals( "AAA59452.1" ) ) {
+ System.out.println( acc.toString() );
+ return false;
+ }
+ n.setName( "GI:94894583" );
+ acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
+ || !acc.getValue().equals( "94894583" ) ) {
+ System.out.println( acc.toString() );
+ return false;
+ }
+ n.setName( "gi|71845847|1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
+ acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
+ || !acc.getValue().equals( "71845847" ) ) {
+ System.out.println( acc.toString() );
+ return false;
+ }
+ n.setName( "gi|71845847|gb|AAZ45343.1| 1,4-alpha-glucan branching enzyme [Dechloromonas aromatica RCB]" );
+ acc = SequenceDbWsTools.obtainSeqAccession( n );
+ if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
+ || !acc.getValue().equals( "AAZ45343.1" ) ) {
+ System.out.println( acc.toString() );
+ return false;
+ }
+ }
+ catch ( final Exception e ) {
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testSequenceDbWsTools2() {
+ try {
+ final PhylogenyNode n1 = new PhylogenyNode( "NP_001025424" );
+ SequenceDbWsTools.obtainSeqInformation( n1 );
+ if ( !n1.getNodeData().getSequence().getName().equals( "Bcl2" ) ) {
+ return false;
+ }
+ if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
+ return false;
+ }
+ if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
+ return false;
+ }
+ if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) {
+ return false;
+ }
+ final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" );
+ SequenceDbWsTools.obtainSeqInformation( n2 );
+ if ( !n2.getNodeData().getSequence().getName()
+ .equals( "Danio rerio B-cell leukemia/lymphoma 2 (bcl2), mRNA" ) ) {
+ return false;
+ }
+ if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
+ return false;
+ }
+ if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
+ return false;
+ }
+ if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) {
+ return false;
+ }
+ final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" );
+ SequenceDbWsTools.obtainSeqInformation( n3 );
+ if ( !n3.getNodeData().getSequence().getName()
+ .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
+ return false;
+ }
+ if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) {
+ return false;
+ }
+ if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
+ return false;
+ }
+ if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) {
+ return false;
+ }
+ }
+ catch ( final IOException e ) {
+ System.out.println();
+ System.out.println( "the following might be due to absence internet connection:" );
+ e.printStackTrace( System.out );
+ return true;
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testSequenceIdParsing() {
+ try {
+ Accession id = SequenceAccessionTools.parseAccessorFromString( "gb_ADF31344_segmented_worms_" );
+ if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+ || !id.getValue().equals( "ADF31344" ) || !id.getSource().equals( "ncbi" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getSource() );
+ }
+ 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" ) ) {
+ if ( id != null ) {
+ System.out.println( "value =" + id.getValue() );
+ System.out.println( "provider=" + id.getSource() );
+ }
+ 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" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
return true;
}
- private static boolean testTreeMethods() {
+ private static boolean testTreeCopy() {
try {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ];
- PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) );
- if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) {
- System.out.println( t0.toNewHampshireX() );
+ final String str_0 = "((((a,b),c),d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=animals]";
+ final Phylogeny t0 = Phylogeny.createInstanceFromNhxString( str_0 );
+ final Phylogeny t1 = t0.copy();
+ if ( !t1.toNewHampshireX().equals( t0.toNewHampshireX() ) ) {
return false;
}
- final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ];
- PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) );
- if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) {
+ if ( !t1.toNewHampshireX().equals( str_0 ) ) {
return false;
}
- if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) {
+ t0.deleteSubtree( t0.getNode( "c" ), true );
+ t0.deleteSubtree( t0.getNode( "a" ), true );
+ t0.getRoot().getNodeData().getTaxonomy().setScientificName( "metazoa" );
+ t0.getNode( "b" ).setName( "Bee" );
+ if ( !t0.toNewHampshireX().equals( "((Bee,d)[&&NHX:S=lizards],e[&&NHX:S=reptiles])r[&&NHX:S=metazoa]" ) ) {
return false;
}
- if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) {
+ if ( !t1.toNewHampshireX().equals( str_0 ) ) {
return false;
}
- }
- catch ( final Exception e ) {
- e.printStackTrace( System.out );
- return false;
- }
- return true;
- }
-
- private static boolean testSequenceDbWsTools1() {
- try {
- final PhylogenyNode n = new PhylogenyNode();
- n.setName( "NP_001025424" );
- Accession acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
- || !acc.getValue().equals( "NP_001025424" ) ) {
- return false;
- }
- n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" );
- acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
- || !acc.getValue().equals( "NP_001025424" ) ) {
- return false;
- }
- n.setName( "NP_001025424.1" );
- acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
- || !acc.getValue().equals( "NP_001025424" ) ) {
- return false;
- }
- n.setName( "NM_001030253" );
- acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
- || !acc.getValue().equals( "NM_001030253" ) ) {
- return false;
- }
- n.setName( "BCL2_HUMAN" );
- acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
- || !acc.getValue().equals( "BCL2_HUMAN" ) ) {
- System.out.println( acc.toString() );
- return false;
- }
- n.setName( "P10415" );
- acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
- || !acc.getValue().equals( "P10415" ) ) {
- System.out.println( acc.toString() );
- return false;
- }
- n.setName( " P10415 " );
- acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
- || !acc.getValue().equals( "P10415" ) ) {
- System.out.println( acc.toString() );
- return false;
- }
- n.setName( "_P10415|" );
- acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
- || !acc.getValue().equals( "P10415" ) ) {
- System.out.println( acc.toString() );
- return false;
- }
- n.setName( "AY695820" );
- acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
- || !acc.getValue().equals( "AY695820" ) ) {
- System.out.println( acc.toString() );
- return false;
- }
- n.setName( "_AY695820_" );
- acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
- || !acc.getValue().equals( "AY695820" ) ) {
- System.out.println( acc.toString() );
- return false;
- }
- n.setName( "AAA59452" );
- acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
- || !acc.getValue().equals( "AAA59452" ) ) {
- System.out.println( acc.toString() );
- return false;
- }
- n.setName( "_AAA59452_" );
- acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
- || !acc.getValue().equals( "AAA59452" ) ) {
- System.out.println( acc.toString() );
- return false;
- }
- n.setName( "AAA59452.1" );
- acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
- || !acc.getValue().equals( "AAA59452.1" ) ) {
- System.out.println( acc.toString() );
- return false;
- }
- n.setName( "_AAA59452.1_" );
- acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
- || !acc.getValue().equals( "AAA59452.1" ) ) {
- System.out.println( acc.toString() );
- return false;
- }
- n.setName( "GI:94894583" );
- acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
- || !acc.getValue().equals( "94894583" ) ) {
- System.out.println( acc.toString() );
- return false;
- }
- }
- catch ( final Exception e ) {
- return false;
- }
- return true;
- }
-
- private static boolean testSequenceDbWsTools2() {
- try {
- final PhylogenyNode n1 = new PhylogenyNode( "NP_001025424" );
- SequenceDbWsTools.obtainSeqInformation( n1 );
- if ( !n1.getNodeData().getSequence().getName().equals( "Bcl2" ) ) {
- return false;
- }
- if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
- return false;
- }
- if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
- return false;
- }
- if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) {
- return false;
- }
- final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" );
- SequenceDbWsTools.obtainSeqInformation( n2 );
- System.out.println( n2.toString() );
- if ( !n2.getNodeData().getSequence().getName()
- .equals( "Danio rerio B-cell leukemia/lymphoma 2 (bcl2), mRNA" ) ) {
- return false;
- }
- if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
- return false;
- }
- if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
- return false;
- }
- if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) {
- return false;
- }
- final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" );
- SequenceDbWsTools.obtainSeqInformation( n3 );
- System.out.println( "n=" + n3.toString() );
- if ( !n3.getNodeData().getSequence().getName()
- .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
- return false;
- }
- if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) {
- return false;
- }
- if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
- return false;
- }
- if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) {
+ t0.deleteSubtree( t0.getNode( "e" ), true );
+ t0.deleteSubtree( t0.getNode( "Bee" ), true );
+ t0.deleteSubtree( t0.getNode( "d" ), true );
+ if ( !t1.toNewHampshireX().equals( str_0 ) ) {
return false;
}
}
- catch ( final IOException e ) {
- System.out.println();
- System.out.println( "the following might be due to absence internet connection:" );
- e.printStackTrace( System.out );
- return true;
- }
catch ( final Exception e ) {
e.printStackTrace();
return false;
return true;
}
- private static boolean testEbiEntryRetrieval() {
+ private static boolean testTreeMethods() {
try {
- final SequenceDatabaseEntry entry = SequenceDbWsTools
- .obtainEmblEntry( new Accession( "AAK41263", Accession.Source.NCBI ) );
- if ( !entry.getAccession().equals( "AAK41263" ) ) {
- System.out.println( entry.getAccession() );
- return false;
- }
- if ( !entry.getTaxonomyScientificName().equals( "Sulfolobus solfataricus P2" ) ) {
- System.out.println( entry.getTaxonomyScientificName() );
- return false;
- }
- if ( !entry.getSequenceName()
- .equals( "Sulfolobus solfataricus P2 Glycogen debranching enzyme, hypothetical (treX-like)" ) ) {
- System.out.println( entry.getSequenceName() );
- return false;
- }
- // if ( !entry.getSequenceSymbol().equals( "" ) ) {
- // System.out.println( entry.getSequenceSymbol() );
- // return false;
- // }
- if ( !entry.getGeneName().equals( "treX-like" ) ) {
- System.out.println( entry.getGeneName() );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final Phylogeny t0 = factory.create( "((((A,B)ab,C)abc,D)abcd,E)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.collapseSubtreeStructure( t0.getNode( "abcd" ) );
+ if ( !t0.toNewHampshireX().equals( "((A,B,C,D)abcd,E)" ) ) {
+ System.out.println( t0.toNewHampshireX() );
return false;
}
- if ( !entry.getTaxonomyIdentifier().equals( "273057" ) ) {
- System.out.println( entry.getTaxonomyIdentifier() );
+ final Phylogeny t1 = factory.create( "((((A:0.1,B)ab:0.2,C)abc:0.3,D)abcd:0.4,E)", new NHXParser() )[ 0 ];
+ PhylogenyMethods.collapseSubtreeStructure( t1.getNode( "abcd" ) );
+ if ( !isEqual( t1.getNode( "A" ).getDistanceToParent(), 0.6 ) ) {
return false;
}
- if ( !entry.getAnnotations().get( 0 ).getRefValue().equals( "3.2.1.33" ) ) {
- System.out.println( entry.getAnnotations().get( 0 ).getRefValue() );
+ if ( !isEqual( t1.getNode( "B" ).getDistanceToParent(), 0.5 ) ) {
return false;
}
- if ( !entry.getAnnotations().get( 0 ).getRefSource().equals( "EC" ) ) {
- System.out.println( entry.getAnnotations().get( 0 ).getRefSource() );
+ if ( !isEqual( t1.getNode( "C" ).getDistanceToParent(), 0.3 ) ) {
return false;
}
}
- catch ( final IOException e ) {
- System.out.println();
- System.out.println( "the following might be due to absence internet connection:" );
- e.printStackTrace( System.out );
- return true;
- }
catch ( final Exception e ) {
- e.printStackTrace();
+ e.printStackTrace( System.out );
return false;
}
return true;
git://source.jalview.org / jalview.git / blobdiff