import java.util.List;
import java.util.Locale;
import java.util.Set;
+import java.util.SortedSet;
import org.forester.application.support_transfer;
-import org.forester.archaeopteryx.AptxUtil;
+import org.forester.archaeopteryx.TreePanelUtil;
import org.forester.development.DevelopmentTools;
import org.forester.evoinference.TestPhylogenyReconstruction;
import org.forester.evoinference.matrix.character.CharacterStateMatrix;
import org.forester.protein.BasicDomain;
import org.forester.protein.BasicProtein;
import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
import org.forester.protein.Protein;
import org.forester.protein.ProteinId;
import org.forester.rio.TestRIO;
import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
import org.forester.util.GeneralTable;
-import org.forester.util.SequenceIdParser;
+import org.forester.util.SequenceAccessionTools;
import org.forester.ws.seqdb.SequenceDatabaseEntry;
import org.forester.ws.seqdb.SequenceDbWsTools;
import org.forester.ws.seqdb.UniProtTaxonomy;
System.exit( -1 );
}
final long start_time = new Date().getTime();
- System.out.print( "Domain id: " );
- if ( !testDomainId() ) {
- System.out.println( "failed." );
- failed++;
- }
- else {
- succeeded++;
- }
- System.out.println( "OK." );
System.out.print( "Protein id: " );
if ( !testProteinId() ) {
System.out.println( "failed." );
private static boolean testBasicDomain() {
try {
final Domain pd = new BasicDomain( "id", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
- if ( !pd.getDomainId().getId().equals( "id" ) ) {
+ if ( !pd.getDomainId().equals( "id" ) ) {
return false;
}
if ( pd.getNumber() != 1 ) {
if ( a1.compareTo( a2 ) != 0 ) {
return false;
}
- if ( a1.compareTo( a3 ) != 0 ) {
+ if ( a1.compareTo( a3 ) == 0 ) {
return false;
}
}
if ( !( t3.getNode( "root node" ).getNodeData().getSequence().getLocation().equals( "12p13-p12" ) ) ) {
return false;
}
+ final SortedSet<Accession> x = t3.getNode( "root node" ).getNodeData().getSequence().getCrossReferences();
+ if ( x.size() != 4 ) {
+ return false;
+ }
+ int c = 0;
+ for( final Accession acc : x ) {
+ if ( c == 0 ) {
+ if ( !acc.getSource().equals( "KEGG" ) ) {
+ return false;
+ }
+ if ( !acc.getValue().equals( "hsa:596" ) ) {
+ return false;
+ }
+ }
+ c++;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
}
if ( ( ( BinaryCharacters ) t3_rt.getNode( "node bb" ).getNodeData().getBinaryCharacters().copy() )
.getLostCount() != BinaryCharacters.COUNT_DEFAULT ) {
- ;
return false;
}
if ( t3_rt.getNode( "node b" ).getNodeData().getBinaryCharacters().getGainedCount() != 1 ) {
.equalsIgnoreCase( "433" ) ) {
return false;
}
+ final SortedSet<Accession> x = t3_rt.getNode( "root node" ).getNodeData().getSequence()
+ .getCrossReferences();
+ if ( x.size() != 4 ) {
+ return false;
+ }
+ int c = 0;
+ for( final Accession acc : x ) {
+ if ( c == 0 ) {
+ if ( !acc.getSource().equals( "KEGG" ) ) {
+ return false;
+ }
+ if ( !acc.getValue().equals( "hsa:596" ) ) {
+ return false;
+ }
+ }
+ c++;
+ }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
if ( !p0.toDomainArchitectureString( "~" ).equals( "a~b~c~d~e~x~y" ) ) {
return false;
}
- // A0 A10 B15 A20 B25 A30 B35 B40 C50 A60 C70 D80
- final Domain A0 = new BasicDomain( "A", 0, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
- final Domain A10 = new BasicDomain( "A", 10, 11, ( short ) 1, ( short ) 4, 0.1, -12 );
- final Domain B15 = new BasicDomain( "B", 11, 16, ( short ) 1, ( short ) 4, 0.1, -12 );
- final Domain A20 = new BasicDomain( "A", 20, 100, ( short ) 1, ( short ) 4, 0.1, -12 );
- final Domain B25 = new BasicDomain( "B", 25, 26, ( short ) 1, ( short ) 4, 0.1, -12 );
- final Domain A30 = new BasicDomain( "A", 30, 31, ( short ) 1, ( short ) 4, 0.1, -12 );
- final Domain B35 = new BasicDomain( "B", 31, 40, ( short ) 1, ( short ) 4, 0.1, -12 );
- final Domain B40 = new BasicDomain( "B", 40, 600, ( short ) 1, ( short ) 4, 0.1, -12 );
- final Domain C50 = new BasicDomain( "C", 50, 59, ( short ) 1, ( short ) 4, 0.1, -12 );
- final Domain A60 = new BasicDomain( "A", 60, 395, ( short ) 1, ( short ) 4, 0.1, -12 );
- final Domain C70 = new BasicDomain( "C", 70, 71, ( short ) 1, ( short ) 4, 0.1, -12 );
- final Domain D80 = new BasicDomain( "D", 80, 81, ( short ) 1, ( short ) 4, 0.1, -12 );
- final BasicProtein p = new BasicProtein( "p", "owl", 0 );
- p.addProteinDomain( B15 );
- p.addProteinDomain( C50 );
- p.addProteinDomain( A60 );
- p.addProteinDomain( A30 );
- p.addProteinDomain( C70 );
- p.addProteinDomain( B35 );
- p.addProteinDomain( B40 );
- p.addProteinDomain( A0 );
- p.addProteinDomain( A10 );
- p.addProteinDomain( A20 );
- p.addProteinDomain( B25 );
- p.addProteinDomain( D80 );
- List<DomainId> domains_ids = new ArrayList<DomainId>();
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "C" ) );
- if ( !p.contains( domains_ids, false ) ) {
+ if ( !p0.toDomainArchitectureString( "~", 3, "=" ).equals( "a~b~c~d~e~x~y" ) ) {
return false;
}
- if ( !p.contains( domains_ids, true ) ) {
+ //
+ final BasicProtein aa0 = new BasicProtein( "aa", "owl", 0 );
+ final Domain a1 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
+ aa0.addProteinDomain( a1 );
+ if ( !aa0.toDomainArchitectureString( "~" ).equals( "a" ) ) {
return false;
}
- domains_ids.add( new DomainId( "X" ) );
- if ( p.contains( domains_ids, false ) ) {
+ if ( !aa0.toDomainArchitectureString( "~", 3, "" ).equals( "a" ) ) {
return false;
}
- if ( p.contains( domains_ids, true ) ) {
+ //
+ final BasicProtein aa1 = new BasicProtein( "aa", "owl", 0 );
+ final Domain a11 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain a12 = new BasicDomain( "a", 2, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
+ aa1.addProteinDomain( a11 );
+ aa1.addProteinDomain( a12 );
+ if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a" ) ) {
return false;
}
- domains_ids = new ArrayList<DomainId>();
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "C" ) );
- domains_ids.add( new DomainId( "D" ) );
- if ( !p.contains( domains_ids, false ) ) {
+ if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "a~a" ) ) {
return false;
}
- if ( !p.contains( domains_ids, true ) ) {
+ aa1.addProteinDomain( new BasicDomain( "a", 20, 30, ( short ) 1, ( short ) 5, 0.1, -12 ) );
+ if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a" ) ) {
return false;
}
- domains_ids = new ArrayList<DomainId>();
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "D" ) );
- domains_ids.add( new DomainId( "C" ) );
- if ( !p.contains( domains_ids, false ) ) {
+ if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
return false;
}
- if ( p.contains( domains_ids, true ) ) {
+ if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "a~a~a" ) ) {
return false;
}
- domains_ids = new ArrayList<DomainId>();
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- if ( !p.contains( domains_ids, false ) ) {
+ aa1.addProteinDomain( new BasicDomain( "a", 30, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
+ if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a" ) ) {
return false;
}
- if ( !p.contains( domains_ids, true ) ) {
+ if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa" ) ) {
return false;
}
- domains_ids = new ArrayList<DomainId>();
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "B" ) );
- if ( !p.contains( domains_ids, false ) ) {
+ if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa" ) ) {
return false;
}
- if ( !p.contains( domains_ids, true ) ) {
+ if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a" ) ) {
return false;
}
- domains_ids = new ArrayList<DomainId>();
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "B" ) );
- if ( !p.contains( domains_ids, false ) ) {
+ aa1.addProteinDomain( new BasicDomain( "b", 32, 40, ( short ) 1, ( short ) 5, 0.1, -12 ) );
+ if ( !aa1.toDomainArchitectureString( "~" ).equals( "a~a~a~a~b" ) ) {
return false;
}
- if ( !p.contains( domains_ids, true ) ) {
+ if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "aaa~b" ) ) {
return false;
}
- domains_ids = new ArrayList<DomainId>();
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "B" ) );
- if ( !p.contains( domains_ids, false ) ) {
+ if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "aaa~b" ) ) {
return false;
}
- if ( p.contains( domains_ids, true ) ) {
+ if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "a~a~a~a~b" ) ) {
return false;
}
- domains_ids = new ArrayList<DomainId>();
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "C" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "C" ) );
- domains_ids.add( new DomainId( "D" ) );
- if ( !p.contains( domains_ids, false ) ) {
+ aa1.addProteinDomain( new BasicDomain( "c", 1, 2, ( short ) 1, ( short ) 5, 0.1, -12 ) );
+ if ( !aa1.toDomainArchitectureString( "~" ).equals( "c~a~a~a~a~b" ) ) {
return false;
}
- if ( !p.contains( domains_ids, true ) ) {
+ if ( !aa1.toDomainArchitectureString( "~", 3, "" ).equals( "c~aaa~b" ) ) {
return false;
}
- domains_ids = new ArrayList<DomainId>();
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "C" ) );
- domains_ids.add( new DomainId( "D" ) );
- if ( !p.contains( domains_ids, false ) ) {
+ if ( !aa1.toDomainArchitectureString( "~", 4, "" ).equals( "c~aaa~b" ) ) {
return false;
}
- if ( !p.contains( domains_ids, true ) ) {
+ if ( !aa1.toDomainArchitectureString( "~", 5, "" ).equals( "c~a~a~a~a~b" ) ) {
+ return false;
+ }
+ //
+ final BasicProtein p00 = new BasicProtein( "p0", "owl", 0 );
+ final Domain a0 = new BasicDomain( "a", 1, 10, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain b0 = new BasicDomain( "b", 11, 20, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain c0 = new BasicDomain( "c", 9, 23, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain d0 = new BasicDomain( "d", 15, 30, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain e0 = new BasicDomain( "e", 60, 70, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain e1 = new BasicDomain( "e", 61, 71, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain e2 = new BasicDomain( "e", 62, 72, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain e3 = new BasicDomain( "e", 63, 73, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain e4 = new BasicDomain( "e", 64, 74, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain e5 = new BasicDomain( "e", 65, 75, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain x0 = new BasicDomain( "x", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain y0 = new BasicDomain( "y", 100, 110, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain y1 = new BasicDomain( "y", 120, 130, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain y2 = new BasicDomain( "y", 140, 150, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain y3 = new BasicDomain( "y", 160, 170, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain z0 = new BasicDomain( "z", 200, 210, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain z1 = new BasicDomain( "z", 300, 310, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain z2 = new BasicDomain( "z", 400, 410, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain zz0 = new BasicDomain( "Z", 500, 510, ( short ) 1, ( short ) 5, 0.1, -12 );
+ final Domain zz1 = new BasicDomain( "Z", 600, 610, ( short ) 1, ( short ) 5, 0.1, -12 );
+ p00.addProteinDomain( y0 );
+ p00.addProteinDomain( e0 );
+ p00.addProteinDomain( b0 );
+ p00.addProteinDomain( c0 );
+ p00.addProteinDomain( d0 );
+ p00.addProteinDomain( a0 );
+ p00.addProteinDomain( x0 );
+ p00.addProteinDomain( y1 );
+ p00.addProteinDomain( y2 );
+ p00.addProteinDomain( y3 );
+ p00.addProteinDomain( e1 );
+ p00.addProteinDomain( e2 );
+ p00.addProteinDomain( e3 );
+ p00.addProteinDomain( e4 );
+ p00.addProteinDomain( e5 );
+ p00.addProteinDomain( z0 );
+ p00.addProteinDomain( z1 );
+ p00.addProteinDomain( z2 );
+ p00.addProteinDomain( zz0 );
+ p00.addProteinDomain( zz1 );
+ if ( !p00.toDomainArchitectureString( "~", 3, "" ).equals( "a~b~c~d~eee~x~yyy~zzz~Z~Z" ) ) {
+ return false;
+ }
+ if ( !p00.toDomainArchitectureString( "~", 4, "" ).equals( "a~b~c~d~eee~x~yyy~z~z~z~Z~Z" ) ) {
+ return false;
+ }
+ if ( !p00.toDomainArchitectureString( "~", 5, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
+ return false;
+ }
+ if ( !p00.toDomainArchitectureString( "~", 6, "" ).equals( "a~b~c~d~eee~x~y~y~y~y~z~z~z~Z~Z" ) ) {
+ return false;
+ }
+ if ( !p00.toDomainArchitectureString( "~", 7, "" ).equals( "a~b~c~d~e~e~e~e~e~e~x~y~y~y~y~z~z~z~Z~Z" ) ) {
return false;
}
- domains_ids = new ArrayList<DomainId>();
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "C" ) );
- domains_ids.add( new DomainId( "C" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "C" ) );
- domains_ids.add( new DomainId( "D" ) );
+ // A0 A10 B15 A20 B25 A30 B35 B40 C50 A60 C70 D80
+ final Domain A0 = new BasicDomain( "A", 0, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain A10 = new BasicDomain( "A", 10, 11, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain B15 = new BasicDomain( "B", 11, 16, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain A20 = new BasicDomain( "A", 20, 100, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain B25 = new BasicDomain( "B", 25, 26, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain A30 = new BasicDomain( "A", 30, 31, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain B35 = new BasicDomain( "B", 31, 40, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain B40 = new BasicDomain( "B", 40, 600, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain C50 = new BasicDomain( "C", 50, 59, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain A60 = new BasicDomain( "A", 60, 395, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain C70 = new BasicDomain( "C", 70, 71, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final Domain D80 = new BasicDomain( "D", 80, 81, ( short ) 1, ( short ) 4, 0.1, -12 );
+ final BasicProtein p = new BasicProtein( "p", "owl", 0 );
+ p.addProteinDomain( B15 );
+ p.addProteinDomain( C50 );
+ p.addProteinDomain( A60 );
+ p.addProteinDomain( A30 );
+ p.addProteinDomain( C70 );
+ p.addProteinDomain( B35 );
+ p.addProteinDomain( B40 );
+ p.addProteinDomain( A0 );
+ p.addProteinDomain( A10 );
+ p.addProteinDomain( A20 );
+ p.addProteinDomain( B25 );
+ p.addProteinDomain( D80 );
+ List<String> domains_ids = new ArrayList<String>();
+ domains_ids.add( "A" );
+ domains_ids.add( "B" );
+ domains_ids.add( "C" );
if ( !p.contains( domains_ids, false ) ) {
return false;
}
- if ( p.contains( domains_ids, true ) ) {
+ if ( !p.contains( domains_ids, true ) ) {
return false;
}
- domains_ids = new ArrayList<DomainId>();
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "C" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "C" ) );
- domains_ids.add( new DomainId( "D" ) );
- if ( !p.contains( domains_ids, false ) ) {
+ domains_ids.add( "X" );
+ if ( p.contains( domains_ids, false ) ) {
return false;
}
if ( p.contains( domains_ids, true ) ) {
return false;
}
- domains_ids = new ArrayList<DomainId>();
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "D" ) );
+ domains_ids = new ArrayList<String>();
+ domains_ids.add( "A" );
+ domains_ids.add( "C" );
+ domains_ids.add( "D" );
if ( !p.contains( domains_ids, false ) ) {
return false;
}
if ( !p.contains( domains_ids, true ) ) {
return false;
}
- domains_ids = new ArrayList<DomainId>();
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "C" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "C" ) );
- domains_ids.add( new DomainId( "D" ) );
- domains_ids.add( new DomainId( "X" ) );
- if ( p.contains( domains_ids, false ) ) {
+ domains_ids = new ArrayList<String>();
+ domains_ids.add( "A" );
+ domains_ids.add( "D" );
+ domains_ids.add( "C" );
+ if ( !p.contains( domains_ids, false ) ) {
return false;
}
if ( p.contains( domains_ids, true ) ) {
return false;
}
- domains_ids = new ArrayList<DomainId>();
- domains_ids.add( new DomainId( "X" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "C" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "C" ) );
- domains_ids.add( new DomainId( "D" ) );
- if ( p.contains( domains_ids, false ) ) {
+ domains_ids = new ArrayList<String>();
+ domains_ids.add( "A" );
+ domains_ids.add( "A" );
+ domains_ids.add( "B" );
+ if ( !p.contains( domains_ids, false ) ) {
return false;
}
- if ( p.contains( domains_ids, true ) ) {
+ if ( !p.contains( domains_ids, true ) ) {
+ return false;
+ }
+ domains_ids = new ArrayList<String>();
+ domains_ids.add( "A" );
+ domains_ids.add( "A" );
+ domains_ids.add( "A" );
+ domains_ids.add( "B" );
+ domains_ids.add( "B" );
+ if ( !p.contains( domains_ids, false ) ) {
+ return false;
+ }
+ if ( !p.contains( domains_ids, true ) ) {
return false;
}
- domains_ids = new ArrayList<DomainId>();
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "B" ) );
- domains_ids.add( new DomainId( "C" ) );
- domains_ids.add( new DomainId( "A" ) );
- domains_ids.add( new DomainId( "C" ) );
- domains_ids.add( new DomainId( "D" ) );
+ domains_ids = new ArrayList<String>();
+ domains_ids.add( "A" );
+ domains_ids.add( "A" );
+ domains_ids.add( "B" );
+ domains_ids.add( "A" );
+ domains_ids.add( "B" );
+ domains_ids.add( "B" );
+ domains_ids.add( "A" );
+ domains_ids.add( "B" );
+ domains_ids.add( "C" );
+ domains_ids.add( "A" );
+ domains_ids.add( "C" );
+ domains_ids.add( "D" );
if ( !p.contains( domains_ids, false ) ) {
return false;
}
try {
final PhylogenyNode n = new PhylogenyNode();
n.setName( "tr|B3RJ64" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) {
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B3RJ64" ) ) {
return false;
}
n.setName( "B0LM41_HUMAN" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) {
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "B0LM41_HUMAN" ) ) {
return false;
}
n.setName( "NP_001025424" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) {
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "NP_001025424" ) ) {
return false;
}
n.setName( "_NM_001030253-" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) {
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "NM_001030253" ) ) {
return false;
}
n.setName( "XM_002122186" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) {
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_NUCCORE + "XM_002122186" ) ) {
return false;
}
n.setName( "dgh_AAA34956_gdg" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
return false;
}
- n.setName( "j40f4_Q06891.1_fndn2 fnr3" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "Q06891.1" ) ) {
+ n.setName( "AAA34956" );
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_PROTEIN + "AAA34956" ) ) {
return false;
}
n.setName( "GI:394892" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
- System.out.println( AptxUtil.createUriForSeqWeb( n, null, null ) );
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
+ System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
return false;
}
n.setName( "gi_394892" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
- System.out.println( AptxUtil.createUriForSeqWeb( n, null, null ) );
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
+ System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
return false;
}
n.setName( "gi6335_gi_394892_56635_Gi_43" );
- if ( !AptxUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
- System.out.println( AptxUtil.createUriForSeqWeb( n, null, null ) );
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.NCBI_GI + "394892" ) ) {
+ System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
+ return false;
+ }
+ n.setName( "P12345" );
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
+ System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
+ return false;
+ }
+ n.setName( "gi_fdgjmn-3jk5-243 mnefmn fg023-0 P12345 4395jtmnsrg02345m1ggi92450jrg890j4t0j240" );
+ if ( !TreePanelUtil.createUriForSeqWeb( n, null, null ).equals( ForesterUtil.UNIPROT_KB + "P12345" ) ) {
+ System.out.println( TreePanelUtil.createUriForSeqWeb( n, null, null ) );
return false;
}
}
return true;
}
- private static boolean testDomainId() {
- try {
- final DomainId id1 = new DomainId( "a" );
- final DomainId id2 = new DomainId( "a" );
- final DomainId id3 = new DomainId( "A" );
- final DomainId id4 = new DomainId( "b" );
- if ( !id1.equals( id1 ) ) {
- return false;
- }
- if ( id1.getId().equals( "x" ) ) {
- return false;
- }
- if ( id1.getId().equals( null ) ) {
- return false;
- }
- if ( !id1.equals( id2 ) ) {
- return false;
- }
- if ( id1.equals( id3 ) ) {
- return false;
- }
- if ( id1.hashCode() != id1.hashCode() ) {
- return false;
- }
- if ( id1.hashCode() != id2.hashCode() ) {
- return false;
- }
- if ( id1.hashCode() == id3.hashCode() ) {
- return false;
- }
- if ( id1.compareTo( id1 ) != 0 ) {
- return false;
- }
- if ( id1.compareTo( id2 ) != 0 ) {
- return false;
- }
- if ( id1.compareTo( id3 ) != 0 ) {
- return false;
- }
- if ( id1.compareTo( id4 ) >= 0 ) {
- return false;
- }
- if ( id4.compareTo( id1 ) <= 0 ) {
- return false;
- }
- if ( !id4.getId().equals( "b" ) ) {
- return false;
- }
- final DomainId id5 = new DomainId( " C " );
- if ( !id5.getId().equals( "C" ) ) {
- return false;
- }
- if ( id5.equals( id1 ) ) {
- return false;
- }
- }
- catch ( final Exception e ) {
- e.printStackTrace( System.out );
- return false;
- }
- return true;
- }
-
private static boolean testEmblEntryRetrieval() {
//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 ( !SequenceIdParser.parseGenbankAccessor( "AY423861" ).equals( "AY423861" ) ) {
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "AY423861" ).equals( "AY423861" ) ) {
return false;
}
- if ( !SequenceIdParser.parseGenbankAccessor( ".AY423861.2" ).equals( "AY423861.2" ) ) {
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( ".AY423861.2" ).equals( "AY423861.2" ) ) {
return false;
}
- if ( !SequenceIdParser.parseGenbankAccessor( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "345_.AY423861.24_345" ).equals( "AY423861.24" ) ) {
return false;
}
- if ( SequenceIdParser.parseGenbankAccessor( "AAY423861" ) != null ) {
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY423861" ) != null ) {
return false;
}
- if ( SequenceIdParser.parseGenbankAccessor( "AY4238612" ) != null ) {
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AY4238612" ) != null ) {
return false;
}
- if ( SequenceIdParser.parseGenbankAccessor( "AAY4238612" ) != null ) {
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "AAY4238612" ) != null ) {
return false;
}
- if ( SequenceIdParser.parseGenbankAccessor( "Y423861" ) != null ) {
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "Y423861" ) != null ) {
return false;
}
- if ( !SequenceIdParser.parseGenbankAccessor( "S12345" ).equals( "S12345" ) ) {
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "S12345" ).equals( "S12345" ) ) {
return false;
}
- if ( !SequenceIdParser.parseGenbankAccessor( "|S12345|" ).equals( "S12345" ) ) {
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "|S12345|" ).equals( "S12345" ) ) {
return false;
}
- if ( SequenceIdParser.parseGenbankAccessor( "|S123456" ) != null ) {
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "|S123456" ) != null ) {
return false;
}
- if ( SequenceIdParser.parseGenbankAccessor( "ABC123456" ) != null ) {
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABC123456" ) != null ) {
return false;
}
- if ( !SequenceIdParser.parseGenbankAccessor( "ABC12345" ).equals( "ABC12345" ) ) {
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "ABC12345" ).equals( "ABC12345" ) ) {
return false;
}
- if ( !SequenceIdParser.parseGenbankAccessor( "&ABC12345&" ).equals( "ABC12345" ) ) {
+ if ( !SequenceAccessionTools.parseGenbankAccessorFromString( "&ABC12345&" ).equals( "ABC12345" ) ) {
return false;
}
- if ( SequenceIdParser.parseGenbankAccessor( "ABCD12345" ) != null ) {
+ if ( SequenceAccessionTools.parseGenbankAccessorFromString( "ABCD12345" ) != null ) {
return false;
}
return true;
try {
PhylogenyNode n = new PhylogenyNode();
n.setName( "tr|B3RJ64" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "tr.B3RJ64" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "tr=B3RJ64" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "tr-B3RJ64" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "tr/B3RJ64" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "tr\\B3RJ64" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "tr_B3RJ64" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( " tr|B3RJ64 " );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "-tr|B3RJ64-" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "-tr=B3RJ64-" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "_tr=B3RJ64_" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( " tr_tr|B3RJ64_sp|123 " );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
- n.setName( "sp|B3RJ64" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ n.setName( "B3RJ64" );
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
- n.setName( "ssp|B3RJ64" );
- if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ n.setName( "sp|B3RJ64" );
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "sp|B3RJ64C" );
- if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
return false;
}
n.setName( "sp B3RJ64" );
- if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n.setName( "sp|B3RJ6X" );
- if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
return false;
}
n.setName( "sp|B3RJ6" );
- if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
return false;
}
n.setName( "K1PYK7_CRAGI" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
return false;
}
n.setName( "K1PYK7_PEA" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PEA" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PEA" ) ) {
return false;
}
n.setName( "K1PYK7_RAT" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_RAT" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_RAT" ) ) {
return false;
}
n.setName( "K1PYK7_PIG" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PIG" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
return false;
}
n.setName( "~K1PYK7_PIG~" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_PIG" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_PIG" ) ) {
return false;
}
n.setName( "123456_ECOLI-K1PYK7_CRAGI-sp" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
return false;
}
n.setName( "K1PYKX_CRAGI" );
- if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
return false;
}
n.setName( "XXXXX_CRAGI" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "XXXXX_CRAGI" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "XXXXX_CRAGI" ) ) {
return false;
}
n.setName( "tr|H3IB65|H3IB65_STRPU~2-2" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "H3IB65" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "H3IB65" ) ) {
return false;
}
n.setName( "jgi|Lacbi2|181470|Lacbi1.estExt_GeneWisePlus_human.C_10729~2-3" );
- if ( ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ) != null ) {
+ if ( SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ) != null ) {
return false;
}
n.setName( "sp|Q86U06|RBM23_HUMAN~2-2" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "Q86U06" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "Q86U06" ) ) {
return false;
}
n = new PhylogenyNode();
org.forester.phylogeny.data.Sequence seq = new org.forester.phylogeny.data.Sequence();
seq.setSymbol( "K1PYK7_CRAGI" );
n.getNodeData().addSequence( seq );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
return false;
}
seq.setSymbol( "tr|B3RJ64" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n = new PhylogenyNode();
seq = new org.forester.phylogeny.data.Sequence();
seq.setName( "K1PYK7_CRAGI" );
n.getNodeData().addSequence( seq );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK7_CRAGI" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK7_CRAGI" ) ) {
return false;
}
seq.setName( "tr|B3RJ64" );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
n = new PhylogenyNode();
seq = new org.forester.phylogeny.data.Sequence();
seq.setAccession( new Accession( "K1PYK8_CRAGI", "?" ) );
n.getNodeData().addSequence( seq );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "K1PYK8_CRAGI" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "K1PYK8_CRAGI" ) ) {
return false;
}
n = new PhylogenyNode();
seq = new org.forester.phylogeny.data.Sequence();
seq.setAccession( new Accession( "tr|B3RJ64", "?" ) );
n.getNodeData().addSequence( seq );
- if ( !ForesterUtil.extractUniProtKbProteinSeqIdentifier( n ).equals( "B3RJ64" ) ) {
+ if ( !SequenceAccessionTools.obtainUniProtAccessorFromDataFields( n ).equals( "B3RJ64" ) ) {
return false;
}
//
n = new PhylogenyNode();
n.setName( "ACP19736" );
- if ( !ForesterUtil.extractGenbankAccessor( n ).equals( "ACP19736" ) ) {
+ if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
return false;
}
n = new PhylogenyNode();
n.setName( "_ACP19736_" );
- if ( !ForesterUtil.extractGenbankAccessor( n ).equals( "ACP19736" ) ) {
+ if ( !SequenceAccessionTools.obtainGenbankAccessorFromDataFields( n ).equals( "ACP19736" ) ) {
return false;
}
}
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" ) ) {
+ 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.getProvider() );
+ System.out.println( "provider=" + id.getSource() );
}
return false;
}
//
- 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" ) ) {
+ 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.getProvider() );
+ System.out.println( "provider=" + id.getSource() );
}
return false;
}
//
- 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" ) ) {
+ 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() );
- System.out.println( "provider=" + id.getProvider() );
+ System.out.println( "provider=" + id.getSource() );
}
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" ) ) {
+ 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" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
- System.out.println( "provider=" + id.getProvider() );
+ System.out.println( "provider=" + id.getSource() );
}
return false;
}
//
- 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" ) ) {
+ 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" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
- System.out.println( "provider=" + id.getProvider() );
+ System.out.println( "provider=" + id.getSource() );
}
return false;
}
//
- 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" ) ) {
+ 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" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
- System.out.println( "provider=" + id.getProvider() );
+ System.out.println( "provider=" + id.getSource() );
}
return false;
}
//
- 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" ) ) {
+ 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" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
- System.out.println( "provider=" + id.getProvider() );
+ System.out.println( "provider=" + id.getSource() );
}
return false;
}
//
- 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( "refseq" ) ) {
+ 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" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
- System.out.println( "provider=" + id.getProvider() );
+ System.out.println( "provider=" + id.getSource() );
}
return false;
}
//
- 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( "refseq" ) ) {
+ 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" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
- System.out.println( "provider=" + id.getProvider() );
+ System.out.println( "provider=" + id.getSource() );
}
return false;
}
//
- id = SequenceIdParser.parse( "P4A123" );
- if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
- || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
+ id = SequenceAccessionTools.parseAccessorFromString( "P4A123" );
+ if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+ || !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "uniprot" ) ) {
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
- System.out.println( "provider=" + id.getProvider() );
+ System.out.println( "provider=" + id.getSource() );
}
return false;
}
//
- id = SequenceIdParser.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
- if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getProvider() )
- || !id.getValue().equals( "P4A123" ) || !id.getProvider().equals( "sp" ) ) {
- if ( id != null ) {
- System.out.println( "value =" + id.getValue() );
- System.out.println( "provider=" + id.getProvider() );
- }
- return false;
- }
+ // id = SequenceAccessionTools.parse( "pllf[pok P4A123_osdjfosnqo035-9233332904i000490 vf tmv x45" );
+ // if ( ( id == null ) || ForesterUtil.isEmpty( id.getValue() ) || ForesterUtil.isEmpty( id.getSource() )
+ // || !id.getValue().equals( "P4A123" ) || !id.getSource().equals( "sp" ) ) {
+ // if ( id != null ) {
+ // System.out.println( "value =" + id.getValue() );
+ // System.out.println( "provider=" + id.getSource() );
+ // }
+ // return false;
+ // }
//
- id = SequenceIdParser.parse( "XP_12345" );
+ id = SequenceAccessionTools.parseAccessorFromString( "XP_12345" );
if ( id != null ) {
System.out.println( "value =" + id.getValue() );
- System.out.println( "provider=" + id.getProvider() );
+ System.out.println( "provider=" + id.getSource() );
return false;
}
// lcl_91970_unknown_
if ( !entry.getSequenceName().equals( "Aspartate aminotransferase, mitochondrial" ) ) {
return false;
}
+ if ( !entry.getSequenceSymbol().equals( "mAspAT" ) ) {
+ return false;
+ }
+ if ( !entry.getGeneName().equals( "GOT2" ) ) {
+ return false;
+ }
if ( !entry.getTaxonomyIdentifier().equals( "9986" ) ) {
return false;
}
System.out.println( results.get( 0 ).getLineage() );
return false;
}
+ //
+ results = null;
+ results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Xenopus tropicalis", 10 );
+ if ( results.size() != 1 ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
+ .equals( "Xenopus tropicalis" ) ) {
+ System.out.println( results.get( 0 ).getLineage() );
+ return false;
+ }
+ //
+ results = null;
+ results = SequenceDbWsTools.getTaxonomiesFromId( "8364", 10 );
+ if ( results.size() != 1 ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
+ .equals( "Xenopus tropicalis" ) ) {
+ System.out.println( results.get( 0 ).getLineage() );
+ return false;
+ }
+ //
+ results = null;
+ results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "XENTR", 10 );
+ if ( results.size() != 1 ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getCode().equals( "XENTR" ) ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getCommonName().equalsIgnoreCase( "Western clawed frog" ) ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getId().equalsIgnoreCase( "8364" ) ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getRank().equalsIgnoreCase( "species" ) ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getScientificName().equals( "Xenopus tropicalis" ) ) {
+ return false;
+ }
+ if ( !results.get( 0 ).getLineage().get( results.get( 0 ).getLineage().size() - 1 )
+ .equals( "Xenopus tropicalis" ) ) {
+ System.out.println( results.get( 0 ).getLineage() );
+ return false;
+ }
}
catch ( final IOException e ) {
System.out.println();