// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.phylogeny.data;
import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.io.writers.PhylogenyWriter;
+import org.forester.sequence.MolecularSequence;
+import org.forester.sequence.MolecularSequence.TYPE;
import org.forester.util.ForesterUtil;
-public class Sequence implements PhylogenyData, MultipleUris {
+public class Sequence implements PhylogenyData, MultipleUris, Comparable<Sequence> {
+ private Accession _accession;
+ private SortedSet<Annotation> _annotations;
+ private DomainArchitecture _da;
+ private String _gene_name;
+ private String _location;
private String _mol_sequence;
private boolean _mol_sequence_is_aligned;
private String _name;
+ private List<SequenceRelation> _seq_relations;
private String _source_id;
- private Accession _accession;
private String _symbol;
- private String _location;
private String _type;
- private SortedSet<Annotation> _annotations;
- private DomainArchitecture _da;
private List<Uri> _uris;
- private List<SequenceRelation> _seq_relations;
+ private SortedSet<Accession> _xrefs;
public Sequence() {
init();
}
- public boolean isEmpty() {
- return ( getAccession() == null ) && ForesterUtil.isEmpty( getName() ) && ForesterUtil.isEmpty( getSymbol() )
- && ForesterUtil.isEmpty( getType() ) && ForesterUtil.isEmpty( getLocation() )
- && ForesterUtil.isEmpty( getSourceId() ) && ForesterUtil.isEmpty( getMolecularSequence() )
- && ( getDomainArchitecture() == null ) && ForesterUtil.isEmpty( _annotations )
- && ForesterUtil.isEmpty( _uris ) && ForesterUtil.isEmpty( _seq_relations );
+ public Sequence( final MolecularSequence mol_seq ) {
+ init();
+ setMolecularSequence( mol_seq.getMolecularSequenceAsString() );
+ setName( mol_seq.getIdentifier() );
+ String type;
+ if ( mol_seq.getType() == TYPE.AA ) {
+ type = "protein";
+ }
+ else if ( mol_seq.getType() == TYPE.DNA ) {
+ type = "dna";
+ }
+ else if ( mol_seq.getType() == TYPE.RNA ) {
+ type = "rna";
+ }
+ else {
+ throw new IllegalArgumentException( "unknown sequence type " + mol_seq.getType() );
+ }
+ try {
+ setType( type );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ throw new IllegalArgumentException( "don't know how to handle type " + mol_seq.getType() );
+ }
}
public void addAnnotation( final Annotation annotation ) {
getAnnotations().add( annotation );
}
+ public void addCrossReference( final Accession cross_reference ) {
+ if ( getCrossReferences() == null ) {
+ setCrossReferences( new TreeSet<Accession>() );
+ }
+ getCrossReferences().add( cross_reference );
+ }
+
+ public void addSequenceRelation( final SequenceRelation sr ) {
+ getSequenceRelations().add( sr );
+ }
+
+ @Override
public void addUri( final Uri uri ) {
if ( getUris() == null ) {
setUris( new ArrayList<Uri>() );
getUris().add( uri );
}
- public void addSequenceRelation( final SequenceRelation sr ) {
- _seq_relations.add( sr );
- }
-
+ @Override
public StringBuffer asSimpleText() {
final StringBuffer sb = new StringBuffer();
if ( getAccession() != null ) {
return sb;
}
+ @Override
public StringBuffer asText() {
return asSimpleText();
}
+ @Override
+ public int compareTo( final Sequence o ) {
+ if ( ( !ForesterUtil.isEmpty( getName() ) ) && ( !ForesterUtil.isEmpty( o.getName() ) ) ) {
+ return getName().compareTo( o.getName() );
+ }
+ if ( ( !ForesterUtil.isEmpty( getSymbol() ) ) && ( !ForesterUtil.isEmpty( o.getSymbol() ) ) ) {
+ return getSymbol().compareTo( o.getSymbol() );
+ }
+ if ( ( !ForesterUtil.isEmpty( getGeneName() ) ) && ( !ForesterUtil.isEmpty( o.getGeneName() ) ) ) {
+ return getGeneName().compareTo( o.getGeneName() );
+ }
+ if ( ( getAccession() != null ) && ( o.getAccession() != null )
+ && !ForesterUtil.isEmpty( getAccession().getValue() )
+ && !ForesterUtil.isEmpty( o.getAccession().getValue() ) ) {
+ return getAccession().getValue().compareTo( o.getAccession().getValue() );
+ }
+ if ( ( !ForesterUtil.isEmpty( getMolecularSequence() ) )
+ && ( !ForesterUtil.isEmpty( o.getMolecularSequence() ) ) ) {
+ return getMolecularSequence().compareTo( o.getMolecularSequence() );
+ }
+ return 0;
+ }
+
/**
* Not a deep copy.
- *
+ *
*/
+ @Override
public PhylogenyData copy() {
final Sequence seq = new Sequence();
seq.setAnnotations( getAnnotations() );
seq.setName( getName() );
- seq.setSymbol( getSymbol() );
+ seq.setGeneName( getGeneName() );
+ try {
+ seq.setSymbol( getSymbol() );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ e.printStackTrace();
+ }
seq.setMolecularSequence( getMolecularSequence() );
seq.setMolecularSequenceAligned( isMolecularSequenceAligned() );
seq.setLocation( getLocation() );
else {
seq.setAccession( null );
}
- seq.setType( getType() );
+ try {
+ seq.setType( getType() );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ e.printStackTrace();
+ }
if ( getUris() != null ) {
seq.setUris( new ArrayList<Uri>() );
for( final Uri uri : getUris() ) {
else {
seq.setDomainArchitecture( null );
}
+ if ( getCrossReferences() != null ) {
+ seq.setCrossReferences( new TreeSet<Accession>() );
+ for( final Accession x : getCrossReferences() ) {
+ if ( x != null ) {
+ seq.getCrossReferences().add( x );
+ }
+ }
+ }
return seq;
}
return _annotations;
}
+ public SortedSet<Accession> getCrossReferences() {
+ return _xrefs;
+ }
+
public DomainArchitecture getDomainArchitecture() {
return _da;
}
+ public String getGeneName() {
+ return _gene_name;
+ }
+
public String getLocation() {
return _location;
}
return _mol_sequence;
}
- public boolean isMolecularSequenceAligned() {
- return _mol_sequence_is_aligned;
- }
-
public String getName() {
return _name;
}
return _seq_relations;
}
- private void setSequenceRelations( final List<SequenceRelation> seq_relations ) {
- _seq_relations = seq_relations;
- }
-
public String getSourceId() {
return _source_id;
}
return _type;
}
- public List<Uri> getUris() {
- return _uris;
- }
-
+ @Override
public Uri getUri( final int index ) {
return getUris().get( index );
}
@Override
+ public List<Uri> getUris() {
+ return _uris;
+ }
+
+ @Override
public int hashCode() {
if ( getAccession() != null ) {
return getAccession().hashCode();
}
- int result = getSymbol().hashCode();
- if ( getName().length() > 0 ) {
+ int result = getName().hashCode();
+ if ( getSymbol().length() > 0 ) {
result ^= getName().hashCode();
}
+ if ( getGeneName().length() > 0 ) {
+ result ^= getGeneName().hashCode();
+ }
if ( getMolecularSequence().length() > 0 ) {
result ^= getMolecularSequence().hashCode();
}
}
public void init() {
- setAnnotations( null );
setName( "" );
+ setGeneName( "" );
setMolecularSequence( "" );
setMolecularSequenceAligned( false );
setLocation( "" );
setAccession( null );
- setSymbol( "" );
- setType( "" );
+ try {
+ setSymbol( "" );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ e.printStackTrace();
+ }
+ try {
+ setType( "" );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ e.printStackTrace();
+ }
setDomainArchitecture( null );
setUris( null );
setSequenceRelations( null );
setSourceId( null );
+ setCrossReferences( null );
+ setAnnotations( null );
}
+ public boolean isEmpty() {
+ return ( getAccession() == null ) && ForesterUtil.isEmpty( getName() ) && ForesterUtil.isEmpty( getSymbol() )
+ && ForesterUtil.isEmpty( getGeneName() ) && ForesterUtil.isEmpty( getType() )
+ && ForesterUtil.isEmpty( getLocation() ) && ForesterUtil.isEmpty( getSourceId() )
+ && ForesterUtil.isEmpty( getMolecularSequence() ) && ( getDomainArchitecture() == null )
+ && ForesterUtil.isEmpty( _annotations ) && ForesterUtil.isEmpty( _uris )
+ && ForesterUtil.isEmpty( _seq_relations )
+ && ( ( getCrossReferences() == null ) || getCrossReferences().isEmpty() );
+ }
+
+ @Override
public boolean isEqual( final PhylogenyData data ) {
if ( this == data ) {
return true;
return getAccession().isEqual( s.getAccession() );
}
return s.getMolecularSequence().equals( getMolecularSequence() ) && s.getName().equals( getName() )
- && s.getSymbol().equals( getSymbol() );
+ && s.getSymbol().equals( getSymbol() ) && s.getGeneName().equals( getGeneName() );
}
- public void setAccession( final Accession accession ) {
- _accession = accession;
+ public boolean isMolecularSequenceAligned() {
+ return _mol_sequence_is_aligned;
}
- private void setAnnotations( final SortedSet<Annotation> annotations ) {
- _annotations = annotations;
+ public void setAccession( final Accession accession ) {
+ _accession = accession;
}
public void setDomainArchitecture( final DomainArchitecture ds ) {
_da = ds;
}
+ public void setGeneName( final String gene_name ) {
+ _gene_name = gene_name;
+ }
+
public void setLocation( final String description ) {
_location = description;
}
_source_id = source_id;
}
- public void setSymbol( final String symbol ) {
+ public void setSymbol( final String symbol ) throws PhyloXmlDataFormatException {
if ( !ForesterUtil.isEmpty( symbol ) && !PhyloXmlUtil.SEQUENCE_SYMBOL_PATTERN.matcher( symbol ).matches() ) {
throw new PhyloXmlDataFormatException( "illegal sequence symbol: [" + symbol + "]" );
}
_symbol = symbol;
}
- public void setType( final String type ) {
+ public void setType( final String type ) throws PhyloXmlDataFormatException {
if ( !ForesterUtil.isEmpty( type ) && !PhyloXmlUtil.SEQUENCE_TYPES.contains( type ) ) {
throw new PhyloXmlDataFormatException( "illegal sequence type: [" + type + "]" );
}
_type = type;
}
+ @Override
public void setUris( final List<Uri> uris ) {
_uris = uris;
}
+ @Override
public StringBuffer toNHX() {
final StringBuffer sb = new StringBuffer();
if ( getName().length() > 0 ) {
if ( getAccession() != null ) {
getAccession().toNHX();
}
- if ( getDomainArchitecture() != null ) {
- sb.append( getDomainArchitecture().toNHX() );
- }
return sb;
}
+ @Override
public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
if ( isEmpty() ) {
return;
if ( !ForesterUtil.isEmpty( getName() ) ) {
PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.SEQUENCE_NAME, getName(), indentation );
}
+ if ( !ForesterUtil.isEmpty( getGeneName() ) ) {
+ PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.SEQUENCE_GENE_NAME, getGeneName(), indentation );
+ }
if ( !ForesterUtil.isEmpty( getLocation() ) ) {
PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.SEQUENCE_LOCATION, getLocation(), indentation );
}
String.valueOf( isMolecularSequenceAligned() ),
indentation );
}
- if ( getUris() != null ) {
+ if ( ( getUris() != null ) && !getUris().isEmpty() ) {
for( final Uri uri : getUris() ) {
if ( uri != null ) {
uri.toPhyloXML( writer, level, indentation );
}
}
}
- if ( _annotations != null ) {
+ if ( ( getAnnotations() != null ) && !getAnnotations().isEmpty() ) {
for( final PhylogenyData annotation : getAnnotations() ) {
annotation.toPhyloXML( writer, level, my_ind );
}
}
+ if ( ( getCrossReferences() != null ) && !getCrossReferences().isEmpty() ) {
+ writer.write( ForesterUtil.LINE_SEPARATOR );
+ writer.write( my_ind );
+ PhylogenyDataUtil.appendOpen( writer, PhyloXmlMapping.SEQUENCE_X_REFS );
+ for( final PhylogenyData x : getCrossReferences() ) {
+ x.toPhyloXML( writer, level, my_ind );
+ }
+ writer.write( ForesterUtil.LINE_SEPARATOR );
+ writer.write( my_ind );
+ PhylogenyDataUtil.appendClose( writer, PhyloXmlMapping.SEQUENCE_X_REFS );
+ }
if ( getDomainArchitecture() != null ) {
getDomainArchitecture().toPhyloXML( writer, level, my_ind );
}
public String toString() {
return asText().toString();
}
+
+ private void setAnnotations( final SortedSet<Annotation> annotations ) {
+ _annotations = annotations;
+ }
+
+ private void setCrossReferences( final TreeSet<Accession> cross_references ) {
+ _xrefs = cross_references;
+ }
+
+ private void setSequenceRelations( final List<SequenceRelation> seq_relations ) {
+ _seq_relations = seq_relations;
+ }
}
git://source.jalview.org / jalview.git / blobdiff