// 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.util.ForesterUtil;
+import org.forester.util.TaxonomyUtil;
public class Taxonomy implements PhylogenyData, MultipleUris, Comparable<Taxonomy> {
private String _taxonomy_code;
private String _rank;
private List<Uri> _uris;
+ private List<String> _lineage;
public Taxonomy() {
init();
}
+ @Override
public StringBuffer asSimpleText() {
return asText();
}
+ @Override
public Uri getUri( final int index ) {
return getUris().get( index );
}
+ @Override
public void addUri( final Uri uri ) {
if ( getUris() == null ) {
setUris( new ArrayList<Uri>() );
getUris().add( uri );
}
+ @Override
public StringBuffer asText() {
final StringBuffer sb = new StringBuffer();
if ( getIdentifier() != null ) {
return sb;
}
+ @Override
public PhylogenyData copy() {
final Taxonomy t = new Taxonomy();
- t.setTaxonomyCode( getTaxonomyCode() );
+ try {
+ t.setTaxonomyCode( getTaxonomyCode() );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ e.printStackTrace();
+ }
t.setScientificName( getScientificName() );
t.setCommonName( getCommonName() );
t.setAuthority( getAuthority() );
else {
t.setIdentifier( null );
}
- t.setRank( new String( getRank() ) );
+ try {
+ t.setRank( new String( getRank() ) );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ e.printStackTrace();
+ }
if ( getUris() != null ) {
t.setUris( new ArrayList<Uri>() );
for( final Uri uri : getUris() ) {
}
}
}
+ if ( getLineage() != null ) {
+ t.setLineage( new ArrayList<String>() );
+ for( final String l : getLineage() ) {
+ if ( l != null ) {
+ t.getLineage().add( l );
+ }
+ }
+ }
return t;
}
return _taxonomy_code;
}
+ @Override
public List<Uri> getUris() {
return _uris;
}
@Override
public int hashCode() {
- if ( getIdentifier() != null ) {
+ if ( ( getIdentifier() != null ) && !ForesterUtil.isEmpty( getIdentifier().getValue() ) ) {
return getIdentifier().hashCode();
}
else if ( !ForesterUtil.isEmpty( getTaxonomyCode() ) ) {
setScientificName( "" );
setCommonName( "" );
setIdentifier( null );
- setRank( "" );
- setTaxonomyCode( "" );
+ try {
+ setRank( "" );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ e.printStackTrace();
+ }
+ try {
+ setTaxonomyCode( "" );
+ }
+ catch ( final PhyloXmlDataFormatException e ) {
+ e.printStackTrace();
+ }
setAuthority( "" );
setSynonyms( null );
setUris( null );
+ setLineage( null );
}
public boolean isEmpty() {
return ( ( getIdentifier() == null ) && ForesterUtil.isEmpty( getTaxonomyCode() )
&& ForesterUtil.isEmpty( getCommonName() ) && ForesterUtil.isEmpty( getScientificName() )
- && ForesterUtil.isEmpty( getRank() ) && ForesterUtil.isEmpty( _uris )
- && ForesterUtil.isEmpty( getAuthority() ) && ForesterUtil.isEmpty( _synonyms ) );
+ && ForesterUtil.isEmpty( _lineage ) );
}
/**
- *
+ *
* If this and taxonomy 'data' has an identifier, comparison will be based on that.
* Otherwise, if this and taxonomy 'data' has a code, comparison will be based on that.
* Otherwise, if Taxonomy 'data' has a scientific name, comparison will be
* Otherwise, if Taxonomy 'data' has a common name, comparison will be
* based on that (case insensitive!).
* (Note. This is important and should not be change without a very good reason.)
- *
+ *
*/
+ @Override
public boolean isEqual( final PhylogenyData data ) {
if ( this == data ) {
return true;
}
final Taxonomy tax = ( Taxonomy ) data;
- if ( ( getIdentifier() != null ) && ( tax.getIdentifier() != null ) ) {
+ if ( ( getIdentifier() != null ) && ( tax.getIdentifier() != null )
+ && !ForesterUtil.isEmpty( getIdentifier().getValue() )
+ && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
return getIdentifier().isEqual( tax.getIdentifier() );
}
else if ( !ForesterUtil.isEmpty( getTaxonomyCode() ) && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
else if ( !ForesterUtil.isEmpty( getCommonName() ) && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
return getCommonName().equalsIgnoreCase( tax.getCommonName() );
}
- else if ( !ForesterUtil.isEmpty( getScientificName() ) && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
- return getScientificName().equalsIgnoreCase( tax.getCommonName() );
- }
- else if ( !ForesterUtil.isEmpty( getCommonName() ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
- return getCommonName().equalsIgnoreCase( tax.getScientificName() );
- }
- throw new RuntimeException( "comparison not possible with empty fields" );
+ //throw new RuntimeException( "comparison not possible with empty fields" );
+ return false;
}
public void setAuthority( final String authority ) {
_identifier = identifier;
}
- public void setRank( final String rank ) {
- if ( !ForesterUtil.isEmpty( rank ) && !PhyloXmlUtil.TAXONOMY_RANKS.contains( rank ) ) {
+ public void setRank( final String rank ) throws PhyloXmlDataFormatException {
+ if ( !ForesterUtil.isEmpty( rank ) && !TaxonomyUtil.TAXONOMY_RANKS_SET.contains( rank ) ) {
throw new PhyloXmlDataFormatException( "illegal rank: [" + rank + "]" );
}
_rank = rank;
_synonyms = synonyms;
}
- public void setTaxonomyCode( final String taxonomy_code ) {
+ public void setTaxonomyCode( String taxonomy_code ) throws PhyloXmlDataFormatException {
if ( !ForesterUtil.isEmpty( taxonomy_code )
&& !PhyloXmlUtil.TAXOMONY_CODE_PATTERN.matcher( taxonomy_code ).matches() ) {
throw new PhyloXmlDataFormatException( "illegal taxonomy code: [" + taxonomy_code + "]" );
_taxonomy_code = taxonomy_code;
}
+ @Override
public void setUris( final List<Uri> uris ) {
_uris = uris;
}
+ @Override
public StringBuffer toNHX() {
final StringBuffer sb = new StringBuffer();
if ( getIdentifier() != null ) {
return sb;
}
+ @Override
public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException {
if ( isEmpty() ) {
return;
PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.TAXONOMY_AUTHORITY, getAuthority(), indentation );
}
if ( !ForesterUtil.isEmpty( getCommonName() ) ) {
- PhylogenyDataUtil
- .appendElement( writer, PhyloXmlMapping.TAXONOMY_COMMON_NAME, getCommonName(), indentation );
+ PhylogenyDataUtil.appendElement( writer,
+ PhyloXmlMapping.TAXONOMY_COMMON_NAME,
+ getCommonName(),
+ indentation );
}
if ( _synonyms != null ) {
for( final String syn : getSynonyms() ) {
if ( equals( o ) ) {
return 0;
}
- else if ( !ForesterUtil.isEmpty( getScientificName() ) && !ForesterUtil.isEmpty( o.getScientificName() ) ) {
+ if ( ( getIdentifier() != null ) && ( o.getIdentifier() != null )
+ && !ForesterUtil.isEmpty( getIdentifier().getValue() )
+ && !ForesterUtil.isEmpty( o.getIdentifier().getValue() ) ) {
+ final int x = getIdentifier().getValuePlusProvider().compareTo( o.getIdentifier().getValuePlusProvider() );
+ if ( x != 0 ) {
+ return x;
+ }
+ }
+ if ( !ForesterUtil.isEmpty( getScientificName() ) && !ForesterUtil.isEmpty( o.getScientificName() ) ) {
return getScientificName().compareToIgnoreCase( o.getScientificName() );
}
- else if ( !ForesterUtil.isEmpty( getCommonName() ) && !ForesterUtil.isEmpty( o.getCommonName() ) ) {
+ if ( !ForesterUtil.isEmpty( getCommonName() ) && !ForesterUtil.isEmpty( o.getCommonName() ) ) {
return getCommonName().compareToIgnoreCase( o.getCommonName() );
}
- else if ( !ForesterUtil.isEmpty( getTaxonomyCode() ) && !ForesterUtil.isEmpty( o.getTaxonomyCode() ) ) {
+ if ( !ForesterUtil.isEmpty( getTaxonomyCode() ) && !ForesterUtil.isEmpty( o.getTaxonomyCode() ) ) {
return getTaxonomyCode().compareToIgnoreCase( o.getTaxonomyCode() );
}
- return 0;
+ if ( ( getIdentifier() != null ) && ( o.getIdentifier() != null )
+ && !ForesterUtil.isEmpty( getIdentifier().getValue() )
+ && !ForesterUtil.isEmpty( o.getIdentifier().getValue() ) ) {
+ return getIdentifier().getValuePlusProvider().compareTo( o.getIdentifier().getValuePlusProvider() );
+ }
+ return 1;
+ }
+
+ public void setLineage( final List<String> lineage ) {
+ _lineage = lineage;
+ }
+
+ public List<String> getLineage() {
+ return _lineage;
}
}
git://source.jalview.org / jalview.git / blobdiff