// 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;
public class Annotation implements PhylogenyData, MultipleUris, Comparable<Annotation> {
+ private Confidence _confidence;
private String _desc;
- private String _type;
- private String _source;
- private final String _ref;
private String _evidence;
- private Confidence _confidence;
private PropertiesMap _properties;
+ private final String _ref_source;
+ private final String _ref_value;
+ private String _source;
+ private String _type;
private List<Uri> _uris;
+ public Annotation() {
+ _ref_value = "";
+ _ref_source = "";
+ init();
+ }
+
public Annotation( final String ref ) {
if ( ForesterUtil.isEmpty( ref ) ) {
- throw new IllegalArgumentException( "illegal attempt to create Annotation with null or empty reference" );
+ throw new IllegalArgumentException( "annotation reference is empty or null" );
}
- if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.length() < 3 ) ) {
- throw new IllegalArgumentException( "illegal format for Annotation reference: [" + ref + "]" );
+ final String s[] = ref.split( ":" );
+ if ( ( s.length != 2 ) || ForesterUtil.isEmpty( s[ 0 ] ) || ForesterUtil.isEmpty( s[ 1 ] ) ) {
+ throw new IllegalArgumentException( "illegal format for annotation reference: [" + ref + "]" );
+ }
+ _ref_source = s[ 0 ];
+ _ref_value = s[ 1 ];
+ init();
+ }
+
+ public Annotation( final String ref_source, final String ref_value ) {
+ if ( ForesterUtil.isEmpty( ref_source ) || ForesterUtil.isEmpty( ref_value ) ) {
+ throw new IllegalArgumentException( "illegal format for annotation reference" );
}
- _ref = ref;
+ _ref_source = ref_source;
+ _ref_value = ref_value;
init();
}
@Override
+ public void addUri( final Uri uri ) {
+ if ( getUris() == null ) {
+ setUris( new ArrayList<Uri>() );
+ }
+ getUris().add( uri );
+ }
+
+ @Override
public StringBuffer asSimpleText() {
- return new StringBuffer( getDesc() );
+ return new StringBuffer( !ForesterUtil.isEmpty( getRef() ) ? getRef() : getDesc() );
}
@Override
public StringBuffer asText() {
- return new StringBuffer( getDesc() );
+ return asSimpleText();
+ }
+
+ @Override
+ public int compareTo( final Annotation o ) {
+ if ( equals( o ) ) {
+ return 0;
+ }
+ if ( getRef().equals( o.getRef() ) ) {
+ return getDesc().compareTo( o.getDesc() );
+ }
+ return getRef().compareTo( o.getRef() );
}
@Override
public PhylogenyData copy() {
- final Annotation ann = new Annotation( new String( getRef() ) );
+ final Annotation ann = new Annotation( getRefSource(), getRefValue() );
if ( getConfidence() != null ) {
ann.setConfidence( ( Confidence ) getConfidence().copy() );
}
else {
ann.setConfidence( null );
}
- ann.setType( new String( getType() ) );
- ann.setDesc( new String( getDesc() ) );
- ann.setEvidence( new String( getEvidence() ) );
+ ann.setType( getType() );
+ ann.setDesc( getDesc() );
+ ann.setEvidence( getEvidence() );
ann.setSource( new String( getSource() ) );
if ( getProperties() != null ) {
ann.setProperties( ( PropertiesMap ) getProperties().copy() );
return ann;
}
+ @Override
+ public boolean equals( final Object o ) {
+ if ( this == o ) {
+ return true;
+ }
+ else if ( o == null ) {
+ return false;
+ }
+ else if ( o.getClass() != this.getClass() ) {
+ throw new IllegalArgumentException( "attempt to check [" + this.getClass() + "] equality to " + o + " ["
+ + o.getClass() + "]" );
+ }
+ else {
+ return isEqual( ( Annotation ) o );
+ }
+ }
+
public Confidence getConfidence() {
return _confidence;
}
}
public String getRef() {
- return _ref;
+ if ( ForesterUtil.isEmpty( _ref_source ) ) {
+ return "";
+ }
+ final StringBuilder sb = new StringBuilder();
+ sb.append( _ref_source );
+ sb.append( ':' );
+ sb.append( _ref_value );
+ return sb.toString();
+ }
+
+ public final String getRefSource() {
+ return _ref_source;
+ }
+
+ public final String getRefValue() {
+ return _ref_value;
}
public String getSource() {
return _type;
}
- private void init() {
- _desc = "";
- _type = "";
- _source = "";
- _evidence = "";
- _confidence = null;
- _properties = null;
- setUris( null );
+ @Override
+ public Uri getUri( final int index ) {
+ return getUris().get( index );
+ }
+
+ @Override
+ public List<Uri> getUris() {
+ return _uris;
}
@Override
}
@Override
+ public void setUris( final List<Uri> uris ) {
+ _uris = uris;
+ }
+
+ @Override
public StringBuffer toNHX() {
throw new UnsupportedOperationException();
}
return asText().toString();
}
- @Override
- public void addUri( final Uri uri ) {
- if ( getUris() == null ) {
- setUris( new ArrayList<Uri>() );
- }
- getUris().add( uri );
- }
-
- @Override
- public Uri getUri( final int index ) {
- return getUris().get( index );
- }
-
- @Override
- public List<Uri> getUris() {
- return _uris;
- }
-
- @Override
- public void setUris( final List<Uri> uris ) {
- _uris = uris;
- }
-
- @Override
- public boolean equals( final Object o ) {
- if ( this == o ) {
- return true;
- }
- else if ( o == null ) {
- return false;
- }
- else if ( o.getClass() != this.getClass() ) {
- throw new IllegalArgumentException( "attempt to check [" + this.getClass() + "] equality to " + o + " ["
- + o.getClass() + "]" );
- }
- else {
- return isEqual( ( Annotation ) o );
- }
- }
-
- @Override
- public int compareTo( final Annotation o ) {
- if ( equals( o ) ) {
- return 0;
- }
- if ( getRef().equals( o.getRef() ) ) {
- return getDesc().compareTo( o.getDesc() );
- }
- return getRef().compareTo( o.getRef() );
+ private void init() {
+ _desc = "";
+ _type = "";
+ _source = "";
+ _evidence = "";
+ _confidence = null;
+ _properties = null;
+ setUris( null );
}
}
git://source.jalview.org / jalview.git / blobdiff