X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2Fdata%2FAnnotation.java;h=652a0348684540277a0d08bbef92f1a64ce99a7d;hb=bdf2d2a11d720d6457f52866af7ff909afe98db4;hp=829707af13f93246d3dea12dfb10423b3f8eb008;hpb=b0fc7a39bd4bdbe8ba7b576a14ce1aaae645ea1b;p=jalview.git

diff --git a/forester/java/src/org/forester/phylogeny/data/Annotation.java b/forester/java/src/org/forester/phylogeny/data/Annotation.java
index 829707a..652a034 100644
--- a/forester/java/src/org/forester/phylogeny/data/Annotation.java
+++ b/forester/java/src/org/forester/phylogeny/data/Annotation.java
@@ -21,7 +21,7 @@
 // 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;
 
@@ -36,53 +36,98 @@ import org.forester.util.ForesterUtil;
 
 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( "annotation reference is empty or null" );
         }
-        if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ref.length() - 2 ) || ( ref.length() < 3 ) ) {
+        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 = ref;
+        _ref_source = s[ 0 ];
+        _ref_value = s[ 1 ];
         init();
     }
 
-    public Annotation() {
-        _ref = "";
+    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_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( !ForesterUtil.isEmpty( getRef() ) ? getRef() : getDesc() );
     }
 
     @Override
     public StringBuffer asText() {
-        return asSimpleText();
+        final StringBuffer sb = new StringBuffer();
+        if ( !ForesterUtil.isEmpty( getDesc() ) && !ForesterUtil.isEmpty( getRef() ) ) {
+            sb.append( getDesc() );
+            sb.append( " (" );
+            sb.append( getRef() );
+            sb.append( ")" );
+        }
+        else if ( !ForesterUtil.isEmpty( getDesc() ) ) {
+            sb.append( getDesc() );
+        }
+        else if ( !ForesterUtil.isEmpty( getRef() ) ) {
+            sb.append( getRef() );
+        }
+        return sb;
+    }
+
+    @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() );
@@ -101,6 +146,23 @@ public class Annotation implements PhylogenyData, MultipleUris, Comparable<Annot
         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;
     }
@@ -118,7 +180,22 @@ public class Annotation implements PhylogenyData, MultipleUris, Comparable<Annot
     }
 
     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() {
@@ -129,14 +206,14 @@ public class Annotation implements PhylogenyData, MultipleUris, Comparable<Annot
         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
@@ -174,6 +251,11 @@ public class Annotation implements PhylogenyData, MultipleUris, Comparable<Annot
     }
 
     @Override
+    public void setUris( final List<Uri> uris ) {
+        _uris = uris;
+    }
+
+    @Override
     public StringBuffer toNHX() {
         throw new UnsupportedOperationException();
     }
@@ -234,54 +316,13 @@ public class Annotation implements PhylogenyData, MultipleUris, Comparable<Annot
         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 );
     }
 }