X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=562440f6a80d140dbd7baf35584bf0e8d6ee03f3;hb=c97b0d0f8b52d2049f81b30df969a64a6d58240c;hp=65537ae5b79cb5a7f4204e48c0cb4397b13afbe0;hpb=8e73c98073451713e9094a80feafd9b9e8bfd917;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 65537ae..562440f 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -33,18 +33,26 @@ public class Sequence implements SequenceI
 {
     SequenceI datasetSequence;
     String name;
-    String sequence;
+    private String sequence;
     String description;
     int start;
     int end;
     Color color = Color.white;
     Vector pdbIds;
     String vamsasId;
-    Vector dbrefs;
+    DBRefEntry [] dbrefs;
 
+    /** This annotation is displayed below the alignment but the
+     * positions are tied to the residues of this sequence */
+    Vector annotation;
 
     /** DOCUMENT ME!! */
-    public Vector sequenceFeatures;
+    public SequenceFeature [] sequenceFeatures;
+
+    /** This array holds hidden sequences
+     * of which this sequence is the representitive member of a group
+     */
+    SequenceGroup hiddenSequences;
 
     /**
      * Creates a new Sequence object.
@@ -133,25 +141,40 @@ public class Sequence implements SequenceI
      *
      * @param v DOCUMENT ME!
      */
-    public void setSequenceFeatures(Vector v)
+    public void setSequenceFeatures(SequenceFeature [] features)
     {
-        sequenceFeatures = v;
+        sequenceFeatures = features;
     }
 
-    public void addSequenceFeature(SequenceFeature sf)
+    public synchronized void addSequenceFeature(SequenceFeature sf)
     {
       if(sequenceFeatures==null)
-        sequenceFeatures = new Vector();
+      {
+        sequenceFeatures = new SequenceFeature[0];
+      }
+
+      for(int i=0; i<sequenceFeatures.length; i++)
+      {
+        if(sequenceFeatures[i].equals(sf))
+        {
+          return;
+        }
+      }
 
-      sequenceFeatures.addElement(sf);
+      SequenceFeature [] temp = new SequenceFeature[sequenceFeatures.length+1];
+      System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
+      temp[sequenceFeatures.length] = sf;
+
+      sequenceFeatures = temp;
     }
 
+
     /**
      * DOCUMENT ME!
      *
      * @return DOCUMENT ME!
      */
-    public Vector getSequenceFeatures()
+    public SequenceFeature [] getSequenceFeatures()
     {
         return sequenceFeatures;
     }
@@ -422,7 +445,7 @@ public class Sequence implements SequenceI
     public int[] gapMap()
     {
         // Returns an int array giving the position of each residue in the sequence in the alignment
-        String seq = jalview.analysis.AlignSeq.extractGaps("-. ", sequence);
+        String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequence);
         int[] map = new int[seq.length()];
         int j = 0;
         int p = 0;
@@ -478,16 +501,6 @@ public class Sequence implements SequenceI
         }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param c DOCUMENT ME!
-     */
-    public void insertCharAt(int i, char c)
-    {
-        insertCharAt(i, c, true);
-    }
 
     /**
      * DOCUMENT ME!
@@ -496,7 +509,7 @@ public class Sequence implements SequenceI
      * @param c DOCUMENT ME!
      * @param chop DOCUMENT ME!
      */
-    public void insertCharAt(int i, char c, boolean chop)
+    public void insertCharAt(int i, char c)
     {
         String tmp = new String(sequence);
 
@@ -547,11 +560,12 @@ public class Sequence implements SequenceI
       vamsasId = id;
     }
 
-    public void setDBRef(Vector dbref)
+    public void setDBRef(DBRefEntry [] dbref)
     {
       dbrefs = dbref;
     }
-    public Vector getDBRef()
+
+    public DBRefEntry [] getDBRef()
     {
       return dbrefs;
     }
@@ -559,9 +573,14 @@ public class Sequence implements SequenceI
     public void addDBRef(DBRefEntry entry)
     {
       if(dbrefs == null)
-        dbrefs = new Vector();
+        dbrefs = new DBRefEntry[0];
+
+      DBRefEntry [] temp = new DBRefEntry[dbrefs.length+1];
+      System.arraycopy(dbrefs, 0, temp, 0, dbrefs.length);
 
-      dbrefs.addElement(entry);
+      temp[temp.length-1] = entry;
+
+      dbrefs = temp;
     }
 
     public void setDatasetSequence(SequenceI seq)
@@ -574,4 +593,104 @@ public class Sequence implements SequenceI
       return datasetSequence;
     }
 
+    public AlignmentAnnotation [] getAnnotation()
+    {
+      if(annotation==null)
+        return null;
+
+      AlignmentAnnotation [] ret = new AlignmentAnnotation[annotation.size()];
+      for(int r = 0; r<ret.length; r++)
+        ret[r] = (AlignmentAnnotation)annotation.elementAt(r);
+
+      return ret;
+    }
+
+    public void addAlignmentAnnotation(AlignmentAnnotation annotation)
+    {
+      if(this.annotation==null)
+        this.annotation = new Vector();
+
+      this.annotation.addElement( annotation );
+    }
+
+    public SequenceGroup getHiddenSequences()
+    {
+      return hiddenSequences;
+    }
+
+    public void addHiddenSequence(SequenceI seq)
+    {
+      if(hiddenSequences==null)
+      {
+        hiddenSequences = new SequenceGroup();
+      }
+      hiddenSequences.addSequence(seq, false);
+    }
+
+    public void showHiddenSequence(SequenceI seq)
+    {
+      hiddenSequences.deleteSequence(seq, false);
+      if (hiddenSequences.getSize(false) < 1)
+      {
+        hiddenSequences = null;
+      }
+    }
+
+    public void changeCase(boolean toUpper, int start, int end)
+    {
+      StringBuffer newSeq = new StringBuffer();
+
+      if(end>sequence.length())
+        end = sequence.length();
+
+      if (start > 0)
+      {
+        newSeq.append(sequence.substring(0, start));
+      }
+
+      if (toUpper)
+        newSeq.append(sequence.substring(start, end).toUpperCase());
+      else
+        newSeq.append(sequence.substring(start, end).toLowerCase());
+
+      if (end < sequence.length())
+        newSeq.append(sequence.substring(end));
+
+      sequence = newSeq.toString();
+    }
+
+    public void toggleCase(int start, int end)
+    {
+      StringBuffer newSeq = new StringBuffer();
+
+     if(end>sequence.length())
+       end = sequence.length();
+
+     if (start > 0)
+     {
+       newSeq.append(sequence.substring(0, start));
+     }
+
+     char nextChar;
+     for(int c=start; c<end; c++)
+     {
+       nextChar = sequence.charAt(c);
+       if(Character.isLetter(nextChar))
+       {
+         if(Character.isUpperCase(nextChar))
+           nextChar = Character.toLowerCase(nextChar);
+         else
+           nextChar = Character.toUpperCase(nextChar);
+       }
+
+
+       newSeq.append(nextChar);
+     }
+
+     if (end < sequence.length())
+       newSeq.append(sequence.substring(end));
+
+     sequence = newSeq.toString();
+    }
+
 }