X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=09c9a696a7de8f5c60c8db5513666360bf1bbec0;hb=daa33859b015a7e4b1295addfff2582bf348b8bc;hp=d35a05bb7cc6df87e94c5f7e949e11c7e6e71357;hpb=68b63b7225615d09b8b870681fd59f11a0167fe7;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index d35a05b..09c9a69 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -47,7 +47,12 @@ public class Sequence implements SequenceI
     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.
@@ -136,25 +141,41 @@ 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)
     {
       if(sequenceFeatures==null)
-        sequenceFeatures = new Vector();
+      {
+        sequenceFeatures = new SequenceFeature[0];
+      }
+
+      for(int i=0; i<sequenceFeatures.length; i++)
+      {
+        if(sequenceFeatures[i].equals(sf))
+        {
+          return;
+        }
+      }
+
+      SequenceFeature [] temp = new SequenceFeature[sequenceFeatures.length+1];
+      System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
+      temp[sequenceFeatures.length] = sf;
+
 
-      sequenceFeatures.addElement(sf);
+      sequenceFeatures = temp;
     }
 
+
     /**
      * DOCUMENT ME!
      *
      * @return DOCUMENT ME!
      */
-    public Vector getSequenceFeatures()
+    public SequenceFeature [] getSequenceFeatures()
     {
         return sequenceFeatures;
     }
@@ -481,16 +502,6 @@ 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!
@@ -499,7 +510,7 @@ 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);
 
@@ -597,4 +608,85 @@ public class Sequence implements SequenceI
       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() < 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();
+    }
+
 }