HiddenSequence methods

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 48057b8..87a9306 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -49,6 +49,11 @@ public class Sequence implements SequenceI
     /** DOCUMENT ME!! */\r
     public SequenceFeature [] sequenceFeatures;\r
 \r
+    /** This array holds hidden sequences\r
+     * of which this sequence is the representitive member of a group\r
+     */\r
+    SequenceGroup hiddenSequences;\r
+\r
     /**\r
      * Creates a new Sequence object.\r
      *\r
@@ -496,16 +501,6 @@ public class Sequence implements SequenceI
         }\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param i DOCUMENT ME!\r
-     * @param c DOCUMENT ME!\r
-     */\r
-    public void insertCharAt(int i, char c)\r
-    {\r
-        insertCharAt(i, c, true);\r
-    }\r
 \r
     /**\r
      * DOCUMENT ME!\r
@@ -514,7 +509,7 @@ public class Sequence implements SequenceI
      * @param c DOCUMENT ME!\r
      * @param chop DOCUMENT ME!\r
      */\r
-    public void insertCharAt(int i, char c, boolean chop)\r
+    public void insertCharAt(int i, char c)\r
     {\r
         String tmp = new String(sequence);\r
 \r
@@ -612,4 +607,27 @@ public class Sequence implements SequenceI
       this.annotation.addElement( annotation );\r
     }\r
 \r
+    public SequenceGroup getHiddenSequences()\r
+    {\r
+      return hiddenSequences;\r
+    }\r
+\r
+    public void addHiddenSequence(SequenceI seq)\r
+    {\r
+      if(hiddenSequences==null)\r
+      {\r
+        hiddenSequences = new SequenceGroup();\r
+      }\r
+      hiddenSequences.addSequence(seq, false);\r
+    }\r
+\r
+    public void showHiddenSequence(SequenceI seq)\r
+    {\r
+      hiddenSequences.deleteSequence(seq, false);\r
+      if (hiddenSequences.getSize() < 1)\r
+      {\r
+        hiddenSequences = null;\r
+      }\r
+\r
+    }\r
 }\r

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 089a5f6..1f7a232 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -183,14 +183,6 @@ public interface SequenceI
      */\r
     public void insertCharAt(int i, char c);\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param i DOCUMENT ME!\r
-     * @param c DOCUMENT ME!\r
-     * @param chop DOCUMENT ME!\r
-     */\r
-    public void insertCharAt(int i, char c, boolean chop);\r
 \r
     /**\r
      * DOCUMENT ME!\r
@@ -256,4 +248,10 @@ public interface SequenceI
 \r
     public void addAlignmentAnnotation(AlignmentAnnotation annotation);\r
 \r
+    public SequenceGroup getHiddenSequences();\r
+\r
+    public void addHiddenSequence(SequenceI seq);\r
+\r
+    public void showHiddenSequence(SequenceI seq);\r
+\r
 }\r