X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=31ccf69ac35c60bb7de8863d7f7a662a4743d4e2;hb=51bbc79eee43d019f9fcb14b7aa6e0a0c2c99f76;hp=df8c6ea9cc4b552dd486854624fb6bf79efa97da;hpb=5da6500eacd4ab3a0e5b156b2e47ae9467343555;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index df8c6ea..31ccf69 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -36,11 +36,12 @@ import java.util.*;
 public class SequenceGroup
 {
     String groupName;
+    String description;
     Conservation conserve;
     Vector aaFrequency;
-    boolean displayBoxes;
-    boolean displayText;
-    boolean colourText;
+    boolean displayBoxes = true;
+    boolean displayText = true;
+    boolean colourText = true;
     private Vector sequences = new Vector();
     int width = -1;
 
@@ -49,17 +50,17 @@ public class SequenceGroup
     int startRes = 0;
     int endRes = 0;
     Color outlineColour = Color.black;
+    public int thresholdTextColour = 0;
+    public Color textColour = Color.black;
+    public Color textColour2 = Color.white;
+
 
     /**
      * Creates a new SequenceGroup object.
      */
     public SequenceGroup()
     {
-        groupName = "Group";
-        this.displayBoxes = true;
-        this.displayText = true;
-        this.colourText = false;
-        cs = null;
+        groupName = "JGroup:"+this.hashCode();
     }
 
     /**
@@ -89,30 +90,6 @@ public class SequenceGroup
         recalcConservation();
     }
 
-    /**
-     * Creates a new SequenceGroup object.
-     *
-     * @param groupName DOCUMENT ME!
-     * @param scheme DOCUMENT ME!
-     * @param displayBoxes DOCUMENT ME!
-     * @param displayText DOCUMENT ME!
-     * @param colourText DOCUMENT ME!
-     * @param start DOCUMENT ME!
-     * @param end DOCUMENT ME!
-     */
-    public SequenceGroup(String groupName, ColourSchemeI scheme,
-        boolean displayBoxes, boolean displayText, boolean colourText,
-        int start, int end)
-    {
-        this.groupName = groupName;
-        this.displayBoxes = displayBoxes;
-        this.displayText = displayText;
-        this.colourText = colourText;
-        this.cs = scheme;
-        startRes = start;
-        endRes = end;
-    }
-
     public SequenceI [] getSelectionAsNewSequences(AlignmentI align)
     {
       int iSize = sequences.size();
@@ -174,25 +151,27 @@ public class SequenceGroup
       return eres;
     }
 
-    public Vector getSequences(boolean includeHidden)
+    public Vector getSequences(Hashtable hiddenReps)
     {
-      if(!includeHidden)
+      if(hiddenReps == null)
         return sequences;
       else
       {
         Vector allSequences = new Vector();
-        SequenceI seq;
+        SequenceI seq, seq2;
         for (int i = 0; i < sequences.size(); i++)
         {
           seq = (SequenceI) sequences.elementAt(i);
           allSequences.addElement(seq);
-          if (seq.getHiddenSequences() != null)
+          if (hiddenReps.containsKey(seq) )
           {
-            for (int h = 0; h < seq.getHiddenSequences().getSize(false); h++)
+            SequenceGroup hsg = (SequenceGroup)hiddenReps.get(seq);
+            for (int h = 0; h < hsg.getSize(); h++)
             {
-              allSequences.addElement(
-                  seq.getHiddenSequences().getSequenceAt(h)
-                  );
+              seq2 = hsg.getSequenceAt(h);
+              if (seq2 != seq
+                  && !allSequences.contains(seq2))
+                allSequences.addElement(seq2);
             }
           }
         }
@@ -201,9 +180,9 @@ public class SequenceGroup
       }
     }
 
-    public SequenceI[] getSequencesAsArray(boolean includeHidden)
+    public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
     {
-      Vector tmp = getSequences(includeHidden);
+      Vector tmp = getSequences(hiddenReps);
       if(tmp==null)
         return null;
       SequenceI [] result = new SequenceI[tmp.size()];
@@ -279,6 +258,11 @@ public class SequenceGroup
         return groupName;
     }
 
+    public String getDescription()
+    {
+      return description;
+    }
+
     /**
      * DOCUMENT ME!
      *
@@ -289,6 +273,11 @@ public class SequenceGroup
         groupName = name;
     }
 
+    public void setDescription(String desc)
+    {
+      description = desc;
+    }
+
     /**
      * DOCUMENT ME!
      *
@@ -448,24 +437,9 @@ public class SequenceGroup
      *
      * @return DOCUMENT ME!
      */
-    public int getSize(boolean includeHidden)
+    public int getSize()
     {
-      if(!includeHidden)
         return sequences.size();
-      else
-      {
-        int total = sequences.size();
-        SequenceI seq;
-        for (int i = 0; i < sequences.size(); i++)
-        {
-          seq = (SequenceI) sequences.elementAt(i);
-          if (seq.getHiddenSequences() != null)
-          {
-            total += seq.getHiddenSequences().getSize(false);
-          }
-        }
-        return total;
-      }
     }
 
     /**