image is panel size

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

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