set icon false if raising windows

[jalview.git] / src / jalview / gui / AlignViewport.java

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index b275611..358d00d 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -112,6 +112,15 @@ public class AlignViewport
     Stack historyList = new Stack();
     Stack redoList = new Stack();
 
+    Hashtable sequenceColours;
+
+    int thresholdTextColour = 0;
+    Color textColour = Color.black;
+    Color textColour2 = Color.white;
+
+    boolean rightAlignIds = false;
+
+
     /**
      * Creates a new AlignViewport object.
      *
@@ -149,6 +158,8 @@ public class AlignViewport
       showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
       showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
 
+      rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+
       autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
       padGaps = Cache.getDefault("PAD_GAPS", true);
@@ -1599,5 +1610,24 @@ public class AlignViewport
     }
 
 
+    public Color getSequenceColour(SequenceI seq)
+    {
+      if(sequenceColours==null || !sequenceColours.containsKey(seq))
+        return Color.white;
+      else
+        return (Color)sequenceColours.get(seq);
+    }
+
+    public void setSequenceColour(SequenceI seq, Color col)
+    {
+      if(sequenceColours==null)
+        sequenceColours = new Hashtable();
+
+      if(col == null)
+        sequenceColours.remove(seq);
+      else
+        sequenceColours.put(seq, col);
+    }
+
 
 }