Colours in viewport

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index fc46386..ca9b447 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -87,7 +87,7 @@ public class AlignViewport
   boolean showHiddenMarkers = true;\r
 \r
 \r
-  public Vector vconsensus;\r
+  public Hashtable [] hconsensus;\r
   AlignmentAnnotation consensus;\r
   AlignmentAnnotation conservation;\r
   AlignmentAnnotation quality;\r
@@ -102,6 +102,8 @@ public class AlignViewport
 \r
   jalview.bin.JalviewLite applet;\r
 \r
+  Hashtable sequenceColours;\r
+\r
   boolean MAC = false;\r
 \r
   public AlignViewport(AlignmentI al, JalviewLite applet)\r
@@ -179,7 +181,7 @@ public class AlignViewport
         globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);\r
         if (globalColourScheme != null)\r
         {\r
-          globalColourScheme.setConsensus(vconsensus);\r
+          globalColourScheme.setConsensus(hconsensus);\r
         }\r
       }\r
 \r
@@ -305,37 +307,28 @@ public class AlignViewport
 \r
   public void updateConsensus()\r
   {\r
-    Annotation[] annotations = new Annotation[alignment.getWidth()];\r
-\r
     // this routine prevents vconsensus becoming a new object each time\r
     // consenus is calculated. Important for speed of Blosum62\r
     // and PID colouring of alignment\r
-    if (vconsensus == null)\r
-    {\r
-      vconsensus = alignment.getAAFrequency();\r
-    }\r
-    else\r
-    {\r
-      Vector temp = alignment.getAAFrequency();\r
-      vconsensus.removeAllElements();\r
-      Enumeration e = temp.elements();\r
-      while (e.hasMoreElements())\r
-      {\r
-        vconsensus.addElement(e.nextElement());\r
-      }\r
-    }\r
-    Hashtable hash = null;\r
-    for (int i = 0; i < alignment.getWidth(); i++)\r
+    int aWidth = alignment.getWidth();\r
+\r
+    Annotation[] annotations = new Annotation[aWidth];\r
+\r
+    hconsensus = new Hashtable[aWidth];\r
+    AAFrequency.calculate(alignment.getSequencesArray(),\r
+                          0, aWidth,\r
+                          hconsensus);\r
+\r
+    for (int i = 0; i < aWidth; i++)\r
     {\r
-      hash = (Hashtable) vconsensus.elementAt(i);\r
       float value = 0;\r
       if(ignoreGapsInConsensusCalculation)\r
-        value = ((Float)hash.get("pid_nogaps")).floatValue();\r
+        value = ((Float)hconsensus[i].get(AAFrequency.PID_NOGAPS)).floatValue();\r
       else\r
-        value = ((Float)hash.get("pid_gaps")).floatValue();\r
+        value = ((Float)hconsensus[i].get(AAFrequency.PID_GAPS)).floatValue();\r
 \r
-      String maxRes = hash.get("maxResidue").toString();\r
-      String mouseOver = hash.get("maxResidue") + " ";\r
+      String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();\r
+      String mouseOver = maxRes;\r
       if (maxRes.length() > 1)\r
       {\r
         mouseOver = "[" + maxRes + "] ";\r
@@ -363,7 +356,7 @@ public class AlignViewport
     }\r
 \r
     if(globalColourScheme!=null)\r
-          globalColourScheme.setConsensus(vconsensus);\r
+          globalColourScheme.setConsensus(hconsensus);\r
 \r
   }\r
   /**\r
@@ -974,8 +967,10 @@ public class AlignViewport
     // object. Refactoring of Cigar and alignment view representation should\r
     // be done to remove redundancy.\r
     CigarArray aligview = getViewAsCigars(selectedOnly);\r
-    if (aligview!=null)\r
-      return new AlignmentView(aligview);\r
+    if (aligview!=null) {\r
+      return new AlignmentView(aligview,\r
+          (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);\r
+    }\r
     return null;\r
   }\r
   /**\r
@@ -1070,5 +1065,23 @@ public class AlignViewport
     showHiddenMarkers = show;\r
   }\r
 \r
+  public Color getSequenceColour(SequenceI seq)\r
+  {\r
+    if (sequenceColours == null || !sequenceColours.containsKey(seq))\r
+      return Color.white;\r
+    else\r
+      return (Color) sequenceColours.get(seq);\r
+  }\r
+\r
+  public void setSequenceColour(SequenceI seq, Color col)\r
+  {\r
+    if (sequenceColours == null)\r
+      sequenceColours = new Hashtable();\r
+\r
+    if (col == null)\r
+      sequenceColours.remove(seq);\r
+    else\r
+      sequenceColours.put(seq, col);\r
+  }\r
 \r
 }\r