update consensus and conservation are in try catch for out of memory error

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index ea974d5..1efb272 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,4 +1,4 @@
-/*\r
+ /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
@@ -176,9 +176,10 @@ public class AlignViewport
      */\r
     public void updateConservation()\r
     {\r
+      try{\r
         Conservation cons = new jalview.analysis.Conservation("All",\r
-                jalview.schemes.ResidueProperties.propHash, 3,\r
-                alignment.getSequences(), 0, alignment.getWidth() - 1);\r
+            jalview.schemes.ResidueProperties.propHash, 3,\r
+            alignment.getSequences(), 0, alignment.getWidth() - 1);\r
         cons.calculate();\r
         cons.verdict(false, ConsPercGaps);\r
         cons.findQuality();\r
@@ -207,71 +208,80 @@ public class AlignViewport
 \r
         for (int i = 0; i < alWidth; i++)\r
         {\r
-            float value = 0;\r
-\r
-            try\r
+          float value = 0;\r
+\r
+          try\r
+          {\r
+            value = Integer.parseInt(sequence.charAt(i) + "");\r
+          }\r
+          catch (Exception ex)\r
+          {\r
+            if (sequence.charAt(i) == '*')\r
             {\r
-                value = Integer.parseInt(sequence.charAt(i) + "");\r
+              value = 11;\r
             }\r
-            catch (Exception ex)\r
-            {\r
-                if (sequence.charAt(i) == '*')\r
-                {\r
-                    value = 11;\r
-                }\r
 \r
-                if (sequence.charAt(i) == '+')\r
-                {\r
-                    value = 10;\r
-                }\r
+            if (sequence.charAt(i) == '+')\r
+            {\r
+              value = 10;\r
             }\r
-\r
-            float vprop = value - min;\r
-            vprop /= max;\r
-            annotations[i] = new Annotation(sequence.charAt(i) + "",\r
-                    String.valueOf(value), ' ', value,\r
-                    new Color(minR + (maxR * vprop), minG + (maxG * vprop),\r
-                        minB + (maxB * vprop)));\r
-\r
-            // Quality calc\r
-            value = ((Double) cons.quality.get(i)).floatValue();\r
-            vprop = value - qmin;\r
-            vprop /= qmax;\r
-            qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',\r
-                    value,\r
-                    new Color(minR + (maxR * vprop), minG + (maxG * vprop),\r
-                        minB + (maxB * vprop)));\r
+          }\r
+\r
+          float vprop = value - min;\r
+          vprop /= max;\r
+          annotations[i] = new Annotation(sequence.charAt(i) + "",\r
+                                          String.valueOf(value), ' ', value,\r
+                                          new Color(minR + (maxR * vprop),\r
+              minG + (maxG * vprop),\r
+              minB + (maxB * vprop)));\r
+\r
+          // Quality calc\r
+          value = ( (Double) cons.quality.get(i)).floatValue();\r
+          vprop = value - qmin;\r
+          vprop /= qmax;\r
+          qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',\r
+                                           value,\r
+                                           new Color(minR + (maxR * vprop),\r
+              minG + (maxG * vprop),\r
+              minB + (maxB * vprop)));\r
         }\r
 \r
         if (conservation == null)\r
         {\r
-            conservation = new AlignmentAnnotation("Conservation",\r
-                    "Conservation of total alignment less than " +\r
-                    ConsPercGaps + "% gaps", annotations, 0f, // cons.qualityRange[0].floatValue(),\r
-                    11f, // cons.qualityRange[1].floatValue()\r
-                    1);\r
-\r
-            if (showConservation)\r
-            {\r
-                alignment.addAnnotation(conservation);\r
-            }\r
-\r
-            quality = new AlignmentAnnotation("Quality",\r
-                    "Alignment Quality based on Blosum62 scores", qannotations,\r
-                    cons.qualityRange[0].floatValue(),\r
-                    cons.qualityRange[1].floatValue(), 1);\r
-\r
-            if (showQuality)\r
-            {\r
-                alignment.addAnnotation(quality);\r
-            }\r
+          conservation = new AlignmentAnnotation("Conservation",\r
+                                                 "Conservation of total alignment less than " +\r
+                                                 ConsPercGaps + "% gaps",\r
+                                                 annotations, 0f, // cons.qualityRange[0].floatValue(),\r
+                                                 11f, // cons.qualityRange[1].floatValue()\r
+                                                 1);\r
+\r
+          if (showConservation)\r
+          {\r
+            alignment.addAnnotation(conservation);\r
+          }\r
+\r
+          quality = new AlignmentAnnotation("Quality",\r
+                                            "Alignment Quality based on Blosum62 scores",\r
+                                            qannotations,\r
+                                            cons.qualityRange[0].floatValue(),\r
+                                            cons.qualityRange[1].floatValue(),\r
+                                            1);\r
+\r
+          if (showQuality)\r
+          {\r
+            alignment.addAnnotation(quality);\r
+          }\r
         }\r
         else\r
         {\r
-            conservation.annotations = annotations;\r
-            quality.annotations = qannotations;\r
-            quality.graphMax = cons.qualityRange[1].floatValue();\r
+          conservation.annotations = annotations;\r
+          quality.annotations = qannotations;\r
+          quality.graphMax = cons.qualityRange[1].floatValue();\r
         }\r
+      }catch(OutOfMemoryError error)\r
+      {\r
+        System.out.println("Out of memory calculating conservation.");\r
+      }\r
     }\r
 \r
     /**\r
@@ -279,6 +289,7 @@ public class AlignViewport
      */\r
     public void updateConsensus()\r
     {\r
+      try{\r
         Annotation[] annotations = new Annotation[alignment.getWidth()];\r
 \r
         // this routine prevents vconsensus becoming a new object each time\r
@@ -286,63 +297,69 @@ public class AlignViewport
         // and PID colouring of alignment\r
         if (vconsensus == null)\r
         {\r
-            vconsensus = alignment.getAAFrequency();\r
+          vconsensus = alignment.getAAFrequency();\r
         }\r
         else\r
         {\r
-            Vector temp = alignment.getAAFrequency();\r
-            vconsensus.clear();\r
+          Vector temp = alignment.getAAFrequency();\r
+          vconsensus.clear();\r
 \r
-            Enumeration e = temp.elements();\r
+          Enumeration e = temp.elements();\r
 \r
-            while (e.hasMoreElements())\r
-            {\r
-                vconsensus.add(e.nextElement());\r
-            }\r
+          while (e.hasMoreElements())\r
+          {\r
+            vconsensus.add(e.nextElement());\r
+          }\r
         }\r
 \r
         Hashtable hash = null;\r
 \r
         for (int i = 0; i < alignment.getWidth(); i++)\r
         {\r
-            hash = (Hashtable) vconsensus.elementAt(i);\r
+          hash = (Hashtable) vconsensus.elementAt(i);\r
 \r
-            float value = 0;\r
-            if(ignoreGapsInConsensusCalculation)\r
-              value = ((Float)hash.get("pid_nogaps")).floatValue();\r
-            else\r
-              value = ((Float)hash.get("pid_gaps")).floatValue();\r
+          float value = 0;\r
+          if (ignoreGapsInConsensusCalculation)\r
+            value = ( (Float) hash.get("pid_nogaps")).floatValue();\r
+          else\r
+            value = ( (Float) hash.get("pid_gaps")).floatValue();\r
 \r
-            String maxRes = hash.get("maxResidue").toString();\r
-            String mouseOver = hash.get("maxResidue")+" ";\r
+          String maxRes = hash.get("maxResidue").toString();\r
+          String mouseOver = hash.get("maxResidue") + " ";\r
 \r
-            if (maxRes.length() > 1)\r
-            {\r
-                mouseOver = "[" + maxRes + "] ";\r
-                maxRes = "+";\r
-            }\r
+          if (maxRes.length() > 1)\r
+          {\r
+            mouseOver = "[" + maxRes + "] ";\r
+            maxRes = "+";\r
+          }\r
 \r
-            mouseOver += ((int) value + "%");\r
-            annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
+          mouseOver += ( (int) value + "%");\r
+          annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
         }\r
 \r
         if (consensus == null)\r
         {\r
-            consensus = new AlignmentAnnotation("Consensus", "PID",\r
-                    annotations, 0f, 100f, 1);\r
+          consensus = new AlignmentAnnotation("Consensus", "PID",\r
+                                              annotations, 0f, 100f, 1);\r
 \r
-            if (showIdentity)\r
-            {\r
-                alignment.addAnnotation(consensus);\r
-            }\r
+          if (showIdentity)\r
+          {\r
+            alignment.addAnnotation(consensus);\r
+          }\r
         }\r
         else\r
         {\r
-            consensus.annotations = annotations;\r
+          consensus.annotations = annotations;\r
         }\r
 \r
-        if(globalColourScheme!=null)\r
+        if (globalColourScheme != null)\r
           globalColourScheme.setConsensus(vconsensus);\r
+\r
+      }catch(OutOfMemoryError error)\r
+      {\r
+        System.out.println("Out of memory calculating consensus.");\r
+      }\r
+\r
     }\r
 \r
     /**\r