Don't parse input id, leave it as it is

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 24d50d4..7f86753 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -43,7 +43,7 @@ public class AlignViewport
     int endRes;\r
     int startSeq;\r
     int endSeq;\r
-    boolean showFullId = false;\r
+    boolean showJVSuffix = true;\r
     boolean showText = true;\r
     boolean showColourText = false;\r
     boolean showBoxes = true;\r
@@ -61,8 +61,7 @@ public class AlignViewport
     SequenceGroup selectionGroup;\r
     int charHeight;\r
     int charWidth;\r
-    int chunkWidth;\r
-    int chunkHeight;\r
+    int wrappedWidth;\r
     Font font = new Font("SansSerif", Font.PLAIN, 10);\r
     AlignmentI alignment;\r
     ColumnSelection colSel = new ColumnSelection();\r
@@ -87,6 +86,15 @@ public class AlignViewport
 \r
     boolean ignoreGapsInConsensusCalculation = false;\r
 \r
+    boolean isDataset = false;\r
+\r
+\r
+    public AlignViewport(AlignmentI al, boolean dataset)\r
+    {\r
+      isDataset = dataset;\r
+      setAlignment(al);\r
+      init();\r
+    }\r
     /**\r
      * Creates a new AlignViewport object.\r
      *\r
@@ -95,20 +103,17 @@ public class AlignViewport
     public AlignViewport(AlignmentI al)\r
     {\r
         setAlignment(al);\r
-        this.startRes = 0;\r
-        this.endRes = al.getWidth() - 1;\r
-        this.startSeq = 0;\r
-        this.endSeq = al.getHeight() - 1;\r
-\r
-        updateFromPreferences();\r
+        init();\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     */\r
-    public void updateFromPreferences()\r
+    void init()\r
     {\r
-      showFullId = Cache.getDefault("SHOW_FULL_ID", true);\r
+        this.startRes = 0;\r
+        this.endRes = alignment.getWidth() - 1;\r
+        this.startSeq = 0;\r
+        this.endSeq = alignment.getHeight() - 1;\r
+\r
+      showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);\r
       showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);\r
       showConservation = Cache.getDefault("SHOW_CONSERVATION", true);\r
 \r
@@ -138,8 +143,11 @@ public class AlignViewport
 \r
         // We must set conservation and consensus before setting colour,\r
         // as Blosum and Clustal require this to be done\r
-        updateConservation();\r
-        updateConsensus();\r
+        if(vconsensus==null && !isDataset)\r
+        {\r
+          updateConservation();\r
+          updateConsensus();\r
+        }\r
 \r
         if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)\r
         {\r
@@ -176,6 +184,9 @@ public class AlignViewport
      */\r
     public void updateConservation()\r
     {\r
+      if(alignment.isNucleotide())\r
+          return;\r
+\r
       try{\r
         Conservation cons = new jalview.analysis.Conservation("All",\r
             jalview.schemes.ResidueProperties.propHash, 3,\r
@@ -278,10 +289,18 @@ public class AlignViewport
           quality.annotations = qannotations;\r
           quality.graphMax = cons.qualityRange[1].floatValue();\r
         }\r
-      }catch(OutOfMemoryError error)\r
+      }\r
+      catch (OutOfMemoryError error)\r
       {\r
-        System.out.println("Out of memory calculating conservation.");\r
+        javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+            "Out of memory calculating conservation!!"\r
+            +\r
+            "\nSee help files for increasing Java Virtual Machine memory."\r
+            , "Out of memory",\r
+            javax.swing.JOptionPane.WARNING_MESSAGE);\r
+        System.out.println("Conservation calculation: " + error);\r
         System.gc();\r
+\r
       }\r
     }\r
 \r
@@ -358,7 +377,13 @@ public class AlignViewport
 \r
       }catch(OutOfMemoryError error)\r
       {\r
-        System.out.println("Out of memory calculating consensus.");\r
+        javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+            "Out of memory calculating consensus!!"\r
+            +\r
+            "\nSee help files for increasing Java Virtual Machine memory."\r
+            , "Out of memory",\r
+            javax.swing.JOptionPane.WARNING_MESSAGE);\r
+        System.out.println("Consensus calculation: " + error);\r
         System.gc();\r
       }\r
 \r
@@ -616,9 +641,9 @@ public class AlignViewport
      *\r
      * @param w DOCUMENT ME!\r
      */\r
-    public void setChunkWidth(int w)\r
+    public void setWrappedWidth(int w)\r
     {\r
-        this.chunkWidth = w;\r
+        this.wrappedWidth = w;\r
     }\r
 \r
     /**\r
@@ -626,30 +651,11 @@ public class AlignViewport
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public int getChunkWidth()\r
+    public int getWrappedWidth()\r
     {\r
-        return chunkWidth;\r
+        return wrappedWidth;\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param h DOCUMENT ME!\r
-     */\r
-    public void setChunkHeight(int h)\r
-    {\r
-        this.chunkHeight = h;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public int getChunkHeight()\r
-    {\r
-        return chunkHeight;\r
-    }\r
 \r
     /**\r
      * DOCUMENT ME!\r
@@ -916,9 +922,9 @@ public class AlignViewport
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public boolean getShowFullId()\r
+    public boolean getShowJVSuffix()\r
     {\r
-        return showFullId;\r
+        return showJVSuffix;\r
     }\r
 \r
     /**\r
@@ -926,11 +932,12 @@ public class AlignViewport
      *\r
      * @param b DOCUMENT ME!\r
      */\r
-    public void setShowFullId(boolean b)\r
+    public void setShowJVSuffix(boolean b)\r
     {\r
-        showFullId = b;\r
+        showJVSuffix = b;\r
     }\r
 \r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -1060,4 +1067,14 @@ public class AlignViewport
     {\r
      return ignoreGapsInConsensusCalculation;\r
     }\r
+\r
+    public void setDataset(boolean b)\r
+    {\r
+      isDataset = b;\r
+    }\r
+\r
+    public boolean isDataset()\r
+    {\r
+      return isDataset;\r
+    }\r
 }\r