X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=cb977d0de63c59c6d8ecbd45473feef06bbc75dd;hb=e25f63a72efddff9e071abdeff0ae5599431e4f8;hp=24d50d446e8c8bbf2febcd17eccafa92cc08789c;hpb=98eb909d0a4fe04ff6ad93f71086f1127fe4a530;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 24d50d4..cb977d0 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -43,7 +43,7 @@ public class AlignViewport
     int endRes;
     int startSeq;
     int endSeq;
-    boolean showFullId = false;
+    boolean showJVSuffix = true;
     boolean showText = true;
     boolean showColourText = false;
     boolean showBoxes = true;
@@ -61,8 +61,7 @@ public class AlignViewport
     SequenceGroup selectionGroup;
     int charHeight;
     int charWidth;
-    int chunkWidth;
-    int chunkHeight;
+    int wrappedWidth;
     Font font = new Font("SansSerif", Font.PLAIN, 10);
     AlignmentI alignment;
     ColumnSelection colSel = new ColumnSelection();
@@ -72,6 +71,12 @@ public class AlignViewport
     boolean scaleAboveWrapped = false;
     boolean scaleLeftWrapped = true;
     boolean scaleRightWrapped = true;
+    boolean hasHiddenColumns = false;
+
+    // The following vector holds the features which are
+    // currently visible, in the correct order or rendering
+    Hashtable featuresDisplayed = null;
+
 
     /** DOCUMENT ME!! */
     public Vector vconsensus;
@@ -87,6 +92,17 @@ public class AlignViewport
 
     boolean ignoreGapsInConsensusCalculation = false;
 
+    boolean isDataset = false;
+
+    boolean antiAlias = false;
+
+
+    public AlignViewport(AlignmentI al, boolean dataset)
+    {
+      isDataset = dataset;
+      setAlignment(al);
+      init();
+    }
     /**
      * Creates a new AlignViewport object.
      *
@@ -95,20 +111,19 @@ public class AlignViewport
     public AlignViewport(AlignmentI al)
     {
         setAlignment(al);
+        init();
+    }
+
+    void init()
+    {
         this.startRes = 0;
-        this.endRes = al.getWidth() - 1;
+        this.endRes = alignment.getWidth() - 1;
         this.startSeq = 0;
-        this.endSeq = al.getHeight() - 1;
+        this.endSeq = alignment.getHeight() - 1;
 
-        updateFromPreferences();
-    }
+      antiAlias = Cache.getDefault("ANTI_ALIAS", false);
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateFromPreferences()
-    {
-      showFullId = Cache.getDefault("SHOW_FULL_ID", true);
+      showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
       showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
       showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
 
@@ -138,8 +153,11 @@ public class AlignViewport
 
         // We must set conservation and consensus before setting colour,
         // as Blosum and Clustal require this to be done
-        updateConservation();
-        updateConsensus();
+        if(vconsensus==null && !isDataset)
+        {
+          updateConservation();
+          updateConsensus();
+        }
 
         if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
         {
@@ -166,16 +184,24 @@ public class AlignViewport
      *
      * @param b DOCUMENT ME!
      */
-    public void showSequenceFeatures(boolean b)
+    public void setShowSequenceFeatures(boolean b)
     {
         showSequenceFeatures = b;
     }
 
+    public boolean getShowSequenceFeatures()
+    {
+      return showSequenceFeatures;
+    }
+
     /**
      * DOCUMENT ME!
      */
     public void updateConservation()
     {
+      if(alignment.isNucleotide())
+          return;
+
       try{
         Conservation cons = new jalview.analysis.Conservation("All",
             jalview.schemes.ResidueProperties.propHash, 3,
@@ -253,7 +279,7 @@ public class AlignViewport
                                                  ConsPercGaps + "% gaps",
                                                  annotations, 0f, // cons.qualityRange[0].floatValue(),
                                                  11f, // cons.qualityRange[1].floatValue()
-                                                 1);
+                                                 AlignmentAnnotation.BAR_GRAPH);
 
           if (showConservation)
           {
@@ -265,7 +291,7 @@ public class AlignViewport
                                             qannotations,
                                             cons.qualityRange[0].floatValue(),
                                             cons.qualityRange[1].floatValue(),
-                                            1);
+                                            AlignmentAnnotation.BAR_GRAPH);
 
           if (showQuality)
           {
@@ -278,10 +304,18 @@ public class AlignViewport
           quality.annotations = qannotations;
           quality.graphMax = cons.qualityRange[1].floatValue();
         }
-      }catch(OutOfMemoryError error)
+      }
+      catch (OutOfMemoryError error)
       {
-        System.out.println("Out of memory calculating conservation.");
+        javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+            "Out of memory calculating conservation!!"
+            +
+            "\nSee help files for increasing Java Virtual Machine memory."
+            , "Out of memory",
+            javax.swing.JOptionPane.WARNING_MESSAGE);
+        System.out.println("Conservation calculation: " + error);
         System.gc();
+
       }
     }
 
@@ -341,7 +375,7 @@ public class AlignViewport
         if (consensus == null)
         {
           consensus = new AlignmentAnnotation("Consensus", "PID",
-                                              annotations, 0f, 100f, 1);
+                                              annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);
 
           if (showIdentity)
           {
@@ -358,7 +392,13 @@ public class AlignViewport
 
       }catch(OutOfMemoryError error)
       {
-        System.out.println("Out of memory calculating consensus.");
+        javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+            "Out of memory calculating consensus!!"
+            +
+            "\nSee help files for increasing Java Virtual Machine memory."
+            , "Out of memory",
+            javax.swing.JOptionPane.WARNING_MESSAGE);
+        System.out.println("Consensus calculation: " + error);
         System.gc();
       }
 
@@ -616,9 +656,9 @@ public class AlignViewport
      *
      * @param w DOCUMENT ME!
      */
-    public void setChunkWidth(int w)
+    public void setWrappedWidth(int w)
     {
-        this.chunkWidth = w;
+        this.wrappedWidth = w;
     }
 
     /**
@@ -626,30 +666,11 @@ public class AlignViewport
      *
      * @return DOCUMENT ME!
      */
-    public int getChunkWidth()
+    public int getWrappedWidth()
     {
-        return chunkWidth;
+        return wrappedWidth;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param h DOCUMENT ME!
-     */
-    public void setChunkHeight(int h)
-    {
-        this.chunkHeight = h;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getChunkHeight()
-    {
-        return chunkHeight;
-    }
 
     /**
      * DOCUMENT ME!
@@ -916,9 +937,9 @@ public class AlignViewport
      *
      * @return DOCUMENT ME!
      */
-    public boolean getShowFullId()
+    public boolean getShowJVSuffix()
     {
-        return showFullId;
+        return showJVSuffix;
     }
 
     /**
@@ -926,11 +947,12 @@ public class AlignViewport
      *
      * @param b DOCUMENT ME!
      */
-    public void setShowFullId(boolean b)
+    public void setShowJVSuffix(boolean b)
     {
-        showFullId = b;
+        showJVSuffix = b;
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -1060,4 +1082,14 @@ public class AlignViewport
     {
      return ignoreGapsInConsensusCalculation;
     }
+
+    public void setDataset(boolean b)
+    {
+      isDataset = b;
+    }
+
+    public boolean isDataset()
+    {
+      return isDataset;
+    }
 }