X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=d4ba5eae69dad4b57ff26efb783afb33910bd380;hb=ea49c8f1b0d681ec87547fc4055eb35a1165aee3;hp=088d4273b8397893f8fd4fea13df5e64b43218c1;hpb=1deb6329192c4750c104d4da8c70f9cb6e3c5a42;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 088d427..d4ba5ea 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -61,8 +61,9 @@ public class AlignViewport
     SequenceGroup selectionGroup;
     int charHeight;
     int charWidth;
+    boolean validCharWidth;
     int wrappedWidth;
-    Font font = new Font("SansSerif", Font.PLAIN, 10);
+    Font font;
     AlignmentI alignment;
     ColumnSelection colSel = new ColumnSelection();
     int threshold;
@@ -71,12 +72,22 @@ public class AlignViewport
     boolean scaleAboveWrapped = false;
     boolean scaleLeftWrapped = true;
     boolean scaleRightWrapped = true;
+    boolean hasHiddenColumns = false;
+    boolean hasHiddenRows = false;
+
+    boolean cursorMode = 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;
     AlignmentAnnotation consensus;
     AlignmentAnnotation conservation;
     AlignmentAnnotation quality;
+    boolean autoCalculateConsensus = true;
 
     /** DOCUMENT ME!! */
     public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
@@ -90,6 +101,8 @@ public class AlignViewport
 
     boolean antiAlias = false;
 
+    boolean padGaps = false;
+
 
     public AlignViewport(AlignmentI al, boolean dataset)
     {
@@ -124,6 +137,10 @@ public class AlignViewport
       showQuality = Cache.getDefault("SHOW_QUALITY", true);
       showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
 
+      autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+
+      padGaps = Cache.getDefault("PAD_GAPS", false);
+
        String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
        String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
        String fontSize = Cache.getDefault("FONT_SIZE", "10");
@@ -178,11 +195,16 @@ 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!
      */
@@ -296,12 +318,19 @@ public class AlignViewport
       }
       catch (OutOfMemoryError error)
       {
-        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);
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            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();
 
@@ -381,12 +410,20 @@ public class AlignViewport
 
       }catch(OutOfMemoryError error)
       {
-        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);
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Out of memory calc45ulating 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();
       }
@@ -588,6 +625,7 @@ public class AlignViewport
         java.awt.FontMetrics fm = c.getFontMetrics(font);
         setCharHeight(fm.getHeight());
         setCharWidth(fm.charWidth('M'));
+        validCharWidth = true;
     }
 
     /**
@@ -1064,7 +1102,6 @@ public class AlignViewport
       {
         globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
       }
-
     }
 
     public boolean getIgnoreGapsConsensus()
@@ -1081,4 +1118,23 @@ public class AlignViewport
     {
       return isDataset;
     }
+
+    public void hideSequence(SequenceI seq)
+    {
+      alignment.getHiddenSequences().hideSequence(seq);
+      hasHiddenRows = true;
+    }
+
+    public void showSequence(int index)
+    {
+      alignment.getHiddenSequences().showSequence(index);
+
+      if(alignment.getHiddenSequences().getSize()<1)
+        hasHiddenRows = false;
+    }
+
+    public int adjustForHiddenSeqs(int alignmentIndex)
+    {
+      return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+    }
 }