X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=f95179203d2bf94f45d5b4d2f0572c1838a32935;hb=f2d10e204281911d5da924b7aa4cdb93102a4e24;hp=904e1e2d05bda4359742efa1b52566e57505cbb1;hpb=ba2255324de03f4f66ed1883c105404c4c97c66b;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 904e1e2..f951792 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -85,6 +85,8 @@ public class AlignViewport
     // JBPNote Prolly only need this in the applet version.
     private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
 
+    boolean ignoreGapsInConsensusCalculation = false;
+
     /**
      * Creates a new AlignViewport object.
      *
@@ -106,52 +108,48 @@ public class AlignViewport
      */
     public void updateFromPreferences()
     {
-        showFullId = Preferences.showFullId;
-        showAnnotation = Preferences.showAnnotation;
-        showConservation = Preferences.showConservation;
-        showQuality = Preferences.showQuality;
-        showIdentity = Preferences.showIdentity;
-        showFullId = Preferences.showFullId;
+      showFullId = Cache.getDefault("SHOW_FULL_ID", true);
+      showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+      showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
 
-        String fontName = Preferences.fontName;
-        String fontStyle = Preferences.fontStyle;
-        String fontSize = Cache.getProperty("FONT_SIZE");
+      showQuality = Cache.getDefault("SHOW_QUALITY", true);
+      showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
 
-        if ((fontName != null) && (fontStyle != null) && (fontSize != null))
-        {
-            int style = 0;
+       String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
+       String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
+       String fontSize = Cache.getDefault("FONT_SIZE", "10");
 
-            if (fontStyle.equals("bold"))
-            {
-                style = 1;
-            }
-            else if (fontStyle.equals("italic"))
-            {
-                style = 2;
-            }
+       int style = 0;
 
-            setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
-        }
-        else
-        {
-            setFont(font);
-        }
+       if (fontStyle.equals("bold"))
+       {
+         style = 1;
+       }
+       else if (fontStyle.equals("italic"))
+       {
+         style = 2;
+       }
+
+       setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+
+
+       alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
 
-        alignment.setGapCharacter(Preferences.gapSymbol);
 
         // We must set conservation and consensus before setting colour,
         // as Blosum and Clustal require this to be done
         updateConservation();
         updateConsensus();
 
-        if (Preferences.defaultColour != null)
+        if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
         {
-            globalColourScheme = ColourSchemeProperty.getColour(alignment,
-                    Preferences.defaultColour);
+          globalColourScheme = ColourSchemeProperty.getColour(alignment,
+              jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
 
             if (globalColourScheme instanceof UserColourScheme)
             {
                 globalColourScheme = UserDefinedColours.loadDefaultColours();
+                ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
             }
 
             if (globalColourScheme != null)
@@ -161,6 +159,8 @@ public class AlignViewport
         }
     }
 
+
+
     /**
      * DOCUMENT ME!
      *
@@ -307,18 +307,19 @@ public class AlignViewport
         {
             hash = (Hashtable) vconsensus.elementAt(i);
 
-            float value = Float.parseFloat(hash.get("maxCount").toString());
-            value /= Float.parseFloat(hash.get("size").toString());
-
-            value *= 100;
+            float value = 0;
+            if(ignoreGapsInConsensusCalculation)
+              value = ((Float)hash.get("pid_nogaps")).floatValue();
+            else
+              value = ((Float)hash.get("pid_gaps")).floatValue();
 
-            String maxRes = hash.get("maxResidue") + " ";
-            String mouseOver = hash.get("maxResidue") + " ";
+            String maxRes = hash.get("maxResidue").toString();
+            String mouseOver = hash.get("maxResidue")+" ";
 
-            if (maxRes.length() > 2)
+            if (maxRes.length() > 1)
             {
                 mouseOver = "[" + maxRes + "] ";
-                maxRes = "+ ";
+                maxRes = "+";
             }
 
             mouseOver += ((int) value + "%");
@@ -339,6 +340,9 @@ public class AlignViewport
         {
             consensus.annotations = annotations;
         }
+
+        if(globalColourScheme!=null)
+          globalColourScheme.setConsensus(vconsensus);
     }
 
     /**
@@ -998,7 +1002,7 @@ public class AlignViewport
     }
 
     /**
-     * DOCUMENT ME!
+     * Property change listener for changes in alignment
      *
      * @param listener DOCUMENT ME!
      */
@@ -1020,7 +1024,7 @@ public class AlignViewport
     }
 
     /**
-     * DOCUMENT ME!
+     * Property change listener for changes in alignment
      *
      * @param prop DOCUMENT ME!
      * @param oldvalue DOCUMENT ME!
@@ -1030,4 +1034,20 @@ public class AlignViewport
     {
         changeSupport.firePropertyChange(prop, oldvalue, newvalue);
     }
+
+    public void setIgnoreGapsConsensus(boolean b)
+    {
+      ignoreGapsInConsensusCalculation = b;
+      updateConsensus();
+      if(globalColourScheme!=null)
+      {
+        globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
+      }
+
+    }
+
+    public boolean getIgnoreGapsConsensus()
+    {
+     return ignoreGapsInConsensusCalculation;
+    }
 }