X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=481a657501204114037cf42065ec41e75555c0a7;hb=245ddd4612033edc65de15acb93ac9c22912a828;hp=e9078dd6b6b4311b2a2a593b2f125ca3e4380003;hpb=de468b0bf50850a89c6a8a7acfa4ff5b689ffed1;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index e9078dd..481a657 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -36,6 +36,9 @@ public class AlignViewport
   int startSeq;
   int endSeq;
 
+
+  boolean cursorMode = false;
+
   boolean showJVSuffix = true;
   boolean showText = true;
   boolean showColourText = false;
@@ -60,6 +63,7 @@ public class AlignViewport
   int wrappedWidth;
 
   Font font = new Font("SansSerif", Font.PLAIN, 10);
+  boolean validCharWidth = true;
   AlignmentI alignment;
 
   ColumnSelection colSel = new ColumnSelection();
@@ -73,11 +77,18 @@ public class AlignViewport
   boolean scaleLeftWrapped = true;
   boolean scaleRightWrapped = true;
 
+  // The following vector holds the features which are
+ // currently visible, in the correct order or rendering
+  Hashtable featuresDisplayed = null;
+
+
   public Vector vconsensus;
   AlignmentAnnotation consensus;
   AlignmentAnnotation conservation;
   AlignmentAnnotation quality;
 
+  boolean autocalculateConsensus = true;
+
   public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
 
   private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
@@ -146,6 +157,11 @@ public class AlignViewport
     showSequenceFeatures = b;
   }
 
+  public boolean getShowSequenceFeatures()
+  {
+    return showSequenceFeatures;
+  }
+
 
   public void updateConservation()
   {
@@ -221,7 +237,7 @@ public class AlignViewport
                                              annotations,
                                              0f, // cons.qualityRange[0].floatValue(),
                                              11f, // cons.qualityRange[1].floatValue()
-                                             AlignmentAnnotation.LINE_GRAPH);
+                                             AlignmentAnnotation.BAR_GRAPH);
       if (showConservation)
       {
         alignment.addAnnotation(conservation);
@@ -231,7 +247,7 @@ public class AlignViewport
                                         qannotations,
                                         cons.qualityRange[0].floatValue(),
                                         cons.qualityRange[1].floatValue(),
-                                        AlignmentAnnotation.LINE_GRAPH);
+                                        AlignmentAnnotation.BAR_GRAPH);
       if (showQuality)
       {
         alignment.addAnnotation(quality);
@@ -294,7 +310,7 @@ public class AlignViewport
     if (consensus == null)
     {
       consensus = new AlignmentAnnotation("Consensus",
-                                          "PID", annotations, 0f, 100f, AlignmentAnnotation.LINE_GRAPH);
+                                          "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       if (showConsensus)
       {
         alignment.addAnnotation(consensus);
@@ -407,12 +423,17 @@ public class AlignViewport
     return endSeq;
   }
 
+  java.awt.Frame nullFrame;
   public void setFont(Font f)
   {
     font = f;
-    java.awt.Frame temp = new java.awt.Frame();
-    temp.addNotify();
-    java.awt.FontMetrics fm = temp.getGraphics().getFontMetrics(font);
+    if(nullFrame == null)
+    {
+      nullFrame = new java.awt.Frame();
+      nullFrame.addNotify();
+    }
+
+    java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
     setCharHeight(fm.getHeight());
     setCharWidth(fm.charWidth('M'));
   }