X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=1bc1b515bc8439254bf29b060e768141784996f8;hb=bf2bf43c980b18a26b724d2a2d51dddc1a79a185;hp=2e0c1cb6306f3844279d967e666d6ba3d1e6d237;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 2e0c1cb..1bc1b51 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;
@@ -53,13 +56,14 @@ public class AlignViewport
   boolean conservationColourSelected = false;
   boolean abovePIDThreshold = false;
 
-  SequenceGroup selectionGroup = new SequenceGroup();
+  SequenceGroup selectionGroup;
 
   int charHeight;
   int charWidth;
   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;
+
+
   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);
@@ -130,14 +141,34 @@ public class AlignViewport
     updateConservation();
     updateConsensus();
 
-    if (applet != null && applet.getParameter("defaultColour") != null)
+
+    if (applet != null)
     {
-      globalColourScheme = ColourSchemeProperty.getColour(alignment,
-          applet.getParameter("defaultColour"));
-      if (globalColourScheme != null)
+      String colour = applet.getParameter("defaultColour");
+
+      if(colour == null)
       {
-        globalColourScheme.setConsensus(vconsensus);
+        colour = applet.getParameter("userDefinedColour");
+        if(colour !=null)
+          colour = "User Defined";
       }
+
+      if(colour != null)
+      {
+        globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
+        if (globalColourScheme != null)
+        {
+          globalColourScheme.setConsensus(vconsensus);
+        }
+      }
+
+      if(applet.getParameter("userDefinedColour")!=null)
+      {
+        ((UserColourScheme)globalColourScheme).parseAppletParameter(
+            applet.getParameter("userDefinedColour"));
+      }
+
+
     }
   }
 
@@ -146,6 +177,11 @@ public class AlignViewport
     showSequenceFeatures = b;
   }
 
+  public boolean getShowSequenceFeatures()
+  {
+    return showSequenceFeatures;
+  }
+
 
   public void updateConservation()
   {
@@ -221,7 +257,7 @@ public class AlignViewport
                                              annotations,
                                              0f, // cons.qualityRange[0].floatValue(),
                                              11f, // cons.qualityRange[1].floatValue()
-                                             1);
+                                             AlignmentAnnotation.BAR_GRAPH);
       if (showConservation)
       {
         alignment.addAnnotation(conservation);
@@ -231,7 +267,7 @@ public class AlignViewport
                                         qannotations,
                                         cons.qualityRange[0].floatValue(),
                                         cons.qualityRange[1].floatValue(),
-                                        1);
+                                        AlignmentAnnotation.BAR_GRAPH);
       if (showQuality)
       {
         alignment.addAnnotation(quality);
@@ -294,7 +330,7 @@ public class AlignViewport
     if (consensus == null)
     {
       consensus = new AlignmentAnnotation("Consensus",
-                                          "PID", annotations, 0f, 100f, 1);
+                                          "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       if (showConsensus)
       {
         alignment.addAnnotation(consensus);
@@ -407,12 +443,17 @@ 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'));
   }