X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=7f8d89d0ec620e648632aa0cc7f77f33957f77fe;hb=559b96a91b710f3f2e116790c9cf7e3aa6c76766;hp=0f9f39308d8aae4b82fd0a0d6951e01bbaf7a6e3;hpb=1236f3fd041e880ca6f48bb79c5934bd3fd03b71;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 0f9f393..7f8d89d 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -78,6 +78,7 @@ public class FeatureRenderer
       renderOrder = fr.renderOrder;
       featureGroups = fr.featureGroups;
       featureColours = fr.featureColours;
+      transparency =  fr.transparency;
     }
 
 
@@ -99,7 +100,7 @@ public class FeatureRenderer
 
       currentColour = null;
 
-      drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1, -1, -1);
+      drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1);
 
       if(currentColour==null)
         return initialCol;
@@ -136,7 +137,7 @@ public class FeatureRenderer
 
       currentColour = null;
 
-      drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1);
+      drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1);
 
       if(currentColour==null)
         return initialCol;
@@ -166,7 +167,7 @@ public class FeatureRenderer
     int sfSize, sfindex, spos, epos;
 
     public void drawSequence(Graphics g, SequenceI seq,
-                             int start, int end, int y1, int width, int height)
+                             int start, int end, int y1)
     {
       if (   seq.getSequenceFeatures() == null
           || seq.getSequenceFeatures().length==0)
@@ -246,13 +247,13 @@ public class FeatureRenderer
                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
                           new Color( ( (Integer) av.featuresDisplayed.get(
                 sequenceFeatures[sfindex].type)).intValue()),
-                          start, end, y1, width, height);
+                          start, end, y1);
             renderFeature(g, seq,
                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,
                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,
                           new Color( ( (Integer) av.featuresDisplayed.get(
                 sequenceFeatures[sfindex].type)).intValue()),
-                          start, end, y1, width, height);
+                          start, end, y1);
 
           }
           else
@@ -260,7 +261,7 @@ public class FeatureRenderer
                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,
                           getColour(sequenceFeatures[sfindex].type),
-                          start, end, y1, width, height);
+                          start, end, y1);
 
         }
       }
@@ -275,7 +276,7 @@ public class FeatureRenderer
     char s;
     int i;
     void renderFeature(Graphics g, SequenceI seq,
-                       int fstart, int fend, Color featureColour, int start, int end,  int y1, int width, int height)
+                       int fstart, int fend, Color featureColour, int start, int end,  int y1)
     {
 
       if (((fstart <= end) && (fend >= start)))
@@ -301,16 +302,16 @@ public class FeatureRenderer
 
             g.setColor(featureColour);
 
-            g.fillRect( (i - start) * width, y1, width, height);
+            g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
 
             if(!av.validCharWidth)
               continue;
 
             g.setColor(Color.white);
-            charOffset = (width - fm.charWidth(s)) / 2;
+            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
             g.drawString(String.valueOf(s),
-                         charOffset + (width * (i - start)),
-                         (y1 + height) - height / 5); //pady = height / 5;
+                         charOffset + (av.charWidth * (i - start)),
+                         (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;
 
           }
       }
@@ -318,6 +319,9 @@ public class FeatureRenderer
 
     void findAllFeatures()
     {
+      jalview.schemes.UserColourScheme ucs = new
+          jalview.schemes.UserColourScheme();
+
       av.featuresDisplayed = new Hashtable();
       Vector allfeatures = new Vector();
       for (int i = 0; i < av.alignment.getHeight(); i++)
@@ -332,6 +336,14 @@ public class FeatureRenderer
         {
           if (!av.featuresDisplayed.containsKey(features[index].getType()))
           {
+            if (getColour(features[index].getType()) == null)
+            {
+              featureColours.put(features[index].getType(),
+                                 ucs.createColourFromName(features[index].
+                  getType()));
+            }
+
+
             av.featuresDisplayed.put(features[index].getType(),
                                   new Integer( getColour(features[index].getType()).getRGB()) );
             allfeatures.addElement(features[index].getType());