X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=7c6032716287cee54db9b9818b34690d2d0628c2;hb=72baa5e02d3f71f1c0259072fdbd0b2bf8250e6c;hp=6fbdee858b359fdd7321ef94a7b8efd49734baf7;hpb=add2f44022857817d1bb9a502f0e37627a34c5d8;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 6fbdee8..7c60327 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -41,17 +41,21 @@ public class FeatureRenderer
     FontMetrics fm;
     int charOffset;
 
+    Hashtable featureColours = new Hashtable();
+
+
     // A higher level for grouping features of a
    // particular type
     Hashtable featureGroups = null;
 
-
     // This is actually an Integer held in the hashtable,
     // Retrieved using the key feature type
     Object currentColour;
 
     String [] renderOrder;
 
+    boolean newFeatureAdded = false;
+
 
     /**
      * Creates a new FeatureRenderer object.
@@ -61,7 +65,6 @@ public class FeatureRenderer
     public FeatureRenderer(AlignViewport av)
     {
         this.av = av;
-        initColours();
     }
 
     public void transferSettings(FeatureRenderer fr)
@@ -76,33 +79,30 @@ public class FeatureRenderer
     boolean offscreenRender = false;
     public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
     {
-      int seqindex = av.alignment.findIndex(seq);
-
       return new Color( findFeatureColour (initialCol.getRGB(),
-                        seqindex, res ));
+                        seq, res ));
     }
 
     /**
-     * This is used by the Molecule Viewer to get the accurate colour
-     * of the rendered sequence
+     * This is used by the Molecule Viewer and Overview to
+     * get the accurate colourof the rendered sequence
      */
-    public int findFeatureColour(int initialCol, int seqIndex, int column)
+    public int findFeatureColour(int initialCol, SequenceI seq, int column)
     {
       if(!av.showSequenceFeatures)
         return initialCol;
 
-      if(seqIndex!=lastSequenceIndex)
+      if(seq!=lastSeq)
       {
-        lastSequence = av.alignment.getSequenceAt(seqIndex);
-        lastSequenceIndex = seqIndex;
-        sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();
+        lastSeq = seq;
+        sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
         if(sequenceFeatures==null)
           return initialCol;
 
         sfSize = sequenceFeatures.length;
       }
 
-      if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
+      if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
         return Color.white.getRGB();
 
 
@@ -120,7 +120,7 @@ public class FeatureRenderer
       {
         offscreenImage.setRGB(0,0,initialCol);
         drawSequence(offscreenImage.getGraphics(),
-                     lastSequence,
+                     lastSeq,
                      column,column,0);
 
         return offscreenImage.getRGB(0,0);
@@ -128,8 +128,8 @@ public class FeatureRenderer
       else
       {
         drawSequence(null,
-                    lastSequence,
-                    lastSequence.findPosition(column),
+                    lastSeq,
+                    lastSeq.findPosition(column),
                     -1, -1);
 
         if (currentColour == null)
@@ -157,8 +157,7 @@ public class FeatureRenderer
      */
    // String type;
    // SequenceFeature sf;
-    int lastSequenceIndex=-1;
-    SequenceI lastSequence;
+    SequenceI lastSeq;
     SequenceFeature [] sequenceFeatures;
     int sfSize, sfindex, spos, epos;
 
@@ -174,7 +173,9 @@ public class FeatureRenderer
         fm = g.getFontMetrics();
 
 
-      if (av.featuresDisplayed == null || renderOrder==null)
+      if (av.featuresDisplayed == null
+          || renderOrder==null
+          || newFeatureAdded)
        {
          findAllFeatures();
          if(av.featuresDisplayed.size()<1)
@@ -184,9 +185,9 @@ public class FeatureRenderer
          sfSize = sequenceFeatures.length;
        }
 
-       if(lastSequence==null || seq!=lastSequence)
+       if(lastSeq==null || seq!=lastSeq)
       {
-        lastSequence = seq;
+        lastSeq = seq;
         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
         sfSize = sequenceFeatures.length;
       }
@@ -202,8 +203,8 @@ public class FeatureRenderer
 
       if(!offscreenRender)
       {
-        spos = lastSequence.findPosition(start);
-        epos = lastSequence.findPosition(end);
+        spos = lastSeq.findPosition(start);
+        epos = lastSeq.findPosition(end);
       }
 
 
@@ -211,6 +212,7 @@ public class FeatureRenderer
       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
        {
         type =  renderOrder[renderIndex];
+
         if(!av.featuresDisplayed.containsKey(type))
           continue;
 
@@ -319,7 +321,7 @@ public class FeatureRenderer
 
             g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);
 
-            if(offscreenRender)
+            if(offscreenRender || !av.validCharWidth)
               continue;
 
             g.setColor(Color.white);
@@ -332,9 +334,24 @@ public class FeatureRenderer
       }
     }
 
-    void findAllFeatures()
+    int count = 0;
+    synchronized public void featuresAdded()
     {
-      av.featuresDisplayed = new Hashtable();
+      newFeatureAdded = true;
+      findAllFeatures();
+      newFeatureAdded = false;
+    }
+
+   synchronized void findAllFeatures()
+   {
+      jalview.schemes.UserColourScheme ucs = new
+          jalview.schemes.UserColourScheme();
+
+      if(av.featuresDisplayed==null)
+        av.featuresDisplayed = new Hashtable();
+
+      av.featuresDisplayed.clear();
+
       Vector allfeatures = new Vector();
       for (int i = 0; i < av.alignment.getHeight(); i++)
       {
@@ -349,9 +366,23 @@ public class FeatureRenderer
         {
           if (!av.featuresDisplayed.containsKey(features[index].getType()))
           {
-            av.featuresDisplayed.put(features[index].getType(),
-                                  new Integer( getColour(features[index].getType()).getRGB()) );
-            allfeatures.addElement(features[index].getType());
+            if(!(features[index].begin == 0 && features[index].end ==0))
+            {
+              // If beginning and end are 0, the feature is for the whole sequence
+              // and we don't want to render the feature in the normal way
+
+              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());
+            }
           }
           index++;
         }
@@ -369,9 +400,11 @@ public class FeatureRenderer
 
     public Color getColour(String featureType)
     {
-      return (Color)featureColours.get(featureType);
+      Color colour = (Color)featureColours.get(featureType);
+      return colour;
     }
 
+
     public void addNewFeature(String name, Color col, String group)
     {
 
@@ -427,47 +460,7 @@ public class FeatureRenderer
 
     }
 
-    Hashtable featureColours = new Hashtable();
-    void initColours()
-    {
-      featureColours.put("active site", new Color(255, 75, 0));
-      featureColours.put("binding site", new Color(245, 85, 0));
-      featureColours.put("calcium-binding region", new Color(235, 95, 0));
-      featureColours.put("chain", new Color(225, 105, 0));
-      featureColours.put("coiled-coil region", new Color(215, 115, 0));
-      featureColours.put("compositionally biased region", new Color(205, 125, 0));
-      featureColours.put("cross-link", new Color(195, 135, 0));
-      featureColours.put("disulfide bond", new Color(230,230,0));
-      featureColours.put("DNA-binding region", new Color(175, 155, 0));
-      featureColours.put("domain", new Color(165, 165, 0));
-      featureColours.put("glycosylation site", new Color(155, 175, 0));
-      featureColours.put("helix", new Color(145, 185, 0));
-      featureColours.put("initiator methionine", new Color(135, 195, 5));
-      featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));
-      featureColours.put("metal ion-binding site", new Color(115, 215, 25));
-      featureColours.put("modified residue", new Color(105, 225, 35));
-      featureColours.put("mutagenesis site", new Color(95, 235, 45));
-      featureColours.put("non-consecutive residues", new Color(85, 245, 55));
-      featureColours.put("non-terminal residue", new Color(75, 255, 65));
-      featureColours.put("nucleotide phosphate-binding region",new Color(65, 245, 75));
-      featureColours.put("peptide", new Color(55, 235, 85));
-      featureColours.put("propeptide", new Color(45, 225, 95));
-      featureColours.put("region of interest", new Color(35, 215, 105));
-      featureColours.put("repeat", new Color(25, 205, 115));
-      featureColours.put("selenocysteine", new Color(15, 195, 125));
-      featureColours.put("sequence conflict", new Color(5, 185, 135));
-      featureColours.put("sequence variant", new Color(0, 175, 145));
-      featureColours.put("short sequence motif", new Color(0, 165, 155));
-      featureColours.put("signal peptide", new Color(0, 155, 165));
-      featureColours.put("site", new Color(0, 145, 175));
-      featureColours.put("splice variant", new Color(0, 135, 185));
-      featureColours.put("strand", new Color(0, 125, 195));
-      featureColours.put("topological domain", new Color(0, 115, 205));
-      featureColours.put("transit peptide", new Color(0, 105, 215));
-      featureColours.put("transmembrane region", new Color(0, 95, 225));
-      featureColours.put("turn", new Color(0, 85, 235));
-      featureColours.put("unsure residue", new Color(0, 75, 245));
-      featureColours.put("zinc finger region", new Color(0, 65, 255));
-    }
+
+
 
 }