X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=b06cace9cd24551ad5567c96480b89a7af39e8bc;hb=e4dca3706ab423352c26ac100f3ca5a3e7c3d2c4;hp=fdbd7eb9eb656f35fcc86531af46e7de4aa399fc;hpb=bd56b8fb21d730b15bb759c529990d244cafbe37;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index fdbd7eb..b06cace 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)
@@ -174,7 +177,9 @@ 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)
@@ -211,6 +216,7 @@ public class FeatureRenderer
       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
        {
         type =  renderOrder[renderIndex];
+
         if(!av.featuresDisplayed.containsKey(type))
           continue;
 
@@ -332,9 +338,24 @@ 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 +370,23 @@ 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 +404,11 @@ 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 +464,7 @@ 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));
-    }
+
+
 
 }