X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=66a9bc247f631c8b26ecdb7105ba04828b261bf9;hb=2ad64bdec4782e3fbfa3b5867a1aa7d1571629fa;hp=900de839e519dfba43a70d156243e9ba9e368bf9;hpb=2df9d1cb0e8975c84486ddc4728062e377adbb1f;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 900de83..66a9bc2 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -35,11 +35,17 @@ public class FeatureRenderer
 {
     AlignViewport av;
 
+    Hashtable featureColours = new Hashtable();
 
     // A higher level for grouping features of a
     // particular type
     Hashtable featureGroups = null;
 
+    // Holds web links for feature groups and feature types
+    // in the form label|link
+    Hashtable featureLinks = null;
+
+
     // This is actually an Integer held in the hashtable,
     // Retrieved using the key feature type
     Object currentColour;
@@ -49,6 +55,10 @@ public class FeatureRenderer
     FontMetrics fm;
     int charOffset;
 
+    float transparency = 1f;
+
+    TransparencySetter transparencySetter = null;
+
     /**
      * Creates a new FeatureRenderer object.
      *
@@ -57,7 +67,9 @@ public class FeatureRenderer
     public FeatureRenderer(AlignViewport av)
     {
         this.av = av;
-        initColours();
+
+        if(!System.getProperty("java.version").startsWith("1.1"))
+             transparencySetter = new TransparencySetter();
     }
 
 
@@ -160,6 +172,10 @@ public class FeatureRenderer
           || seq.getSequenceFeatures().length==0)
         return;
 
+      if(transparencySetter!=null && g!=null)
+      {
+        transparencySetter.setTransparency(g, transparency);
+      }
 
       if (av.featuresDisplayed == null || renderOrder==null)
        {
@@ -248,6 +264,11 @@ public class FeatureRenderer
 
         }
       }
+
+      if(transparencySetter!=null && g!=null)
+      {
+        transparencySetter.setTransparency(g, 1.0f);
+      }
     }
 
 
@@ -297,6 +318,9 @@ 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++)
@@ -311,6 +335,14 @@ 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());
@@ -373,52 +405,19 @@ public class FeatureRenderer
             renderOrder[data.length - i - 1] = type;
           }
     }
+}
 
-    Hashtable featureColours = new Hashtable();
-    void initColours()
+  class TransparencySetter
+  {
+    void setTransparency(Graphics g, float value)
     {
-      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(185, 145, 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));
+      Graphics2D g2 = (Graphics2D) g;
+      g2.setComposite(
+          AlphaComposite.getInstance(
+              AlphaComposite.SRC_OVER, value));
     }
+  }
 
-}