X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=551dea7d93d6e77bcbdc7e59104324b7af3f0d69;hb=df9b85c1cf39894039018499fe802406cc37f209;hp=0b504be57b500af56ebac59cb8f562b70a763d2a;hpb=be9cbda993c0cb66255c0eb8274ee2bfa9199220;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 0b504be..551dea7 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,3 +1,4 @@
+
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -34,11 +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;
@@ -48,6 +55,10 @@ public class FeatureRenderer
     FontMetrics fm;
     int charOffset;
 
+    float transparency = 1f;
+
+    TransparencySetter transparencySetter = null;
+
     /**
      * Creates a new FeatureRenderer object.
      *
@@ -56,12 +67,23 @@ public class FeatureRenderer
     public FeatureRenderer(AlignViewport av)
     {
         this.av = av;
-        initColours();
+
+        if(!System.getProperty("java.version").startsWith("1.1"))
+             transparencySetter = new TransparencySetter();
+    }
+
+
+    public void transferSettings(FeatureRenderer fr)
+    {
+      renderOrder = fr.renderOrder;
+      featureGroups = fr.featureGroups;
+      featureColours = fr.featureColours;
     }
 
 
     public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
     {
+      overview = true;
       if(!av.showSequenceFeatures)
         return initialCol;
 
@@ -150,6 +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)
        {
@@ -187,10 +213,7 @@ public class FeatureRenderer
           if (!sequenceFeatures[sfindex].type.equals(type))
             continue;
 
-          if(sequenceFeatures[sfindex]==null)
-          {
-          }
-          else  if (featureGroups != null
+          if (featureGroups != null
               && sequenceFeatures[sfindex].featureGroup != null
               &&
               featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
@@ -207,9 +230,8 @@ public class FeatureRenderer
 
           if (overview)
           {
-
-            if (sequenceFeatures[sfindex].begin - 1 <= start &&
-                sequenceFeatures[sfindex].end + 1 >= start)
+            if (sequenceFeatures[sfindex].begin <= start &&
+                sequenceFeatures[sfindex].end >= start)
             {
               currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
                   type);
@@ -240,9 +262,12 @@ public class FeatureRenderer
                           getColour(sequenceFeatures[sfindex].type),
                           start, end, y1, width, height);
 
-
         }
+      }
 
+      if(transparencySetter!=null && g!=null)
+      {
+        transparencySetter.setTransparency(g, 1.0f);
       }
     }
 
@@ -278,6 +303,9 @@ public class FeatureRenderer
 
             g.fillRect( (i - start) * width, y1, width, height);
 
+            if(!av.validCharWidth)
+              continue;
+
             g.setColor(Color.white);
             charOffset = (width - fm.charWidth(s)) / 2;
             g.drawString(String.valueOf(s),
@@ -366,52 +394,19 @@ 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));
     }
+  }
 
-}