X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;fp=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=829bafb0d4ecf3c781003fcefe5cf9499aec7f5d;hb=7daa352541756250e798b0d7479b2bc7f807de0b;hp=372ecd7d6dd52c5aa807e3f2c86555f1bd72c012;hpb=5e8e52baf2ac3df23cc3180a44425d0e05334b03;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 372ecd7..829bafb 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -39,6 +39,8 @@ public class FeatureRenderer
     Color resBoxColour;
     Graphics graphics;
     float transparency = 1.0f;
+    FontMetrics fm;
+    int charOffset;
 
     // The following vector holds the features which are
     // to be added, in the correct order or rendering
@@ -75,6 +77,8 @@ public class FeatureRenderer
       if (seq.getDatasetSequence().getSequenceFeatures() == null)
         return;
 
+      fm = g.getFontMetrics();
+
       if (transparency != 1)
       {
         Graphics2D g2 = (Graphics2D) g;
@@ -83,88 +87,52 @@ public class FeatureRenderer
                 AlphaComposite.SRC_OVER, transparency));
       }
 
-      Enumeration e, e2;
       String type;
       SequenceFeature sf;
-      if (featuresDisplayed != null)
-      {
-           e = featuresDisplayed.elements();
-           while(e.hasMoreElements())
-           {
-             type = e.nextElement().toString();
-             e2 = seq.getDatasetSequence().getSequenceFeatures().elements();
-             while(e2.hasMoreElements())
-             {
-               sf = (SequenceFeature) e2.nextElement();
-               if(!type.equals(sf.getType() ) )
-                  continue;
-
-               if (sf.getBegin() > seq.getEnd())
-                  continue;
-
-               renderFeature(g,seq,
-                         seq.findIndex(sf.getBegin()) - 1,
-                         seq.findIndex(sf.getEnd()) - 1,
-                         type,start,end,x1,y1,width,height);
-             }
-           }
-      }
-      else
+      if (featuresDisplayed == null || featuresDisplayed.size()==0)
+        findAllFeatures();
+
+      Enumeration e = featuresDisplayed.elements(), e2;
+
+      // Loop through each visible feature
+      while (e.hasMoreElements())
       {
-        e = seq.getDatasetSequence().getSequenceFeatures().elements();
-        while (e.hasMoreElements())
+
+        type = e.nextElement().toString();
+        e2 = seq.getDatasetSequence().getSequenceFeatures().elements();
+        // loop through all features in sequence to find
+        // current feature to render
+          while (e2.hasMoreElements())
         {
-          sf = (SequenceFeature) e.nextElement();
-          type = sf.getType();
+
+          sf = (SequenceFeature) e2.nextElement();
+          if (!type.equals(sf.getType()))
+            continue;
 
           if (sf.getBegin() > seq.getEnd())
-          {
             continue;
-          }
 
-          renderFeature(g,seq,
-                        seq.findIndex(sf.getBegin()) - 1,
-                        seq.findIndex(sf.getEnd()) - 1,
-                        type,start,end,x1,y1,width,height);
+          if (type.equals("disulfide bond"))
+          {
+
+            renderFeature(g, seq,
+                          seq.findIndex(sf.getBegin()) - 1,
+                          seq.findIndex(sf.getBegin()) - 1,
+                          type, start, end, x1, y1, width, height);
+            renderFeature(g, seq,
+                          seq.findIndex(sf.getEnd()) - 1,
+                          seq.findIndex(sf.getEnd()) - 1,
+                          type, start, end, x1, y1, width, height);
 
+          }
+          else
+            renderFeature(g, seq,
+                          seq.findIndex(sf.getBegin()) - 1,
+                          seq.findIndex(sf.getEnd()) - 1,
+                          type, start, end, x1, y1, width, height);
         }
       }
 
-   /*       while (e.hasMoreElements())
-        {
-            SequenceFeature sf=null;
-            if(featuresDisplayed!=null)
-            {
-              e2 = seq.getDatasetSequence().getSequenceFeatures().elements();
-              type = e.nextElement().toString();
-              while(e2.hasMoreElements())
-              {
-                sf = (SequenceFeature) e2.nextElement();
-                if(sf.getType().equals(type))
-                  break;
-                else
-                  sf = null;
-              }
-            }
-            else
-            {
-              sf = (SequenceFeature) e.nextElement();
-              type = sf.getType();
-            }
-
-            if(sf==null)
-              continue;
-
-
-            if (sf.getBegin() > seq.getEnd())
-            {
-                continue;
-            }
-
-            int fstart = seq.findIndex(sf.getBegin()) - 1;
-            int fend = seq.findIndex(sf.getEnd()) - 1;
-*/
-
         if(transparency!=1.0f)
         {
           Graphics2D g2 = (Graphics2D) g;
@@ -174,9 +142,11 @@ public class FeatureRenderer
         }
     }
 
+
     void renderFeature(Graphics g, SequenceI seq,
                        int fstart, int fend, String type, int start, int end, int x1, int y1, int width, int height)
     {
+
       if (((fstart <= end) && (fend >= start)))
       {
           if (fstart < start)
@@ -186,48 +156,53 @@ public class FeatureRenderer
 
           if (fend >= end)
           {
-              fend = end;
+            fend = end;
           }
-
-          if (fstart == fend)
+          for (int i = fstart; i <= fend; i++)
           {
-              g.setColor(getColour(type));
-              g.fillRoundRect((fstart - start) * width, y1, width,
-                  height, 4, 4);
-              g.setColor(Color.white);
-
-              char s = seq.getSequence().charAt(fstart);
-              FontMetrics fm = g.getFontMetrics();
-              int charOffset = (width - fm.charWidth(s)) / 2;
-              int pady = height / 5;
-              g.drawString(String.valueOf(s),
-                  charOffset + x1 + (width * (fstart - start)),
-                  (y1 + height) - pady);
+            char s = seq.getSequence().charAt(i);
+
+            if (jalview.util.Comparison.isGap(s))
+            {
+              continue;
+            }
+
+            g.setColor(getColour(type));
+
+            g.fillRect( (i - start) * width, y1, width, height);
+
+            g.setColor(Color.white);
+
+            charOffset = (width - fm.charWidth(s)) / 2;
+            g.drawString(String.valueOf(s),
+                         charOffset + x1 + (width * (i - start)),
+                         (y1 + height) - height/5);//pady = height / 5;
           }
-          else
+        }
+    }
+
+    void findAllFeatures()
+    {
+      Vector features = new Vector();
+      SequenceFeature sf;
+      featuresDisplayed = new Vector();
+      Enumeration e;
+      for (int i = 0; i < av.alignment.getHeight(); i++)
+      {
+        features = av.alignment.getSequenceAt(i).getDatasetSequence().
+            getSequenceFeatures();
+        if (features == null)
+          continue;
+
+        e = features.elements();
+        while (e.hasMoreElements())
+        {
+          sf = (SequenceFeature) e.nextElement();
+          if (!featuresDisplayed.contains(sf.getType()))
           {
-              for (int i = fstart; i <= fend; i++)
-              {
-                  char s = seq.getSequence().charAt(i);
-
-                  if (jalview.util.Comparison.isGap(s))
-                  {
-                      continue;
-                  }
-
-                  g.setColor(getColour(type));
-                  g.fillRect((i - start) * width, y1, width, height);
-
-                  g.setColor(Color.white);
-
-                  FontMetrics fm = g.getFontMetrics();
-                  int charOffset = (width - fm.charWidth(s)) / 2;
-                  int pady = height / 5;
-                  g.drawString(String.valueOf(s),
-                      charOffset + x1 + (width * (i - start)),
-                      (y1 + height) - pady);
-              }
+            featuresDisplayed.addElement(sf.getType());
           }
+        }
       }
     }
 
@@ -276,7 +251,7 @@ public class FeatureRenderer
       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("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));
@@ -288,8 +263,7 @@ public class FeatureRenderer
       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("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));