X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=c126e246d8910bc7437e62254d098076fcc30896;hb=acc9fa6c42fcdde3d55b483f1dea91e0058be06e;hp=405fe9871999c467a6520e040d3a26affc52bf4b;hpb=391968dd70ca76090306df9b5852bbef10ab4ede;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 405fe98..c126e24 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -24,6 +24,8 @@ import java.awt.*;
 
 import java.util.*;
 
+import java.awt.image.*;
+
 
 /**
  * DOCUMENT ME!
@@ -39,18 +41,19 @@ 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;
 
-
     /**
      * Creates a new FeatureRenderer object.
      *
@@ -59,70 +62,80 @@ public class FeatureRenderer
     public FeatureRenderer(AlignViewport av)
     {
         this.av = av;
-        initColours();
     }
 
-
-    public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+    public void transferSettings(FeatureRenderer fr)
     {
-      if(!av.showSequenceFeatures)
-        return initialCol;
-
-        lastSequence = seq;
-        sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();
-        if(sequenceFeatures==null)
-          return initialCol;
-
-        sfSize = sequenceFeatures.length;
-
-      if(jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))
-        return Color.white;
-
-      currentColour = null;
-
-      drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1, -1, -1);
-
-      if(currentColour==null)
-        return initialCol;
+      renderOrder = fr.renderOrder;
+      featureGroups = fr.featureGroups;
+      featureColours = fr.featureColours;
+      transparency =  fr.transparency;
+    }
 
-      return new Color( ((Integer)currentColour).intValue() );
+    BufferedImage offscreenImage;
+    boolean offscreenRender = false;
+    public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
+    {
+      return new Color( findFeatureColour (initialCol.getRGB(),
+                        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
      */
-
-    boolean overview = false;
-
-    int white = Color.white.getRGB();
-    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();
 
+
+      //Only bother making an offscreen image if transparency is applied
+      if(transparency!=1.0f && offscreenImage==null)
+      {
+        offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);
+      }
+
       currentColour = null;
 
-      drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1);
+      offscreenRender = true;
+
+      if(offscreenImage!=null)
+      {
+        offscreenImage.setRGB(0,0,initialCol);
+        drawSequence(offscreenImage.getGraphics(),
+                     lastSeq,
+                     column,column,0);
+
+        return offscreenImage.getRGB(0,0);
+      }
+      else
+      {
+        drawSequence(null,
+                    lastSeq,
+                    lastSeq.findPosition(column),
+                    -1, -1);
+
+        if (currentColour == null)
+          return initialCol;
+        else
+          return  ((Integer)currentColour).intValue();
+      }
 
-      if(currentColour==null)
-        return initialCol;
 
-      return  ((Integer)currentColour).intValue();
     }
 
 
@@ -141,33 +154,36 @@ public class FeatureRenderer
      */
    // String type;
    // SequenceFeature sf;
-    int lastSequenceIndex=-1;
-    SequenceI lastSequence;
+    SequenceI lastSeq;
     SequenceFeature [] sequenceFeatures;
     int sfSize, sfindex, spos, epos;
 
     public void drawSequence(Graphics g, SequenceI seq,
-                             int start, int end, int y1, int width, int height)
+                             int start, int end, int y1)
     {
-      if (   seq.getDatasetSequence().getSequenceFeatures() == null
+      if ( seq.getDatasetSequence().getSequenceFeatures() == null
           || seq.getDatasetSequence().getSequenceFeatures().length==0)
         return;
 
-
       if(g!=null)
         fm = g.getFontMetrics();
 
 
-      if (av.featuresDisplayed == null || renderOrder==null)
+      if (av.featuresDisplayed == null
+          || renderOrder==null
+          || newFeatureAdded)
        {
          findAllFeatures();
+         if(av.featuresDisplayed.size()<1)
+           return;
+
          sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
          sfSize = sequenceFeatures.length;
        }
 
-       if(lastSequence==null || seq!=lastSequence)
+       if(lastSeq==null || seq!=lastSeq)
       {
-        lastSequence = seq;
+        lastSeq = seq;
         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
         sfSize = sequenceFeatures.length;
       }
@@ -181,21 +197,29 @@ public class FeatureRenderer
                 AlphaComposite.SRC_OVER, transparency));
       }
 
-      if(!overview)
+      if(!offscreenRender)
       {
-        spos = lastSequence.findPosition(start);
-        epos = lastSequence.findPosition(end);
+        spos = lastSeq.findPosition(start);
+        epos = lastSeq.findPosition(end);
       }
 
+
       String type;
       for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
        {
         type =  renderOrder[renderIndex];
 
+        if(!av.featuresDisplayed.containsKey(type))
+          continue;
+
         // loop through all features in sequence to find
         // current feature to render
         for (sfindex = 0; sfindex < sfSize; sfindex++)
         {
+          if(sequenceFeatures.length<=sfindex)
+          {
+            continue;
+          }
           if (!sequenceFeatures[sfindex].type.equals(type))
             continue;
 
@@ -210,20 +234,18 @@ public class FeatureRenderer
             continue;
           }
 
-          if (!overview && (sequenceFeatures[sfindex].getBegin() > epos
+          if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
                             || sequenceFeatures[sfindex].getEnd() < spos))
             continue;
 
-          if (overview)
+          if (offscreenRender && offscreenImage==null)
           {
-
-            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);
+                 type);
             }
-
           }
           else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
           {
@@ -233,13 +255,13 @@ public class FeatureRenderer
                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
                           new Color( ( (Integer) av.featuresDisplayed.get(
                 sequenceFeatures[sfindex].type)).intValue()),
-                          start, end, y1, width, height);
+                          start, end, y1);
             renderFeature(g, seq,
                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,
                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,
                           new Color( ( (Integer) av.featuresDisplayed.get(
                 sequenceFeatures[sfindex].type)).intValue()),
-                          start, end, y1, width, height);
+                          start, end, y1);
 
           }
           else
@@ -247,7 +269,7 @@ public class FeatureRenderer
                           seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
                           seq.findIndex(sequenceFeatures[sfindex].end) - 1,
                           getColour(sequenceFeatures[sfindex].type),
-                          start, end, y1, width, height);
+                          start, end, y1);
 
 
         }
@@ -267,7 +289,7 @@ public class FeatureRenderer
     char s;
     int i;
     void renderFeature(Graphics g, SequenceI seq,
-                       int fstart, int fend, Color featureColour, int start, int end,  int y1, int width, int height)
+                       int fstart, int fend, Color featureColour, int start, int end,  int y1)
     {
 
       if (((fstart <= end) && (fend >= start)))
@@ -281,7 +303,7 @@ public class FeatureRenderer
         {
           fend = end;
         }
-
+          int pady = (y1 + av.charHeight) - av.charHeight / 5;
           for (i = fstart; i <= fend; i++)
           {
             s = seq.getSequence().charAt(i);
@@ -293,25 +315,54 @@ public class FeatureRenderer
 
             g.setColor(featureColour);
 
-            g.fillRect( (i - start) * width, y1, width, height);
+            g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);
+
+            if(offscreenRender || !av.validCharWidth)
+              continue;
 
             g.setColor(Color.white);
-            charOffset = (width - fm.charWidth(s)) / 2;
+            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
             g.drawString(String.valueOf(s),
-                         charOffset + (width * (i - start)),
-                         (y1 + height) - height / 5); //pady = height / 5;
+                         charOffset + (av.charWidth * (i - start)),
+                         pady);
 
           }
       }
     }
 
-    void findAllFeatures()
+
+    boolean newFeatureAdded = false;
+
+    public void featuresAdded()
     {
-      av.featuresDisplayed = new Hashtable();
+      findAllFeatures();
+    }
+
+   boolean findingFeatures = false;
+   synchronized void findAllFeatures()
+   {
+      newFeatureAdded = false;
+
+      if(findingFeatures)
+      {
+        newFeatureAdded = true;
+        return;
+      }
+
+      findingFeatures = true;
+      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++)
       {
-        SequenceFeature [] features = av.alignment.getSequenceAt(i).getDatasetSequence().
-            getSequenceFeatures();
+        SequenceFeature [] features
+            = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
 
         if (features == null)
           continue;
@@ -321,37 +372,58 @@ public class FeatureRenderer
         {
           if (!av.featuresDisplayed.containsKey(features[index].getType()))
           {
-            av.featuresDisplayed.put(features[index].getType(),
-                                  new Integer( getColour(features[index].getType()).getRGB()) );
+            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++;
         }
       }
 
-      renderOrder = new String[av.featuresDisplayed.size()];
-      Enumeration en = av.featuresDisplayed.keys();
-      int i = 0;
+      renderOrder = new String[allfeatures.size()];
+      Enumeration en = allfeatures.elements();
+      int i = allfeatures.size()-1;
       while(en.hasMoreElements())
       {
         renderOrder[i] = en.nextElement().toString();
-        i++;
+        i--;
       }
+
+      findingFeatures = false;
     }
 
     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)
+
+    public void addNewFeature(String name, Color col, String group)
     {
 
       setColour(name, col);
       if(av.featuresDisplayed==null)
         av.featuresDisplayed = new Hashtable();
 
+      if(group == null)
+        group = "NOGROUP";
 
-      av.featuresDisplayed.put(name, "NOGROUP");
+      av.featuresDisplayed.put(name, new Integer(col.getRGB()));
     }
 
     public void setColour(String featureType, Color col)
@@ -374,65 +446,29 @@ public class FeatureRenderer
       // The feature table will display high priority
       // features at the top, but theses are the ones
       // we need to render last, so invert the data
-      av.featuresDisplayed.clear();
+      if(av.featuresDisplayed!=null)
+        av.featuresDisplayed.clear();
+      else
+        av.featuresDisplayed = new Hashtable();
 
       renderOrder = new String[data.length];
 
-      if(data.length>0)
-      for(int i=data.length-1; i>-1; i--)
-      {
-       String type = data[i][0].toString();
-       setColour(type, (Color)data[i][1]);
-       if( ((Boolean)data[i][2]).booleanValue() )
-       {
-         av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
-       }
-       renderOrder[i] = type;
-      }
+      if (data.length > 0)
+        for (int i = 0; i < data.length; i++)
+        {
+          String type = data[i][0].toString();
+          setColour(type, (Color) data[i][1]);
+          if ( ( (Boolean) data[i][2]).booleanValue())
+          {
+            av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
+          }
 
-    }
+          renderOrder[data.length - i - 1] = type;
+        }
 
-    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));
     }
 
+
+
+
 }