X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=6fbdee858b359fdd7321ef94a7b8efd49734baf7;hb=add2f44022857817d1bb9a502f0e37627a34c5d8;hp=3f332b5fddfe0e32bd1bb09a8794938947d53bab;hpb=d03971168d7f0192862cf5b57602ecf3e341b457;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 3f332b5..6fbdee8 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -40,11 +40,18 @@ public class FeatureRenderer
     float transparency = 1.0f;
     FontMetrics fm;
     int charOffset;
-    boolean drawText = true;
 
-    // The following vector holds the features which are
-    // to be added, in the correct order or rendering
-    Vector featuresDisplayed = null;
+    // 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.
@@ -57,27 +64,81 @@ public class FeatureRenderer
         initColours();
     }
 
+    public void transferSettings(FeatureRenderer fr)
+    {
+      renderOrder = fr.renderOrder;
+      featureGroups = fr.featureGroups;
+      featureColours = fr.featureColours;
+      transparency =  fr.transparency;
+    }
+
+    BufferedImage offscreenImage;
+    boolean offscreenRender = false;
+    public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
+    {
+      int seqindex = av.alignment.findIndex(seq);
+
+      return new Color( findFeatureColour (initialCol.getRGB(),
+                        seqindex, res ));
+    }
+
     /**
      * This is used by the Molecule Viewer to get the accurate colour
      * of the rendered sequence
      */
-    BufferedImage bi;
-    public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+    public int findFeatureColour(int initialCol, int seqIndex, int column)
     {
       if(!av.showSequenceFeatures)
         return initialCol;
 
-      if (bi == null)
-        bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);
+      if(seqIndex!=lastSequenceIndex)
+      {
+        lastSequence = av.alignment.getSequenceAt(seqIndex);
+        lastSequenceIndex = seqIndex;
+        sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();
+        if(sequenceFeatures==null)
+          return initialCol;
+
+        sfSize = sequenceFeatures.length;
+      }
 
-      bi.setRGB(0,0, initialCol.getRGB());
+      if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
+        return Color.white.getRGB();
 
-      drawText = false;
 
-      drawSequence(bi.getGraphics(), seq, i, i, 0, 0, 1, 1);
-      drawText = true;
+      //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;
+
+      offscreenRender = true;
+
+      if(offscreenImage!=null)
+      {
+        offscreenImage.setRGB(0,0,initialCol);
+        drawSequence(offscreenImage.getGraphics(),
+                     lastSequence,
+                     column,column,0);
+
+        return offscreenImage.getRGB(0,0);
+      }
+      else
+      {
+        drawSequence(null,
+                    lastSequence,
+                    lastSequence.findPosition(column),
+                    -1, -1);
+
+        if (currentColour == null)
+          return initialCol;
+        else
+          return  ((Integer)currentColour).intValue();
+      }
+
 
-      return new Color(bi.getRGB(0, 0));
     }
 
 
@@ -94,18 +155,44 @@ public class FeatureRenderer
      * @param width DOCUMENT ME!
      * @param height DOCUMENT ME!
      */
+   // String type;
+   // SequenceFeature sf;
+    int lastSequenceIndex=-1;
+    SequenceI lastSequence;
+    SequenceFeature [] sequenceFeatures;
+    int sfSize, sfindex, spos, epos;
+
     public void drawSequence(Graphics g, SequenceI seq,
-                             int start, int end, int x1, int y1, int width, int height)
+                             int start, int end, int y1)
     {
-
-//System.out.println(start+" "+end+" "+x1+" "+y1);
-      if (seq.getDatasetSequence().getSequenceFeatures() == null
-          || seq.getDatasetSequence().getSequenceFeatures().size()==0)
+      if ( seq.getDatasetSequence().getSequenceFeatures() == null
+          || seq.getDatasetSequence().getSequenceFeatures().length==0)
         return;
 
-      fm = g.getFontMetrics();
 
-      if (transparency != 1)
+      if(g!=null)
+        fm = g.getFontMetrics();
+
+
+      if (av.featuresDisplayed == null || renderOrder==null)
+       {
+         findAllFeatures();
+         if(av.featuresDisplayed.size()<1)
+           return;
+
+         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+         sfSize = sequenceFeatures.length;
+       }
+
+       if(lastSequence==null || seq!=lastSequence)
+      {
+        lastSequence = seq;
+        sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+        sfSize = sequenceFeatures.length;
+      }
+
+
+      if (transparency != 1 && g!=null)
       {
         Graphics2D g2 = (Graphics2D) g;
         g2.setComposite(
@@ -113,53 +200,85 @@ public class FeatureRenderer
                 AlphaComposite.SRC_OVER, transparency));
       }
 
-      String type;
-      SequenceFeature sf;
-      if (featuresDisplayed == null)
-        findAllFeatures();
+      if(!offscreenRender)
+      {
+        spos = lastSequence.findPosition(start);
+        epos = lastSequence.findPosition(end);
+      }
 
-      Enumeration e = featuresDisplayed.elements(), e2;
 
-      // Loop through each visible feature
-      while (e.hasMoreElements())
-      {
+      String type;
+      for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
+       {
+        type =  renderOrder[renderIndex];
+        if(!av.featuresDisplayed.containsKey(type))
+          continue;
 
-        type = e.nextElement().toString();
-        e2 = seq.getDatasetSequence().getSequenceFeatures().elements();
         // loop through all features in sequence to find
         // current feature to render
-          while (e2.hasMoreElements())
+        for (sfindex = 0; sfindex < sfSize; sfindex++)
         {
+          if(sequenceFeatures.length<=sfindex)
+          {
+            continue;
+          }
+          if (!sequenceFeatures[sfindex].type.equals(type))
+            continue;
 
-          sf = (SequenceFeature) e2.nextElement();
-          if (!type.equals(sf.getType()))
+          if (featureGroups != null
+              && sequenceFeatures[sfindex].featureGroup != null
+              &&
+              featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
+              &&
+              ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).
+              booleanValue())
+          {
             continue;
+          }
 
-          if (sf.getBegin() > seq.getEnd())
+          if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
+                            || sequenceFeatures[sfindex].getEnd() < spos))
             continue;
 
-          if (type.equals("disulfide bond"))
+          if (offscreenRender && offscreenImage==null)
+          {
+            if (sequenceFeatures[sfindex].begin <= start &&
+                sequenceFeatures[sfindex].end  >= start)
+            {
+              currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
+                 type);
+            }
+          }
+          else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
           {
 
             renderFeature(g, seq,
-                          seq.findIndex(sf.getBegin()) - 1,
-                          seq.findIndex(sf.getBegin()) - 1,
-                          type, start, end, x1, y1, width, height);
+                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                          new Color( ( (Integer) av.featuresDisplayed.get(
+                sequenceFeatures[sfindex].type)).intValue()),
+                          start, end, y1);
             renderFeature(g, seq,
-                          seq.findIndex(sf.getEnd()) - 1,
-                          seq.findIndex(sf.getEnd()) - 1,
-                          type, start, end, x1, y1, width, height);
+                          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);
 
           }
           else
             renderFeature(g, seq,
-                          seq.findIndex(sf.getBegin()) - 1,
-                          seq.findIndex(sf.getEnd()) - 1,
-                          type, start, end, x1, y1, width, height);
+                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                          seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                          getColour(sequenceFeatures[sfindex].type),
+                          start, end, y1);
+
+
         }
+
       }
 
-        if(transparency!=1.0f)
+        if(transparency!=1.0f && g!=null)
         {
           Graphics2D g2 = (Graphics2D) g;
           g2.setComposite(
@@ -169,69 +288,83 @@ public class FeatureRenderer
     }
 
 
+    char s;
+    int i;
     void renderFeature(Graphics g, SequenceI seq,
-                       int fstart, int fend, String type, int start, int end, int x1, int y1, int width, int height)
+                       int fstart, int fend, Color featureColour, int start, int end,  int y1)
     {
 
       if (((fstart <= end) && (fend >= start)))
       {
-          if (fstart < start)
-          { // fix for if the feature we have starts before the sequence start,
-              fstart = start; // but the feature end is still valid!!
-          }
+        if (fstart < start)
+        { // fix for if the feature we have starts before the sequence start,
+          fstart = start; // but the feature end is still valid!!
+        }
 
-          if (fend >= end)
-          {
-            fend = end;
-          }
-          for (int i = fstart; i <= fend; i++)
+        if (fend >= end)
+        {
+          fend = end;
+        }
+          int pady = (y1 + av.charHeight) - av.charHeight / 5;
+          for (i = fstart; i <= fend; i++)
           {
-            char s = seq.getSequence().charAt(i);
+            s = seq.getSequence().charAt(i);
 
             if (jalview.util.Comparison.isGap(s))
             {
               continue;
             }
 
-            g.setColor(getColour(type));
+            g.setColor(featureColour);
+
+            g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);
 
-            g.fillRect( (i - start) * width, y1, width, height);
+            if(offscreenRender)
+              continue;
+
+            g.setColor(Color.white);
+            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+            g.drawString(String.valueOf(s),
+                         charOffset + (av.charWidth * (i - start)),
+                         pady);
 
-            if(drawText)
-           {
-             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;
-           }
           }
-        }
+      }
     }
 
     void findAllFeatures()
     {
-      Vector features = new Vector();
-      SequenceFeature sf;
-      featuresDisplayed = new Vector();
-      Enumeration e;
+      av.featuresDisplayed = new Hashtable();
+      Vector allfeatures = new Vector();
       for (int i = 0; i < av.alignment.getHeight(); i++)
       {
-        features = av.alignment.getSequenceAt(i).getDatasetSequence().
-            getSequenceFeatures();
+        SequenceFeature [] features
+            = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
+
         if (features == null)
           continue;
 
-        e = features.elements();
-        while (e.hasMoreElements())
+        int index = 0;
+        while (index < features.length)
         {
-          sf = (SequenceFeature) e.nextElement();
-          if (!featuresDisplayed.contains(sf.getType()))
+          if (!av.featuresDisplayed.containsKey(features[index].getType()))
           {
-            featuresDisplayed.addElement(sf.getType());
+            av.featuresDisplayed.put(features[index].getType(),
+                                  new Integer( getColour(features[index].getType()).getRGB()) );
+            allfeatures.addElement(features[index].getType());
           }
+          index++;
         }
       }
+
+      renderOrder = new String[allfeatures.size()];
+      Enumeration en = allfeatures.elements();
+      int i = allfeatures.size()-1;
+      while(en.hasMoreElements())
+      {
+        renderOrder[i] = en.nextElement().toString();
+        i--;
+      }
     }
 
     public Color getColour(String featureType)
@@ -239,6 +372,19 @@ public class FeatureRenderer
       return (Color)featureColours.get(featureType);
     }
 
+    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, new Integer(col.getRGB()));
+    }
+
     public void setColour(String featureType, Color col)
     {
       featureColours.put(featureType, col);
@@ -259,14 +405,26 @@ 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
-      featuresDisplayed.clear();
-      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() )
-         featuresDisplayed.addElement(type);
-      }
+      if(av.featuresDisplayed!=null)
+        av.featuresDisplayed.clear();
+      else
+        av.featuresDisplayed = new Hashtable();
+
+      renderOrder = new String[data.length];
+
+      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();