X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=47fbb0db946cd166180af6bfa632685f812c134d;hb=6c4bc68ae8b1c5005e79661bb2d8246515cb787d;hp=091a1270931aad62682f475639876521ec1a5942;hpb=d355ad106f73e0de0abc3fb3f375af4eaf352591;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 091a127..47fbb0d 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,6 +1,7 @@
+
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -33,20 +34,31 @@ import java.util.*;
 public class FeatureRenderer
 {
     AlignViewport av;
-    SequenceGroup currentSequenceGroup = null;
-    SequenceGroup[] allGroups = null;
-    Graphics graphics;
 
-    // The following vector holds the features which are
-    // to be added, in the correct order or rendering
-    Vector featuresDisplayed;
+    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;
 
-    Color currentColour = null;
 
-    boolean drawText = true;
+    // This is actually an Integer held in the hashtable,
+    // Retrieved using the key feature type
+    Object currentColour;
+
+    String [] renderOrder;
+
     FontMetrics fm;
     int charOffset;
 
+    float transparency = 1f;
+
+    TransparencySetter transparencySetter = null;
+
     /**
      * Creates a new FeatureRenderer object.
      *
@@ -55,10 +67,85 @@ 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;
+      transparency =  fr.transparency;
+    }
+
+
+    public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+    {
+      overview = true;
+      if(!av.showSequenceFeatures)
+        return initialCol;
+
+        lastSequence = seq;
+        sequenceFeatures = lastSequence.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);
+
+      if(currentColour==null)
+        return initialCol;
+
+      return new Color( ((Integer)currentColour).intValue() );
+    }
+
+    /**
+     * This is used by the Molecule Viewer to get the accurate colour
+     * of the rendered sequence
+     */
+    boolean overview = false;
+
+    int white = Color.white.getRGB();
+    public int findFeatureColour(int initialCol, int seqIndex, int column)
+    {
+      if(!av.showSequenceFeatures)
+        return initialCol;
+
+      if(seqIndex!=lastSequenceIndex)
+      {
+        lastSequence = av.alignment.getSequenceAt(seqIndex);
+        lastSequenceIndex = seqIndex;
+        sequenceFeatures = lastSequence.getSequenceFeatures();
+        if(sequenceFeatures==null)
+          return initialCol;
+
+        sfSize = sequenceFeatures.length;
+      }
+
+
+      if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
+        return Color.white.getRGB();
+
+      currentColour = null;
+
+      drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1);
+
+      if(currentColour==null)
+        return initialCol;
+
+      return  ((Integer)currentColour).intValue();
     }
 
-    //boolean highlightTransparent = true;
+
     /**
      * DOCUMENT ME!
      *
@@ -72,80 +159,127 @@ 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)
     {
-      fm = g.getFontMetrics();
-
-        if(seq.getSequenceFeatures()==null)
-          return;
+      if (   seq.getSequenceFeatures() == null
+          || seq.getSequenceFeatures().length==0)
+        return;
 
-        Enumeration e = null, e2;
-        String type;
-        if(featuresDisplayed!=null)
-          e = featuresDisplayed.elements();
-        else
-         e = seq.getSequenceFeatures().elements();
+      if(transparencySetter!=null && g!=null)
+      {
+        transparencySetter.setTransparency(g, transparency);
+      }
 
+      if (av.featuresDisplayed == null || renderOrder==null)
+       {
+         findAllFeatures();
+         if(av.featuresDisplayed.size()<1)
+           return;
 
-        while (e.hasMoreElements())
+         sequenceFeatures = seq.getSequenceFeatures();
+         sfSize = sequenceFeatures.length;
+       }
+       if(lastSequence==null || seq!=lastSequence)
+      {
+        lastSequence = seq;
+        sequenceFeatures = seq.getSequenceFeatures();
+        sfSize = sequenceFeatures.length;
+      }
+      if(!overview)
+      {
+        spos = lastSequence.findPosition(start);
+        epos = lastSequence.findPosition(end);
+        if(g!=null)
+          fm = g.getFontMetrics();
+      }
+      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++)
         {
-            SequenceFeature sf=null;
-            if(featuresDisplayed!=null)
-            {
-              e2 = seq.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 (!sequenceFeatures[sfindex].type.equals(type))
+            continue;
 
-            if(sf==null)
-              continue;
+          if (featureGroups != null
+              && sequenceFeatures[sfindex].featureGroup != null
+              &&
+              featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
+              &&
+              ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).
+              booleanValue())
+          {
+            continue;
+          }
 
+          if (!overview && (sequenceFeatures[sfindex].getBegin() > epos
+                            || sequenceFeatures[sfindex].getEnd() < spos))
+            continue;
 
-            if (sf.getBegin() > seq.getEnd())
+          if (overview)
+          {
+            if (sequenceFeatures[sfindex].begin <= start &&
+                sequenceFeatures[sfindex].end >= start)
             {
-                continue;
+              currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
+                  type);
             }
 
-            if (type.equals("disulfide bond"))
-            {
+          }
+          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);
-              renderFeature(g, seq,
-                            seq.findIndex(sf.getEnd()) - 1,
-                            seq.findIndex(sf.getEnd()) - 1,
-                            type, start, end, x1, y1, width, height);
+            renderFeature(g, seq,
+                          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(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);
+          }
+          else
+            renderFeature(g, seq,
+                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                          seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                          getColour(sequenceFeatures[sfindex].type),
+                          start, end, y1);
 
+        }
+      }
+
+      if(transparencySetter!=null && g!=null)
+      {
+        transparencySetter.setTransparency(g, 1.0f);
       }
     }
 
+
+    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 <= end) && (fend >= start)))
       {
         if (fstart < start)
         { // fix for if the feature we have starts before the sequence start,
@@ -156,135 +290,135 @@ public class FeatureRenderer
         {
           fend = end;
         }
-        for (int i = fstart; i <= fend; i++)
-        {
-          char s = seq.getSequence().charAt(i);
 
-          if (jalview.util.Comparison.isGap(s))
+          for (i = fstart; i <= fend; i++)
           {
-            continue;
-          }
+            s = seq.getCharAt(i);
 
-          currentColour = getColour(type);
+            if (jalview.util.Comparison.isGap(s))
+            {
+              continue;
+            }
 
-          g.setColor(currentColour);
+            g.setColor(featureColour);
 
-          g.fillRect( (i - start) * width, y1, width, height);
+            g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
+
+            if(!av.validCharWidth)
+              continue;
 
-          if (drawText)
-          {
             g.setColor(Color.white);
-            charOffset = (width - fm.charWidth(s)) / 2;
+            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
             g.drawString(String.valueOf(s),
-                         charOffset + x1 + (width * (i - start)),
-                         (y1 + height) - height / 5);
+                         charOffset + (av.charWidth * (i - start)),
+                         (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;
+
           }
-        }
       }
     }
 
-    Image offscreen;
-    Frame nullframe;
-    public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+    void findAllFeatures()
     {
-      currentColour = initialCol;
-      if(offscreen == null)
+      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++)
       {
-        nullframe = new Frame();
-        nullframe.addNotify();
-        offscreen = nullframe.createImage(1, 1);
-      }
+        SequenceFeature [] features = av.alignment.getSequenceAt(i).getSequenceFeatures();
 
-      drawSequence(offscreen.getGraphics(), seq, i, i, 0, 0, 1, 1);
-      return currentColour;
-    }
+        if (features == null)
+          continue;
+
+        int index = 0;
+        while (index < features.length)
+        {
+          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());
+          }
+          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)
     {
       return (Color)featureColours.get(featureType);
     }
 
-    public void setColour(String featureType, Color col)
+    public void addNewFeature(String name, Color col)
     {
-      featureColours.put(featureType, col);
-    }
 
- /*   public void setTransparency(float value)
-    {
-      transparency = value;
+      setColour(name, col);
+      if(av.featuresDisplayed==null)
+        av.featuresDisplayed = new Hashtable();
+
+
+      av.featuresDisplayed.put(name, "NOGROUP");
     }
 
-    public float getTransparency()
+    public void setColour(String featureType, Color col)
     {
-      return transparency;
-    }*/
+      featureColours.put(featureType, col);
+    }
 
     public void setFeaturePriority(Object [][] data)
     {
-      // 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
-      if(featuresDisplayed!=null)
-        featuresDisplayed.removeAllElements();
-      else
-        featuresDisplayed = new Vector();
-
-      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);
-      }
+        // 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
+        if(av.featuresDisplayed!=null)
+          av.featuresDisplayed.clear();
+
+        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();
-    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));*/
     }
+  }
 
-}