X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=c71a3ccc2088be6fbffcf52fc14d6fe15a8885e2;hb=9175e97621ea51c3e98145545b3957842126c09e;hp=4a97e43b4e00355f59b4bcde416b159a98d7d377;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 4a97e43..c71a3cc 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -24,7 +24,6 @@ import java.awt.*;
 
 import java.util.*;
 
-
 /**
  * DOCUMENT ME!
  *
@@ -34,15 +33,20 @@ import java.util.*;
 public class FeatureRenderer
 {
     AlignViewport av;
-    SequenceGroup currentSequenceGroup = null;
-    SequenceGroup[] allGroups = null;
-    Color resBoxColour;
-    Graphics graphics;
-    float transparency = .4f;
 
-    // The following vector holds the features which are
-    // to be added, in the correct order or rendering
-    Vector featuresDisplayed;
+
+    // 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;
+
+    FontMetrics fm;
+    int charOffset;
 
     /**
      * Creates a new FeatureRenderer object.
@@ -53,13 +57,72 @@ public class FeatureRenderer
     {
         this.av = av;
         initColours();
-        String version = System.getProperty("java.version");
-        if (version.indexOf("1.1") == 0)
-          highlightTransparent = false;
+    }
+
+
+    public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+    {
+      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, -1, -1);
+
+      if(currentColour==null)
+        return initialCol;
+
+      return new Color( ((Integer)currentColour).intValue() );
     }
 
-boolean highlightTransparent = true;
+    /**
+     * 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, -1, -1);
+
+      if(currentColour==null)
+        return initialCol;
+
+      return  ((Integer)currentColour).intValue();
+    }
+
+
     /**
      * DOCUMENT ME!
      *
@@ -73,118 +136,184 @@ boolean highlightTransparent = true;
      * @param width DOCUMENT ME!
      * @param height DOCUMENT ME!
      */
-    public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
-        int start, int end, int x1, int y1, int width, int height)
+   // 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 y1, int width, int height)
     {
+      if (   seq.getSequenceFeatures() == null
+          || seq.getSequenceFeatures().length==0)
+        return;
 
-        if(seq.getSequenceFeatures()==null)
-          return;
 
-        Enumeration e = null, e2;
-        String type;
-        if(featuresDisplayed!=null)
-          e = featuresDisplayed.elements();
-        else
-         e = seq.getSequenceFeatures().elements();
+      if (av.featuresDisplayed == null || renderOrder==null)
+       {
+         findAllFeatures();
+         if(av.featuresDisplayed.size()<1)
+           return;
 
-       if(highlightTransparent)
+         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++)
         {
-        //  MyGraphics.SetTransparency(g, transparency);
-        }
+          if (!sequenceFeatures[sfindex].type.equals(type))
+            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;
 
-        while (e.hasMoreElements())
-        {
-            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
+          if (overview)
+          {
+            if (sequenceFeatures[sfindex].begin <= start &&
+                sequenceFeatures[sfindex].end >= start)
             {
-              sf = (SequenceFeature) e.nextElement();
-              type = sf.getType();
+              currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
+                  type);
             }
 
-            if(sf==null)
-              continue;
+          }
+          else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
+          {
 
+            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, width, height);
+            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);
 
-            if (sf.getBegin() > seq.getEnd())
-            {
-                continue;
-            }
+          }
+          else
+            renderFeature(g, seq,
+                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                          seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                          getColour(sequenceFeatures[sfindex].type),
+                          start, end, y1, width, height);
 
-            int fstart = seq.findIndex(sf.getBegin()) - 1;
-            int fend = seq.findIndex(sf.getEnd()) - 1;
+        }
+      }
+    }
+
+
+    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)
+    {
+
+      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 (fend >= end)
+        {
+          fend = end;
+        }
 
-            if (((fstart <= end) && (fend >= start)))
+          for (i = fstart; i <= fend; i++)
+          {
+            s = seq.getSequence().charAt(i);
+
+            if (jalview.util.Comparison.isGap(s))
             {
-                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;
-                }
-
-                if (fstart == fend)
-                {
-                    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);
-                }
-                else
-                {
-                    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);
-                    }
-                }
+              continue;
             }
+
+            g.setColor(featureColour);
+
+            g.fillRect( (i - start) * width, y1, width, height);
+
+            g.setColor(Color.white);
+            charOffset = (width - fm.charWidth(s)) / 2;
+            g.drawString(String.valueOf(s),
+                         charOffset + (width * (i - start)),
+                         (y1 + height) - height / 5); //pady = height / 5;
+
           }
+      }
+    }
+
+    void findAllFeatures()
+    {
+      av.featuresDisplayed = new Hashtable();
+      Vector allfeatures = new Vector();
+      for (int i = 0; i < av.alignment.getHeight(); i++)
+      {
+        SequenceFeature [] features = av.alignment.getSequenceAt(i).getSequenceFeatures();
 
-          if (highlightTransparent)
+        if (features == null)
+          continue;
+
+        int index = 0;
+        while (index < features.length)
+        {
+          if (!av.featuresDisplayed.containsKey(features[index].getType()))
           {
-        //    MyGraphics.SetTransparency(g, 1.0f);
+            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)
@@ -192,34 +321,44 @@ boolean highlightTransparent = true;
       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
-      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();