X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=7f8d89d0ec620e648632aa0cc7f77f33957f77fe;hb=3caa3405a5822c7248bab517b8d1a7776e0dc210;hp=291ce5fbc944d3b99daa97765ef3362be34c344f;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 291ce5f..7f8d89d 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,3 +1,4 @@
+
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
@@ -16,94 +17,408 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.appletgui;
 
-import java.util.*;
+import jalview.datamodel.*;
 
 import java.awt.*;
 
-import jalview.datamodel.*;
+import java.util.*;
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class FeatureRenderer
 {
-  AlignViewport av;
+    AlignViewport av;
 
-  SequenceGroup currentSequenceGroup = null;
-  SequenceGroup[] allGroups = null;
-  Color resBoxColour;
-  Graphics graphics;
+    Hashtable featureColours = new Hashtable();
 
-  public FeatureRenderer(AlignViewport av)
-  {
-    this.av = av;
-  }
+    // A higher level for grouping features of a
+    // particular type
+    Hashtable featureGroups = null;
 
-  public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
-                           int start, int end, int x1, int y1, int width,
-                           int height)
-  {
-    Vector features = seq.getSequenceFeatures();
-    Enumeration e = features.elements();
-    while (e.hasMoreElements())
+    // Holds web links for feature groups and feature types
+    // in the form label|link
+    Hashtable featureLinks = null;
+
+
+    // 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.
+     *
+     * @param av DOCUMENT ME!
+     */
+    public FeatureRenderer(AlignViewport av)
+    {
+        this.av = av;
+
+        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)
     {
-      SequenceFeature sf = (SequenceFeature) e.nextElement();
-      if (sf.getStart() > seq.getEnd())
+      if(!av.showSequenceFeatures)
+        return initialCol;
+
+      if(seqIndex!=lastSequenceIndex)
       {
-        continue;
+        lastSequence = av.alignment.getSequenceAt(seqIndex);
+        lastSequenceIndex = seqIndex;
+        sequenceFeatures = lastSequence.getSequenceFeatures();
+        if(sequenceFeatures==null)
+          return initialCol;
+
+        sfSize = sequenceFeatures.length;
       }
 
-      int fstart = seq.findIndex(sf.getStart()) - 1;
-      int fend = seq.findIndex(sf.getEnd()) - 1;
 
-      if ( (fstart <= end && fend >= start))
+      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();
+    }
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     * @param seq DOCUMENT ME!
+     * @param sg DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     * @param x1 DOCUMENT ME!
+     * @param y1 DOCUMENT ME!
+     * @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 y1)
+    {
+      if (   seq.getSequenceFeatures() == null
+          || seq.getSequenceFeatures().length==0)
+        return;
+
+      if(transparencySetter!=null && g!=null)
       {
-        if (fstart < 0) // fix for if the feature we have starts before the sequence start,
+        transparencySetter.setTransparency(g, transparency);
+      }
+
+      if (av.featuresDisplayed == null || renderOrder==null)
+       {
+         findAllFeatures();
+         if(av.featuresDisplayed.size()<1)
+           return;
+
+         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++)
         {
-          fstart = 0; // but the feature end is still valid!!
+          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;
+
+          if (overview)
+          {
+            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(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(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);
+      }
+    }
 
-        if (fstart == fend)
-        {
-          g.setColor(Color.red);
-          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;
+    int i;
+    void renderFeature(Graphics g, SequenceI seq,
+                       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!!
         }
-        else
+
+        if (fend >= end)
         {
-          for (int i = fstart; i <= fend; i++)
+          fend = end;
+        }
+
+          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(Color.blue);
-            g.fillRect( (i - start) * width, y1, width, height);
+            g.setColor(featureColour);
 
-            g.setColor(Color.white);
+            g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
 
-            FontMetrics fm = g.getFontMetrics();
-            int charOffset = (width - fm.charWidth(s)) / 2;
-            int pady = height / 5;
+            if(!av.validCharWidth)
+              continue;
+
+            g.setColor(Color.white);
+            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
             g.drawString(String.valueOf(s),
-                         charOffset + x1 + width * (i - start),
-                         y1 + height - pady);
+                         charOffset + (av.charWidth * (i - start)),
+                         (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;
+
           }
+      }
+    }
+
+    void findAllFeatures()
+    {
+      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++)
+      {
+        SequenceFeature [] features = av.alignment.getSequenceAt(i).getSequenceFeatures();
+
+        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 addNewFeature(String name, Color col)
+    {
+
+      setColour(name, col);
+      if(av.featuresDisplayed==null)
+        av.featuresDisplayed = new Hashtable();
+
+
+      av.featuresDisplayed.put(name, "NOGROUP");
+    }
+
+    public void setColour(String featureType, Color col)
+    {
+      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(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;
+          }
+    }
 }
+
+  class TransparencySetter
+  {
+    void setTransparency(Graphics g, float value)
+    {
+      Graphics2D g2 = (Graphics2D) g;
+      g2.setComposite(
+          AlphaComposite.getInstance(
+              AlphaComposite.SRC_OVER, value));
+    }
+  }
+
+
+
+