X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=16de45f603960d65dfbbead4166ce06c59929182;hb=8c0f35fa0bee850e670c157157cc335d8a1a49ae;hp=2e193aab98523b2161f067e7d4dde13489ba4d3b;hpb=74f2c25a0ad46ce7286cca6d976f3592952d36ad;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 2e193aa..16de45f 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,7 +1,6 @@
-
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -19,11 +18,11 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.*;
+import java.util.*;
 
 import java.awt.*;
 
-import java.util.*;
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -33,392 +32,426 @@ import java.util.*;
  */
 public class FeatureRenderer
 {
-    AlignViewport av;
+  AlignViewport av;
 
-    Hashtable featureColours = new Hashtable();
+  Hashtable featureColours = new Hashtable();
 
-    // A higher level for grouping features of a
-    // particular type
-    Hashtable featureGroups = null;
+  // 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;
+  // 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;
 
-    // This is actually an Integer held in the hashtable,
-    // Retrieved using the key feature type
-    Object currentColour;
+  String[] renderOrder;
 
-    String [] renderOrder;
+  FontMetrics fm;
+  int charOffset;
 
-    FontMetrics fm;
-    int charOffset;
+  float transparency = 1f;
 
-    float transparency = 1f;
+  TransparencySetter transparencySetter = null;
 
-    TransparencySetter transparencySetter = null;
+  /**
+   * Creates a new FeatureRenderer object.
+   *
+   * @param av DOCUMENT ME!
+   */
+  public FeatureRenderer(AlignViewport av)
+  {
+    this.av = av;
 
-    /**
-     * Creates a new FeatureRenderer object.
-     *
-     * @param av DOCUMENT ME!
-     */
-    public FeatureRenderer(AlignViewport av)
+    if (!System.getProperty("java.version").startsWith("1.1"))
     {
-        this.av = av;
-
-        if(!System.getProperty("java.version").startsWith("1.1"))
-             transparencySetter = new TransparencySetter();
+      transparencySetter = new TransparencySetter();
     }
+  }
 
+  public void transferSettings(FeatureRenderer fr)
+  {
+    renderOrder = fr.renderOrder;
+    featureGroups = fr.featureGroups;
+    featureColours = fr.featureColours;
+    transparency = fr.transparency;
+  }
 
-    public void transferSettings(FeatureRenderer fr)
+  public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+  {
+    overview = true;
+    if (!av.showSequenceFeatures)
     {
-      renderOrder = fr.renderOrder;
-      featureGroups = fr.featureGroups;
-      featureColours = fr.featureColours;
-      transparency =  fr.transparency;
+      return initialCol;
     }
 
-
-    public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+    lastSequence = seq;
+    sequenceFeatures = lastSequence.getSequenceFeatures();
+    if (sequenceFeatures == null)
     {
-      overview = true;
-      if(!av.showSequenceFeatures)
-        return initialCol;
-
-        lastSequence = seq;
-        sequenceFeatures = lastSequence.getSequenceFeatures();
-        if(sequenceFeatures==null)
-          return initialCol;
-
-        sfSize = sequenceFeatures.length;
+      return initialCol;
+    }
 
-      if(jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))
-        return Color.white;
+    sfSize = sequenceFeatures.length;
 
-      currentColour = null;
+    if (jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))
+    {
+      return Color.white;
+    }
 
-      drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1);
+    currentColour = null;
 
-      if(currentColour==null)
-        return initialCol;
+    drawSequence(null, lastSequence, lastSequence.findPosition(i), -1, -1);
 
-      return new Color( ((Integer)currentColour).intValue() );
+    if (currentColour == null)
+    {
+      return initialCol;
     }
 
-    /**
-     * This is used by the Molecule Viewer to get the accurate colour
-     * of the rendered sequence
-     */
-    boolean overview = false;
+    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)
+  int white = Color.white.getRGB();
+  public int findFeatureColour(int initialCol, int seqIndex, int column)
+  {
+    if (!av.showSequenceFeatures)
     {
-      if(!av.showSequenceFeatures)
-        return initialCol;
+      return initialCol;
+    }
 
-      if(seqIndex!=lastSequenceIndex)
+    if (seqIndex != lastSequenceIndex)
+    {
+      lastSequence = av.alignment.getSequenceAt(seqIndex);
+      lastSequenceIndex = seqIndex;
+      sequenceFeatures = lastSequence.getSequenceFeatures();
+      if (sequenceFeatures == null)
       {
-        lastSequence = av.alignment.getSequenceAt(seqIndex);
-        lastSequenceIndex = seqIndex;
-        sequenceFeatures = lastSequence.getSequenceFeatures();
-        if(sequenceFeatures==null)
-          return initialCol;
-
-        sfSize = sequenceFeatures.length;
+        return initialCol;
       }
 
+      sfSize = sequenceFeatures.length;
+    }
 
-      if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
-        return Color.white.getRGB();
-
-      currentColour = null;
+    if (jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
+    {
+      return Color.white.getRGB();
+    }
 
-      drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1);
+    currentColour = null;
 
-      if(currentColour==null)
-        return initialCol;
+    drawSequence(null, lastSequence, lastSequence.findPosition(column), -1, -1);
 
-      return  ((Integer)currentColour).intValue();
+    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)
+  /**
+   * 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)
     {
-      if (   seq.getSequenceFeatures() == null
-          || seq.getSequenceFeatures().length==0)
-        return;
+      return;
+    }
 
-      if(transparencySetter!=null && g!=null)
+    if (transparencySetter != null && g != null)
+    {
+      transparencySetter.setTransparency(g, transparency);
+    }
+
+    if (av.featuresDisplayed == null || renderOrder == null)
+    {
+      findAllFeatures();
+      if (av.featuresDisplayed.size() < 1)
       {
-        transparencySetter.setTransparency(g, transparency);
+        return;
       }
 
-      if (av.featuresDisplayed == null || renderOrder==null)
-       {
-         findAllFeatures();
-         if(av.featuresDisplayed.size()<1)
-           return;
-
-         sequenceFeatures = seq.getSequenceFeatures();
-         sfSize = sequenceFeatures.length;
-       }
-       if(lastSequence==null || seq!=lastSequence)
+      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)
       {
-        lastSequence = seq;
-        sequenceFeatures = seq.getSequenceFeatures();
-        sfSize = sequenceFeatures.length;
+        fm = g.getFontMetrics();
       }
-      if(!overview)
+    }
+    String type;
+    for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
+    {
+      type = renderOrder[renderIndex];
+      if (!av.featuresDisplayed.containsKey(type))
       {
-        spos = lastSequence.findPosition(start);
-        epos = lastSequence.findPosition(end);
-        if(g!=null)
-          fm = g.getFontMetrics();
+        continue;
       }
-      String type;
-      for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
-       {
-        type =  renderOrder[renderIndex];
-        if(!av.featuresDisplayed.containsKey(type))
+
+      // loop through all features in sequence to find
+      // current feature to render
+      for (sfindex = 0; sfindex < sfSize; sfindex++)
+      {
+        if (!sequenceFeatures[sfindex].type.equals(type))
+        {
           continue;
+        }
 
-        // loop through all features in sequence to find
-        // current feature to render
-        for (sfindex = 0; sfindex < sfSize; sfindex++)
+        if (featureGroups != null
+            && sequenceFeatures[sfindex].featureGroup != null
+            &&
+            featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
+            &&
+            ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
+                                            featureGroup)).
+            booleanValue())
         {
-          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;
-          }
+          continue;
+        }
 
-          if (!overview && (sequenceFeatures[sfindex].getBegin() > epos
-                            || sequenceFeatures[sfindex].getEnd() < spos))
-            continue;
+        if (!overview && (sequenceFeatures[sfindex].getBegin() > epos
+                          || sequenceFeatures[sfindex].getEnd() < spos))
+        {
+          continue;
+        }
 
-          if (overview)
+        if (overview)
+        {
+          if (sequenceFeatures[sfindex].begin <= start &&
+              sequenceFeatures[sfindex].end >= start)
           {
-            if (sequenceFeatures[sfindex].begin <= start &&
-                sequenceFeatures[sfindex].end >= start)
-            {
-              currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
-                  type);
-            }
-
+            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 if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
+        {
 
-          }
-          else
-            renderFeature(g, seq,
-                          seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
-                          seq.findIndex(sequenceFeatures[sfindex].end) - 1,
-                          getColour(sequenceFeatures[sfindex].type),
-                          start, end, y1);
+          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 (transparencySetter != null && g != null)
+    {
+      transparencySetter.setTransparency(g, 1.0f);
+    }
+  }
+
+  char s;
+  int i;
+  void renderFeature(Graphics g, SequenceI seq,
+                     int fstart, int fend, Color featureColour, int start,
+                     int end, int y1)
+  {
 
-    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!!
+      }
 
-      if (((fstart <= end) && (fend >= start)))
+      if (fend >= end)
       {
-        if (fstart < start)
-        { // fix for if the feature we have starts before the sequence start,
-          fstart = start; // but the feature end is still valid!!
-        }
+        fend = end;
+      }
+
+      for (i = fstart; i <= fend; i++)
+      {
+        s = seq.getCharAt(i);
 
-        if (fend >= end)
+        if (jalview.util.Comparison.isGap(s))
         {
-          fend = end;
+          continue;
         }
 
-          for (i = fstart; i <= fend; i++)
-          {
-            s = seq.getSequence().charAt(i);
-
-            if (jalview.util.Comparison.isGap(s))
-            {
-              continue;
-            }
+        g.setColor(featureColour);
 
-            g.setColor(featureColour);
+        g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
 
-            g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
-
-            if(!av.validCharWidth)
-              continue;
+        if (!av.validCharWidth)
+        {
+          continue;
+        }
 
-            g.setColor(Color.white);
-            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
-            g.drawString(String.valueOf(s),
-                         charOffset + (av.charWidth * (i - start)),
-                         (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;
+        g.setColor(Color.white);
+        charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+        g.drawString(String.valueOf(s),
+                     charOffset + (av.charWidth * (i - start)),
+                     (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;
 
-          }
       }
     }
+  }
+
+  void findAllFeatures()
+  {
+    jalview.schemes.UserColourScheme ucs = new
+        jalview.schemes.UserColourScheme();
 
-    void findAllFeatures()
+    av.featuresDisplayed = new Hashtable();
+    Vector allfeatures = new Vector();
+    for (int i = 0; i < av.alignment.getHeight(); i++)
     {
-      jalview.schemes.UserColourScheme ucs = new
-          jalview.schemes.UserColourScheme();
+      SequenceFeature[] features = av.alignment.getSequenceAt(i).
+          getSequenceFeatures();
 
-      av.featuresDisplayed = new Hashtable();
-      Vector allfeatures = new Vector();
-      for (int i = 0; i < av.alignment.getHeight(); i++)
+      if (features == null)
       {
-        SequenceFeature [] features = av.alignment.getSequenceAt(i).getSequenceFeatures();
-
-        if (features == null)
-          continue;
+        continue;
+      }
 
-        int index = 0;
-        while (index < features.length)
+      int index = 0;
+      while (index < features.length)
+      {
+        if (!av.featuresDisplayed.containsKey(features[index].getType()))
         {
-          if (!av.featuresDisplayed.containsKey(features[index].getType()))
+          if (getColour(features[index].getType()) == null)
           {
-            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());
+            featureColours.put(features[index].getType(),
+                               ucs.createColourFromName(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--;
+          av.featuresDisplayed.put(features[index].getType(),
+                                   new Integer(getColour(features[index].
+              getType()).getRGB()));
+          allfeatures.addElement(features[index].getType());
+        }
+        index++;
       }
     }
 
-    public Color getColour(String featureType)
+    renderOrder = new String[allfeatures.size()];
+    Enumeration en = allfeatures.elements();
+    int i = allfeatures.size() - 1;
+    while (en.hasMoreElements())
     {
-      return (Color)featureColours.get(featureType);
+      renderOrder[i] = en.nextElement().toString();
+      i--;
     }
+  }
 
-    public void addNewFeature(String name, Color col)
-    {
-
-      setColour(name, col);
-      if(av.featuresDisplayed==null)
-        av.featuresDisplayed = new Hashtable();
-
+  public Color getColour(String featureType)
+  {
+    return (Color) featureColours.get(featureType);
+  }
 
-      av.featuresDisplayed.put(name, "NOGROUP");
-    }
+  public void addNewFeature(String name, Color col)
+  {
 
-    public void setColour(String featureType, Color col)
+    setColour(name, col);
+    if (av.featuresDisplayed == null)
     {
-      featureColours.put(featureType, col);
+      av.featuresDisplayed = new Hashtable();
     }
 
-    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];
+    av.featuresDisplayed.put(name, "NOGROUP");
+  }
 
-        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;
-          }
-    }
-}
+  public void setColour(String featureType, Color col)
+  {
+    featureColours.put(featureType, col);
+  }
 
-  class TransparencySetter
+  public void setFeaturePriority(Object[][] data)
   {
-    void setTransparency(Graphics g, float value)
+    // 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)
     {
-     //Graphics2D g2 = (Graphics2D) g;
-    // g2.setComposite(
-     //   AlphaComposite.getInstance(
-     //        AlphaComposite.SRC_OVER, value));
+      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));
+  }
+}