X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=7ad5f4d0608f2dd1bab2a28df66b0ae7993a622a;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=4cb4f4304dc97774991b36061040589315611514;hpb=50b746c8bfb7cd8febdf438e6dc616687684364e;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 4cb4f43..7ad5f4d 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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
@@ -18,11 +18,11 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.*;
+import java.util.*;
 
 import java.awt.*;
 
-import java.util.*;
+import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
@@ -32,280 +32,426 @@ 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;
-
-    // A higher level for grouping features of a
-    // particular type
-    Hashtable featureGroups = null;
-
-    Color currentColour = null;
-
-    boolean drawText = true;
-    FontMetrics fm;
-    int charOffset;
-
-    /**
-     * Creates a new FeatureRenderer object.
-     *
-     * @param av DOCUMENT ME!
-     */
-    public FeatureRenderer(AlignViewport av)
+  AlignViewport av;
+
+  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;
+
+  // 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)
     {
-        this.av = av;
-        initColours();
+      return initialCol;
     }
 
-    //boolean highlightTransparent = true;
-    /**
-     * 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!
-     */
-    public void drawSequence(Graphics g, SequenceI seq,
-        int start, int end, int x1, int y1, int width, int height)
+    lastSequence = seq;
+    sequenceFeatures = lastSequence.getSequenceFeatures();
+    if (sequenceFeatures == null)
     {
-      fm = g.getFontMetrics();
+      return initialCol;
+    }
 
-        if(seq.getSequenceFeatures()==null)
-          return;
+    sfSize = sequenceFeatures.length;
 
-        Enumeration e = null, e2;
-        String type;
-        if(featuresDisplayed!=null)
-          e = featuresDisplayed.elements();
-        else
-         e = seq.getSequenceFeatures().elements();
+    if (jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))
+    {
+      return Color.white;
+    }
 
+    currentColour = null;
 
-        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
-            {
-              sf = (SequenceFeature) e.nextElement();
-              type = sf.getType();
-            }
-
-            if(sf==null)
-              continue;
-
-            if(featureGroups!=null
-               && sf.getFeatureGroup()!=null
-               && featureGroups.containsKey(sf.getFeatureGroup())
-               && !((Boolean)featureGroups.get(sf.getFeatureGroup())).booleanValue())
-            {
-              continue;
-            }
-
-
-            if (sf.getBegin() > seq.getEnd())
-            {
-                continue;
-            }
-
-            if (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);
-
-            }
-            else
-              renderFeature(g, seq,
-                            seq.findIndex(sf.getBegin()) - 1,
-                            seq.findIndex(sf.getEnd()) - 1,
-                          type, start, end, x1, y1, width, height);
+    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();
     }
 
-    void renderFeature(Graphics g, SequenceI seq,
-                       int fstart, int fend, String type, int start, int end,
-                       int x1, int y1, int width, int height)
+    currentColour = null;
+
+    drawSequence(null, lastSequence, lastSequence.findPosition(column), -1, -1);
+
+    if (currentColour == null)
     {
-      if ( ( (fstart <= end) && (fend >= start)))
+      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)
+    {
+      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++)
       {
-        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 (!sequenceFeatures[sfindex].type.equals(type))
+        {
+          continue;
         }
 
-        if (fend >= end)
+        if (featureGroups != null
+            && sequenceFeatures[sfindex].featureGroup != null
+            &&
+            featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
+            &&
+            ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
+                                            featureGroup)).
+            booleanValue())
         {
-          fend = end;
+          continue;
         }
-        for (int i = fstart; i <= fend; i++)
+
+        if (!overview && (sequenceFeatures[sfindex].getBegin() > epos
+                          || sequenceFeatures[sfindex].getEnd() < spos))
         {
-          char s = seq.getSequence().charAt(i);
+          continue;
+        }
 
-          if (jalview.util.Comparison.isGap(s))
+        if (overview)
+        {
+          if (sequenceFeatures[sfindex].begin <= start &&
+              sequenceFeatures[sfindex].end >= start)
           {
-            continue;
+            currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
+                type);
           }
 
-          currentColour = getColour(type);
-
-          g.setColor(currentColour);
+        }
+        else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
+        {
 
-          g.fillRect( (i - start) * width, 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);
 
-          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);
-          }
         }
+        else
+        {
+          renderFeature(g, seq,
+                        seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+                        seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+                        getColour(sequenceFeatures[sfindex].type),
+                        start, end, y1);
+        }
+
       }
     }
 
-    Image offscreen;
-    Frame nullframe;
-    public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+    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)
+  {
+
+    if ( ( (fstart <= end) && (fend >= start)))
     {
-      currentColour = initialCol;
-      if(offscreen == null)
+      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)
       {
-        nullframe = new Frame();
-        nullframe.addNotify();
-        offscreen = nullframe.createImage(1, 1);
+        fend = end;
       }
 
-      drawSequence(offscreen.getGraphics(), seq, i, i, 0, 0, 1, 1);
-      return currentColour;
-    }
+      for (i = fstart; i <= fend; i++)
+      {
+        s = seq.getCharAt(i);
 
+        if (jalview.util.Comparison.isGap(s))
+        {
+          continue;
+        }
 
+        g.setColor(featureColour);
 
-    public Color getColour(String featureType)
-    {
-      return (Color)featureColours.get(featureType);
+        g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
+
+        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;
+
+      }
     }
+  }
+
+  void findAllFeatures()
+  {
+    jalview.schemes.UserColourScheme ucs = new
+        jalview.schemes.UserColourScheme();
 
-    public void setColour(String featureType, Color col)
+    av.featuresDisplayed = new Hashtable();
+    Vector allfeatures = new Vector();
+    for (int i = 0; i < av.alignment.getHeight(); i++)
     {
-      featureColours.put(featureType, col);
+      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++;
+      }
     }
 
-    public void addNewFeature(String name, Color col)
+    renderOrder = new String[allfeatures.size()];
+    Enumeration en = allfeatures.elements();
+    int i = allfeatures.size() - 1;
+    while (en.hasMoreElements())
     {
-      setColour(name, col);
-      if (featuresDisplayed == null)
-        featuresDisplayed = new Vector();
-      featuresDisplayed.insertElementAt(name, 0);
+      renderOrder[i] = en.nextElement().toString();
+      i--;
     }
+  }
+
+  public Color getColour(String featureType)
+  {
+    return (Color) featureColours.get(featureType);
+  }
 
+  public void addNewFeature(String name, Color col)
+  {
 
- /*   public void setTransparency(float value)
+    setColour(name, col);
+    if (av.featuresDisplayed == null)
     {
-      transparency = value;
+      av.featuresDisplayed = new Hashtable();
     }
 
-    public float getTransparency()
-    {
-      return transparency;
-    }*/
+    av.featuresDisplayed.put(name, "NOGROUP");
+  }
 
-    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);
-      }
-    }
+  public void setColour(String featureType, Color col)
+  {
+    featureColours.put(featureType, col);
+  }
 
-    Hashtable featureColours = new Hashtable();
-    void initColours()
+  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)
     {
-      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));
+      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));*/
+  }
+}