X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=6fbdee858b359fdd7321ef94a7b8efd49734baf7;hb=add2f44022857817d1bb9a502f0e37627a34c5d8;hp=6e38f1b9eabfb7788d78e4ecba5547283e7b7224;hpb=22be3f466cd70cb03d5eae619ede8589ae69716a;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 6e38f1b..6fbdee8 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,71 +1,473 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * 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.gui;
 
 import jalview.datamodel.*;
-import jalview.schemes.*;
+
 import java.awt.*;
+
 import java.util.*;
 
-public class FeatureRenderer implements RendererI
+import java.awt.image.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer
 {
-  AlignViewport av;
+    AlignViewport av;
+    Color resBoxColour;
+    float transparency = 1.0f;
+    FontMetrics fm;
+    int charOffset;
+
+    // A higher level for grouping features of a
+   // particular type
+    Hashtable featureGroups = null;
 
-  SequenceGroup currentSequenceGroup = null;
-  SequenceGroup [] allGroups = null;
-  Color resBoxColour;
-  Graphics graphics;
 
-  public FeatureRenderer(AlignViewport av)
-  {
-    this.av = av;
-  }
+    // This is actually an Integer held in the hashtable,
+    // Retrieved using the key feature type
+    Object currentColour;
 
+    String [] renderOrder;
+
+
+    /**
+     * Creates a new FeatureRenderer object.
+     *
+     * @param av DOCUMENT ME!
+     */
+    public FeatureRenderer(AlignViewport av)
+    {
+        this.av = av;
+        initColours();
+    }
 
-  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)
-  {
-    Vector features = seq.getSequenceFeatures();
-    Enumeration e = features.elements();
-    while( e.hasMoreElements() )
+    public void transferSettings(FeatureRenderer fr)
     {
-      SequenceFeature sf = (SequenceFeature)e.nextElement();
-      int fstart = seq.findIndex(sf.getStart())-1;
-      int fend = seq.findIndex(sf.getEnd())-1;
+      renderOrder = fr.renderOrder;
+      featureGroups = fr.featureGroups;
+      featureColours = fr.featureColours;
+      transparency =  fr.transparency;
+    }
+
+    BufferedImage offscreenImage;
+    boolean offscreenRender = false;
+    public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
+    {
+      int seqindex = av.alignment.findIndex(seq);
+
+      return new Color( findFeatureColour (initialCol.getRGB(),
+                        seqindex, res ));
+    }
+
+    /**
+     * This is used by the Molecule Viewer to get the accurate colour
+     * of the rendered sequence
+     */
+    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.getDatasetSequence().getSequenceFeatures();
+        if(sequenceFeatures==null)
+          return initialCol;
+
+        sfSize = sequenceFeatures.length;
+      }
+
+      if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
+        return Color.white.getRGB();
+
 
-      if(    (fstart>=start&&fstart<=end) || (fend>=start&&fend<=end))
+      //Only bother making an offscreen image if transparency is applied
+      if(transparency!=1.0f && offscreenImage==null)
       {
-        if(fstart==fend)
+        offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);
+      }
+
+      currentColour = null;
+
+      offscreenRender = true;
+
+      if(offscreenImage!=null)
+      {
+        offscreenImage.setRGB(0,0,initialCol);
+        drawSequence(offscreenImage.getGraphics(),
+                     lastSequence,
+                     column,column,0);
+
+        return offscreenImage.getRGB(0,0);
+      }
+      else
+      {
+        drawSequence(null,
+                    lastSequence,
+                    lastSequence.findPosition(column),
+                    -1, -1);
+
+        if (currentColour == null)
+          return initialCol;
+        else
+          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.getDatasetSequence().getSequenceFeatures() == null
+          || seq.getDatasetSequence().getSequenceFeatures().length==0)
+        return;
+
+
+      if(g!=null)
+        fm = g.getFontMetrics();
+
+
+      if (av.featuresDisplayed == null || renderOrder==null)
+       {
+         findAllFeatures();
+         if(av.featuresDisplayed.size()<1)
+           return;
+
+         sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+         sfSize = sequenceFeatures.length;
+       }
+
+       if(lastSequence==null || seq!=lastSequence)
+      {
+        lastSequence = seq;
+        sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+        sfSize = sequenceFeatures.length;
+      }
+
+
+      if (transparency != 1 && g!=null)
+      {
+        Graphics2D g2 = (Graphics2D) g;
+        g2.setComposite(
+            AlphaComposite.getInstance(
+                AlphaComposite.SRC_OVER, transparency));
+      }
+
+      if(!offscreenRender)
+      {
+        spos = lastSequence.findPosition(start);
+        epos = lastSequence.findPosition(end);
+      }
+
+
+      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(sequenceFeatures.length<=sfindex)
+          {
+            continue;
+          }
+          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 (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
+                            || sequenceFeatures[sfindex].getEnd() < spos))
+            continue;
+
+          if (offscreenRender && offscreenImage==null)
+          {
+            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(transparency!=1.0f && g!=null)
         {
-          g.setColor(Color.red);
-          g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);
-          g.setColor(Color.white);
+          Graphics2D g2 = (Graphics2D) g;
+          g2.setComposite(
+              AlphaComposite.getInstance(
+                  AlphaComposite.SRC_OVER, 1.0f));
+        }
+    }
 
-          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;
+        }
+          int pady = (y1 + av.charHeight) - av.charHeight / 5;
+          for (i = fstart; i <= fend; i++)
           {
-            g.setColor(Color.blue);
-            g.fillRect( (i-start) * width, y1, width, height);
+            s = seq.getSequence().charAt(i);
+
+            if (jalview.util.Comparison.isGap(s))
+            {
+              continue;
+            }
+
+            g.setColor(featureColour);
+
+            g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);
+
+            if(offscreenRender)
+              continue;
 
             g.setColor(Color.white);
-            char s = seq.getSequence().charAt(i);
-            FontMetrics fm = g.getFontMetrics();
-            int charOffset = (width - fm.charWidth(s)) / 2;
-            int pady = height / 5;
+            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)),
+                         pady);
 
           }
+      }
+    }
+
+    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).getDatasetSequence().getSequenceFeatures();
+
+        if (features == null)
+          continue;
+
+        int index = 0;
+        while (index < features.length)
+        {
+          if (!av.featuresDisplayed.containsKey(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, String group)
+    {
+
+      setColour(name, col);
+      if(av.featuresDisplayed==null)
+        av.featuresDisplayed = new Hashtable();
+
+      if(group == null)
+        group = "NOGROUP";
+
+      av.featuresDisplayed.put(name, new Integer(col.getRGB()));
+    }
+
+    public void setColour(String featureType, Color col)
+    {
+      featureColours.put(featureType, col);
+    }
+
+    public void setTransparency(float value)
+    {
+      transparency = value;
+    }
+
+    public float getTransparency()
+    {
+      return transparency;
+    }
+
+    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();
+      else
+        av.featuresDisplayed = new Hashtable();
+
+      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()
+    {
+      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(230,230,0));
+      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));
     }
-   }
 
 }