X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=03080bdf2e27c7e32000e4a9ed4be5f08c26ddfb;hb=eacce9627f059fc2f9e880c81d8d1bdfbe7fe5b3;hp=8a94a895aadded33776f94672513d8ec8d7cb52e;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 8a94a89..03080bd 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -24,6 +24,8 @@ import java.awt.*;
 
 import java.util.*;
 
+import java.awt.image.*;
+
 
 /**
  * DOCUMENT ME!
@@ -34,10 +36,15 @@ import java.util.*;
 public class FeatureRenderer
 {
     AlignViewport av;
-    SequenceGroup currentSequenceGroup = null;
-    SequenceGroup[] allGroups = null;
     Color resBoxColour;
-    Graphics graphics;
+    float transparency = 1.0f;
+    FontMetrics fm;
+    int charOffset;
+    boolean drawText = true;
+
+    // The following vector holds the features which are
+    // to be added, in the correct order or rendering
+    Vector featuresDisplayed = null;
 
     /**
      * Creates a new FeatureRenderer object.
@@ -47,8 +54,33 @@ public class FeatureRenderer
     public FeatureRenderer(AlignViewport av)
     {
         this.av = av;
+        initColours();
+    }
+
+    /**
+     * This is used by the Molecule Viewer to get the accurate colour
+     * of the rendered sequence
+     */
+    BufferedImage bi;
+    public synchronized Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+    {
+      if(!av.showSequenceFeatures)
+        return initialCol;
+
+      if (bi == null)
+        bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);
+
+      bi.setRGB(0,0, initialCol.getRGB());
+
+      drawText = false;
+
+      drawSequence(bi.getGraphics(), seq, i, i, 0, 0, 1, 1);
+      drawText = true;
+
+      return new Color(bi.getRGB(0, 0));
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -62,76 +94,222 @@ public class FeatureRenderer
      * @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)
+    public void drawSequence(Graphics g, SequenceI seq,
+                             int start, int end, int x1, int y1, int width, int height)
     {
-        Vector features = seq.getSequenceFeatures();
-        Enumeration e = features.elements();
 
-        while (e.hasMoreElements())
+//System.out.println(start+" "+end+" "+x1+" "+y1);
+      if (seq.getDatasetSequence().getSequenceFeatures() == null
+          || seq.getDatasetSequence().getSequenceFeatures().size()==0)
+        return;
+
+      fm = g.getFontMetrics();
+
+      if (transparency != 1)
+      {
+        Graphics2D g2 = (Graphics2D) g;
+        g2.setComposite(
+            AlphaComposite.getInstance(
+                AlphaComposite.SRC_OVER, transparency));
+      }
+
+      String type;
+      SequenceFeature sf;
+      if (featuresDisplayed == null)
+        findAllFeatures();
+
+      Enumeration e = featuresDisplayed.elements(), e2;
+
+      // Loop through each visible feature
+      while (e.hasMoreElements())
+      {
+
+        type = e.nextElement().toString();
+        e2 = seq.getDatasetSequence().getSequenceFeatures().elements();
+        // loop through all features in sequence to find
+        // current feature to render
+          while (e2.hasMoreElements())
         {
-            SequenceFeature sf = (SequenceFeature) e.nextElement();
 
-            if (sf.getStart() > seq.getEnd())
-            {
-                continue;
-            }
+          sf = (SequenceFeature) e2.nextElement();
+          if (!type.equals(sf.getType()))
+            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);
+        }
+      }
+
+        if(transparency!=1.0f)
+        {
+          Graphics2D g2 = (Graphics2D) g;
+          g2.setComposite(
+              AlphaComposite.getInstance(
+                  AlphaComposite.SRC_OVER, 1.0f));
+        }
+    }
+
 
-            int fstart = seq.findIndex(sf.getStart()) - 1;
-            int fend = seq.findIndex(sf.getEnd()) - 1;
+    void renderFeature(Graphics g, SequenceI seq,
+                       int fstart, int fend, String type, int start, int end, int x1, 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 (((fstart <= end) && (fend >= start)))
+          if (fend >= end)
+          {
+            fend = end;
+          }
+          for (int i = fstart; i <= fend; i++)
+          {
+            char 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(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);
-                }
-                else
-                {
-                    for (int i = fstart; i <= fend; i++)
-                    {
-                        char 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(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(getColour(type));
+
+            g.fillRect( (i - start) * width, y1, width, height);
+
+            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); //pady = height / 5;
+           }
+          }
+        }
+    }
+
+    void findAllFeatures()
+    {
+      Vector features = new Vector();
+      SequenceFeature sf;
+      featuresDisplayed = new Vector();
+      Enumeration e;
+      for (int i = 0; i < av.alignment.getHeight(); i++)
+      {
+        features = av.alignment.getSequenceAt(i).getDatasetSequence().
+            getSequenceFeatures();
+        if (features == null)
+          continue;
+
+        e = features.elements();
+        while (e.hasMoreElements())
+        {
+          sf = (SequenceFeature) e.nextElement();
+          if (!featuresDisplayed.contains(sf.getType()))
+          {
+            featuresDisplayed.addElement(sf.getType());
+          }
         }
+      }
+    }
+
+    public Color getColour(String featureType)
+    {
+      return (Color)featureColours.get(featureType);
     }
+
+    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
+      featuresDisplayed.clear();
+      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);
+      }
+    }
+
+    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));
+    }
+
 }