X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=fc31fdfe8b2139db0627b5b51a33c26320b67ccd;hb=e7ed63f1ea56432246a6ed1553f0fe56d26f56ea;hp=cd754c706a87aa38570ce6b9ebdd063b2ca6f0d2;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index cd754c7..fc31fdf 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -5,81 +5,76 @@ import jalview.schemes.*;
 import java.awt.*;
 import java.util.*;
 
-public class FeatureRenderer implements RendererI {
+public class FeatureRenderer implements RendererI
+{
+  AlignViewport av;
+
+  SequenceGroup currentSequenceGroup = null;
+  SequenceGroup [] allGroups = null;
+  Color resBoxColour;
+  Graphics graphics;
+
+  public FeatureRenderer(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+
+  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() )
+    {
+      SequenceFeature sf = (SequenceFeature)e.nextElement();
+      if(sf.getStart()>seq.getEnd())
+        continue;
+
+      int fstart = seq.findIndex(sf.getStart())-1;
+      int fend = seq.findIndex(sf.getEnd())-1;
+
+      if(   (fstart<=end && fend>=start)  )
+      {
+        if(fstart<0) // fix for if the feature we have starts before the sequence start,
+          fstart = 0;// but the feature end is still valid!!
+
+        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);
 
-
-    public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) {
-	Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null);
-	return c;
-    }
-
-    public void drawSequence(Graphics g,ColourSchemeI cs,SequenceI seq,int start, int end, int x1, int y1, double width, int height,boolean showScores, boolean displayBoxes, boolean displayText,Vector pid, int seqnum,AlignViewport av) {
-
-	int i      = start;
-	int length = seq.getLength();
-
-	Color currentColor = Color.black;
-
-
-	int    prev   = -1;
-        int    fstart = 0;
-        char   prevc   = '-';
-
-	g.setColor(Color.magenta);
-
-	while (i <= end && i < length) {
-            char c = seq.getCharAt(i);
-	    if (c != '-') {
-
-              if (prevc != c) {
-
-                if (prevc == 'F') {
-                  g.setColor(Color.green);
-                } else if (prevc == 'R') {
-                  g.setColor(Color.cyan);
-                } else if (prevc == 'M') {
-                  g.setColor(Color.magenta);
-                } else if (prevc == 'P') {
-                  g.setColor(Color.yellow);
-                }
-		g.fillRect(x1+(int)(width*(i-fstart)),y1+height/4,(int)((prev-fstart+1)*width),height/2);
-
-                prevc   = c;
-                fstart = i;
-            }
-          } else if (prevc != '-') {
-                if (prevc == 'F') {
-                  g.setColor(Color.green);
-                } else if (prevc == 'R') {
-                  g.setColor(Color.cyan);
-                } else if (prevc == 'M') {
-                  g.setColor(Color.magenta);
-                } else if (prevc == 'P') {
-                  g.setColor(Color.yellow);
-                }
-		g.fillRect(x1+(int)(width*(fstart-start)),y1+height/4,(int)((i-fstart+1)*width),height/2);
-
-                prevc = c;
-          } else {
-            fstart = -1;
+        }
+        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);
           }
-	    i++;
-	}
-
-        if (fstart != -1) {
-        if (prevc == 'F') {
-          g.setColor(Color.green);
-        } else if (prevc == 'R') {
-          g.setColor(Color.cyan);
-        } else if (prevc == 'M') {
-          g.setColor(Color.magenta);
-        } else if (prevc == 'P') {
-          g.setColor(Color.yellow);
         }
+      }
 
-	//g.fillRect(x1+(int)(width*(fstart-start)),y1+height/4,(int)((end-fstart+1)*width),height/2);
-
-        }
     }
+   }
 
 }