paintFlag removed

[jalview.git] / src / jalview / gui / FeatureRenderer.java

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index cd754c7..fc31fdf 100755 (executable)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -5,81 +5,76 @@ import jalview.schemes.*;
 import java.awt.*;\r
 import java.util.*;\r
 \r
-public class FeatureRenderer implements RendererI {\r
+public class FeatureRenderer implements RendererI\r
+{\r
+  AlignViewport av;\r
+\r
+  SequenceGroup currentSequenceGroup = null;\r
+  SequenceGroup [] allGroups = null;\r
+  Color resBoxColour;\r
+  Graphics graphics;\r
+\r
+  public FeatureRenderer(AlignViewport av)\r
+  {\r
+    this.av = av;\r
+  }\r
+\r
+\r
+  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)\r
+  {\r
+    Vector features = seq.getSequenceFeatures();\r
+    Enumeration e = features.elements();\r
+    while( e.hasMoreElements() )\r
+    {\r
+      SequenceFeature sf = (SequenceFeature)e.nextElement();\r
+      if(sf.getStart()>seq.getEnd())\r
+        continue;\r
+\r
+      int fstart = seq.findIndex(sf.getStart())-1;\r
+      int fend = seq.findIndex(sf.getEnd())-1;\r
+\r
+      if(   (fstart<=end && fend>=start)  )\r
+      {\r
+        if(fstart<0) // fix for if the feature we have starts before the sequence start,\r
+          fstart = 0;// but the feature end is still valid!!\r
+\r
+        if(fstart==fend)\r
+        {\r
+          g.setColor(Color.red);\r
+          g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);\r
+          g.setColor(Color.white);\r
+\r
+          char s = seq.getSequence().charAt(fstart);\r
+          FontMetrics fm = g.getFontMetrics();\r
+          int charOffset =  (width - fm.charWidth(s))/2;\r
+          int pady = height/5;\r
+          g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady);\r
 \r
-\r
-    public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) {\r
-       Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null);\r
-       return c;\r
-    }\r
-\r
-    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) {\r
-\r
-       int i      = start;\r
-       int length = seq.getLength();\r
-\r
-       Color currentColor = Color.black;\r
-\r
-\r
-       int    prev   = -1;\r
-        int    fstart = 0;\r
-        char   prevc   = '-';\r
-\r
-       g.setColor(Color.magenta);\r
-\r
-       while (i <= end && i < length) {\r
-            char c = seq.getCharAt(i);\r
-           if (c != '-') {\r
-\r
-              if (prevc != c) {\r
-\r
-                if (prevc == 'F') {\r
-                  g.setColor(Color.green);\r
-                } else if (prevc == 'R') {\r
-                  g.setColor(Color.cyan);\r
-                } else if (prevc == 'M') {\r
-                  g.setColor(Color.magenta);\r
-                } else if (prevc == 'P') {\r
-                  g.setColor(Color.yellow);\r
-                }\r
-               g.fillRect(x1+(int)(width*(i-fstart)),y1+height/4,(int)((prev-fstart+1)*width),height/2);\r
-\r
-                prevc   = c;\r
-                fstart = i;\r
-            }\r
-          } else if (prevc != '-') {\r
-                if (prevc == 'F') {\r
-                  g.setColor(Color.green);\r
-                } else if (prevc == 'R') {\r
-                  g.setColor(Color.cyan);\r
-                } else if (prevc == 'M') {\r
-                  g.setColor(Color.magenta);\r
-                } else if (prevc == 'P') {\r
-                  g.setColor(Color.yellow);\r
-                }\r
-               g.fillRect(x1+(int)(width*(fstart-start)),y1+height/4,(int)((i-fstart+1)*width),height/2);\r
-\r
-                prevc = c;\r
-          } else {\r
-            fstart = -1;\r
+        }\r
+        else\r
+        {\r
+          for (int i = fstart; i <= fend; i++)\r
+          {\r
+            char s = seq.getSequence().charAt(i);\r
+            if( jalview.util.Comparison.isGap(s) )\r
+              continue;\r
+\r
+            g.setColor(Color.blue);\r
+            g.fillRect( (i-start) * width, y1, width, height);\r
+\r
+            g.setColor(Color.white);\r
+\r
+            FontMetrics fm = g.getFontMetrics();\r
+            int charOffset = (width - fm.charWidth(s)) / 2;\r
+            int pady = height / 5;\r
+            g.drawString(String.valueOf(s),\r
+                         charOffset + x1 + width * (i-start),\r
+                         y1 + height - pady);\r
           }\r
-           i++;\r
-       }\r
-\r
-        if (fstart != -1) {\r
-        if (prevc == 'F') {\r
-          g.setColor(Color.green);\r
-        } else if (prevc == 'R') {\r
-          g.setColor(Color.cyan);\r
-        } else if (prevc == 'M') {\r
-          g.setColor(Color.magenta);\r
-        } else if (prevc == 'P') {\r
-          g.setColor(Color.yellow);\r
         }\r
+      }\r
 \r
-       //g.fillRect(x1+(int)(width*(fstart-start)),y1+height/4,(int)((end-fstart+1)*width),height/2);\r
-\r
-        }\r
     }\r
+   }\r
 \r
 }\r