Use the isGap method in utils

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

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 4264c64..5022050 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -27,9 +27,10 @@ public class SequenceRenderer implements RendererI
   public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
   {\r
    Color c = Color.white;\r
-    try{\r
-       c = cs.findColour(seq, seq.getSequence(i, i + 1), i, null);\r
-    }catch(Exception ex){}\r
+try{\r
+     if (cs != null)\r
+       c = cs.findColour(seq.getSequence(i, i + 1), i, av.getConsensus(false));\r
+   }catch(Exception ex){}\r
 \r
     return c;\r
   }\r
@@ -54,50 +55,18 @@ public class SequenceRenderer implements RendererI
     int curStart = x1;\r
     int curWidth = width;\r
 \r
-    if(currentSequenceGroup!=null && currentSequenceGroup.getDisplayBoxes())\r
-    {\r
-      curStart = currentSequenceGroup.getStartRes();\r
-      curWidth = currentSequenceGroup.getEndRes();\r
-    }\r
-\r
-  //  int threshold = 80;\r
-\r
     while (i <= end && i < length)\r
     {\r
+      color = color.white;\r
+\r
       if(inCurrentSequenceGroup(i))\r
       {\r
-        color = getResidueBoxColour(currentSequenceGroup.cs, seq, i);\r
+        if( currentSequenceGroup.getDisplayBoxes())\r
+             color = getResidueBoxColour(currentSequenceGroup.cs, seq, i);\r
       }\r
-      else\r
-        color = getResidueBoxColour(av.getGlobalColourScheme(), seq, i);\r
-\r
-    //  Hashtable hash  = (Hashtable)freq.elementAt(i-start);\r
-    //  String    s     = (String)hash.get("maxResidue");\r
-    //  int       count = ((Integer)hash.get("maxCount")).intValue();\r
-  //    int       max   = ((Integer)hash.get("size")).intValue();\r
-   //   int       nongap = ((Integer)hash.get("nongap")).intValue();\r
-   //   float     frac  = (float)(count*1.0/(1.0*nongap));\r
-\r
-      //System.out.println("Frac/count/nongap " + frac + " " + count + " " + nongap);\r
-    /*  if (!seq.getSequence().substring(i,i+1).equals(s) ||\r
-         s.equals("-") ||\r
-         s.equals(".") ||\r
-         s.equals(" "))\r
-      {\r
-       c = Color.white;\r
-      } else {\r
-       if (frac > 0.9) {\r
-         c = Color.red;\r
-       } else if (frac > 0.8) {\r
-         c = Color.orange;\r
-       } else if (frac > 0.7) {\r
-         c = Color.pink;\r
-       } else if (frac > 0.5) {\r
-         c = Color.yellow;\r
-       } else if (frac> 0.3) {\r
-           c = Color.lightGray;\r
-       }\r
-      }*/\r
+      else if(av.getShowBoxes())\r
+           color = getResidueBoxColour(av.getGlobalColourScheme(), seq, i);\r
+\r
 \r
       if (color != currentColor || color != null)\r
       {\r
@@ -132,9 +101,10 @@ public class SequenceRenderer implements RendererI
         else\r
           s = ' ';\r
 \r
-        if(!renderGaps && (s=='-' || s=='.' || s==' '))\r
+        if(!renderGaps && jalview.util.Comparison.isGap(s))\r
           continue;\r
 \r
+        g.setColor(Color.black);\r
 \r
         if (inCurrentSequenceGroup(i))\r
         {\r
@@ -145,7 +115,13 @@ public class SequenceRenderer implements RendererI
             g.setColor(getResidueBoxColour(currentSequenceGroup.cs, seq, i).darker());\r
         }\r
         else\r
-          g.setColor(Color.black);\r
+        {\r
+          if(!av.getShowText())\r
+            continue;\r
+\r
+          if(av.getColourText())\r
+            g.setColor(getResidueBoxColour(av.getGlobalColourScheme(), seq, i).darker());\r
+        }\r
 \r
       charOffset =  (width - fm.charWidth(s))/2;\r
       g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);\r