X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=6c7fb37cd615f5a85e52eab5f2be52076f20c43d;hb=b69e028fe41a867e72cda2a6d69182ff0c6bd90e;hp=739187bcd53af277812f6ee524abb06452a3fadf;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 739187b..6c7fb37 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -104,7 +104,7 @@ public class SequenceRenderer
     {
         if (cs != null)
         {
-            resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
+            resBoxColour = cs.findColour(seq.getCharAt(i), i);
         }
         else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
         {
@@ -227,24 +227,30 @@ public class SequenceRenderer
 
         if(end+1>=seq.getLength())
           end = seq.getLength()-1;
-        graphics.setColor(Color.black);
+        graphics.setColor(av.textColour);
 
 
-        if(monospacedFont && av.showText && allGroups.length==0 && !av.getColourText())
+        if(monospacedFont
+           && av.showText
+           && allGroups.length==0
+           && !av.getColourText()
+           && av.thresholdTextColour==0)
         {
-          if(av.renderGaps)
-          graphics.drawString(seq.getSequence(start, end + 1), 0, y1);
-         else
+          if (av.renderGaps)
+            graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
+          else
          {
            char gap = av.getGapCharacter();
-           graphics.drawString( seq.getSequence(start, end+1).replace(gap, ' '), 0, y1);
+           graphics.drawString( seq.getSequenceAsString(start, end+1).replace(gap, ' '), 0, y1);
          }
         }
         else
         {
+          boolean getboxColour = false;
           for (int i = start; i <= end; i++)
           {
-            graphics.setColor(Color.black);
+            graphics.setColor(av.textColour);
+            getboxColour = false;
             s = seq.getCharAt(i);
             if (!renderGaps && jalview.util.Comparison.isGap(s))
             {
@@ -258,11 +264,26 @@ public class SequenceRenderer
                 continue;
               }
 
-              if (currentSequenceGroup.getColourText())
+              if (currentSequenceGroup.thresholdTextColour > 0
+                  || currentSequenceGroup.getColourText())
               {
+                getboxColour = true;
                 getBoxColour(currentSequenceGroup.cs, seq, i);
-                graphics.setColor(resBoxColour.darker());
+
+                if (currentSequenceGroup.getColourText())
+                  graphics.setColor(resBoxColour.darker());
+
+                if (currentSequenceGroup.thresholdTextColour > 0)
+                {
+                  if (resBoxColour.getRed() +
+                      resBoxColour.getBlue() +
+                      resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour)
+                    graphics.setColor(currentSequenceGroup.textColour2);
+                }
               }
+              else
+                  graphics.setColor(currentSequenceGroup.textColour);
+
             }
             else
             {
@@ -273,6 +294,7 @@ public class SequenceRenderer
 
               if (av.getColourText())
               {
+                getboxColour = true;
                 getBoxColour(av.globalColourScheme, seq, i);
 
                 if (av.getShowBoxes())
@@ -284,17 +306,28 @@ public class SequenceRenderer
                   graphics.setColor(resBoxColour);
                 }
               }
+
+              if (av.thresholdTextColour > 0)
+              {
+                if (!getboxColour)
+                  getBoxColour(av.globalColourScheme, seq, i);
+
+                if (resBoxColour.getRed() +
+                    resBoxColour.getBlue() +
+                    resBoxColour.getGreen() < av.thresholdTextColour)
+                  graphics.setColor(av.textColour2);
+              }
+
             }
 
-            charOffset = (av.charWidth - fm.charWidth(s)) / 2;
 
-          //  System.out.print(s);
-            graphics.drawString(String.valueOf(s),
-                                charOffset + av.charWidth * (i - start),
-                                y1);
+
+          charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+          graphics.drawString(String.valueOf(s),
+                              charOffset + av.charWidth * (i - start),
+                              y1);
 
           }
-        //  System.out.println("\n");
         }
     }
 
@@ -354,7 +387,7 @@ public class SequenceRenderer
           {
             if (i < seq.getLength())
             {
-              s = seq.getSequence().charAt(i);
+              s = seq.getCharAt(i);
             }
 
             charOffset = (av.charWidth - fm.charWidth(s)) / 2;