From 2f96585f0cd39dc5cac42011d602b08740148518 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 13 Nov 2006 11:11:22 +0000
Subject: [PATCH] Colour text

---
 src/jalview/gui/RotatableCanvas.java  |    4 +--
 src/jalview/gui/SequenceRenderer.java |   55 ++++++++++++++++++++++++++-------
 2 files changed, 46 insertions(+), 13 deletions(-)

diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 458d971..b30dc34 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -397,13 +397,13 @@ public class RotatableCanvas extends JPanel implements MouseListener,
                 halfheight;
             float z = sp.coord[1] - centre[2];
 
-            if (sp.sequence.getColor() == Color.black)
+            if (av.getSequenceColour(sp.sequence) == Color.black)
             {
                 g.setColor(Color.white);
             }
             else
             {
-                g.setColor(sp.sequence.getColor());
+                g.setColor(av.getSequenceColour(sp.sequence));
             }
 
             if (av.getSelectionGroup() != null)
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 739187b..8d7755c 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -227,10 +227,14 @@ 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);
@@ -242,9 +246,11 @@ public class SequenceRenderer
         }
         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");
         }
     }
 
-- 
1.7.10.2