{\r
if (cs != null)\r
{\r
- resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);\r
+ resBoxColour = cs.findColour(seq.getCharAt(i), i);\r
}\r
else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))\r
{\r
\r
if(end+1>=seq.getLength())\r
end = seq.getLength()-1;\r
- graphics.setColor(Color.black);\r
+ graphics.setColor(av.textColour);\r
\r
\r
- if(monospacedFont && av.showText && allGroups.length==0 && !av.getColourText())\r
+ if(monospacedFont\r
+ && av.showText\r
+ && allGroups.length==0\r
+ && !av.getColourText()\r
+ && av.thresholdTextColour==0)\r
{\r
- if(av.renderGaps)\r
- graphics.drawString(seq.getSequence(start, end + 1), 0, y1);\r
- else\r
+ if (av.renderGaps)\r
+ graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);\r
+ else\r
{\r
char gap = av.getGapCharacter();\r
- graphics.drawString( seq.getSequence(start, end+1).replace(gap, ' '), 0, y1);\r
+ graphics.drawString( seq.getSequenceAsString(start, end+1).replace(gap, ' '), 0, y1);\r
}\r
}\r
else\r
{\r
+ boolean getboxColour = false;\r
for (int i = start; i <= end; i++)\r
{\r
- graphics.setColor(Color.black);\r
+ graphics.setColor(av.textColour);\r
+ getboxColour = false;\r
s = seq.getCharAt(i);\r
if (!renderGaps && jalview.util.Comparison.isGap(s))\r
{\r
continue;\r
}\r
\r
- if (currentSequenceGroup.getColourText())\r
+ if (currentSequenceGroup.thresholdTextColour > 0\r
+ || currentSequenceGroup.getColourText())\r
{\r
+ getboxColour = true;\r
getBoxColour(currentSequenceGroup.cs, seq, i);\r
- graphics.setColor(resBoxColour.darker());\r
+\r
+ if (currentSequenceGroup.getColourText())\r
+ graphics.setColor(resBoxColour.darker());\r
+\r
+ if (currentSequenceGroup.thresholdTextColour > 0)\r
+ {\r
+ if (resBoxColour.getRed() +\r
+ resBoxColour.getBlue() +\r
+ resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour)\r
+ graphics.setColor(currentSequenceGroup.textColour2);\r
+ }\r
}\r
+ else\r
+ graphics.setColor(currentSequenceGroup.textColour);\r
+\r
}\r
else\r
{\r
\r
if (av.getColourText())\r
{\r
+ getboxColour = true;\r
getBoxColour(av.globalColourScheme, seq, i);\r
\r
if (av.getShowBoxes())\r
graphics.setColor(resBoxColour);\r
}\r
}\r
+\r
+ if (av.thresholdTextColour > 0)\r
+ {\r
+ if (!getboxColour)\r
+ getBoxColour(av.globalColourScheme, seq, i);\r
+\r
+ if (resBoxColour.getRed() +\r
+ resBoxColour.getBlue() +\r
+ resBoxColour.getGreen() < av.thresholdTextColour)\r
+ graphics.setColor(av.textColour2);\r
+ }\r
+\r
}\r
\r
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
\r
- // System.out.print(s);\r
- graphics.drawString(String.valueOf(s),\r
- charOffset + av.charWidth * (i - start),\r
- y1);\r
+\r
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
+ graphics.drawString(String.valueOf(s),\r
+ charOffset + av.charWidth * (i - start),\r
+ y1);\r
\r
}\r
- // System.out.println("\n");\r
}\r
}\r
\r
{\r
if (i < seq.getLength())\r
{\r
- s = seq.getSequence().charAt(i);\r
+ s = seq.getCharAt(i);\r
}\r
\r
charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r