{\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
&& !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
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