renderGaps = b;\r
}\r
\r
- public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
+ public Color getResidueBoxColour(SequenceI seq, int i)\r
{\r
- getBoxColour(cs, seq, i);\r
+ allGroups = av.alignment.findAllGroups(seq);\r
+\r
+ if (inCurrentSequenceGroup(i))\r
+ {\r
+ if (currentSequenceGroup.getDisplayBoxes())\r
+ {\r
+ getBoxColour(currentSequenceGroup.cs, seq, i);\r
+ }\r
+ }\r
+ else if (av.getShowBoxes())\r
+ {\r
+ getBoxColour(av.globalColourScheme, seq, i);\r
+ }\r
+\r
return resBoxColour;\r
- }\r
+ }\r
\r
void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
{\r
}\r
}\r
\r
+ public Color findSequenceColour(SequenceI seq, int i)\r
+ {\r
+ allGroups = av.alignment.findAllGroups(seq);\r
+ drawBoxes(seq, i,i, 0, 0, 1,1);\r
+ return resBoxColour;\r
+ }\r
+\r
public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
int start, int end, int x1, int y1, int width,\r
int height)\r
public void drawText(SequenceI seq, int start, int end, int x1, int y1,\r
int width, int height)\r
{\r
- int pady = height / 5;\r
- int charOffset = 0;\r
- char s=' ';\r
- // Need to find the sequence position here.\r
\r
- String sequence = seq.getSequence();\r
+ y1 += height - height / 5; // height/5 replaces pady\r
+\r
+ int charOffset = 0;\r
\r
+ // Need to find the sequence position here.\r
if(end+1>=seq.getLength())\r
end = seq.getLength()-1;\r
\r
+ char s = ' ';\r
+\r
for (int i = start; i <= end; i++)\r
{\r
graphics.setColor(Color.black);\r
\r
- s = sequence.charAt(i);\r
-\r
+ s = seq.getCharAt(i);\r
if (!renderGaps && jalview.util.Comparison.isGap(s))\r
{\r
continue;\r
\r
charOffset = (width - fm.charWidth(s)) / 2;\r
graphics.drawString(String.valueOf(s),\r
- charOffset + x1 + width * (i - start),\r
- y1 + height - pady);\r
+ charOffset + x1 + width * (i - start),\r
+ y1 );\r
}\r
\r
}\r