/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
}\r
else\r
{\r
- gg.setColor(s.getColor());\r
+ gg.setColor(av.getSequenceColour(s));\r
gg.fillRect(0, ((i - starty) * charHeight) + ypos,\r
getSize().width, charHeight);\r
gg.setColor(Color.black);\r
//Now draw the id strings\r
\r
//Now draw the id strings\r
+ SequenceI seq;\r
for (int i = starty; i < endy; i++)\r
{\r
if (av.hasHiddenRows)\r
setHiddenFont(i);\r
}\r
\r
+ seq = av.alignment.getSequenceAt(i);\r
+\r
// Selected sequence colours\r
if ( (searchResults != null) &&\r
- searchResults.contains(av.alignment.getSequenceAt(i)))\r
+ searchResults.contains(seq))\r
{\r
currentColor = Color.black;\r
currentTextColor = Color.white;\r
}\r
else if ( (av.getSelectionGroup() != null) &&\r
- av.getSelectionGroup().getSequences(false).contains(\r
- av.alignment.getSequenceAt(i)))\r
+ av.getSelectionGroup().getSequences(false).contains(seq))\r
{\r
currentColor = Color.lightGray;\r
currentTextColor = Color.black;\r
}\r
else\r
{\r
- currentColor = av.alignment.getSequenceAt(i).getColor();\r
+ currentColor = av.getSequenceColour(seq);\r
currentTextColor = Color.black;\r
}\r
\r
\r
gg.setColor(currentTextColor);\r
\r
- String string = av.alignment.getSequenceAt(i).getDisplayId(av.\r
- getShowJVSuffix());\r
\r
- gg.drawString(string, 0,\r
+ gg.drawString(seq.getDisplayId(av.getShowJVSuffix()),\r
+ 0,\r
( ( (i - starty) * av.charHeight) + av.charHeight) -\r
(av.charHeight / 5));\r
\r
\r
void drawMarker(int i, int starty, int yoffset)\r
{\r
- int hiddenIndex = av.adjustForHiddenSeqs(i);\r
- int lastIndex = av.adjustForHiddenSeqs(i - 1);\r
- int nextIndex = av.adjustForHiddenSeqs(i + 1);\r
+ SequenceI [] hseqs = av.alignment.getHiddenSequences().hiddenSequences;\r
+ //Use this method here instead of calling hiddenSeq adjust\r
+ //3 times.\r
+ int hSize = hseqs.length;\r
+\r
+ int hiddenIndex = i;\r
+ int lastIndex = i - 1;\r
+ int nextIndex = i + 1;\r
\r
boolean below = (hiddenIndex > lastIndex + 1);\r
- boolean above = (nextIndex>hiddenIndex+1);\r
+ boolean above = (nextIndex > hiddenIndex + 1);\r
+\r
+\r
+\r
+ for(int j=0; j<hSize; j++)\r
+ {\r
+ if (hseqs[j] != null)\r
+ {\r
+ if(j-1<hiddenIndex)\r
+ hiddenIndex++;\r
+ if(j-1<lastIndex)\r
+ lastIndex++;\r
+ if(j-1<nextIndex)\r
+ nextIndex++;\r
+ }\r
+ }\r
\r
gg.setColor(Color.blue);\r
if(below)\r