/*\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
setLayout(new BorderLayout());\r
this.av = av;\r
- PaintRefresher.Register(this, av.alignment);\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
}\r
\r
/**\r
* @param starty DOCUMENT ME!\r
* @param ypos DOCUMENT ME!\r
*/\r
- public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,\r
- int ypos)\r
+ public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty, int ypos)\r
{\r
int charHeight = av.charHeight;\r
\r
\r
gg.drawString( s.getDisplayId(av.getShowJVSuffix()),\r
0, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));\r
+\r
+ if (av.hasHiddenRows && av.showHiddenMarkers)\r
+ drawMarker(i, starty, ypos);\r
+\r
+\r
}\r
\r
/**\r
return;\r
}\r
\r
+ int oldHeight = imgHeight;\r
+\r
imgHeight = getHeight();\r
imgHeight -= (imgHeight % av.charHeight);\r
\r
return;\r
}\r
\r
- image = new BufferedImage(getWidth(), imgHeight,\r
- BufferedImage.TYPE_INT_RGB);\r
- gg = (Graphics2D) image.getGraphics();\r
+ if(oldHeight!=imgHeight || image.getWidth(this)!=getWidth())\r
+ {\r
+ image = new BufferedImage(getWidth(), imgHeight,\r
+ BufferedImage.TYPE_INT_RGB);\r
+ }\r
\r
+ gg = (Graphics2D) image.getGraphics();\r
//Fill in the background\r
gg.setColor(Color.white);\r
gg.fillRect(0, 0, getWidth(), imgHeight);\r
\r
-\r
drawIds(av.getStartSeq(), av.endSeq);\r
\r
g.drawImage(image, 0, 0, this);\r
{\r
if (av.hasHiddenRows)\r
{\r
- setHiddenFont(i, starty);\r
+ setHiddenFont(i);\r
}\r
else\r
gg.setFont(italic);\r
labels.drawComponent(gg, getWidth());\r
gg.translate(0, -ypos-(alheight * av.charHeight));\r
}\r
+\r
+\r
}\r
}\r
else\r
{\r
+ //Now draw the id strings\r
+\r
//Now draw the id strings\r
for (int i = starty; i < endy; i++)\r
{\r
if (av.hasHiddenRows)\r
{\r
- setHiddenFont(i, starty);\r
+ setHiddenFont(i);\r
}\r
\r
// Selected sequence colours\r
gg.drawString(string, 0,\r
(((i - starty) * av.charHeight) + av.charHeight) -\r
(av.charHeight / 5));\r
+\r
+ if(av.hasHiddenRows && av.showHiddenMarkers)\r
+ drawMarker(i, starty, 0);\r
+\r
}\r
\r
}\r
}\r
\r
- void setHiddenFont(int i, int starty)\r
+ void drawMarker(int i, int starty, int yoffset)\r
{\r
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
- av.getFont().getSize());\r
- Font bold = new Font(av.getFont().getName(), Font.BOLD,\r
- av.getFont().getSize());\r
\r
- int tmp, hiddenIndex = starty;\r
- tmp = av.adjustForHiddenSeqs(i);\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
- if (av.adjustForHiddenSeqs(i - 1) == tmp - 1)\r
- {\r
- hiddenIndex = tmp;\r
- }\r
+ int hiddenIndex = i;\r
+ int lastIndex = i - 1;\r
+ int nextIndex = i + 1;\r
\r
- if (hiddenIndex != tmp)\r
+ for(int j=0; j<hSize; j++)\r
{\r
- hiddenIndex = tmp;\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
- hiddenIndex++;\r
+ boolean below = (hiddenIndex > lastIndex + 1);\r
+ boolean above = (nextIndex > hiddenIndex+1);\r
+\r
+\r
+ gg.setColor(Color.blue);\r
+ if(below)\r
+ {\r
+ gg.fillPolygon(new int[]\r
+ {getWidth()- av.charHeight,\r
+ getWidth()- av.charHeight,\r
+ getWidth()},\r
+ new int[]\r
+ {\r
+ (i - starty) * av.charHeight +yoffset,\r
+ (i - starty) * av.charHeight +yoffset+ av.charHeight / 4,\r
+ (i - starty) * av.charHeight+yoffset\r
+ }, 3);\r
+ }\r
+ if(above)\r
+ {\r
+ gg.fillPolygon(new int[]\r
+ {getWidth()- av.charHeight,\r
+ getWidth()- av.charHeight,\r
+ getWidth() },\r
+ new int[]\r
+ {\r
+ (i - starty+1) * av.charHeight +yoffset,\r
+ (i - starty+1) * av.charHeight +yoffset- av.charHeight / 4,\r
+ (i - starty+1) * av.charHeight +yoffset\r
+ }, 3);\r
+\r
+ }\r
+ }\r
+\r
+ void setHiddenFont(int i)\r
+ {\r
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
+ av.getFont().getSize());\r
+ Font bold = new Font(av.getFont().getName(), Font.BOLD,\r
+ av.getFont().getSize());\r
+\r
\r
- if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)\r
+ if (av.alignment.getSequenceAt(i)!=null\r
+ && av.alignment.getSequenceAt(i).getHiddenSequences() != null)\r
gg.setFont(bold);\r
else\r
gg.setFont(italic);\r