/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 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(null);\r
this.av = av;\r
- PaintRefresher.Register(this, av.alignment);\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
}\r
\r
public void drawIdString(Graphics gg, SequenceI s, int i, int starty,\r
if (searchResults != null && searchResults.contains(s))\r
{\r
gg.setColor(Color.black);\r
- gg.fillRect(0, ((i - starty) * charHeight) + ypos,\r
+ gg.fillRect(0, ( (i - starty) * charHeight) + ypos,\r
getSize().width, charHeight);\r
gg.setColor(Color.white);\r
}\r
else if (av.getSelectionGroup() != null &&\r
- av.getSelectionGroup().getSequences(false).contains(s))\r
+ av.getSelectionGroup().getSequences(null).contains(s))\r
{\r
gg.setColor(Color.lightGray);\r
- gg.fillRect(0, ((i - starty) * charHeight) + ypos,\r
+ gg.fillRect(0, ( (i - starty) * charHeight) + ypos,\r
getSize().width, charHeight);\r
gg.setColor(Color.white);\r
}\r
else\r
{\r
- gg.setColor(s.getColor());\r
- gg.fillRect(0, ((i - starty) * charHeight) + ypos,\r
+ gg.setColor(av.getSequenceColour(s));\r
+ gg.fillRect(0, ( (i - starty) * charHeight) + ypos,\r
getSize().width, charHeight);\r
gg.setColor(Color.black);\r
}\r
\r
-\r
- gg.drawString( s.getDisplayId(av.getShowJVSuffix()), 0,\r
- ((i - starty) * charHeight) + ypos +\r
+ gg.drawString(s.getDisplayId(av.getShowJVSuffix()), 0,\r
+ ( (i - starty) * charHeight) + ypos +\r
charHeight - (charHeight / 5));\r
\r
if (av.hasHiddenRows && av.showHiddenMarkers)\r
- drawMarker(i, starty, ypos);\r
+ {\r
+ drawMarker(i, starty, ypos);\r
+ }\r
\r
}\r
\r
int alheight = av.alignment.getHeight();\r
\r
if (av.hasHiddenColumns)\r
+ {\r
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ }\r
\r
int annotationHeight = 0;\r
AnnotationLabels labels = null;\r
\r
int hgap = av.charHeight;\r
if (av.scaleAboveWrapped)\r
+ {\r
hgap += av.charHeight;\r
+ }\r
\r
int cHeight = alheight * av.charHeight\r
+ hgap\r
setHiddenFont(i);\r
}\r
else\r
+ {\r
gg.setFont(italic);\r
+ }\r
\r
SequenceI s = av.alignment.getSequenceAt(i);\r
drawIdString(gg, s, i, 0, ypos);\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
+ if (seq == null)\r
+ {\r
+ continue;\r
+ }\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(null).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
if (av.hasHiddenRows && av.showHiddenMarkers)\r
+ {\r
drawMarker(i, starty, 0);\r
+ }\r
}\r
}\r
}\r
\r
void drawMarker(int i, int starty, int yoffset)\r
{\r
- SequenceI [] hseqs = av.alignment.getHiddenSequences().hiddenSequences;\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
boolean below = (hiddenIndex > lastIndex + 1);\r
boolean above = (nextIndex > hiddenIndex + 1);\r
\r
-\r
-\r
- for(int j=0; j<hSize; j++)\r
+ for (int j = 0; j < hSize; j++)\r
{\r
if (hseqs[j] != null)\r
{\r
- if(j-1<hiddenIndex)\r
+ if (j - 1 < hiddenIndex)\r
+ {\r
hiddenIndex++;\r
- if(j-1<lastIndex)\r
+ }\r
+ if (j - 1 < lastIndex)\r
+ {\r
lastIndex++;\r
- if(j-1<nextIndex)\r
+ }\r
+ if (j - 1 < nextIndex)\r
+ {\r
nextIndex++;\r
+ }\r
}\r
- }\r
+ }\r
\r
- gg.setColor(Color.blue);\r
- if(below)\r
- {\r
- gg.fillPolygon(new int[]\r
- {getSize().width- av.charHeight,\r
- getSize().width- av.charHeight,\r
- getSize().width},\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
- {getSize().width- av.charHeight,\r
- getSize().width - av.charHeight,\r
- getSize().width },\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
+ gg.setColor(Color.blue);\r
+ if (below)\r
+ {\r
+ gg.fillPolygon(new int[]\r
+ {getSize().width - av.charHeight,\r
+ getSize().width - av.charHeight,\r
+ getSize().width},\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
+ {getSize().width - av.charHeight,\r
+ getSize().width - av.charHeight,\r
+ getSize().width},\r
+ new int[]\r
+ {\r
+ (i - starty + 1) * av.charHeight + yoffset,\r
+ (i - starty + 1) * av.charHeight + yoffset -\r
+ av.charHeight / 4,\r
+ (i - starty + 1) * av.charHeight + yoffset\r
+ }, 3);\r
\r
- }\r
+ }\r
}\r
\r
void setHiddenFont(int i)\r
{\r
- /* System.out.println(i+" "+av.alignment.getHeight());\r
- if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)\r
- gg.setFont(new Font(av.getFont().getName(), Font.BOLD,\r
- av.getFont().getSize()));\r
- else\r
- gg.setFont(new Font(av.getFont().getName(), Font.ITALIC,\r
- av.getFont().getSize()));*/\r
+ /* System.out.println(i+" "+av.alignment.getHeight());\r
+ if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)\r
+ gg.setFont(new Font(av.getFont().getName(), Font.BOLD,\r
+ av.getFont().getSize()));\r
+ else\r
+ gg.setFont(new Font(av.getFont().getName(), Font.ITALIC,\r
+ av.getFont().getSize()));*/\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff