/*\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
setLayout(null);\r
\r
sr = new SequenceRenderer(av);\r
- sr.renderGaps( false );\r
+ sr.renderGaps = false;\r
sr.forOverview = true;\r
fr = new FeatureRenderer(av);\r
- fr.overview = true;\r
-\r
\r
// scale the initial size of overviewpanel to shape of alignment\r
float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight();\r
{\r
public void mouseDragged(MouseEvent evt)\r
{\r
- if(!av.wrapAlignment)\r
- doMouseDragged(evt);\r
+ if (!av.wrapAlignment)\r
+ {\r
+ boxX = evt.getX();\r
+ boxY = evt.getY();\r
+ checkValid();\r
+ }\r
}\r
});\r
\r
public void mousePressed(MouseEvent evt)\r
{\r
if(!av.wrapAlignment)\r
- doMousePressed(evt);\r
- }\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- if(!av.wrapAlignment)\r
- doMouseReleased(evt);\r
+ {\r
+ boxX = evt.getX();\r
+ boxY = evt.getY();\r
+ checkValid();\r
+ }\r
}\r
});\r
\r
updateOverviewImage();\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void doMousePressed(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
-\r
- checkValid();\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void doMouseReleased(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
- checkValid();\r
-\r
- if(av.hasHiddenColumns)\r
- {\r
- int col = (int) ( boxX / scalew / av.getCharWidth());\r
-\r
- if(av.getColumnSelection().isVisible(col))\r
- {\r
- ap.setScrollValues(\r
- av.getColumnSelection().findColumnPosition(col),\r
- (int) (boxY / scaleh / av.getCharHeight()));\r
- }\r
- else\r
- System.out.println(col +" not visible");\r
- }\r
- else\r
- ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),\r
- (int) (boxY / scaleh / av.getCharHeight()));\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void doMouseDragged(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
- checkValid();\r
-\r
- if(av.hasHiddenColumns)\r
- {\r
- int col = (int) ( boxX / scalew / av.getCharWidth());\r
-\r
- if(!av.getColumnSelection().isVisible(col))\r
- {\r
- return;\r
- }\r
-\r
- ap.setScrollValues(\r
- av.getColumnSelection().findColumnPosition( col ),\r
- (int) (boxY / scaleh / av.getCharHeight()));\r
- }\r
- else\r
- ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),\r
- (int) (boxY / scaleh / av.getCharHeight()));\r
- repaint();\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
boxWidth = (int) ( (av.endRes - av.startRes + 1) *\r
av.getCharWidth() * scalew);\r
}\r
-\r
boxX = width - boxWidth;\r
}\r
+\r
+ int col = (int) (boxX / scalew / av.getCharWidth());\r
+ int row = (int) (boxY / scaleh / av.getCharHeight());\r
+\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ if (!av.getColumnSelection().isVisible(col))\r
+ {\r
+ return;\r
+ }\r
+\r
+ col = av.getColumnSelection().findColumnPosition(col);\r
+ }\r
+\r
+ if( av.hasHiddenRows )\r
+ {\r
+ row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);\r
+ }\r
+\r
+ ap.setScrollValues( col, row );\r
+\r
}\r
\r
/**\r
}\r
\r
setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));\r
- // setBoxPosition();\r
\r
Thread thread = new Thread(this);\r
thread.start();\r
\r
if (av.showSequenceFeatures)\r
{\r
- fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;\r
- fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;\r
- fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;\r
- fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;\r
+ fr.transferSettings( ap.seqPanel.seqCanvas.getFeatureRenderer() );\r
}\r
\r
int alwidth = av.alignment.getWidth();\r
seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);\r
if (seq == null)\r
{\r
-\r
int index =\r
av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(lastrow);\r
\r
-\r
seq = av.alignment.getSequenceAt(index);\r
}\r
else\r
seq, lastcol).getRGB();\r
\r
if (av.showSequenceFeatures)\r
- color = fr.findFeatureColour(color, lastrow, lastcol);\r
+ color = fr.findFeatureColour(color, seq, lastcol);\r
}\r
else\r
{\r
endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);\r
}\r
\r
+ int startSeq = av.startSeq;\r
+ int endSeq = av.endSeq;\r
+\r
+ if (av.hasHiddenRows)\r
+ {\r
+ startSeq =\r
+ av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);\r
+\r
+ endSeq =\r
+ av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);\r
+\r
+ }\r
+\r
\r
scalew = (float) width / (float) fullsizeWidth;\r
scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
\r
boxX = (int) (startRes * av.getCharWidth() * scalew);\r
- boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);\r
+ boxY = (int) (startSeq * av.getCharHeight() * scaleh);\r
+\r
+\r
\r
if(av.hasHiddenColumns)\r
boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);\r
else\r
boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);\r
\r
- boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) -\r
- boxY;\r
+\r
+ boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);\r
+\r
+\r
repaint();\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff