switch (evt.getKeyCode())\r
{\r
case 27: // escape key\r
- av.setSelectionGroup(null);\r
- repaint();\r
+ alignFrame.deselectAllSequenceMenuItem_actionPerformed(null);\r
\r
break;\r
\r
if(!av.cursorMode)\r
{\r
alignFrame.cut_actionPerformed(null);\r
- seqPanel.seqCanvas.repaint();\r
}\r
else\r
seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());\r
}\r
break;\r
case KeyEvent.VK_C:\r
- if(av.cursorMode)\r
+ if(av.cursorMode && !evt.isControlDown())\r
{\r
seqPanel.setCursorColumn();\r
}\r
*/\r
public void adjustmentValueChanged(AdjustmentEvent evt)\r
{\r
+\r
int oldX = av.getStartRes();\r
int oldY = av.getStartSeq();\r
\r
\r
if (av.getWrapAlignment())\r
{\r
- int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.\r
- seqCanvas.getWidth());\r
- av.setStartRes(vscroll.getValue() * rowSize);\r
- av.setEndRes( (vscroll.getValue() + 1) * rowSize);\r
+ if(offy>-1)\r
+ {\r
+ int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.\r
+ seqCanvas.getWidth());\r
+ av.setStartRes(offy * rowSize);\r
+ av.setEndRes( (offy + 1) * rowSize);\r
+ }\r
+ else\r
+ {\r
+ //This is only called if file loaded is a jar file that\r
+ //was wrapped when saved and user has wrap alignment true\r
+ //as preference setting\r
+ SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ setScrollValues(av.getStartRes(), av.getStartSeq());\r
+ }\r
+ });\r
+ }\r
}\r
else\r
{\r
\r
if (av.getWrapAlignment())\r
{\r
- int max = av.alignment.getWidth() /\r
- seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;\r
+ int maxwidth = av.alignment.getWidth();\r
+\r
+ if (av.hasHiddenColumns)\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+\r
+ int max = maxwidth /\r
+ seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +\r
+ 1;\r
\r
\r
vscroll.setMaximum(max);\r
for (int i = startSeq; i < endSeq; i++)\r
{\r
if ( (av.getSelectionGroup() != null) &&\r
- av.getSelectionGroup().sequences.contains(\r
+ av.getSelectionGroup().getSequences(false).contains(\r
av.getAlignment().getSequenceAt(i)))\r
{\r
currentColor = Color.gray;\r
\r
int idWidth = calculateIdWidth().width + 4;\r
\r
+ int maxwidth = av.alignment.getWidth();\r
+ if (av.hasHiddenColumns)\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+\r
+\r
int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -\r
idWidth);\r
\r
- int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);\r
+ int totalHeight = cHeight * (maxwidth / resWidth + 1);\r
\r
pg.setColor(Color.white);\r
pg.fillRect(0, 0, pwidth, pheight);\r
\r
void makeAlignmentImage(int type, File file)\r
{\r
+ int maxwidth = av.alignment.getWidth();\r
+ if (av.hasHiddenColumns)\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);\r
+\r
int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
- int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);\r
+ int width = idPanel.getWidth() + (maxwidth * av.charWidth);\r
if (idPanel.getWidth() == 0)\r
{\r
width += calculateIdWidth().getWidth() + 4;\r
width = alignFrame.getWidth() - 22;\r
}\r
else\r
-\r
width = seqPanel.getWidth() + idPanel.getWidth();\r
\r
}\r
+ hgap\r
+ annotationHeight;\r
\r
- int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;\r
+ int maxwidth = av.alignment.getWidth();\r
+ if (av.hasHiddenColumns)\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+\r
+\r
+ int height = ( (maxwidth / chunkWidth) + 1) * cHeight;\r
\r
return height;\r
}\r