\r
public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
{\r
- this.addKeyListener(new KeyAdapter()\r
- {\r
- public void keyPressed(KeyEvent ke)\r
- {\r
- System.out.println("Align Panel "+ke);\r
- }\r
- });\r
-\r
try\r
{\r
jbInit();\r
annotationPanel = new AnnotationPanel(this);\r
alabels = new AnnotationLabels(this);\r
\r
+ setAnnotationVisible(av.showAnnotation);\r
+\r
idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);\r
annotationScroller.add(annotationPanel);\r
{\r
// set idCanvas bufferedImage to null\r
// to prevent drawing old image\r
+ idPanel.idCanvas.image =null;\r
FontMetrics fm = getFontMetrics(av.getFont());\r
\r
scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));\r
idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));\r
\r
- annotationPanel.adjustPanelHeight();\r
+ int ap = annotationPanel.adjustPanelHeight();\r
annotationPanel.repaint();\r
Dimension d = calculateIdWidth();\r
d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);\r
+ alabels.setSize(d.width+4, ap );\r
idPanel.idCanvas.setSize(d);\r
hscrollFillerPanel.setSize(d);\r
\r
- alignFrame.pack();\r
+ validate();\r
+ repaint();\r
\r
if(overviewPanel!=null)\r
overviewPanel.updateOverviewImage();\r
return new Dimension(idWidth, idPanel.idCanvas.getSize().height);\r
}\r
\r
- public void highlightSearchResults(int[] results)\r
+ public void highlightSearchResults(SearchResults results)\r
{\r
seqPanel.seqCanvas.highlightSearchResults(results);\r
\r
- // do we need to scroll the panel?\r
+ // do we need to scroll the panel?\r
if (results != null)\r
{\r
- SequenceI seq = av.alignment.getSequenceAt(results[0]);\r
- int start = seq.findIndex(results[1]) - 1;\r
- int end = seq.findIndex(results[2]) - 1;\r
- if (av.getStartRes() > start\r
- || av.getEndRes() < end\r
- || (av.getStartSeq() > results[0]\r
- || av.getEndSeq() < results[0]))\r
- {\r
- setScrollValues(start, results[0]);\r
- }\r
+ SequenceI seq = results.getResultSequence(0);\r
+ int seqIndex = av.alignment.findIndex(seq);\r
+ int start = seq.findIndex(results.getResultStart(0)) - 1;\r
+ int end = seq.findIndex(results.getResultEnd(0)) - 1;\r
+\r
+ if(!av.wrapAlignment)\r
+ {\r
+ if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||\r
+ ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))\r
+ {\r
+ if (start > av.alignment.getWidth() - hextent)\r
+ {\r
+ start = av.alignment.getWidth() - hextent;\r
+ if (start < 0)\r
+ start = 0;\r
+ }\r
+ if (seqIndex > av.alignment.getHeight() - vextent)\r
+ {\r
+ seqIndex = av.alignment.getHeight() - vextent;\r
+ if (seqIndex < 0)\r
+ seqIndex = 0;\r
+ }\r
+ setScrollValues(start, seqIndex);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.\r
+ seqCanvas.getSize().width);\r
+ if (start < av.getStartRes() || start > (av.getStartRes() + cwidth))\r
+ {\r
+ vscroll.setValue(start / cwidth);\r
+ av.startRes = vscroll.getValue() * cwidth;\r
+ }\r
+ }\r
}\r
\r
+ repaint();\r
}\r
\r
public OverviewPanel getOverviewPanel()\r
{\r
av.startSeq = 0;\r
scalePanelHolder.setVisible(!wrap);\r
+\r
+\r
hscroll.setVisible(!wrap);\r
idwidthAdjuster.setVisible(!wrap);\r
\r
annotationSpaceFillerHolder.setVisible(true);\r
}\r
\r
+\r
idSpaceFillerPanel1.setVisible(!wrap);\r
\r
+ fontChanged();//This is so that the scalePanel is resized correctly\r
+\r
validate();\r
repaint();\r
\r
int oldX = av.getStartRes();\r
int oldY = av.getStartSeq();\r
\r
- if (evt.getSource() == hscroll)\r
+ if (evt==null || evt.getSource() == hscroll)\r
{\r
int x = hscroll.getValue();\r
av.setStartRes(x);\r
1);\r
}\r
\r
- if (evt.getSource() == vscroll)\r
+ if (evt==null || evt.getSource() == vscroll)\r
{\r
int offy = vscroll.getValue();\r
if (av.getWrapAlignment())\r
overviewPanel.setBoxPosition();\r
}\r
\r
+ int scrollX = av.startRes - oldX;\r
+ int scrollY = av.startSeq - oldY;\r
+\r
if (av.getWrapAlignment() || !fastPaint || MAC)\r
{\r
repaint();\r
}\r
- else\r
+ else if(!seqPanel.seqCanvas.fastPaint)\r
{\r
- idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);\r
- seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,\r
- av.getStartSeq() - oldY);\r
+ // Make sure we're not trying to draw a panel\r
+ // larger than the visible window\r
+ if(scrollX>av.endRes-av.startRes)\r
+ scrollX = av.endRes-av.startRes;\r
+ else if(scrollX<av.startRes-av.endRes)\r
+ scrollX = av.startRes - av.endRes;\r
+\r
+ idPanel.idCanvas.fastPaint(scrollY);\r
+ seqPanel.seqCanvas.fastPaint(scrollX,\r
+ scrollY);\r
\r
scalePanel.repaint();\r
if (av.getShowAnnotation())\r
}\r
\r
alabels.repaint();\r
- idPanel.idCanvas.repaint();\r
+\r
seqPanel.seqCanvas.repaint();\r
scalePanel.repaint();\r
annotationPanel.repaint();\r
+ idPanel.idCanvas.repaint();\r
\r
if (getBounds() == g.getClipBounds())\r
{\r