annotationPanel = new AnnotationPanel(this);\r
alabels = new AnnotationLabels(this);\r
\r
- annotationSpaceFillerHolder.setPreferredSize(annotationPanel.\r
- getPreferredSize());\r
- annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());\r
+\r
annotationScroller.setViewportView(annotationPanel);\r
annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);\r
\r
*\r
* @param results DOCUMENT ME!\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
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
+ 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.getStartRes() > start) || (av.getEndRes() < end) ||\r
- ( (av.getStartSeq() > results[0]) ||\r
- (av.getEndSeq() < results[0])))\r
+ if(!av.wrapAlignment)\r
{\r
- setScrollValues(start, results[0]);\r
+ if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||\r
+ ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))\r
+ {\r
+ setScrollValues(start, seqIndex);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\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
overviewPanel.setBoxPosition();\r
}\r
\r
- int xShift = av.getStartRes() - oldX;\r
- int yShift = av.getStartSeq() - oldY;\r
+ int scrollX = av.startRes - oldX;\r
+ int scrollY = av.startSeq - oldY;\r
\r
- if ( (xShift != 0 && yShift != 0) ||\r
- (Math.abs(xShift) > av.getEndRes() - av.getStartRes()\r
- || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq())\r
- || av.getWrapAlignment()\r
- || !fastPaint)\r
+ if (av.getWrapAlignment() || !fastPaint)\r
{\r
- // Either no shift at all, or shift greater than visible amount\r
repaint();\r
}\r
else\r
{\r
- idPanel.idCanvas.fastPaint(yShift);\r
- seqPanel.seqCanvas.fastPaint(xShift, yShift);\r
-\r
- scalePanel.repaint();\r
-\r
- if (av.getShowAnnotation())\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
+ if(scrollX!=0 || scrollY!=0)\r
{\r
- annotationPanel.fastPaint(xShift);\r
+ idPanel.idCanvas.fastPaint(scrollY);\r
+ seqPanel.seqCanvas.fastPaint(scrollX,\r
+ scrollY);\r
+ scalePanel.repaint();\r
+\r
+ if (av.getShowAnnotation())\r
+ {\r
+ annotationPanel.fastPaint(scrollX);\r
+ }\r
}\r
}\r
}\r
Color currentColor = null;\r
Color currentTextColor = null;\r
\r
+ pg.setFont(new Font(av.getFont().getName(),\r
+ Font.ITALIC,\r
+ av.getFont().getSize()));\r
for (int i = startSeq; i < endSeq; i++)\r
{\r
if ( (av.getSelectionGroup() != null) &&\r
(av.getCharHeight() / 5));\r
}\r
\r
+ pg.setFont(av.getFont());\r
+\r
// draw main sequence panel\r
pg.translate(idWidth, 0);\r
- seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,\r
- startRes, startSeq, 0);\r
+ seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);\r
\r
if (av.showAnnotation && (endSeq == av.alignment.getHeight()))\r
{\r
- pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight + 3);\r
+ pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);\r
alabels.drawComponent( (Graphics2D) pg, idWidth);\r
- pg.translate(idWidth, 0);\r
+ pg.translate(idWidth+3, 0);\r
annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +\r
1);\r
}\r
}\r
if (labels != null)\r
{\r
- pg.translate(0,\r
+ pg.translate(-3,\r
ypos +\r
(av.getAlignment().getHeight() * av.charHeight));\r
\r
pg.setFont(av.getFont());\r
labels.drawComponent(pg, idWidth);\r
pg.setFont(italic);\r
- pg.translate(0,\r
+ pg.translate(+3,\r
-ypos -\r
(av.getAlignment().getHeight() * av.charHeight));\r
}\r
if (av.getWrapAlignment())\r
{\r
if(im.getGraphics()!=null)\r
+ {\r
printWrappedAlignment(im.getGraphics(), width, height, 0);\r
+ im.writeImage();\r
+ }\r
}\r
else\r
{\r
if(im.getGraphics()!=null)\r
+ {\r
printUnwrapped(im.getGraphics(), width, height, 0);\r
+ im.writeImage();\r
+ }\r
}\r
-\r
- im.writeImage();\r
}\r
catch (OutOfMemoryError err)\r
{\r
sy = s * av.charHeight + scaleHeight;\r
\r
SequenceI seq = av.alignment.getSequenceAt(s);\r
- java.util.Vector features = seq.getDatasetSequence().getSequenceFeatures();\r
+ SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();\r
SequenceGroup[] groups = av.alignment.findAllGroups(seq);\r
for(res =0; res<alwidth; res++)\r
{\r
+ " onMouseOver=\"toolTip('"\r
+ alIndex + " " + triplet );\r
}\r
- fSize = features.size();\r
+ fSize = features.length;\r
for (f = 0; f < fSize; f++)\r
{\r
- SequenceFeature sf = (SequenceFeature) features.elementAt(f);\r
\r
- if ( (sf.getBegin() <= seq.findPosition(res)) &&\r
- (sf.getEnd() >= seq.findPosition(res)))\r
+ if ( (features[f].getBegin() <= seq.findPosition(res)) &&\r
+ (features[f].getEnd() >= seq.findPosition(res)))\r
{\r
- if (sf.getType().equals("disulfide bond"))\r
+ if (features[f].getType().equals("disulfide bond"))\r
{\r
- if (sf.getBegin() == seq.findPosition(res)\r
- || sf.getEnd() == seq.findPosition(res))\r
+ if (features[f].getBegin() == seq.findPosition(res)\r
+ || features[f].getEnd() == seq.findPosition(res))\r
{\r
- text.append("<br>disulfide bond " + sf.getBegin() + ":" +\r
- sf.getEnd());\r
+ text.append("<br>disulfide bond " + features[f].getBegin() + ":" +\r
+ features[f].getEnd());\r
}\r
}\r
else\r
{\r
text.append("<br>");\r
- text.append(sf.getType());\r
- if (sf.getDescription() != null && !sf.getType().equals(sf.getDescription()))\r
- text.append(" " + sf.getDescription());\r
+ text.append(features[f].getType());\r
+ if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))\r
+ text.append(" " + features[f].getDescription());\r
\r
- if (sf.getStatus() != null && sf.getStatus().length()>0)\r
+ if (features[f].getStatus() != null && features[f].getStatus().length()>0)\r
{\r
- text.append(" (" + sf.getStatus() + ")");\r
+ text.append(" (" + features[f].getStatus() + ")");\r
}\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff