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
setScrollValues(0, 0);\r
\r
- annotationPanel.adjustPanelHeight();\r
- annotationSpaceFillerHolder.setPreferredSize(annotationPanel.\r
- getPreferredSize());\r
- annotationScroller.setPreferredSize(annotationPanel.\r
- getPreferredSize());\r
+ adjustAnnotationHeight();\r
+\r
setAnnotationVisible(av.getShowAnnotation());\r
\r
hscroll.addAdjustmentListener(this);\r
{\r
public void keyPressed(KeyEvent evt)\r
{\r
+ if(av.cursorMode\r
+ && evt.getKeyCode()>=KeyEvent.VK_0\r
+ && evt.getKeyCode()<=KeyEvent.VK_9)\r
+ {\r
+ seqPanel.numberPressed(evt.getKeyChar());\r
+ }\r
+\r
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
case KeyEvent.VK_DOWN:\r
- alignFrame.moveSelectedSequences(false);\r
-\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.moveCursor(0,1);\r
+ }\r
+ else\r
+ alignFrame.moveSelectedSequences(false);\r
break;\r
\r
case KeyEvent.VK_UP:\r
- alignFrame.moveSelectedSequences(true);\r
+ if (av.cursorMode)\r
+ {\r
+ seqPanel.moveCursor(0,-1);\r
+ }\r
+ else\r
+ alignFrame.moveSelectedSequences(true);\r
+ break;\r
\r
+ case KeyEvent.VK_LEFT:\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.moveCursor(-1,0);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_RIGHT:\r
+ if (av.cursorMode)\r
+ {\r
+ seqPanel.moveCursor(1,0);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_SPACE:\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.insertGapAtCursor(evt.isControlDown() || evt.isShiftDown());\r
+ }\r
break;\r
\r
- case KeyEvent.VK_BACK_SPACE:\r
case KeyEvent.VK_DELETE:\r
- alignFrame.cut_actionPerformed(null);\r
+ case KeyEvent.VK_BACK_SPACE:\r
+ if(!av.cursorMode)\r
+ {\r
+ alignFrame.cut_actionPerformed(null);\r
+ }\r
+ else\r
+ seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());\r
+\r
break;\r
\r
+ case KeyEvent.VK_S:\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.setCursorRow();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_C:\r
+ if(av.cursorMode && !evt.isControlDown())\r
+ {\r
+ seqPanel.setCursorColumn();\r
+ }\r
+ break;\r
case KeyEvent.VK_P:\r
- seqPanel.seqCanvas.increaseAARatio();\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.setCursorPosition();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_ENTER:\r
+ case KeyEvent.VK_COMMA:\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.setCursorRowAndColumn();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Q:\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.setSelectionAreaAtCursor(true);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_M:\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.setSelectionAreaAtCursor(false);\r
+ }\r
break;\r
- case KeyEvent.VK_L:\r
- seqPanel.seqCanvas.decreaseAARation();\r
+\r
+ case KeyEvent.VK_F2:\r
+ av.cursorMode = ! av.cursorMode;\r
+ alignFrame.statusBar.setText("Keyboard editing mode is "+\r
+ (av.cursorMode ? "on" : "off"));\r
+ if(av.cursorMode)\r
+ {\r
+ seqPanel.seqCanvas.cursorX = av.startRes;\r
+ seqPanel.seqCanvas.cursorY = av.startSeq;\r
+ }\r
+ seqPanel.seqCanvas.repaint();\r
+ break;\r
+\r
+ case KeyEvent.VK_F1:\r
+ try\r
+ {\r
+ ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
+ java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");\r
+ javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);\r
+\r
+ javax.help.HelpBroker hb = hs.createHelpBroker();\r
+ hb.setCurrentID("home");\r
+ hb.setDisplayed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_H:\r
+ {\r
+ boolean toggleSeqs = !evt.isControlDown();\r
+ boolean toggleCols = !evt.isShiftDown();\r
+\r
+ boolean hide = false;\r
+\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+ if(toggleSeqs)\r
+ {\r
+ if(sg != null && sg.getSize(false) != av.alignment.getHeight())\r
+ {\r
+ alignFrame.hideSelSequences_actionPerformed(null);\r
+ hide = true;\r
+ }\r
+ else if (!(toggleCols && av.colSel.getSelected().size() > 0))\r
+ alignFrame.showAllSeqs_actionPerformed(null);\r
+ }\r
+\r
+ if (toggleCols)\r
+ {\r
+ if(av.colSel.getSelected().size() > 0)\r
+ {\r
+ alignFrame.hideSelColumns_actionPerformed(null);\r
+ if(!toggleSeqs)\r
+ av.selectionGroup = sg;\r
+ }\r
+ else if(!hide)\r
+ alignFrame.showAllColumns_actionPerformed(null);\r
+ }\r
break;\r
+ }\r
+\r
}\r
}\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
+ 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
- setScrollValues(start, results[0]);\r
+ scrollToWrappedVisible(start);\r
}\r
}\r
}\r
\r
+ void scrollToWrappedVisible(int res)\r
+ {\r
+ int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
+ if( res<=av.getStartRes() || res>=(av.getStartRes()+cwidth) )\r
+ {\r
+ vscroll.setValue(res / cwidth);\r
+ av.startRes = vscroll.getValue() * cwidth;\r
+ }\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
repaint();\r
}\r
\r
+ public void adjustAnnotationHeight()\r
+ {\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ while(alignFrame.getHeight()==0)\r
+ {\r
+ Thread.yield();\r
+ }\r
+\r
+ int height = annotationPanel.adjustPanelHeight();\r
+\r
+ if (height > alignFrame.getHeight() / 2)\r
+ {\r
+ height = alignFrame.getHeight() / 2;\r
+ }\r
+\r
+ annotationScroller.setPreferredSize(\r
+ new Dimension(annotationScroller.getWidth(),\r
+ height));\r
+\r
+ annotationSpaceFillerHolder.setPreferredSize(new Dimension(\r
+ annotationSpaceFillerHolder.getWidth(),\r
+ height));\r
+\r
+ annotationPanel.repaint();\r
+ }\r
+ });\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
public boolean scrollRight(boolean right)\r
{\r
- if (right)\r
+ if (!right)\r
{\r
if (hscroll.getValue() < 1)\r
{\r
*/\r
public void setScrollValues(int x, int y)\r
{\r
- av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -\r
- 1);\r
+\r
+ int width = av.alignment.getWidth();\r
+ int height = av.alignment.getHeight();\r
+\r
+ if(av.hasHiddenColumns)\r
+ width = av.getColumnSelection().findColumnPosition(width);\r
+\r
+ av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) -1);\r
\r
hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;\r
vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;\r
\r
- if (hextent > av.alignment.getWidth())\r
+ if (hextent > width)\r
{\r
- hextent = av.alignment.getWidth();\r
+ hextent = width;\r
}\r
\r
- if (vextent > av.alignment.getHeight())\r
+ if (vextent > height)\r
{\r
- vextent = av.alignment.getHeight();\r
+ vextent = height;\r
}\r
\r
- if ( (hextent + x) > av.getAlignment().getWidth())\r
+ if ( (hextent + x) > width)\r
{\r
- x = av.getAlignment().getWidth() - hextent;\r
+ x = width - hextent;\r
}\r
\r
- if ( (vextent + y) > av.getAlignment().getHeight())\r
+ if ( (vextent + y) > height)\r
{\r
- y = av.getAlignment().getHeight() - vextent;\r
+ y = height - vextent;\r
}\r
\r
if (y < 0)\r
x = 0;\r
}\r
\r
- hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());\r
- vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());\r
+ hscroll.setValues(x, hextent, 0, width);\r
+ vscroll.setValues(y, vextent, 0, height);\r
}\r
\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
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
\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
vscroll.setUnitIncrement(1);\r
vscroll.setVisibleAmount(1);\r
setScrollValues(av.getStartRes(), av.getStartSeq());\r
}\r
\r
-\r
- if( this.getVisibleRect().getBounds() == g.getClipBounds() )\r
- {\r
- if (overviewPanel != null)\r
+ if( this.getVisibleRect().getBounds() == g.getClipBounds()\r
+ && overviewPanel != null)\r
overviewPanel.updateOverviewImage();\r
- }\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.getSelectionGroup().sequences.contains(\r
+ av.getSelectionGroup().getSequences(false).contains(\r
av.getAlignment().getSequenceAt(i)))\r
{\r
currentColor = Color.gray;\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
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
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
\r
void makeAlignmentImage(int type, File file)\r
{\r
- int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
- int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);\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() + (maxwidth * av.charWidth);\r
if (idPanel.getWidth() == 0)\r
{\r
width += calculateIdWidth().getWidth() + 4;\r
if (av.getWrapAlignment())\r
{\r
height = getWrappedHeight();\r
- width = seqPanel.getWidth() + idPanel.getWidth();\r
+ if (System.getProperty("java.awt.headless") != null\r
+ && System.getProperty("java.awt.headless").equals("true"))\r
+ {\r
+ width = alignFrame.getWidth() - 22;\r
+ }\r
+ else\r
+ width = seqPanel.getWidth() + idPanel.getWidth();\r
+\r
}\r
else if (av.getShowAnnotation())\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].getValue("status") != null )\r
{\r
- text.append(" (" + sf.getStatus() + ")");\r
+ text.append(" (" + features[f].getValue("status") + ")");\r
}\r
}\r
}\r
\r
int getWrappedHeight()\r
{\r
+ int seqPanelWidth = seqPanel.seqCanvas.getWidth();\r
+\r
+ //If headless, seqPanel will have 0 width\r
+ if (System.getProperty("java.awt.headless") != null\r
+ && System.getProperty("java.awt.headless").equals("true"))\r
+ {\r
+ int idWidth = calculateIdWidth().width + 4;\r
+ seqPanelWidth = alignFrame.getWidth() - idWidth;\r
+ }\r
\r
int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(\r
- seqPanel.seqCanvas.getWidth());\r
+ seqPanelWidth\r
+ );\r
\r
int hgap = av.charHeight;\r
if (av.scaleAboveWrapped)\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
git://source.jalview.org / jalview.git / blobdiff