/*\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) 2007 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
import java.awt.*;\r
import java.awt.event.*;\r
\r
-import jalview.analysis.*;\r
import jalview.datamodel.*;\r
-import jalview.jbappletgui.*;\r
-import jalview.schemes.*;\r
\r
public class AlignmentPanel\r
- extends GAlignmentPanel implements AdjustmentListener\r
+ extends Panel implements AdjustmentListener\r
{\r
\r
AlignViewport av;\r
\r
public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
{\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
alignFrame = af;\r
this.av = av;\r
seqPanel = new SeqPanel(av, this);\r
scalePanel = new ScalePanel(av, this);\r
idwidthAdjuster = new IdwidthAdjuster(this);\r
annotationPanel = new AnnotationPanel(this);\r
+\r
+ sequenceHolderPanel.add(annotationPanel, BorderLayout.SOUTH);\r
+\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
annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);\r
scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
hscroll.addAdjustmentListener(this);\r
vscroll.addAdjustmentListener(this);\r
\r
- seqPanel.seqCanvas.addKeyListener(new MyKeyAdapter());\r
- idPanel.idCanvas.addKeyListener(new MyKeyAdapter());\r
-\r
addComponentListener(new ComponentAdapter()\r
{\r
public void componentResized(ComponentEvent evt)\r
idPanel.idCanvas.setSize(d);\r
\r
hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);\r
- annotationScroller.setSize(annotationPanel.getSize());\r
\r
idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);\r
annotationSpaceFillerHolder.setSize(d.width,\r
annotationPanel.getSize().height);\r
alabels.setSize(d.width, annotationPanel.getSize().height);\r
\r
+ final AlignmentPanel ap = this;\r
+ av.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
+ {\r
+ public void propertyChange(java.beans.PropertyChangeEvent evt)\r
+ {\r
+ if (evt.getPropertyName().equals("alignment"))\r
+ {\r
+ PaintRefresher.Refresh(ap,\r
+ av.getSequenceSetId(),\r
+ true,\r
+ true);\r
+ alignmentChanged();\r
+ }\r
+ }\r
+ });\r
+\r
}\r
\r
- class MyKeyAdapter\r
- extends KeyAdapter\r
+ public void alignmentChanged()\r
{\r
- public void keyPressed(KeyEvent evt)\r
- {\r
- // System.out.println(evt.getKeyCode()); log.\r
- switch (evt.getKeyCode())\r
- {\r
- case 27: // escape key\r
- av.setSelectionGroup(null);\r
- alignFrame.alignPanel.repaint();\r
- break;\r
- case KeyEvent.VK_X:\r
- if (evt.isControlDown())\r
- {\r
- alignFrame.cut_actionPerformed(null);\r
- }\r
- break;\r
- case KeyEvent.VK_C:\r
- if (evt.isControlDown())\r
- {\r
- alignFrame.copy_actionPerformed(null);\r
- }\r
- break;\r
- case KeyEvent.VK_V:\r
- if (evt.isControlDown())\r
- {\r
- alignFrame.paste(true);\r
- }\r
- break;\r
- case KeyEvent.VK_A:\r
- if (evt.isControlDown())\r
- {\r
- alignFrame.selectAllSequenceMenuItem_actionPerformed(null);\r
- }\r
- break;\r
- case KeyEvent.VK_DOWN:\r
- alignFrame.moveSelectedSequences(false);\r
- break;\r
- case KeyEvent.VK_UP:\r
- alignFrame.moveSelectedSequences(true);\r
- break;\r
- case KeyEvent.VK_F:\r
- if (evt.isControlDown())\r
- {\r
- alignFrame.findMenuItem_actionPerformed(null);\r
- }\r
- break;\r
- case KeyEvent.VK_BACK_SPACE:\r
- case KeyEvent.VK_DELETE:\r
- alignFrame.cut_actionPerformed(null);\r
- break;\r
+ av.alignmentChanged(this);\r
\r
- }\r
+ if (overviewPanel != null)\r
+ {\r
+ overviewPanel.updateOverviewImage();\r
}\r
+\r
+ alignFrame.updateEditMenuBar();\r
+\r
+ repaint();\r
}\r
\r
public void fontChanged()\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
+ annotationPanel.image = null;\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
+ {\r
+ overviewPanel.updateOverviewImage();\r
+ }\r
}\r
\r
public void setIdWidth(int w, int h)\r
\r
Dimension calculateIdWidth()\r
{\r
- Frame frame = new Frame();\r
- frame.addNotify();\r
- Graphics g = frame.getGraphics();\r
- if (g == null)\r
+ if (av.nullFrame == null)\r
{\r
- Frame f = new Frame();\r
- f.addNotify();\r
- g = f.getGraphics();\r
+ av.nullFrame = new Frame();\r
+ av.nullFrame.addNotify();\r
}\r
\r
+ Graphics g = av.nullFrame.getGraphics();\r
+\r
FontMetrics fm = g.getFontMetrics(av.font);\r
AlignmentI al = av.getAlignment();\r
\r
while (i < al.getHeight() && al.getSequenceAt(i) != null)\r
{\r
SequenceI s = al.getSequenceAt(i);\r
- if (av.getShowFullId())\r
- {\r
- id = s.getDisplayId();\r
- }\r
- else\r
- {\r
- id = s.getName();\r
- }\r
+ id = s.getDisplayId(av.getShowJVSuffix());\r
\r
if (fm.stringWidth(id) > idWidth)\r
{\r
i = 0;\r
if (al.getAlignmentAnnotation() != null)\r
{\r
- fm = g.getFontMetrics(frame.getFont());\r
+ fm = g.getFontMetrics(av.nullFrame.getFont());\r
while (i < al.getAlignmentAnnotation().length)\r
{\r
String label = al.getAlignmentAnnotation()[i].label;\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
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
+ 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
+ {\r
+ start = 0;\r
+ }\r
+ }\r
+ if (seqIndex > av.alignment.getHeight() - vextent)\r
+ {\r
+ seqIndex = av.alignment.getHeight() - vextent;\r
+ if (seqIndex < 0)\r
+ {\r
+ seqIndex = 0;\r
+ }\r
+ }\r
+ setScrollValues(start, seqIndex);\r
+ }\r
+ }\r
+ else\r
{\r
- setScrollValues(start, results[0]);\r
+ scrollToWrappedVisible(start);\r
}\r
}\r
\r
+ repaint();\r
+ }\r
+\r
+ void scrollToWrappedVisible(int res)\r
+ {\r
+ int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.\r
+ getSize().width);\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
public OverviewPanel getOverviewPanel()\r
\r
public void setAnnotationVisible(boolean b)\r
{\r
- annotationSpaceFillerHolder.setVisible(b);\r
- annotationScroller.setVisible(b);\r
+ if (!av.wrapAlignment)\r
+ {\r
+ annotationSpaceFillerHolder.setVisible(b);\r
+ annotationPanel.setVisible(b);\r
+ }\r
validate();\r
repaint();\r
}\r
\r
public void setWrapAlignment(boolean wrap)\r
{\r
+ av.startSeq = 0;\r
+ av.startRes = 0;\r
scalePanelHolder.setVisible(!wrap);\r
+\r
hscroll.setVisible(!wrap);\r
idwidthAdjuster.setVisible(!wrap);\r
\r
- av.setShowAnnotation(!wrap);\r
- annotationScroller.setVisible(!wrap);\r
- annotationSpaceFillerHolder.setVisible(!wrap);\r
- idSpaceFillerPanel1.setVisible(!wrap);\r
-\r
- validate();\r
- repaint();\r
-\r
- }\r
-\r
- public void setColourScheme()\r
- {\r
- ColourSchemeI cs = av.getGlobalColourScheme();\r
-\r
- if (av.getConservationSelected())\r
+ if (wrap)\r
{\r
+ annotationPanel.setVisible(false);\r
+ annotationSpaceFillerHolder.setVisible(false);\r
+ }\r
+ else if (av.showAnnotation)\r
+ {\r
+ annotationPanel.setVisible(true);\r
+ annotationSpaceFillerHolder.setVisible(true);\r
+ }\r
\r
- Alignment al = (Alignment) av.getAlignment();\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- al.getSequences(), 0,\r
- al.getWidth());\r
-\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, cs);\r
-\r
- av.setGlobalColourScheme(ccs);\r
+ idSpaceFillerPanel1.setVisible(!wrap);\r
\r
- }\r
+ fontChanged(); //This is so that the scalePanel is resized correctly\r
\r
+ validate();\r
repaint();\r
+\r
}\r
\r
int hextent = 0;\r
{\r
return false;\r
}\r
- fastPaint = false;\r
- vscroll.setValue(vscroll.getValue() - 1);\r
+ setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);\r
}\r
else\r
{\r
{\r
return false;\r
}\r
- fastPaint = false;\r
- vscroll.setValue(vscroll.getValue() + 1);\r
+ setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);\r
}\r
- fastPaint = true;\r
+\r
+ repaint();\r
return true;\r
}\r
\r
public boolean scrollRight(boolean right)\r
{\r
-\r
- if (right)\r
+ if (!right)\r
{\r
if (hscroll.getValue() < 1)\r
{\r
return false;\r
}\r
- fastPaint = false;\r
- hscroll.setValue(hscroll.getValue() - 1);\r
+ setScrollValues(hscroll.getValue() - 1, vscroll.getValue());\r
}\r
else\r
{\r
{\r
return false;\r
}\r
- fastPaint = false;\r
- hscroll.setValue(hscroll.getValue() + 1);\r
+ setScrollValues(hscroll.getValue() + 1, vscroll.getValue());\r
}\r
- fastPaint = true;\r
+\r
+ repaint();\r
return true;\r
}\r
\r
public void setScrollValues(int x, int y)\r
{\r
+ int width = av.alignment.getWidth();\r
+ int height = av.alignment.getHeight();\r
+\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ width = av.getColumnSelection().findColumnPosition(width);\r
+ }\r
\r
av.setStartRes(x);\r
- av.setStartSeq(y);\r
- av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() - 1);\r
+ av.setEndRes( (x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);\r
\r
hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;\r
vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;\r
\r
- if (hextent > av.alignment.getWidth())\r
+ if (hextent > width)\r
{\r
- hextent = av.alignment.getWidth();\r
+ hextent = width;\r
}\r
- if (vextent > av.alignment.getHeight())\r
+\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
+ av.setStartSeq(y);\r
+\r
int endSeq = y + vextent;\r
if (endSeq > av.alignment.getHeight())\r
{\r
}\r
\r
av.setEndSeq(endSeq);\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
+ if (overviewPanel != null)\r
+ {\r
+ overviewPanel.setBoxPosition();\r
+ }\r
\r
}\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
- if (av.getWrapAlignment() || !fastPaint)\r
+ int scrollX = av.startRes - oldX;\r
+ int scrollY = av.startSeq - oldY;\r
+\r
+ if (av.getWrapAlignment() || !fastPaint || av.MAC)\r
{\r
repaint();\r
}\r
else\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
+ {\r
+ scrollX = av.endRes - av.startRes;\r
+ }\r
+ else if (scrollX < av.startRes - av.endRes)\r
+ {\r
+ scrollX = av.startRes - av.endRes;\r
+ }\r
+\r
+ idPanel.idCanvas.fastPaint(scrollY);\r
+ seqPanel.seqCanvas.fastPaint(scrollX,\r
+ scrollY);\r
\r
scalePanel.repaint();\r
if (av.getShowAnnotation())\r
\r
public void paint(Graphics g)\r
{\r
+ invalidate();\r
Dimension d = idPanel.idCanvas.getSize();\r
idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);\r
annotationSpaceFillerHolder.setSize(d.width,\r
annotationPanel.getSize().height);\r
- alabels.setSize(d.width, annotationPanel.getSize().height);\r
\r
- alabels.repaint();\r
- idPanel.idCanvas.repaint();\r
- seqPanel.seqCanvas.repaint();\r
- scalePanel.repaint();\r
- annotationPanel.repaint();\r
+ alabels.setSize(d.width, annotationPanel.getSize().height);\r
\r
if (av.getWrapAlignment())\r
{\r
- int max = av.alignment.getWidth() /\r
- seqPanel.seqCanvas.\r
- getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);\r
- vscroll.setMaximum(max);\r
- vscroll.setUnitIncrement(1);\r
- vscroll.setVisibleAmount(1);\r
+ int maxwidth = av.alignment.getWidth();\r
+\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ }\r
+\r
+ int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth\r
+ (seqPanel.seqCanvas.getSize().width);\r
+\r
+ if (canvasWidth > 0)\r
+ {\r
+ int max = maxwidth / canvasWidth;\r
+ vscroll.setMaximum(max);\r
+ vscroll.setUnitIncrement(1);\r
+ vscroll.setVisibleAmount(1);\r
+ }\r
}\r
else\r
{\r
setScrollValues(av.getStartRes(), av.getStartSeq());\r
}\r
\r
+ alabels.repaint();\r
+\r
+ seqPanel.seqCanvas.repaint();\r
+ scalePanel.repaint();\r
+ annotationPanel.repaint();\r
+ idPanel.idCanvas.repaint();\r
+\r
+ if (getBounds() == g.getClipBounds())\r
+ {\r
+ if (overviewPanel != null)\r
+ {\r
+ overviewPanel.updateOverviewImage();\r
+ }\r
+ }\r
+\r
}\r
+\r
+ protected Panel sequenceHolderPanel = new Panel();\r
+ protected Scrollbar vscroll = new Scrollbar();\r
+ protected Scrollbar hscroll = new Scrollbar();\r
+ protected Panel seqPanelHolder = new Panel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ BorderLayout borderLayout3 = new BorderLayout();\r
+ protected Panel scalePanelHolder = new Panel();\r
+ protected Panel idPanelHolder = new Panel();\r
+ BorderLayout borderLayout5 = new BorderLayout();\r
+ protected Panel idSpaceFillerPanel1 = new Panel();\r
+ public Panel annotationSpaceFillerHolder = new Panel();\r
+ BorderLayout borderLayout6 = new BorderLayout();\r
+ BorderLayout borderLayout7 = new BorderLayout();\r
+ Panel hscrollHolder = new Panel();\r
+ BorderLayout borderLayout10 = new BorderLayout();\r
+ protected Panel hscrollFillerPanel = new Panel();\r
+ BorderLayout borderLayout11 = new BorderLayout();\r
+ BorderLayout borderLayout4 = new BorderLayout();\r
+ BorderLayout borderLayout2 = new BorderLayout();\r
+\r
+ private void jbInit()\r
+ throws Exception\r
+ {\r
+ // idPanelHolder.setPreferredSize(new Dimension(70, 10));\r
+ this.setLayout(borderLayout7);\r
+\r
+ // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));\r
+ sequenceHolderPanel.setLayout(borderLayout3);\r
+ seqPanelHolder.setLayout(borderLayout1);\r
+ scalePanelHolder.setBackground(Color.white);\r
+\r
+ // scalePanelHolder.setPreferredSize(new Dimension(10, 30));\r
+ scalePanelHolder.setLayout(borderLayout6);\r
+ idPanelHolder.setLayout(borderLayout5);\r
+ idSpaceFillerPanel1.setBackground(Color.white);\r
+\r
+ // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));\r
+ idSpaceFillerPanel1.setLayout(borderLayout11);\r
+ annotationSpaceFillerHolder.setBackground(Color.white);\r
+\r
+ // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));\r
+ annotationSpaceFillerHolder.setLayout(borderLayout4);\r
+ hscroll.setOrientation(Scrollbar.HORIZONTAL);\r
+ hscrollHolder.setLayout(borderLayout10);\r
+ hscrollFillerPanel.setBackground(Color.white);\r
+\r
+ // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));\r
+ hscrollHolder.setBackground(Color.white);\r
+\r
+ // annotationScroller.setPreferredSize(new Dimension(10, 80));\r
+ // this.setPreferredSize(new Dimension(220, 166));\r
+ seqPanelHolder.setBackground(Color.white);\r
+ idPanelHolder.setBackground(Color.white);\r
+ sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);\r
+ sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);\r
+ seqPanelHolder.add(vscroll, BorderLayout.EAST);\r
+\r
+ // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);\r
+ this.add(idPanelHolder, BorderLayout.WEST);\r
+ idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);\r
+ idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);\r
+ this.add(hscrollHolder, BorderLayout.SOUTH);\r
+ hscrollHolder.add(hscroll, BorderLayout.CENTER);\r
+ hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);\r
+ this.add(sequenceHolderPanel, BorderLayout.CENTER);\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff