/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 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
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.jbappletgui.GAlignmentPanel;\r
-import jalview.schemes.*;\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener\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
{\r
\r
- AlignViewport av;\r
+ AlignViewport av;\r
OverviewPanel overviewPanel;\r
- SeqPanel seqPanel;\r
- IdPanel idPanel;\r
+ SeqPanel seqPanel;\r
+ IdPanel idPanel;\r
IdwidthAdjuster idwidthAdjuster;\r
public AlignFrame alignFrame;\r
ScalePanel scalePanel;\r
public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
{\r
alignFrame = af;\r
- this.av = av;\r
- seqPanel = new SeqPanel (av, this);\r
- idPanel = new IdPanel (av, this);\r
- scalePanel = new ScalePanel(av, this);\r
+ this.av = av;\r
+ seqPanel = new SeqPanel(av, this);\r
+ idPanel = new IdPanel(av, this);\r
+ scalePanel = new ScalePanel(av, this);\r
idwidthAdjuster = new IdwidthAdjuster(this);\r
annotationPanel = new AnnotationPanel(this);\r
- alabels = new AnnotationLabels(this);\r
-\r
+ alabels = new AnnotationLabels(this);\r
\r
idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);\r
hscroll.addAdjustmentListener(this);\r
vscroll.addAdjustmentListener(this);\r
\r
- seqPanel.seqCanvas.addKeyListener( new MyKeyAdapter() );\r
- idPanel.idCanvas.addKeyListener( new MyKeyAdapter() );\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
- {\r
- setScrollValues(av.getStartRes(), av.getStartSeq());\r
- repaint();\r
- }\r
- });\r
+ addComponentListener(new ComponentAdapter()\r
+ {\r
+ public void componentResized(ComponentEvent evt)\r
+ {\r
+ setScrollValues(av.getStartRes(), av.getStartSeq());\r
+ repaint();\r
+ }\r
+ });\r
\r
- Dimension d = calculateIdWidth();\r
- idPanel.idCanvas.setSize(d);\r
+ Dimension d = calculateIdWidth();\r
+ idPanel.idCanvas.setSize(d);\r
\r
- hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);\r
- annotationScroller.setSize(annotationPanel.getSize());\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,annotationPanel.getSize().height);\r
- alabels.setSize(d.width,annotationPanel.getSize().height);\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
}\r
\r
- class MyKeyAdapter extends KeyAdapter\r
+ class MyKeyAdapter\r
+ extends KeyAdapter\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
- alignFrame.cut_actionPerformed(null);\r
- break;\r
- case KeyEvent.VK_C:\r
- if(evt.isControlDown())\r
- alignFrame.copy_actionPerformed(null);\r
- break;\r
- case KeyEvent.VK_V:\r
- if(evt.isControlDown())\r
- alignFrame.paste(true);\r
- break;\r
- case KeyEvent.VK_A:\r
- if(evt.isControlDown())\r
- alignFrame.selectAllSequenceMenuItem_actionPerformed(null);\r
- break;\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
alignFrame.moveSelectedSequences(true);\r
break;\r
case KeyEvent.VK_F:\r
- if(evt.isControlDown())\r
- alignFrame.findMenuItem_actionPerformed(null);\r
+ if (evt.isControlDown())\r
+ {\r
+ alignFrame.findMenuItem_actionPerformed(null);\r
+ }\r
break;\r
- }\r
- }\r
+ }\r
+ }\r
}\r
\r
public void fontChanged()\r
// to prevent drawing old image\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
+ 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.repaint();\r
\r
public void setIdWidth(int w, int h)\r
{\r
- idPanel.idCanvas.setSize(w,h);\r
- idPanelHolder.setSize(w,idPanelHolder.getSize().height);\r
- alabels.setSize(w,alabels.getSize().height);\r
+ idPanel.idCanvas.setSize(w, h);\r
+ idPanelHolder.setSize(w, idPanelHolder.getSize().height);\r
+ alabels.setSize(w, alabels.getSize().height);\r
validate();\r
}\r
+\r
Dimension calculateIdWidth()\r
{\r
Frame frame = new Frame();\r
frame.addNotify();\r
Graphics g = frame.getGraphics();\r
- if(g==null)\r
+ if (g == null)\r
{\r
Frame f = new Frame();\r
f.addNotify();\r
FontMetrics fm = g.getFontMetrics(av.font);\r
AlignmentI al = av.getAlignment();\r
\r
- int i = 0;\r
- int idWidth = 0;\r
- String id;\r
- while (i < al.getHeight() && al.getSequenceAt(i) != null)\r
- {\r
- SequenceI s = al.getSequenceAt(i);\r
- if(av.getShowFullId())\r
- id = s.getDisplayId();\r
- else\r
- id = s.getName();\r
-\r
- if (fm.stringWidth(id) > idWidth)\r
- idWidth = fm.stringWidth(id);\r
- i++;\r
- }\r
-\r
- // Also check annotation label widths\r
- i=0;\r
- if(al.getAlignmentAnnotation()!=null)\r
- {\r
- fm = g.getFontMetrics(frame.getFont());\r
- while (i < al.getAlignmentAnnotation().length)\r
- {\r
- String label = al.getAlignmentAnnotation()[i].label;\r
- if (fm.stringWidth(label) > idWidth)\r
- idWidth = fm.stringWidth(label);\r
- i++;\r
- }\r
- }\r
-\r
- return new Dimension(idWidth, idPanel.idCanvas.getSize().height);\r
- }\r
+ int i = 0;\r
+ int idWidth = 0;\r
+ String id;\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
\r
+ if (fm.stringWidth(id) > idWidth)\r
+ {\r
+ idWidth = fm.stringWidth(id);\r
+ }\r
+ i++;\r
+ }\r
\r
- public void highlightSearchResults(int [] results)\r
- {\r
- seqPanel.seqCanvas.highlightSearchResults( results );\r
+ // Also check annotation label widths\r
+ i = 0;\r
+ if (al.getAlignmentAnnotation() != null)\r
+ {\r
+ fm = g.getFontMetrics(frame.getFont());\r
+ while (i < al.getAlignmentAnnotation().length)\r
+ {\r
+ String label = al.getAlignmentAnnotation()[i].label;\r
+ if (fm.stringWidth(label) > idWidth)\r
+ {\r
+ idWidth = fm.stringWidth(label);\r
+ }\r
+ i++;\r
+ }\r
+ }\r
+\r
+ return new Dimension(idWidth, idPanel.idCanvas.getSize().height);\r
+ }\r
+\r
+ public void highlightSearchResults(int[] results)\r
+ {\r
+ seqPanel.seqCanvas.highlightSearchResults(results);\r
\r
- // do we need to scroll the panel?\r
- if(results!=null)\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
+ 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
+ || av.getEndSeq() < results[0]))\r
+ {\r
setScrollValues(start, results[0]);\r
+ }\r
}\r
\r
- }\r
-\r
-\r
- public OverviewPanel getOverviewPanel()\r
- {\r
- return overviewPanel;\r
- }\r
+ }\r
\r
- public void setOverviewPanel(OverviewPanel op)\r
- {\r
- overviewPanel = op;\r
- }\r
+ public OverviewPanel getOverviewPanel()\r
+ {\r
+ return overviewPanel;\r
+ }\r
\r
+ public void setOverviewPanel(OverviewPanel op)\r
+ {\r
+ overviewPanel = op;\r
+ }\r
\r
public void setAnnotationVisible(boolean b)\r
{\r
repaint();\r
}\r
\r
-\r
public void setWrapAlignment(boolean wrap)\r
{\r
scalePanelHolder.setVisible(!wrap);\r
\r
}\r
\r
-\r
public void setColourScheme()\r
{\r
ColourSchemeI cs = av.getGlobalColourScheme();\r
\r
- if(av.getConservationSelected())\r
+ if (av.getConservationSelected())\r
{\r
\r
- Alignment al = (Alignment)av.getAlignment();\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3, al.getSequences(), 0,\r
- al.getWidth() );\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
+ c.calculate();\r
+ c.verdict(false, av.ConsPercGaps);\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c, cs);\r
\r
- av.setGlobalColourScheme( ccs );\r
+ av.setGlobalColourScheme(ccs);\r
\r
}\r
\r
repaint();\r
}\r
\r
-\r
int hextent = 0;\r
int vextent = 0;\r
\r
// return value is true if the scroll is valid\r
public boolean scrollUp(boolean up)\r
{\r
- if(up)\r
+ if (up)\r
{\r
- if(vscroll.getValue()<1)\r
+ if (vscroll.getValue() < 1)\r
+ {\r
return false;\r
- fastPaint = false;\r
+ }\r
+ fastPaint = false;\r
vscroll.setValue(vscroll.getValue() - 1);\r
}\r
else\r
{\r
- if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())\r
- return false;\r
- fastPaint = false;\r
+ if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())\r
+ {\r
+ return false;\r
+ }\r
+ fastPaint = false;\r
vscroll.setValue(vscroll.getValue() + 1);\r
}\r
fastPaint = true;\r
if (right)\r
{\r
if (hscroll.getValue() < 1)\r
+ {\r
return false;\r
+ }\r
fastPaint = false;\r
hscroll.setValue(hscroll.getValue() - 1);\r
}\r
else\r
{\r
if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())\r
+ {\r
return false;\r
+ }\r
fastPaint = false;\r
hscroll.setValue(hscroll.getValue() + 1);\r
}\r
return true;\r
}\r
\r
-\r
public void setScrollValues(int x, int y)\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.getCharWidth() - 1);\r
\r
- hextent = seqPanel.seqCanvas.getSize().width/av.charWidth;\r
- vextent = seqPanel.seqCanvas.getSize().height/av.charHeight;\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 > av.alignment.getWidth())\r
+ {\r
hextent = av.alignment.getWidth();\r
- if(vextent > av.alignment.getHeight())\r
+ }\r
+ if (vextent > av.alignment.getHeight())\r
+ {\r
vextent = av.alignment.getHeight();\r
+ }\r
\r
- if(hextent+x > av.getAlignment().getWidth())\r
- x = av.getAlignment().getWidth()- hextent;\r
+ if (hextent + x > av.getAlignment().getWidth())\r
+ {\r
+ x = av.getAlignment().getWidth() - hextent;\r
+ }\r
\r
- if(vextent+y > av.getAlignment().getHeight())\r
+ if (vextent + y > av.getAlignment().getHeight())\r
+ {\r
y = av.getAlignment().getHeight() - vextent;\r
+ }\r
\r
- if(y<0)\r
+ if (y < 0)\r
+ {\r
y = 0;\r
+ }\r
\r
- if(x<0)\r
- x=0;\r
-\r
+ if (x < 0)\r
+ {\r
+ x = 0;\r
+ }\r
\r
int endSeq = y + vextent;\r
- if(endSeq>av.alignment.getHeight())\r
+ if (endSeq > av.alignment.getHeight())\r
+ {\r
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
+ av.setEndSeq(endSeq);\r
+ hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());\r
+ vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());\r
\r
}\r
\r
-\r
public void adjustmentValueChanged(AdjustmentEvent evt)\r
{\r
int oldX = av.getStartRes();\r
{\r
int x = hscroll.getValue();\r
av.setStartRes(x);\r
- av.setEndRes(x + seqPanel.seqCanvas.getSize().width/av.getCharWidth()-1);\r
+ av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() -\r
+ 1);\r
}\r
\r
if (evt.getSource() == vscroll)\r
int offy = vscroll.getValue();\r
if (av.getWrapAlignment())\r
{\r
- int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);\r
- av.setStartRes( vscroll.getValue() * rowSize );\r
- av.setEndRes( (vscroll.getValue()+1) * rowSize );\r
+ int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.\r
+ seqCanvas.getSize().width);\r
+ av.setStartRes(vscroll.getValue() * rowSize);\r
+ av.setEndRes( (vscroll.getValue() + 1) * rowSize);\r
}\r
else\r
{\r
av.setStartSeq(offy);\r
- av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height / av.getCharHeight());\r
+ av.setEndSeq(offy +\r
+ seqPanel.seqCanvas.getSize().height / av.getCharHeight());\r
}\r
}\r
\r
- if(overviewPanel!=null)\r
+ if (overviewPanel != null)\r
+ {\r
overviewPanel.setBoxPosition();\r
+ }\r
\r
- if(av.getWrapAlignment() || !fastPaint)\r
+ if (av.getWrapAlignment() || !fastPaint)\r
+ {\r
repaint();\r
+ }\r
else\r
{\r
idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);\r
\r
scalePanel.repaint();\r
if (av.getShowAnnotation())\r
+ {\r
annotationPanel.fastPaint(av.getStartRes() - oldX);\r
+ }\r
}\r
\r
}\r
\r
public void update(Graphics g)\r
{\r
- paint (g);\r
+ paint(g);\r
}\r
\r
-\r
public void paint(Graphics g)\r
{\r
Dimension d = idPanel.idCanvas.getSize();\r
idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);\r
- annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);\r
- alabels.setSize(d.width,annotationPanel.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
scalePanel.repaint();\r
annotationPanel.repaint();\r
\r
-\r
if (av.getWrapAlignment())\r
{\r
- int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);\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
setScrollValues(av.getStartRes(), av.getStartSeq());\r
}\r
\r
-\r
-\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff