+/*\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
package jalview.gui;\r
\r
-import jalview.jbgui.GAlignmentPanel;\r
-import jalview.schemes.*;\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
+import java.io.*;\r
+import javax.imageio.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.awt.print.*;\r
-import java.io.*;\r
import java.awt.image.*;\r
-import org.jibble.epsgraphics.*;\r
-import javax.imageio.*;\r
+import java.awt.print.*;\r
import javax.swing.*;\r
\r
+import org.jibble.epsgraphics.*;\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.jbgui.*;\r
+import jalview.schemes.*;\r
\r
-\r
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable\r
+public class AlignmentPanel\r
+ extends GAlignmentPanel implements AdjustmentListener, Printable\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
AnnotationLabels alabels;\r
\r
// this value is set false when selection area being dragged\r
- boolean fastPaint = true;\r
+ boolean fastPaint = false;\r
+ int hextent = 0;\r
+ int vextent = 0;\r
\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
+ this.av = av;\r
+ seqPanel = new SeqPanel(av, this);\r
+ idPanel = new IdPanel(av, this);\r
\r
scalePanel = new ScalePanel(av, this);\r
\r
annotationPanel = new AnnotationPanel(this);\r
alabels = new AnnotationLabels(this);\r
\r
- annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());\r
+ annotationSpaceFillerHolder.setPreferredSize(annotationPanel.\r
+ getPreferredSize());\r
annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());\r
annotationScroller.setViewportView(annotationPanel);\r
annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);\r
hscroll.addAdjustmentListener(this);\r
vscroll.addAdjustmentListener(this);\r
\r
- setFocusable(true);\r
- addKeyListener(new KeyAdapter()\r
- {\r
- public void keyPressed(KeyEvent evt)\r
- {\r
- switch(evt.getKeyCode())\r
- {\r
- case 27: // escape key\r
- av.setSelectionGroup(null);\r
- repaint();\r
- break;\r
-\r
- case KeyEvent.VK_DOWN:\r
- alignFrame.moveSelectedSequences(false);\r
- break;\r
- case KeyEvent.VK_UP:\r
- alignFrame.moveSelectedSequences(true);\r
- break;\r
- }\r
- }\r
- });\r
+ setFocusable(true);\r
+ addKeyListener(new KeyAdapter()\r
+ {\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
+ switch (evt.getKeyCode())\r
+ {\r
+ case 27: // escape key\r
+ av.setSelectionGroup(null);\r
+ repaint();\r
+\r
+ break;\r
+\r
+ case KeyEvent.VK_DOWN:\r
+ alignFrame.moveSelectedSequences(false);\r
+\r
+ break;\r
+\r
+ case KeyEvent.VK_UP:\r
+ alignFrame.moveSelectedSequences(true);\r
+\r
+ break;\r
+ }\r
+ }\r
+ });\r
}\r
\r
public void fontChanged()\r
// to prevent drawing old image\r
FontMetrics fm = getFontMetrics(av.getFont());\r
\r
- scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight+fm.getDescent()));\r
- idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight+fm.getDescent()));\r
+ scalePanelHolder.setPreferredSize(new Dimension(10,\r
+ av.charHeight + fm.getDescent()));\r
+ idSpaceFillerPanel1.setPreferredSize(new Dimension(10,\r
+ av.charHeight + fm.getDescent()));\r
\r
idPanel.idCanvas.gg = null;\r
annotationPanel.adjustPanelHeight();\r
+\r
Dimension d = calculateIdWidth();\r
d.setSize(d.width + 4, d.height);\r
idPanel.idCanvas.setPreferredSize(d);\r
repaint();\r
}\r
\r
-\r
Dimension calculateIdWidth()\r
{\r
Graphics g = this.getGraphics();\r
- if(g==null)\r
+\r
+ if (g == null)\r
{\r
javax.swing.JFrame f = new javax.swing.JFrame();\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(alabels.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, 12);\r
- }\r
+ int i = 0;\r
+ int idWidth = 0;\r
+ String id;\r
\r
+ while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))\r
+ {\r
+ SequenceI s = al.getSequenceAt(i);\r
\r
- public void highlightSearchResults(int [] results)\r
- {\r
- seqPanel.seqCanvas.highlightSearchResults( results );\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
+\r
+ i++;\r
+ }\r
\r
- // do we need to scroll the panel?\r
- if(results!=null)\r
+ // Also check annotation label widths\r
+ i = 0;\r
+\r
+ if (al.getAlignmentAnnotation() != 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
- setScrollValues(start, results[0]);\r
+ fm = g.getFontMetrics(alabels.getFont());\r
+\r
+ while (i < al.getAlignmentAnnotation().length)\r
+ {\r
+ String label = al.getAlignmentAnnotation()[i].label;\r
+\r
+ if (fm.stringWidth(label) > idWidth)\r
+ {\r
+ idWidth = fm.stringWidth(label);\r
+ }\r
+\r
+ i++;\r
+ }\r
}\r
\r
- }\r
+ return new Dimension(idWidth, 12);\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
+ {\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
\r
- public OverviewPanel getOverviewPanel()\r
- {\r
- return overviewPanel;\r
- }\r
+ if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||\r
+ ( (av.getStartSeq() > results[0]) ||\r
+ (av.getEndSeq() < results[0])))\r
+ {\r
+ setScrollValues(start, results[0]);\r
+ }\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
annotationScroller.setVisible(b);\r
}\r
\r
-\r
public void setWrapAlignment(boolean wrap)\r
{\r
scalePanelHolder.setVisible(!wrap);\r
idSpaceFillerPanel1.setVisible(!wrap);\r
\r
repaint();\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
+ Alignment al = (Alignment) av.getAlignment();\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth());\r
\r
- Alignment al = (Alignment)av.getAlignment();\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3, 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
\r
- av.setGlobalColourScheme( ccs );\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c, cs);\r
\r
+ av.setGlobalColourScheme(ccs);\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
+\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
+\r
+ fastPaint = false;\r
vscroll.setValue(vscroll.getValue() + 1);\r
}\r
+\r
fastPaint = true;\r
+\r
return true;\r
}\r
\r
public boolean scrollRight(boolean right)\r
{\r
-\r
if (right)\r
{\r
if (hscroll.getValue() < 1)\r
+ {\r
return false;\r
+ }\r
+\r
fastPaint = false;\r
hscroll.setValue(hscroll.getValue() - 1);\r
}\r
else\r
{\r
- if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())\r
+ if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())\r
+ {\r
return false;\r
+ }\r
+\r
fastPaint = false;\r
hscroll.setValue(hscroll.getValue() + 1);\r
}\r
+\r
fastPaint = true;\r
+\r
return true;\r
}\r
\r
-\r
public void setScrollValues(int x, int y)\r
{\r
- av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);\r
+ av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -\r
+ 1);\r
\r
- hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;\r
- vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;\r
+ hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;\r
+ vextent = seqPanel.seqCanvas.getHeight() / 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
+\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
- hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());\r
- vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );\r
-\r
-\r
+ if (x < 0)\r
+ {\r
+ x = 0;\r
+ }\r
\r
+ hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());\r
+ vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());\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.getWidth()/av.getCharWidth()-1);\r
+ av.setEndRes( (x +\r
+ (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);\r
}\r
\r
if (evt.getSource() == vscroll)\r
{\r
int offy = vscroll.getValue();\r
+\r
if (av.getWrapAlignment())\r
{\r
- int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
- av.setStartRes( vscroll.getValue() * rowSize );\r
- av.setEndRes( (vscroll.getValue()+1) * rowSize );\r
+ int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.\r
+ seqCanvas.getWidth());\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.getHeight() / av.getCharHeight());\r
+ av.setEndSeq(offy +\r
+ (seqPanel.seqCanvas.getHeight() / 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
av.getStartSeq() - oldY);\r
\r
scalePanel.repaint();\r
+\r
if (av.getShowAnnotation())\r
+ {\r
annotationPanel.fastPaint(av.getStartRes() - oldX);\r
+ }\r
}\r
-\r
}\r
\r
-\r
public void paintComponent(Graphics g)\r
{\r
invalidate();\r
+\r
Dimension d = idPanel.idCanvas.getPreferredSize();\r
idPanelHolder.setPreferredSize(d);\r
hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));\r
\r
if (av.getWrapAlignment())\r
{\r
- int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
+ int max = av.alignment.getWidth() /\r
+ seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
vscroll.setMaximum(max);\r
vscroll.setUnitIncrement(1);\r
vscroll.setVisibleAmount(1);\r
{\r
setScrollValues(av.getStartRes(), av.getStartSeq());\r
}\r
-\r
-\r
-\r
}\r
\r
- public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException\r
+ public int print(Graphics pg, PageFormat pf, int pi)\r
+ throws PrinterException\r
{\r
- pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());\r
+ pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());\r
\r
int pwidth = (int) pf.getImageableWidth();\r
int pheight = (int) pf.getImageableHeight();\r
\r
if (av.getWrapAlignment())\r
- return printWrappedAlignment(pg, pwidth,pheight, pi);\r
+ {\r
+ return printWrappedAlignment(pg, pwidth, pheight, pi);\r
+ }\r
else\r
- return printUnwrapped(pg,pwidth, pheight,pi);\r
+ {\r
+ return printUnwrapped(pg, pwidth, pheight, pi);\r
+ }\r
}\r
\r
- public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException\r
+ public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)\r
+ throws PrinterException\r
{\r
+ int idWidth = calculateIdWidth().width + 4;\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ int scaleHeight = av.charHeight + fm.getDescent();\r
\r
- int idWidth = calculateIdWidth().width + 4;\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
- int scaleHeight = av.charHeight + fm.getDescent();\r
+ pg.setColor(Color.white);\r
+ pg.fillRect(0, 0, pwidth, pheight);\r
+ pg.setFont(av.getFont());\r
\r
- pg.setColor(Color.white);\r
- pg.fillRect(0, 0, pwidth, pheight);\r
- pg.setFont(av.getFont());\r
+ ////////////////////////////////////\r
+ /// How many sequences and residues can we fit on a printable page?\r
+ int totalRes = (pwidth - idWidth) / av.getCharWidth();\r
\r
- ////////////////////////////////////\r
- /// How many sequences and residues can we fit on a printable page?\r
- int totalRes = (pwidth - idWidth) / av.getCharWidth();\r
+ int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -\r
+ 1;\r
\r
- int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) - 1;\r
+ int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;\r
\r
- int pagesWide = av.getAlignment().getWidth() / totalRes + 1;\r
+ /////////////////////////////\r
+ /// Only print these sequences and residues on this page\r
+ int startRes;\r
\r
- /////////////////////////////\r
- /// Only print these sequences and residues on this page\r
- int startRes, endRes, startSeq, endSeq;\r
- startRes = (pi % pagesWide) * totalRes;\r
- endRes = startRes + totalRes - 1;\r
- if (endRes > av.getAlignment().getWidth()-1)\r
- endRes = av.getAlignment().getWidth()-1;\r
+ /////////////////////////////\r
+ /// Only print these sequences and residues on this page\r
+ int endRes;\r
\r
- startSeq = (pi / pagesWide) * totalSeq;\r
- endSeq = startSeq + totalSeq;\r
- if (endSeq > av.getAlignment().getHeight())\r
- endSeq = av.getAlignment().getHeight();\r
+ /////////////////////////////\r
+ /// Only print these sequences and residues on this page\r
+ int startSeq;\r
\r
- int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;\r
+ /////////////////////////////\r
+ /// Only print these sequences and residues on this page\r
+ int endSeq;\r
+ startRes = (pi % pagesWide) * totalRes;\r
+ endRes = (startRes + totalRes) - 1;\r
\r
- if (av.showAnnotation)\r
- pagesHigh += annotationPanel.getHeight();\r
+ if (endRes > (av.getAlignment().getWidth() - 1))\r
+ {\r
+ endRes = av.getAlignment().getWidth() - 1;\r
+ }\r
\r
- pagesHigh /= pheight;\r
+ startSeq = (pi / pagesWide) * totalSeq;\r
+ endSeq = startSeq + totalSeq;\r
\r
- if (pi >= pagesWide * pagesHigh)\r
- return Printable.NO_SUCH_PAGE;\r
+ if (endSeq > av.getAlignment().getHeight())\r
+ {\r
+ endSeq = av.getAlignment().getHeight();\r
+ }\r
\r
- //draw Scale\r
- pg.translate(idWidth, 0);\r
- scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);\r
- pg.translate( -idWidth, scaleHeight);\r
- ////////////////\r
- // Draw the ids\r
- Color currentColor = null;\r
- Color currentTextColor = null;\r
- for (int i = startSeq; i < endSeq; i++)\r
- {\r
- if (av.getSelectionGroup() != null &&\r
- av.getSelectionGroup().sequences.\r
- contains(av.getAlignment().getSequenceAt(i)))\r
- {\r
- currentColor = Color.gray;\r
- currentTextColor = Color.black;\r
- }\r
- else\r
- {\r
- currentColor = av.getAlignment().getSequenceAt(i).getColor();\r
- currentTextColor = Color.black;\r
- }\r
+ int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;\r
+\r
+ if (av.showAnnotation)\r
+ {\r
+ pagesHigh += annotationPanel.getHeight();\r
+ }\r
\r
- pg.setColor(currentColor);\r
- pg.fillRect(0,\r
- jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,\r
- av.getCharHeight()),\r
- idWidth,\r
- av.getCharHeight());\r
+ pagesHigh /= pheight;\r
\r
- pg.setColor(currentTextColor);\r
+ if (pi >= (pagesWide * pagesHigh))\r
+ {\r
+ return Printable.NO_SUCH_PAGE;\r
+ }\r
\r
- String string = av.getAlignment().getSequenceAt(i).getName();\r
- if (av.getShowFullId())\r
- string = av.getAlignment().getSequenceAt(i).getDisplayId();\r
+ //draw Scale\r
+ pg.translate(idWidth, 0);\r
+ scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);\r
+ pg.translate( -idWidth, scaleHeight);\r
\r
- pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight\r
- (startSeq, i, av.getCharHeight()) + av.getCharHeight() -\r
- (av.getCharHeight() / 5));\r
+ ////////////////\r
+ // Draw the ids\r
+ Color currentColor = null;\r
+ Color currentTextColor = null;\r
+\r
+ for (int i = startSeq; i < endSeq; i++)\r
+ {\r
+ if ( (av.getSelectionGroup() != null) &&\r
+ av.getSelectionGroup().sequences.contains(\r
+ av.getAlignment().getSequenceAt(i)))\r
+ {\r
+ currentColor = Color.gray;\r
+ currentTextColor = Color.black;\r
+ }\r
+ else\r
+ {\r
+ currentColor = av.getAlignment().getSequenceAt(i).getColor();\r
+ currentTextColor = Color.black;\r
}\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
+ pg.setColor(currentColor);\r
+ pg.fillRect(0,\r
+ jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,\r
+ av.getCharHeight()), idWidth, av.getCharHeight());\r
+\r
+ pg.setColor(currentTextColor);\r
\r
+ String string = av.getAlignment().getSequenceAt(i).getName();\r
\r
- if (av.showAnnotation && endSeq == av.alignment.getHeight())\r
+ if (av.getShowFullId())\r
{\r
- pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight);\r
- alabels.drawComponent( (Graphics2D) pg);\r
- pg.translate(idWidth, 0);\r
- annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes+1);\r
+ string = av.getAlignment().getSequenceAt(i).getDisplayId();\r
}\r
\r
- return Printable.PAGE_EXISTS;\r
+ pg.drawString(string, 0,\r
+ (jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,\r
+ av.getCharHeight()) + av.getCharHeight()) -\r
+ (av.getCharHeight() / 5));\r
+ }\r
\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
\r
+ if (av.showAnnotation && (endSeq == av.alignment.getHeight()))\r
+ {\r
+ pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight);\r
+ alabels.drawComponent( (Graphics2D) pg);\r
+ pg.translate(idWidth, 0);\r
+ annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +\r
+ 1);\r
+ }\r
\r
- public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException\r
+ return Printable.PAGE_EXISTS;\r
+ }\r
+\r
+ public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,\r
+ int pi)\r
+ throws PrinterException\r
{\r
- int idWidth = calculateIdWidth().width + 4;\r
+ int idWidth = calculateIdWidth().width + 4;\r
\r
- int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - idWidth);\r
- int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *\r
- ( (av.alignment.getWidth()\r
- / resWidth) + 1) * av.charHeight;\r
+ int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -\r
+ idWidth);\r
+ int totalHeight = totalHeight = (av.alignment.getHeight() + 2) *\r
+ ( (av.alignment.getWidth() / resWidth) +\r
+ 1) * av.charHeight;\r
\r
+ pg.setColor(Color.white);\r
+ pg.fillRect(0, 0, pwidth, pheight);\r
+ pg.setFont(av.getFont());\r
\r
- pg.setColor(Color.white);\r
- pg.fillRect(0, 0, pwidth, pheight);\r
- pg.setFont(av.getFont());\r
+ ////////////////\r
+ // Draw the ids\r
+ pg.setColor(Color.black);\r
\r
- ////////////////\r
- // Draw the ids\r
- pg.setColor(Color.black);\r
+ pg.translate(0, -pi * pheight);\r
\r
- pg.translate(0, -pi * pheight);\r
+ pg.setClip(0, pi * pheight, pwidth, pheight);\r
\r
- pg.setClip(0,pi*pheight,pwidth, pheight);\r
+ int ypos = 2 * av.charHeight;\r
\r
- int ypos = 2 * av.charHeight;\r
- do\r
+ do\r
+ {\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceI s = av.alignment.getSequenceAt(i);\r
- String string = s.getName();\r
- if (av.getShowFullId())\r
- string = s.getDisplayId();\r
-\r
- pg.drawString(string, 0,\r
- AlignmentUtil.getPixelHeight(0, i, av.charHeight) +\r
- ypos +\r
- av.charHeight - (av.charHeight / 5));\r
+ SequenceI s = av.alignment.getSequenceAt(i);\r
+ String string = s.getName();\r
\r
+ if (av.getShowFullId())\r
+ {\r
+ string = s.getDisplayId();\r
}\r
\r
- ypos += (av.alignment.getHeight() + 2) * av.charHeight;\r
-\r
+ pg.drawString(string, 0,\r
+ (AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +\r
+ av.charHeight) - (av.charHeight / 5));\r
}\r
- while (ypos < totalHeight);\r
-\r
- pg.translate(idWidth, 0);\r
-\r
- seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);\r
\r
- if (pi * pheight < totalHeight)\r
- return Printable.PAGE_EXISTS;\r
- else\r
- return Printable.NO_SUCH_PAGE;\r
+ ypos += ( (av.alignment.getHeight() + 2) * av.charHeight);\r
+ }\r
+ while (ypos < totalHeight);\r
\r
+ pg.translate(idWidth, 0);\r
\r
+ seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);\r
\r
+ if ( (pi * pheight) < totalHeight)\r
+ {\r
+ return Printable.PAGE_EXISTS;\r
+ }\r
+ else\r
+ {\r
+ return Printable.NO_SUCH_PAGE;\r
+ }\r
}\r
\r
-\r
public void makeEPS()\r
{\r
- int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;\r
+ int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *\r
+ av.chunkHeight;\r
int width = seqPanel.getWidth() + idPanel.getWidth();\r
\r
if (!av.getWrapAlignment())\r
{\r
- height = (av.alignment.getHeight()+1) * av.charHeight + 30;\r
- width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;\r
+ height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
+ width = idPanel.getWidth() +\r
+ (av.alignment.getWidth() * av.charWidth);\r
+ }\r
+\r
+ if (av.getShowAnnotation())\r
+ {\r
+ height += annotationPanel.getPreferredSize().height;\r
}\r
- if(av.getShowAnnotation())\r
- {\r
- height += annotationPanel.getPreferredSize().height;\r
- }\r
\r
try\r
{\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"),\r
- new String[]{"eps"},\r
- new String[]{"Encapsulated Postscript"},\r
- "Encapsulated Postscript");\r
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"eps"},\r
+ new String[]\r
+ {"Encapsulated Postscript"},\r
+ "Encapsulated Postscript");\r
chooser.setFileView(new jalview.io.JalviewFileView());\r
chooser.setDialogTitle("Create EPS file from alignment");\r
chooser.setToolTipText("Save");\r
\r
int value = chooser.showSaveDialog(this);\r
+\r
if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
return;\r
+ }\r
\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
- EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
\r
- if (av.getWrapAlignment())\r
- printWrappedAlignment(pg, width, height, 0);\r
- else\r
- printUnwrapped(pg, width, height, 0);\r
+ FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
+ EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,\r
+ height);\r
\r
+ if (av.getWrapAlignment())\r
+ {\r
+ printWrappedAlignment(pg, width, height, 0);\r
+ }\r
+ else\r
+ {\r
+ printUnwrapped(pg, width, height, 0);\r
+ }\r
\r
- pg.flush();\r
- pg.close();\r
+ pg.flush();\r
+ pg.close();\r
}\r
catch (Exception ex)\r
{\r
\r
public void makePNG()\r
{\r
- int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;\r
- int width = seqPanel.getWidth() + idPanel.getWidth();\r
-\r
- if (!av.getWrapAlignment())\r
- {\r
- height = (av.alignment.getHeight()+1) * av.charHeight + 30;\r
- width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;\r
- }\r
-\r
- if(av.getShowAnnotation())\r
- {\r
- height += annotationPanel.getPreferredSize().height;\r
- }\r
+ int height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *\r
+ av.chunkHeight;\r
+ int width = seqPanel.getWidth() + idPanel.getWidth();\r
\r
+ if (!av.getWrapAlignment())\r
+ {\r
+ height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
+ width = idPanel.getWidth() +\r
+ (av.alignment.getWidth() * av.charWidth);\r
+ }\r
\r
+ if (av.getShowAnnotation())\r
+ {\r
+ height += annotationPanel.getPreferredSize().height;\r
+ }\r
\r
try\r
{\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"),\r
- new String[]{"png"},\r
- new String[]{"Portable network graphics"},\r
- "Portable network graphics");\r
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"png"},\r
+ new String[]\r
+ {"Portable network graphics"},\r
+ "Portable network graphics");\r
chooser.setFileView(new jalview.io.JalviewFileView());\r
chooser.setDialogTitle("Create EPS file from alignment");\r
chooser.setToolTipText("Save");\r
\r
int value = chooser.showSaveDialog(this);\r
+\r
if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
return;\r
+ }\r
+\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());\r
FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
\r
- BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);\r
- Graphics2D png = (Graphics2D)bi.getGraphics();\r
+ BufferedImage bi = new BufferedImage(width, height,\r
+ BufferedImage.TYPE_INT_RGB);\r
+ Graphics2D png = (Graphics2D) bi.getGraphics();\r
\r
- png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);\r
+ png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
\r
- if (av.getWrapAlignment())\r
- printWrappedAlignment(png, width, height, 0);\r
- else\r
- printUnwrapped(png, width, height, 0);\r
+ if (av.getWrapAlignment())\r
+ {\r
+ printWrappedAlignment(png, width, height, 0);\r
+ }\r
+ else\r
+ {\r
+ printUnwrapped(png, width, height, 0);\r
+ }\r
\r
- ImageIO.write(bi, "png", out);\r
- out.close();\r
+ ImageIO.write(bi, "png", out);\r
+ out.close();\r
}\r
catch (Exception ex)\r
{\r
ex.printStackTrace();\r
}\r
}\r
-\r
}\r
\r
-class Preview extends JFrame\r
+class Preview\r
+ extends JFrame\r
{\r
-\r
public Preview(Image image)\r
{\r
setResizable(true);\r
}\r
}\r
\r
-class PreviewPanel extends JPanel\r
+class PreviewPanel\r
+ extends JPanel\r
{\r
Image image;\r
+\r
public PreviewPanel(Image image)\r
{\r
this.image = image;\r
}\r
+\r
public void paintComponent(Graphics g)\r
{\r
- if(image!=null)\r
- g.drawImage(image,0,0,this);\r
+ if (image != null)\r
+ {\r
+ g.drawImage(image, 0, 0, this);\r
+ }\r
else\r
+ {\r
System.out.println("DEBUG:image is null");\r
+ }\r
}\r
}\r
-\r
-\r
-\r
-\r