+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 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
+\r
+import jalview.jbgui.*;\r
+\r
+import jalview.schemes.*;\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 javax.swing.*;\r
+import java.beans.*;\r
\r
\r
\r
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class AlignmentPanel extends GAlignmentPanel\r
+ implements AdjustmentListener, Printable\r
{\r
-\r
- AlignViewport av;\r
+ public AlignViewport av;\r
OverviewPanel overviewPanel;\r
- SeqPanel seqPanel;\r
- IdPanel idPanel;\r
+ SeqPanel seqPanel;\r
+ IdPanel idPanel;\r
IdwidthAdjuster idwidthAdjuster;\r
+\r
+ /** DOCUMENT ME!! */\r
public AlignFrame alignFrame;\r
ScalePanel scalePanel;\r
AnnotationPanel annotationPanel;\r
\r
// this value is set false when selection area being dragged\r
boolean fastPaint = true;\r
+ int hextent = 0;\r
+ int vextent = 0;\r
\r
+ /**\r
+ * Creates a new AlignmentPanel object.\r
+ *\r
+ * @param af DOCUMENT ME!\r
+ * @param av DOCUMENT ME!\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
- annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());\r
annotationScroller.setViewportView(annotationPanel);\r
annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);\r
\r
fontChanged();\r
\r
scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
- seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
+ seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
\r
setScrollValues(0, 0);\r
\r
+ setAnnotationVisible(av.getShowAnnotation());\r
+\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
- 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
- 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
- alignFrame.findMenuItem_actionPerformed(null);\r
- break;\r
- }\r
- }\r
- });\r
+ final AlignmentPanel ap = this;\r
+ av.addPropertyChangeListener(new PropertyChangeListener()\r
+ {\r
+ public void propertyChange(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
+ adjustAnnotationHeight();\r
+\r
}\r
\r
+ public void alignmentChanged()\r
+ {\r
+ av.alignmentChanged(this);\r
+\r
+ if (overviewPanel != null)\r
+ overviewPanel.updateOverviewImage();\r
+\r
+ alignFrame.updateEditMenuBar();\r
+\r
+ repaint();\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
public void fontChanged()\r
{\r
// set idCanvas bufferedImage to null\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
+ seqPanel.seqCanvas.img = null;\r
annotationPanel.adjustPanelHeight();\r
+\r
Dimension d = calculateIdWidth();\r
d.setSize(d.width + 4, d.height);\r
idPanel.idCanvas.setPreferredSize(d);\r
hscrollFillerPanel.setPreferredSize(d);\r
+\r
+ if (overviewPanel != null)\r
+ overviewPanel.setBoxPosition();\r
+\r
repaint();\r
}\r
\r
-\r
- Dimension calculateIdWidth()\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Dimension calculateIdWidth()\r
{\r
- Graphics g = this.getGraphics();\r
- if(g==null)\r
- {\r
- javax.swing.JFrame f = new javax.swing.JFrame();\r
- f.addNotify();\r
- g = f.getGraphics();\r
- }\r
+ Container c = new Container();\r
+\r
+ FontMetrics fm = c.getFontMetrics(\r
+ new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));\r
\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
+ id = s.getDisplayId(av.getShowJVSuffix());\r
\r
- // do we need to scroll the panel?\r
- if(results!=null && (av.getStartSeq()>results[0]\r
- || av.getEndSeq()<results[0]\r
- || av.getStartRes()>results[1]\r
- || av.getEndRes()<results[2]))\r
- setScrollValues(results[1], results[0]);\r
+ if (fm.stringWidth(id) > idWidth)\r
+ {\r
+ idWidth = fm.stringWidth(id);\r
+ }\r
\r
+ i++;\r
+ }\r
\r
- }\r
+ // Also check annotation label widths\r
+ i = 0;\r
\r
+ if (al.getAlignmentAnnotation() != null)\r
+ {\r
+ fm = c.getFontMetrics(alabels.getFont());\r
\r
- public OverviewPanel getOverviewPanel()\r
- {\r
- return overviewPanel;\r
- }\r
+ while (i < al.getAlignmentAnnotation().length)\r
+ {\r
+ String label = al.getAlignmentAnnotation()[i].label;\r
\r
- public void setOverviewPanel(OverviewPanel op)\r
- {\r
- overviewPanel = op;\r
- }\r
+ if (fm.stringWidth(label) > idWidth)\r
+ {\r
+ idWidth = fm.stringWidth(label);\r
+ }\r
\r
+ i++;\r
+ }\r
+ }\r
\r
- public void setAnnotationVisible(boolean b)\r
- {\r
- annotationSpaceFillerHolder.setVisible(b);\r
- annotationScroller.setVisible(b);\r
+ return new Dimension(idWidth, 12);\r
}\r
\r
-\r
- public void setWrapAlignment(boolean wrap)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param results DOCUMENT ME!\r
+ */\r
+ public void highlightSearchResults(SearchResults results)\r
{\r
- scalePanelHolder.setVisible(!wrap);\r
- hscroll.setVisible(!wrap);\r
- idwidthAdjuster.setVisible(!wrap);\r
+ seqPanel.seqCanvas.highlightSearchResults(results);\r
\r
- av.setShowAnnotation(!wrap);\r
- annotationScroller.setVisible(!wrap);\r
- annotationSpaceFillerHolder.setVisible(!wrap);\r
- idSpaceFillerPanel1.setVisible(!wrap);\r
+ // do we need to scroll the panel?\r
+ if (results != null)\r
+ {\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
- repaint();\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
+ 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
+ * @return DOCUMENT ME!\r
+ */\r
+ public OverviewPanel getOverviewPanel()\r
+ {\r
+ return overviewPanel;\r
+ }\r
\r
- public void setColourScheme()\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param op DOCUMENT ME!\r
+ */\r
+ public void setOverviewPanel(OverviewPanel op)\r
{\r
- ColourSchemeI cs = av.getGlobalColourScheme();\r
+ overviewPanel = op;\r
+ }\r
\r
- if(av.getConservationSelected())\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param b DOCUMENT ME!\r
+ */\r
+ public void setAnnotationVisible(boolean b)\r
+ {\r
+ if (!av.wrapAlignment)\r
{\r
+ annotationSpaceFillerHolder.setVisible(b);\r
+ annotationScroller.setVisible(b);\r
+ }\r
+ repaint();\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
-\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, cs);\r
+ public void adjustAnnotationHeight()\r
+ {\r
+ if (alignFrame.getHeight() == 0)\r
+ {\r
+ System.out.println("NEEDS FIXING");\r
+ }\r
\r
- av.setGlobalColourScheme( ccs );\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
repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param wrap DOCUMENT ME!\r
+ */\r
+ public void setWrapAlignment(boolean wrap)\r
+ {\r
+ av.startSeq = 0;\r
+ scalePanelHolder.setVisible(!wrap);\r
+ hscroll.setVisible(!wrap);\r
+ idwidthAdjuster.setVisible(!wrap);\r
\r
- int hextent = 0;\r
- int vextent = 0;\r
+ if (wrap)\r
+ {\r
+ annotationScroller.setVisible(false);\r
+ annotationSpaceFillerHolder.setVisible(false);\r
+ }\r
+ else if (av.showAnnotation)\r
+ {\r
+ annotationScroller.setVisible(true);\r
+ annotationSpaceFillerHolder.setVisible(true);\r
+ }\r
+\r
+ idSpaceFillerPanel1.setVisible(!wrap);\r
+\r
+ repaint();\r
+ }\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param right DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\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
+\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param x DOCUMENT ME!\r
+ * @param y DOCUMENT ME!\r
+ */\r
public void setScrollValues(int x, int y)\r
{\r
- av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);\r
\r
- hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;\r
- vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;\r
+ int width = av.alignment.getWidth();\r
+ int height = av.alignment.getHeight();\r
\r
- if(hextent > av.alignment.getWidth())\r
- hextent = av.alignment.getWidth();\r
- if(vextent > av.alignment.getHeight())\r
- vextent = av.alignment.getHeight();\r
+ if(av.hasHiddenColumns)\r
+ width = av.getColumnSelection().findColumnPosition(width);\r
\r
- if(hextent+x > av.getAlignment().getWidth())\r
- x = av.getAlignment().getWidth()- hextent;\r
+ av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) -1);\r
\r
- if(vextent+y > av.getAlignment().getHeight())\r
- y = av.getAlignment().getHeight() - vextent;\r
+ hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;\r
+ vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;\r
\r
- if(y<0)\r
- y = 0;\r
+ if (hextent > width)\r
+ {\r
+ hextent = width;\r
+ }\r
\r
- if(x<0)\r
- x=0;\r
+ if (vextent > height)\r
+ {\r
+ vextent = height;\r
+ }\r
\r
- hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());\r
- vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );\r
+ if ( (hextent + x) > width)\r
+ {\r
+ x = width - hextent;\r
+ }\r
+\r
+ if ( (vextent + y) > height)\r
+ {\r
+ y = height - vextent;\r
+ }\r
\r
+ if (y < 0)\r
+ {\r
+ y = 0;\r
+ }\r
\r
+ if (x < 0)\r
+ {\r
+ x = 0;\r
+ }\r
\r
+ hscroll.setValues(x, hextent, 0, width);\r
+ vscroll.setValues(y, vextent, 0, height);\r
}\r
\r
-\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
public void adjustmentValueChanged(AdjustmentEvent evt)\r
{\r
+\r
int oldX = av.getStartRes();\r
int oldY = av.getStartSeq();\r
\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
+ 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
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
+ int scrollX = av.startRes - oldX;\r
+ int scrollY = av.startSeq - oldY;\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
- 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
+ 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
+ idPanel.idCanvas.fastPaint(scrollY);\r
+ seqPanel.seqCanvas.fastPaint(scrollX,\r
+ scrollY);\r
+ scalePanel.repaint();\r
\r
- scalePanel.repaint();\r
- if (av.getShowAnnotation())\r
- annotationPanel.fastPaint(av.getStartRes() - oldX);\r
+ if (av.getShowAnnotation())\r
+ {\r
+ annotationPanel.fastPaint(scrollX);\r
+ }\r
+ }\r
}\r
-\r
}\r
\r
-\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\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
- vscroll.setMaximum(max);\r
- vscroll.setUnitIncrement(1);\r
- vscroll.setVisibleAmount(1);\r
+ int maxwidth = av.alignment.getWidth();\r
+\r
+ if (av.hasHiddenColumns)\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+\r
+ int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
+ if(canvasWidth>0)\r
+ {\r
+ int max = maxwidth /\r
+ seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.\r
+ getWidth()) +\r
+ 1;\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
-\r
-\r
+ if( this.getVisibleRect().getBounds() == g.getClipBounds()\r
+ && overviewPanel != null)\r
+ overviewPanel.updateOverviewImage();\r
}\r
\r
- public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pg DOCUMENT ME!\r
+ * @param pf DOCUMENT ME!\r
+ * @param pi DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ *\r
+ * @throws PrinterException DOCUMENT ME!\r
+ */\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pg DOCUMENT ME!\r
+ * @param pwidth DOCUMENT ME!\r
+ * @param pheight DOCUMENT ME!\r
+ * @param pi DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ *\r
+ * @throws PrinterException DOCUMENT ME!\r
+ */\r
+ public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)\r
+ throws PrinterException\r
{\r
+ int idWidth = getVisibleIdWidth();\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
- pg.setColor(currentColor);\r
- pg.fillRect(0,\r
- jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i,\r
- av.getCharHeight()),\r
- idWidth,\r
- av.getCharHeight());\r
+ if (av.showAnnotation)\r
+ {\r
+ pagesHigh += annotationPanel.adjustPanelHeight() + 3;\r
+ }\r
\r
- pg.setColor(currentTextColor);\r
+ pagesHigh /= pheight;\r
\r
- String string = av.getAlignment().getSequenceAt(i).getName();\r
- if (av.getShowFullId())\r
- string = av.getAlignment().getSequenceAt(i).getDisplayId();\r
+ if (pi >= (pagesWide * pagesHigh))\r
+ {\r
+ return Printable.NO_SUCH_PAGE;\r
+ }\r
\r
- pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight\r
- (startSeq, i, av.getCharHeight()) + av.getCharHeight() -\r
- (av.getCharHeight() / 5));\r
+ //draw Scale\r
+ pg.translate(idWidth, 0);\r
+ scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);\r
+ pg.translate( -idWidth, scaleHeight);\r
+\r
+ ////////////////\r
+ // Draw the ids\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
+ SequenceI seq;\r
+ for (int i = startSeq; i < endSeq; i++)\r
+ {\r
+ seq = av.getAlignment().getSequenceAt(i);\r
+ if ( (av.getSelectionGroup() != null) &&\r
+ av.getSelectionGroup().getSequences(null).contains(seq))\r
+ {\r
+ currentColor = Color.gray;\r
+ currentTextColor = Color.black;\r
+ }\r
+ else\r
+ {\r
+ currentColor = av.getSequenceColour(seq);\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, (i - startSeq) * av.charHeight, idWidth,\r
+ av.getCharHeight());\r
\r
+ pg.setColor(currentTextColor);\r
\r
- if (av.showAnnotation && endSeq == av.alignment.getHeight())\r
+ int xPos = 0;\r
+ if (av.rightAlignIds)\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
+ fm = pg.getFontMetrics();\r
+ xPos = idWidth - fm.stringWidth(\r
+ seq.getDisplayId(av.getShowJVSuffix())\r
+ ) - 4;\r
}\r
\r
- return Printable.PAGE_EXISTS;\r
+ pg.drawString(seq.getDisplayId( av.getShowJVSuffix()),\r
+ xPos,\r
+ ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -\r
+ (av.getCharHeight() / 5));\r
+ }\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, 0);\r
+\r
+ if (av.showAnnotation && (endSeq == av.alignment.getHeight()))\r
+ {\r
+ pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);\r
+ alabels.drawComponent( (Graphics2D) pg, idWidth);\r
+ pg.translate(idWidth+3, 0);\r
+ annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +\r
+ 1);\r
+ }\r
\r
+ return Printable.PAGE_EXISTS;\r
+ }\r
\r
- public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pg DOCUMENT ME!\r
+ * @param pwidth DOCUMENT ME!\r
+ * @param pheight DOCUMENT ME!\r
+ * @param pi DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ *\r
+ * @throws PrinterException DOCUMENT ME!\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
\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 annotationHeight = 0;\r
+ AnnotationLabels labels = null;\r
+ if (av.showAnnotation)\r
+ {\r
+ annotationHeight = annotationPanel.adjustPanelHeight();\r
+ labels = new AnnotationLabels(av);\r
+ }\r
\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
\r
- pg.setColor(Color.white);\r
- pg.fillRect(0, 0, pwidth, pheight);\r
- pg.setFont(av.getFont());\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+ + hgap\r
+ + annotationHeight;\r
\r
- ////////////////\r
- // Draw the ids\r
- pg.setColor(Color.black);\r
+ int idWidth = getVisibleIdWidth();\r
\r
- pg.translate(0, -pi * pheight);\r
+ int maxwidth = av.alignment.getWidth();\r
+ if (av.hasHiddenColumns)\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
\r
- pg.setClip(0,pi*pheight,pwidth, pheight);\r
\r
- int ypos = 2 * av.charHeight;\r
- do\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
+ int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -\r
+ idWidth);\r
\r
- pg.drawString(string, 0,\r
- AlignmentUtil.getPixelHeight(0, i, av.charHeight) +\r
- ypos +\r
- av.charHeight - (av.charHeight / 5));\r
+ int totalHeight = cHeight * (maxwidth / resWidth + 1);\r
\r
- }\r
+ pg.setColor(Color.white);\r
+ pg.fillRect(0, 0, pwidth, pheight);\r
+ pg.setFont(av.getFont());\r
\r
- ypos += (av.alignment.getHeight() + 2) * av.charHeight;\r
+ ////////////////\r
+ // Draw the ids\r
+ pg.setColor(Color.black);\r
\r
- }\r
- while (ypos < totalHeight);\r
+ pg.translate(0, -pi * pheight);\r
\r
- pg.translate(idWidth, 0);\r
+ pg.setClip(0, pi * pheight, pwidth, pheight);\r
\r
- seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);\r
+ int ypos = hgap;\r
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
+ av.getFont().getSize());\r
+ pg.setFont(italic);\r
\r
- if (pi * pheight < totalHeight)\r
- return Printable.PAGE_EXISTS;\r
- else\r
- return Printable.NO_SUCH_PAGE;\r
+ do\r
+ {\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\r
+ SequenceI s = av.alignment.getSequenceAt(i);\r
+ String string = s.getDisplayId( av.getShowJVSuffix());\r
+ int xPos = 0;\r
+ if (av.rightAlignIds)\r
+ {\r
+ FontMetrics fm = getFontMetrics(italic);\r
+ xPos = idWidth - fm.stringWidth( string ) - 4;\r
+ }\r
+ pg.drawString(string, xPos,\r
+ ( (i * av.charHeight) + ypos + av.charHeight) -\r
+ (av.charHeight / 5));\r
+ }\r
+ if (labels != null)\r
+ {\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(+3,\r
+ -ypos -\r
+ (av.getAlignment().getHeight() * av.charHeight));\r
+ }\r
+\r
+ ypos += cHeight;\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
+ }\r
+ else\r
+ {\r
+ return Printable.NO_SUCH_PAGE;\r
+ }\r
}\r
\r
+ int getVisibleIdWidth()\r
+ {\r
+ return\r
+ idPanel.getWidth() > 0 ? idPanel.getWidth() :\r
+ calculateIdWidth().width + 4;\r
+ }\r
\r
- public void makeEPS()\r
+ void makeAlignmentImage(int type, File file)\r
{\r
- int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;\r
- int width = seqPanel.getWidth() + idPanel.getWidth();\r
+ int maxwidth = av.alignment.getWidth();\r
+ if (av.hasHiddenColumns)\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);\r
\r
- if (!av.getWrapAlignment())\r
+ int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
+ int width = getVisibleIdWidth() + (maxwidth * av.charWidth);\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 = getWrappedHeight();\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() + getVisibleIdWidth();\r
+\r
+ }\r
+ else if (av.getShowAnnotation())\r
+ {\r
+ height += annotationPanel.adjustPanelHeight() + 3;\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"), new String[]{"eps"}, "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
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
- return;\r
\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());\r
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
- EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);\r
-\r
- if (av.getWrapAlignment())\r
- printWrappedAlignment(pg, width, height, 0);\r
- else\r
- printUnwrapped(pg, width, height, 0);\r
+ jalview.util.ImageMaker im;\r
+ if(type==jalview.util.ImageMaker.PNG)\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.PNG,\r
+ "Create PNG image from alignment",\r
+ width, height, file, null);\r
+ else\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.EPS,\r
+ "Create EPS file from alignment",\r
+ width, height, file, alignFrame.getTitle() );\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
+ catch (OutOfMemoryError err)\r
+ {\r
+ System.out.println("########################\n"\r
+ + "OUT OF MEMORY " + file + "\n"\r
+ + "########################");\r
+\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Out of Memory Creating Image!!"\r
+ +\r
+ "\nSee help files for increasing Java Virtual Machine memory."\r
+ , "Out of memory",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ System.out.println("Create IMAGE: " + err);\r
+ System.gc();\r
\r
- pg.flush();\r
- pg.close();\r
}\r
catch (Exception ex)\r
{\r
ex.printStackTrace();\r
}\r
}\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void makeEPS(File epsFile)\r
+ {\r
+ makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);\r
+ }\r
\r
- public void makePNG()\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void makePNG(File pngFile)\r
{\r
- int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;\r
- int width = seqPanel.getWidth() + idPanel.getWidth();\r
+ makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);\r
+ }\r
\r
- if (!av.getWrapAlignment())\r
+ public void makePNGImageMap(File imgMapFile, String imageName)\r
+ {\r
+ ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS\r
+ //////////////////////////////////////////////\r
+ int idWidth = getVisibleIdWidth();\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ int scaleHeight = av.charHeight + fm.getDescent();\r
+\r
+ // Gen image map\r
+ //////////////////////////////////\r
+ if (imgMapFile != null)\r
+ {\r
+ try\r
{\r
- height = (av.alignment.getHeight()+1) * av.charHeight + 30;\r
- width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;\r
- }\r
+ int s, sSize = av.alignment.getHeight(),\r
+ res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;\r
+ StringBuffer text = new StringBuffer();\r
+ PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));\r
+ out.println(jalview.io.HTMLOutput.getImageMapHTML());\r
+ out.println("<img src=\"" + imageName +\r
+ "\" border=\"0\" usemap=\"#Map\" >"\r
+ + "<map name=\"Map\">");\r
+\r
+ for (s = 0; s < sSize; s++)\r
+ {\r
+ sy = s * av.charHeight + scaleHeight;\r
+\r
+ SequenceI seq = av.alignment.getSequenceAt(s);\r
+ SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();\r
+ SequenceGroup[] groups = av.alignment.findAllGroups(seq);\r
+ for(res =0; res<alwidth; res++)\r
+ {\r
+ text = new StringBuffer();\r
+ Object obj = null;\r
+ if(av.alignment.isNucleotide())\r
+ obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );\r
+ else\r
+ obj = ResidueProperties.aa2Triplet.get(\r
+ seq.getCharAt(res) + "");\r
+\r
+ if (obj == null)\r
+ continue;\r
+\r
+ String triplet = obj.toString();\r
+ int alIndex = seq.findPosition(res);\r
+ gSize = groups.length;\r
+ for (g = 0; g < gSize; g++)\r
+ {\r
+ if(text.length()<1)\r
+ {\r
+ text.append("<area shape=\"rect\" coords=\""\r
+ + (idWidth + res * av.charWidth) + ","\r
+ + sy + ","\r
+ + (idWidth + (res + 1) * av.charWidth) + ","\r
+ + (av.charHeight + sy) + "\""\r
+ + " onMouseOver=\"toolTip('"\r
+ + alIndex + " " + triplet );\r
+ }\r
+\r
+ if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)\r
+ text.append("<br><em>" + groups[g].getName() + "</em>");\r
+ }\r
+\r
+ if (features != null)\r
+ {\r
+ if(text.length()<1)\r
+ {\r
+ text.append("<area shape=\"rect\" coords=\""\r
+ + (idWidth + res * av.charWidth) + ","\r
+ + sy + ","\r
+ + (idWidth + (res + 1) * av.charWidth) + ","\r
+ + (av.charHeight + sy) + "\""\r
+ + " onMouseOver=\"toolTip('"\r
+ + alIndex + " " + triplet );\r
+ }\r
+ fSize = features.length;\r
+ for (f = 0; f < fSize; f++)\r
+ {\r
+\r
+ if ( (features[f].getBegin() <= seq.findPosition(res)) &&\r
+ (features[f].getEnd() >= seq.findPosition(res)))\r
+ {\r
+ if (features[f].getType().equals("disulfide bond"))\r
+ {\r
+ if (features[f].getBegin() == seq.findPosition(res)\r
+ || features[f].getEnd() == seq.findPosition(res))\r
+ {\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(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 (features[f].getValue("status") != null )\r
+ {\r
+ text.append(" (" + features[f].getValue("status") + ")");\r
+ }\r
+ }\r
+ }\r
+\r
+ }\r
+ }\r
+ if(text.length()>1)\r
+ {\r
+ text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");\r
+ out.println(text.toString());\r
+ }\r
+ }\r
+ }\r
+ out.println("</map></body></html>");\r
+ out.close();\r
\r
- if(av.getShowAnnotation())\r
+ }\r
+ catch (Exception ex)\r
{\r
- height += annotationPanel.getPreferredSize().height;\r
+ ex.printStackTrace();\r
}\r
+ } ///////////END OF IMAGE MAP\r
\r
+ }\r
\r
+ int getWrappedHeight()\r
+ {\r
+ int seqPanelWidth = seqPanel.seqCanvas.getWidth();\r
\r
- try\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
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[]{"png"}, "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
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
- return;\r
-\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());\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
+ seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth();\r
+ }\r
\r
- png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);\r
+ int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(\r
+ seqPanelWidth\r
+ );\r
\r
- if (av.getWrapAlignment())\r
- printWrappedAlignment(png, width, height, 0);\r
- else\r
- printUnwrapped(png, width, height, 0);\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
\r
- ImageIO.write(bi, "png", out);\r
- out.close();\r
- }\r
- catch (Exception ex)\r
+ int annotationHeight = 0;\r
+ if (av.showAnnotation)\r
{\r
- ex.printStackTrace();\r
+ annotationHeight = annotationPanel.adjustPanelHeight();\r
}\r
- }\r
\r
-}\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+ + hgap\r
+ + annotationHeight;\r
\r
-class Preview extends JFrame\r
-{\r
+ int maxwidth = av.alignment.getWidth();\r
+ if (av.hasHiddenColumns)\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
\r
- public Preview(Image image)\r
- {\r
- setResizable(true);\r
- setSize(image.getWidth(this), image.getHeight(this));\r
- setVisible(true);\r
- getContentPane().setLayout(new BorderLayout());\r
- getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);\r
- validate();\r
- repaint();\r
+\r
+ int height = ( (maxwidth / chunkWidth) + 1) * cHeight;\r
+\r
+ return height;\r
}\r
-}\r
\r
-class PreviewPanel extends JPanel\r
-{\r
- Image image;\r
- public PreviewPanel(Image image)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+ class Preview\r
+ extends JFrame\r
{\r
- this.image = image;\r
+ /**\r
+ * Creates a new Preview object.\r
+ *\r
+ * @param image DOCUMENT ME!\r
+ */\r
+ public Preview(Image image)\r
+ {\r
+ setResizable(true);\r
+ setSize(image.getWidth(this), image.getHeight(this));\r
+ setVisible(true);\r
+ getContentPane().setLayout(new BorderLayout());\r
+ getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);\r
+ validate();\r
+ repaint();\r
+ }\r
}\r
- public void paintComponent(Graphics g)\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+ class PreviewPanel\r
+ extends JPanel\r
{\r
- if(image!=null)\r
- g.drawImage(image,0,0,this);\r
- else\r
- System.out.println("image is null");\r
+ Image image;\r
+\r
+ /**\r
+ * Creates a new PreviewPanel object.\r
+ *\r
+ * @param image DOCUMENT ME!\r
+ */\r
+ public PreviewPanel(Image image)\r
+ {\r
+ this.image = image;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ */\r
+ public void paintComponent(Graphics g)\r
+ {\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
-\r
git://source.jalview.org / jalview.git / blobdiff