-package jalview.gui;\r
-\r
-import jalview.jbgui.GAlignmentPanel;\r
-import jalview.schemes.*;\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\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
-\r
-\r
-\r
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable\r
-{\r
-\r
- AlignViewport av;\r
- OverviewPanel overviewPanel;\r
- SeqPanel seqPanel;\r
- IdPanel idPanel;\r
- IdwidthAdjuster idwidthAdjuster;\r
- public AlignFrame alignFrame;\r
- ScalePanel scalePanel;\r
- AnnotationPanel annotationPanel;\r
- AnnotationLabels alabels;\r
-\r
- // this value is set false when selection area being dragged\r
- boolean fastPaint = true;\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
-\r
- scalePanel = new ScalePanel(av, this);\r
-\r
- idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
- idwidthAdjuster = new IdwidthAdjuster(this);\r
- idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);\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
- Dimension d = calculateIdWidth();\r
- d.setSize( d.width+4, d.height);\r
- idPanel.idCanvas.setPreferredSize( d );\r
- hscrollFillerPanel.setPreferredSize( d );\r
-\r
- scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
- seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
-\r
- javax.swing.SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- {\r
- invalidate();\r
- setScrollValues(0,0);\r
- Dimension d = calculateIdWidth();\r
- d.setSize( d.width+4, d.height);\r
- idPanel.idCanvas.setPreferredSize( d );\r
- RefreshPanels();\r
- }\r
- });\r
-\r
-\r
- hscroll.addAdjustmentListener(this);\r
- vscroll.addAdjustmentListener(this);\r
-\r
- addComponentListener(new ComponentAdapter()\r
- {\r
- public void componentResized(ComponentEvent evt)\r
- {\r
- RefreshPanels();\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
- RefreshPanels();\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
- }\r
-\r
- 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
-\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
-\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 && (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
-\r
-\r
- }\r
-\r
-\r
- public OverviewPanel getOverviewPanel()\r
- {\r
- return overviewPanel;\r
- }\r
-\r
- public void setOverviewPanel(OverviewPanel op)\r
- {\r
- overviewPanel = op;\r
- }\r
-\r
-\r
- public void setAnnotationVisible(boolean b)\r
- {\r
- annotationSpaceFillerHolder.setVisible(b);\r
- annotationScroller.setVisible(b);\r
- javax.swing.SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- {\r
- RefreshPanels();\r
- }\r
- });\r
-\r
- }\r
-\r
-\r
- public void setWrapAlignment(boolean wrap)\r
- {\r
- scalePanelHolder.setVisible(!wrap);\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
- javax.swing.SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- {\r
- RefreshPanels();\r
- }\r
- });\r
-\r
- }\r
-\r
-\r
- public void setColourScheme()\r
- {\r
- ColourSchemeI cs = av.getGlobalColourScheme();\r
-\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
-\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, cs);\r
-\r
- av.setGlobalColourScheme( ccs );\r
-\r
- }\r
-\r
- RefreshPanels();\r
- }\r
-\r
-\r
- public void RefreshPanels()\r
- {\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.setValues(0, 1, 0, max);\r
- }\r
- else\r
- {\r
- if (overviewPanel != null)\r
- overviewPanel.updateOverviewImage();\r
- setScrollValues(av.getStartRes(), av.getStartSeq());\r
- }\r
-\r
- validate();\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
- {\r
- if(vscroll.getValue()<1)\r
- return false;\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
- vscroll.setValue(vscroll.getValue() + 1);\r
- }\r
- fastPaint = true;\r
- return true;\r
- }\r
-\r
- public boolean scrollRight(boolean right)\r
- {\r
-\r
- if (right)\r
- {\r
- if (hscroll.getValue() < 1)\r
- return false;\r
- fastPaint = false;\r
- hscroll.setValue(hscroll.getValue() - 1);\r
- }\r
- else\r
- {\r
- if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())\r
- return false;\r
- fastPaint = false;\r
- hscroll.setValue(hscroll.getValue() + 1);\r
- }\r
- fastPaint = true;\r
- return true;\r
- }\r
-\r
-\r
- public void setScrollValues(int x, int y)\r
- {\r
- hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;\r
- vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;\r
-\r
- if(hextent > av.alignment.getWidth())\r
- hextent = av.alignment.getWidth();\r
- if(vextent > av.alignment.getHeight())\r
- vextent = av.alignment.getHeight();\r
-\r
- if(hextent+x > av.getAlignment().getWidth())\r
- x = av.getAlignment().getWidth()- hextent;\r
-\r
- if(vextent+y > av.getAlignment().getHeight())\r
- y = av.getAlignment().getHeight() - vextent;\r
-\r
- if(y<0)\r
- y = 0;\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
-\r
-\r
- public void adjustmentValueChanged(AdjustmentEvent evt)\r
- {\r
- int oldX = av.getStartRes();\r
- int oldY = av.getStartSeq();\r
-\r
- if (evt.getSource() == hscroll)\r
- {\r
- int x = hscroll.getValue();\r
- av.setStartRes(x);\r
- av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);\r
- }\r
-\r
- if (evt.getSource() == vscroll)\r
- {\r
- int offy = vscroll.getValue();\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
- }\r
- else\r
- {\r
- av.setStartSeq(offy);\r
- av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());\r
- }\r
- }\r
-\r
-\r
- if(overviewPanel!=null)\r
- overviewPanel.setBoxPosition();\r
-\r
- if(av.getWrapAlignment() || !fastPaint)\r
- repaint();\r
- else\r
- {\r
- seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,\r
- av.getStartSeq() - oldY);\r
- idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);\r
- scalePanel.repaint();\r
- if (av.getShowAnnotation())\r
- annotationPanel.fastPaint(av.getStartRes() - oldX);\r
- }\r
-\r
- }\r
-\r
- public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException\r
- {\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
- else\r
- return printUnwrapped(pg,pwidth, pheight,pi);\r
- }\r
-\r
- public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException\r
- {\r
-\r
- int idWidth = calculateIdWidth().width + 4;\r
-\r
-\r
- pg.setColor(Color.white);\r
- pg.fillRect(0,0,pwidth, pheight);\r
- pg.setFont( av.getFont() );\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 - 30)/av.getCharHeight())-1;\r
- int pagesWide = av.getAlignment().getWidth() / totalRes +1;\r
- int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;\r
-\r
- if (pi >= pagesWide*pagesHigh)\r
- return Printable.NO_SUCH_PAGE;\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())\r
- endRes = av.getAlignment().getWidth();\r
-\r
- startSeq = (pi / pagesWide) * totalSeq;\r
- endSeq = startSeq + totalSeq;\r
- if(endSeq > av.getAlignment().getHeight())\r
- endSeq = av.getAlignment().getHeight();\r
-\r
-\r
- ////////////////\r
- //draw Scale\r
- pg.translate(idWidth,0);\r
- scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);\r
-\r
- pg.translate(-idWidth, 30);\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 && av.getSelectionGroup().sequences.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
-\r
- pg.setColor(currentColor);\r
- pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),\r
- idWidth,\r
- av.getCharHeight());\r
-\r
- pg.setColor(currentTextColor);\r
-\r
- String string = av.getAlignment().getSequenceAt(i).getName();\r
- if(av.getShowFullId())\r
- string = av.getAlignment().getSequenceAt(i).getDisplayId();\r
-\r
- pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight\r
- (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));\r
- }\r
-\r
- // draw main sequence panel\r
- pg.translate(idWidth,0);\r
- seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);\r
-\r
-\r
- if(av.getShowAnnotation())\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
- }\r
-\r
- return Printable.PAGE_EXISTS;\r
- }\r
-\r
-\r
- public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException\r
- {\r
-\r
- int idWidth = calculateIdWidth().width+4;\r
-\r
- if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)\r
- pwidth = seqPanel.seqCanvas.getWidth() + idWidth;\r
-\r
-\r
- pg.setColor(Color.white);\r
- pg.fillRect(0,0,pwidth, pheight);\r
- pg.setFont( av.getFont() );\r
-\r
- ////////////////////////////////////\r
- /// How many sequences and residues can we fit on a printable page?\r
- AlignmentI da = av.alignment;\r
- int endy = da.getHeight();\r
- int chunkHeight = (da.getHeight() + 2)*av.charHeight;\r
- int chunkWidth = (pwidth-idWidth)/av.charWidth;\r
-\r
- int noChunksOnPage = pheight / chunkHeight;\r
- int totalChunks = da.getWidth() / chunkWidth;\r
-\r
- if ( pi*noChunksOnPage > totalChunks )\r
- return Printable.NO_SUCH_PAGE;\r
-\r
- ////////////////\r
- // Draw the ids\r
- pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);\r
-\r
- pg.setColor(Color.black);\r
-\r
- int rowSize = av.getEndRes() - av.getStartRes();\r
- // Draw the rest of the panels\r
-\r
- for(int ypos=2*av.charHeight, row=av.getEndRes(); row<av.alignment.getWidth();\r
- ypos += av.chunkHeight, row+=rowSize )\r
- {\r
- for (int i = 0; i < endy; i++)\r
- {\r
- SequenceI s = da.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) + ypos +\r
- av.charHeight - (av.charHeight / 5));\r
- }\r
- }\r
-\r
- // draw main sequence panel\r
- pg.translate(idWidth,0);\r
- seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);\r
-\r
-\r
- return Printable.PAGE_EXISTS;\r
-\r
- }\r
-\r
-\r
- public void makeEPS()\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
- 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
-\r
-\r
- pg.flush();\r
- pg.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\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
-\r
-\r
-System.out.println(width +" "+height);\r
-\r
- try\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
- Graphics png = bi.getGraphics();\r
-\r
-\r
- if (av.getWrapAlignment())\r
- printWrappedAlignment(png, width, height, 0);\r
- else\r
- printUnwrapped(png, width, height, 0);\r
-\r
- ImageIO.write(bi, "png", out);\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
-}\r
-\r
-\r
-\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import java.beans.*;
+import java.io.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.print.*;
+import javax.swing.*;
+
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignmentPanel
+ extends GAlignmentPanel implements AdjustmentListener, Printable
+{
+ public AlignViewport av;
+ OverviewPanel overviewPanel;
+ SeqPanel seqPanel;
+ IdPanel idPanel;
+ IdwidthAdjuster idwidthAdjuster;
+
+ /** DOCUMENT ME!! */
+ public AlignFrame alignFrame;
+ ScalePanel scalePanel;
+ AnnotationPanel annotationPanel;
+ AnnotationLabels alabels;
+
+ // this value is set false when selection area being dragged
+ boolean fastPaint = true;
+ int hextent = 0;
+ int vextent = 0;
+
+ /**
+ * Creates a new AlignmentPanel object.
+ *
+ * @param af DOCUMENT ME!
+ * @param av DOCUMENT ME!
+ */
+ public AlignmentPanel(AlignFrame af, final AlignViewport av)
+ {
+ alignFrame = af;
+ this.av = av;
+ seqPanel = new SeqPanel(av, this);
+ idPanel = new IdPanel(av, this);
+
+ scalePanel = new ScalePanel(av, this);
+
+ idPanelHolder.add(idPanel, BorderLayout.CENTER);
+ idwidthAdjuster = new IdwidthAdjuster(this);
+ idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
+
+ annotationPanel = new AnnotationPanel(this);
+ alabels = new AnnotationLabels(this);
+
+ annotationScroller.setViewportView(annotationPanel);
+ annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
+
+ scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
+ seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
+
+ setScrollValues(0, 0);
+
+ setAnnotationVisible(av.getShowAnnotation());
+
+ hscroll.addAdjustmentListener(this);
+ vscroll.addAdjustmentListener(this);
+
+ final AlignmentPanel ap = this;
+ av.addPropertyChangeListener(new PropertyChangeListener()
+ {
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (evt.getPropertyName().equals("alignment"))
+ {
+ PaintRefresher.Refresh(ap,
+ av.getSequenceSetId(),
+ true,
+ true);
+ alignmentChanged();
+ }
+ }
+ });
+
+ fontChanged();
+ adjustAnnotationHeight();
+
+ }
+
+ public void alignmentChanged()
+ {
+ av.alignmentChanged(this);
+
+ alignFrame.updateEditMenuBar();
+
+ paintAlignment(true);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void fontChanged()
+ {
+ // set idCanvas bufferedImage to null
+ // to prevent drawing old image
+ FontMetrics fm = getFontMetrics(av.getFont());
+
+ scalePanelHolder.setPreferredSize(new Dimension(10,
+ av.charHeight + fm.getDescent()));
+ idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
+ av.charHeight + fm.getDescent()));
+
+ idPanel.idCanvas.gg = null;
+ seqPanel.seqCanvas.img = null;
+ annotationPanel.adjustPanelHeight();
+
+ Dimension d = calculateIdWidth();
+ d.setSize(d.width + 4, d.height);
+ idPanel.idCanvas.setPreferredSize(d);
+ hscrollFillerPanel.setPreferredSize(d);
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.setBoxPosition();
+ }
+
+ repaint();
+ }
+
+ /**
+ * Calculate the width of the alignment labels based on the displayed names and any bounds on label width set in preferences.
+ *
+ * @return Dimension giving the maximum width of the alignment label panel that should be used.
+ */
+ public Dimension calculateIdWidth()
+ {
+ Container c = new Container();
+
+ FontMetrics fm = c.getFontMetrics(
+ new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
+
+ AlignmentI al = av.getAlignment();
+ int afwidth = (alignFrame!=null ? alignFrame.getWidth() : 300);
+ int maxwidth = Math.max(20,Math.min(afwidth-200,(int) 2*afwidth/3));
+ int i = 0;
+ int idWidth = 0;
+ String id;
+
+ while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
+ {
+ SequenceI s = al.getSequenceAt(i);
+
+ id = s.getDisplayId(av.getShowJVSuffix());
+
+ if (fm.stringWidth(id) > idWidth)
+ {
+ idWidth = fm.stringWidth(id);
+ }
+
+ i++;
+ }
+
+ // Also check annotation label widths
+ i = 0;
+
+ if (al.getAlignmentAnnotation() != null)
+ {
+ fm = c.getFontMetrics(alabels.getFont());
+
+ while (i < al.getAlignmentAnnotation().length)
+ {
+ String label = al.getAlignmentAnnotation()[i].label;
+
+ if (fm.stringWidth(label) > idWidth)
+ {
+ idWidth = fm.stringWidth(label);
+ }
+
+ i++;
+ }
+ }
+
+ return new Dimension(Math.min(maxwidth, idWidth), 12);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param results DOCUMENT ME!
+ */
+ public void highlightSearchResults(SearchResults results)
+ {
+ seqPanel.seqCanvas.highlightSearchResults(results);
+
+ // do we need to scroll the panel?
+ if (results != null)
+ {
+ SequenceI seq = results.getResultSequence(0);
+ int seqIndex = av.alignment.findIndex(seq);
+ int start = seq.findIndex(results.getResultStart(0)) - 1;
+ int end = seq.findIndex(results.getResultEnd(0)) - 1;
+
+ if (!av.wrapAlignment)
+ {
+ if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
+ ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+ {
+ setScrollValues(start, seqIndex);
+ }
+ }
+ else
+ {
+ scrollToWrappedVisible(start);
+ }
+ }
+
+ paintAlignment(true);
+ }
+
+ void scrollToWrappedVisible(int res)
+ {
+ int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
+ getWidth());
+ if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
+ {
+ vscroll.setValue(res / cwidth);
+ av.startRes = vscroll.getValue() * cwidth;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public OverviewPanel getOverviewPanel()
+ {
+ return overviewPanel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param op DOCUMENT ME!
+ */
+ public void setOverviewPanel(OverviewPanel op)
+ {
+ overviewPanel = op;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setAnnotationVisible(boolean b)
+ {
+ if (!av.wrapAlignment)
+ {
+ annotationSpaceFillerHolder.setVisible(b);
+ annotationScroller.setVisible(b);
+ }
+ repaint();
+ }
+
+ public void adjustAnnotationHeight()
+ {
+ //TODO: display vertical annotation scrollbar if necessary
+ // this is called after loading new annotation onto alignment
+ if (alignFrame.getHeight() == 0)
+ {
+ System.out.println("NEEDS FIXING");
+ }
+
+ int height = annotationPanel.adjustPanelHeight();
+
+ if (hscroll.isVisible())
+ {
+ height += hscroll.getPreferredSize().height;
+ }
+ if (height > alignFrame.getHeight() / 2)
+ {
+ height = alignFrame.getHeight() / 2;
+ }
+
+ hscroll.addNotify();
+
+ annotationScroller.setPreferredSize(
+ new Dimension(annotationScroller.getWidth(), height));
+
+
+ annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+ annotationSpaceFillerHolder.getWidth(),
+ height));
+ annotationScroller.validate();// repaint();
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param wrap DOCUMENT ME!
+ */
+ public void setWrapAlignment(boolean wrap)
+ {
+ av.startSeq = 0;
+ scalePanelHolder.setVisible(!wrap);
+ hscroll.setVisible(!wrap);
+ idwidthAdjuster.setVisible(!wrap);
+
+ if (wrap)
+ {
+ annotationScroller.setVisible(false);
+ annotationSpaceFillerHolder.setVisible(false);
+ }
+ else if (av.showAnnotation)
+ {
+ annotationScroller.setVisible(true);
+ annotationSpaceFillerHolder.setVisible(true);
+ }
+
+ idSpaceFillerPanel1.setVisible(!wrap);
+
+ repaint();
+ }
+
+ // return value is true if the scroll is valid
+ public boolean scrollUp(boolean up)
+ {
+ if (up)
+ {
+ if (vscroll.getValue() < 1)
+ {
+ return false;
+ }
+
+ fastPaint = false;
+ vscroll.setValue(vscroll.getValue() - 1);
+ }
+ else
+ {
+ if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
+ {
+ return false;
+ }
+
+ fastPaint = false;
+ vscroll.setValue(vscroll.getValue() + 1);
+ }
+
+ fastPaint = true;
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param right DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean scrollRight(boolean right)
+ {
+ if (!right)
+ {
+ if (hscroll.getValue() < 1)
+ {
+ return false;
+ }
+
+ fastPaint = false;
+ hscroll.setValue(hscroll.getValue() - 1);
+ }
+ else
+ {
+ if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
+ {
+ return false;
+ }
+
+ fastPaint = false;
+ hscroll.setValue(hscroll.getValue() + 1);
+ }
+
+ fastPaint = true;
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x DOCUMENT ME!
+ * @param y DOCUMENT ME!
+ */
+ public void setScrollValues(int x, int y)
+ {
+
+ int width = av.alignment.getWidth();
+ int height = av.alignment.getHeight();
+
+ if (av.hasHiddenColumns)
+ {
+ width = av.getColumnSelection().findColumnPosition(width);
+ }
+
+ av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
+
+ hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
+ vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
+
+ if (hextent > width)
+ {
+ hextent = width;
+ }
+
+ if (vextent > height)
+ {
+ vextent = height;
+ }
+
+ if ( (hextent + x) > width)
+ {
+ x = width - hextent;
+ }
+
+ if ( (vextent + y) > height)
+ {
+ y = height - vextent;
+ }
+
+ if (y < 0)
+ {
+ y = 0;
+ }
+
+ if (x < 0)
+ {
+ x = 0;
+ }
+
+ hscroll.setValues(x, hextent, 0, width);
+ vscroll.setValues(y, vextent, 0, height);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+
+ int oldX = av.getStartRes();
+ int oldY = av.getStartSeq();
+
+ if (evt.getSource() == hscroll)
+ {
+ int x = hscroll.getValue();
+ av.setStartRes(x);
+ av.setEndRes( (x +
+ (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
+ }
+
+ if (evt.getSource() == vscroll)
+ {
+ int offy = vscroll.getValue();
+
+ if (av.getWrapAlignment())
+ {
+ if (offy > -1)
+ {
+ int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
+ seqCanvas.getWidth());
+ av.setStartRes(offy * rowSize);
+ av.setEndRes( (offy + 1) * rowSize);
+ }
+ else
+ {
+ //This is only called if file loaded is a jar file that
+ //was wrapped when saved and user has wrap alignment true
+ //as preference setting
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ setScrollValues(av.getStartRes(), av.getStartSeq());
+ }
+ });
+ }
+ }
+ else
+ {
+ av.setStartSeq(offy);
+ av.setEndSeq(offy +
+ (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
+ }
+ }
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.setBoxPosition();
+ }
+
+ int scrollX = av.startRes - oldX;
+ int scrollY = av.startSeq - oldY;
+
+ if (av.getWrapAlignment() || !fastPaint)
+ {
+ repaint();
+ }
+ else
+ {
+ // Make sure we're not trying to draw a panel
+ // larger than the visible window
+ if (scrollX > av.endRes - av.startRes)
+ {
+ scrollX = av.endRes - av.startRes;
+ }
+ else if (scrollX < av.startRes - av.endRes)
+ {
+ scrollX = av.startRes - av.endRes;
+ }
+
+ if (scrollX != 0 || scrollY != 0)
+ {
+ idPanel.idCanvas.fastPaint(scrollY);
+ seqPanel.seqCanvas.fastPaint(scrollX,
+ scrollY);
+ scalePanel.repaint();
+
+ if (av.getShowAnnotation())
+ {
+ annotationPanel.fastPaint(scrollX);
+ }
+ }
+ }
+ }
+
+ public void paintAlignment(boolean updateOverview)
+ {
+ repaint();
+
+ if(updateOverview)
+ {
+ jalview.structure.StructureSelectionManager.getStructureSelectionManager()
+ .sequenceColoursChanged(this);
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.updateOverviewImage();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void paintComponent(Graphics g)
+ {
+ invalidate();
+
+ Dimension d = idPanel.idCanvas.getPreferredSize();
+ idPanelHolder.setPreferredSize(d);
+ hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+ validate();
+
+ if (av.getWrapAlignment())
+ {
+ int maxwidth = av.alignment.getWidth();
+
+ if (av.hasHiddenColumns)
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
+ seqCanvas.getWidth());
+ if (canvasWidth > 0)
+ {
+ int max = maxwidth /
+ seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
+ getWidth()) +
+ 1;
+ vscroll.setMaximum(max);
+ vscroll.setUnitIncrement(1);
+ vscroll.setVisibleAmount(1);
+ }
+ }
+ else
+ {
+ setScrollValues(av.getStartRes(), av.getStartSeq());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg DOCUMENT ME!
+ * @param pf DOCUMENT ME!
+ * @param pi DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException DOCUMENT ME!
+ */
+ public int print(Graphics pg, PageFormat pf, int pi)
+ throws PrinterException
+ {
+ pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
+
+ int pwidth = (int) pf.getImageableWidth();
+ int pheight = (int) pf.getImageableHeight();
+
+ if (av.getWrapAlignment())
+ {
+ return printWrappedAlignment(pg, pwidth, pheight, pi);
+ }
+ else
+ {
+ return printUnwrapped(pg, pwidth, pheight, pi);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg DOCUMENT ME!
+ * @param pwidth DOCUMENT ME!
+ * @param pheight DOCUMENT ME!
+ * @param pi DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException DOCUMENT ME!
+ */
+ public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
+ throws PrinterException
+ {
+ int idWidth = getVisibleIdWidth();
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int scaleHeight = av.charHeight + fm.getDescent();
+
+ pg.setColor(Color.white);
+ pg.fillRect(0, 0, pwidth, pheight);
+ pg.setFont(av.getFont());
+
+ ////////////////////////////////////
+ /// How many sequences and residues can we fit on a printable page?
+ int totalRes = (pwidth - idWidth) / av.getCharWidth();
+
+ int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
+ 1;
+
+ int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
+
+ /////////////////////////////
+ /// Only print these sequences and residues on this page
+ int startRes;
+
+ /////////////////////////////
+ /// Only print these sequences and residues on this page
+ int endRes;
+
+ /////////////////////////////
+ /// Only print these sequences and residues on this page
+ int startSeq;
+
+ /////////////////////////////
+ /// Only print these sequences and residues on this page
+ int endSeq;
+ startRes = (pi % pagesWide) * totalRes;
+ endRes = (startRes + totalRes) - 1;
+
+ if (endRes > (av.getAlignment().getWidth() - 1))
+ {
+ endRes = av.getAlignment().getWidth() - 1;
+ }
+
+ startSeq = (pi / pagesWide) * totalSeq;
+ endSeq = startSeq + totalSeq;
+
+ if (endSeq > av.getAlignment().getHeight())
+ {
+ endSeq = av.getAlignment().getHeight();
+ }
+
+ int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
+
+ if (av.showAnnotation)
+ {
+ pagesHigh += annotationPanel.adjustPanelHeight() + 3;
+ }
+
+ pagesHigh /= pheight;
+
+ if (pi >= (pagesWide * pagesHigh))
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
+
+ //draw Scale
+ pg.translate(idWidth, 0);
+ scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
+ pg.translate( -idWidth, scaleHeight);
+
+ ////////////////
+ // Draw the ids
+ Color currentColor = null;
+ Color currentTextColor = null;
+
+ pg.setFont(idPanel.idCanvas.idfont);
+
+ SequenceI seq;
+ for (int i = startSeq; i < endSeq; i++)
+ {
+ seq = av.getAlignment().getSequenceAt(i);
+ if ( (av.getSelectionGroup() != null) &&
+ av.getSelectionGroup().getSequences(null).contains(seq))
+ {
+ currentColor = Color.gray;
+ currentTextColor = Color.black;
+ }
+ else
+ {
+ currentColor = av.getSequenceColour(seq);
+ currentTextColor = Color.black;
+ }
+
+ pg.setColor(currentColor);
+ pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+ av.getCharHeight());
+
+ pg.setColor(currentTextColor);
+
+ int xPos = 0;
+ if (av.rightAlignIds)
+ {
+ fm = pg.getFontMetrics();
+ xPos = idWidth - fm.stringWidth(
+ seq.getDisplayId(av.getShowJVSuffix())
+ ) - 4;
+ }
+
+ pg.drawString(seq.getDisplayId(av.getShowJVSuffix()),
+ xPos,
+ ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
+ (av.getCharHeight() / 5));
+ }
+
+ pg.setFont(av.getFont());
+
+ // draw main sequence panel
+ pg.translate(idWidth, 0);
+ seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
+
+ if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
+ {
+ pg.translate( -idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
+ alabels.drawComponent( (Graphics2D) pg, idWidth);
+ pg.translate(idWidth + 3, 0);
+ annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
+ 1);
+ }
+
+ return Printable.PAGE_EXISTS;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg DOCUMENT ME!
+ * @param pwidth DOCUMENT ME!
+ * @param pheight DOCUMENT ME!
+ * @param pi DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException DOCUMENT ME!
+ */
+ public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
+ int pi)
+ throws PrinterException
+ {
+
+ int annotationHeight = 0;
+ AnnotationLabels labels = null;
+ if (av.showAnnotation)
+ {
+ annotationHeight = annotationPanel.adjustPanelHeight();
+ labels = new AnnotationLabels(av);
+ }
+
+ int hgap = av.charHeight;
+ if (av.scaleAboveWrapped)
+ {
+ hgap += av.charHeight;
+ }
+
+ int cHeight = av.getAlignment().getHeight() * av.charHeight
+ + hgap
+ + annotationHeight;
+
+ int idWidth = getVisibleIdWidth();
+
+ int maxwidth = av.alignment.getWidth();
+ if (av.hasHiddenColumns)
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
+ idWidth);
+
+ int totalHeight = cHeight * (maxwidth / resWidth + 1);
+
+ pg.setColor(Color.white);
+ pg.fillRect(0, 0, pwidth, pheight);
+ pg.setFont(av.getFont());
+
+ ////////////////
+ // Draw the ids
+ pg.setColor(Color.black);
+
+ pg.translate(0, -pi * pheight);
+
+ pg.setClip(0, pi * pheight, pwidth, pheight);
+
+ int ypos = hgap;
+
+ do
+ {
+ for (int i = 0; i < av.alignment.getHeight(); i++)
+ {
+ pg.setFont(idPanel.idCanvas.idfont);
+ SequenceI s = av.alignment.getSequenceAt(i);
+ String string = s.getDisplayId(av.getShowJVSuffix());
+ int xPos = 0;
+ if (av.rightAlignIds)
+ {
+ FontMetrics fm = pg.getFontMetrics();
+ xPos = idWidth - fm.stringWidth(string) - 4;
+ }
+ pg.drawString(string, xPos,
+ ( (i * av.charHeight) + ypos + av.charHeight) -
+ (av.charHeight / 5));
+ }
+ if (labels != null)
+ {
+ pg.translate( -3,
+ ypos +
+ (av.getAlignment().getHeight() * av.charHeight));
+
+ pg.setFont(av.getFont());
+ labels.drawComponent(pg, idWidth);
+ pg.translate( +3,
+ -ypos -
+ (av.getAlignment().getHeight() * av.charHeight));
+ }
+
+ ypos += cHeight;
+ }
+ while (ypos < totalHeight);
+
+ pg.translate(idWidth, 0);
+
+ seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
+
+ if ( (pi * pheight) < totalHeight)
+ {
+ return Printable.PAGE_EXISTS;
+
+ }
+ else
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
+ }
+
+ int getVisibleIdWidth()
+ {
+ return
+ idPanel.getWidth() > 0 ? idPanel.getWidth() :
+ calculateIdWidth().width + 4;
+ }
+
+ void makeAlignmentImage(int type, File file)
+ {
+ int maxwidth = av.alignment.getWidth();
+ if (av.hasHiddenColumns)
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+ }
+
+ int height = ( (av.alignment.getHeight() + 1) * av.charHeight)
+ + scalePanel.getHeight();
+ int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
+
+ if (av.getWrapAlignment())
+ {
+ height = getWrappedHeight();
+ if (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
+ {
+ width = alignFrame.getWidth()
+ - vscroll.getPreferredSize().width
+ - alignFrame.getInsets().left
+ - alignFrame.getInsets().right;
+ }
+ else
+ {
+ width = seqPanel.getWidth() + getVisibleIdWidth();
+ }
+
+ }
+ else if (av.getShowAnnotation())
+ {
+ height += annotationPanel.adjustPanelHeight() + 3;
+ }
+
+ try
+ {
+
+ jalview.util.ImageMaker im;
+ if (type == jalview.util.ImageMaker.PNG)
+ {
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.PNG,
+ "Create PNG image from alignment",
+ width, height, file, null);
+ }
+ else
+ {
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.EPS,
+ "Create EPS file from alignment",
+ width, height, file,
+ alignFrame.getTitle());
+ }
+
+ if (av.getWrapAlignment())
+ {
+ if (im.getGraphics() != null)
+ {
+ printWrappedAlignment(im.getGraphics(), width, height, 0);
+ im.writeImage();
+ }
+ }
+ else
+ {
+ if (im.getGraphics() != null)
+ {
+ printUnwrapped(im.getGraphics(), width, height, 0);
+ im.writeImage();
+ }
+ }
+ }
+ catch (OutOfMemoryError err)
+ {
+ // Be noisy here.
+ System.out.println("########################\n"
+ + "OUT OF MEMORY " + file + "\n"
+ + "########################");
+ new OOMWarning("Creating Image for "+file,err);
+ // System.out.println("Create IMAGE: " + err);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void makeEPS(File epsFile)
+ {
+ makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void makePNG(File pngFile)
+ {
+ makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
+ }
+
+ public void makePNGImageMap(File imgMapFile, String imageName)
+ {
+ ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+ //////////////////////////////////////////////
+ int idWidth = getVisibleIdWidth();
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int scaleHeight = av.charHeight + fm.getDescent();
+
+ // Gen image map
+ //////////////////////////////////
+ if (imgMapFile != null)
+ {
+ try
+ {
+ int s, sSize = av.alignment.getHeight(),
+ res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
+ StringBuffer text = new StringBuffer();
+ PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
+ out.println(jalview.io.HTMLOutput.getImageMapHTML());
+ out.println("<img src=\"" + imageName +
+ "\" border=\"0\" usemap=\"#Map\" >"
+ + "<map name=\"Map\">");
+
+ for (s = 0; s < sSize; s++)
+ {
+ sy = s * av.charHeight + scaleHeight;
+
+ SequenceI seq = av.alignment.getSequenceAt(s);
+ SequenceFeature[] features = seq.getDatasetSequence().
+ getSequenceFeatures();
+ SequenceGroup[] groups = av.alignment.findAllGroups(seq);
+ for (res = 0; res < alwidth; res++)
+ {
+ text = new StringBuffer();
+ Object obj = null;
+ if (av.alignment.isNucleotide())
+ {
+ obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) +
+ "");
+ }
+ else
+ {
+ obj = ResidueProperties.aa2Triplet.get(
+ seq.getCharAt(res) + "");
+ }
+
+ if (obj == null)
+ {
+ continue;
+ }
+
+ String triplet = obj.toString();
+ int alIndex = seq.findPosition(res);
+ gSize = groups.length;
+ for (g = 0; g < gSize; g++)
+ {
+ if (text.length() < 1)
+ {
+ text.append("<area shape=\"rect\" coords=\""
+ + (idWidth + res * av.charWidth) + ","
+ + sy + ","
+ + (idWidth + (res + 1) * av.charWidth) + ","
+ + (av.charHeight + sy) + "\""
+ + " onMouseOver=\"toolTip('"
+ + alIndex + " " + triplet);
+ }
+
+ if (groups[g].getStartRes() < res && groups[g].getEndRes() > res)
+ {
+ text.append("<br><em>" + groups[g].getName() + "</em>");
+ }
+ }
+
+ if (features != null)
+ {
+ if (text.length() < 1)
+ {
+ text.append("<area shape=\"rect\" coords=\""
+ + (idWidth + res * av.charWidth) + ","
+ + sy + ","
+ + (idWidth + (res + 1) * av.charWidth) + ","
+ + (av.charHeight + sy) + "\""
+ + " onMouseOver=\"toolTip('"
+ + alIndex + " " + triplet);
+ }
+ fSize = features.length;
+ for (f = 0; f < fSize; f++)
+ {
+
+ if ( (features[f].getBegin() <= seq.findPosition(res)) &&
+ (features[f].getEnd() >= seq.findPosition(res)))
+ {
+ if (features[f].getType().equals("disulfide bond"))
+ {
+ if (features[f].getBegin() == seq.findPosition(res)
+ || features[f].getEnd() == seq.findPosition(res))
+ {
+ text.append("<br>disulfide bond " + features[f].getBegin() +
+ ":" +
+ features[f].getEnd());
+ }
+ }
+ else
+ {
+ text.append("<br>");
+ text.append(features[f].getType());
+ if (features[f].getDescription() != null &&
+ !features[f].
+ getType().equals(features[f].getDescription()))
+ {
+ text.append(" " + features[f].getDescription());
+ }
+
+ if (features[f].getValue("status") != null)
+ {
+ text.append(" (" + features[f].getValue("status") + ")");
+ }
+ }
+ }
+
+ }
+ }
+ if (text.length() > 1)
+ {
+ text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
+ out.println(text.toString());
+ }
+ }
+ }
+ out.println("</map></body></html>");
+ out.close();
+
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ } ///////////END OF IMAGE MAP
+
+ }
+
+ int getWrappedHeight()
+ {
+ int seqPanelWidth = seqPanel.seqCanvas.getWidth();
+
+ if (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
+ {
+ seqPanelWidth = alignFrame.getWidth()
+ - getVisibleIdWidth()
+ - vscroll.getPreferredSize().width
+ - alignFrame.getInsets().left
+ - alignFrame.getInsets().right;
+ }
+
+ int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
+ seqPanelWidth
+ );
+
+ int hgap = av.charHeight;
+ if (av.scaleAboveWrapped)
+ {
+ hgap += av.charHeight;
+ }
+
+ int annotationHeight = 0;
+ if (av.showAnnotation)
+ {
+ annotationHeight = annotationPanel.adjustPanelHeight();
+ }
+
+ int cHeight = av.getAlignment().getHeight() * av.charHeight
+ + hgap
+ + annotationHeight;
+
+ int maxwidth = av.alignment.getWidth();
+ if (av.hasHiddenColumns)
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ int height = ( (maxwidth / chunkWidth) + 1) * cHeight;
+
+ return height;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff