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.image.*;\r
import java.awt.event.*;\r
import java.awt.print.*;\r
-import javax.swing.*;\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
OverviewPanel overviewPanel;\r
SeqPanel seqPanel;\r
IdPanel idPanel;\r
+ IdwidthAdjuster idwidthAdjuster;\r
public AlignFrame alignFrame;\r
ScalePanel scalePanel;\r
- ScorePanel scorePanel;\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, AlignViewport av)\r
+ public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
{\r
alignFrame = af;\r
this.av = av;\r
seqPanel = new SeqPanel (av, this);\r
idPanel = new IdPanel (av, this);\r
- scalePanel = new ScalePanel(av);\r
- scorePanel = new ScorePanel(av);\r
+\r
+ scalePanel = new ScalePanel(av, this);\r
\r
idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
- idPanel.addNotify();\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
- scorePanelHolder.add(scorePanel, BorderLayout.CENTER);\r
seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
- setScrollValues(0,0);\r
+\r
+\r
+ if(seqPanel.seqCanvas.getWidth()==0)\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\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
+ 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
+ return new Dimension(idWidth, 12);\r
+ }\r
+\r
+\r
public void highlightSearchResults(int [] results)\r
{\r
seqPanel.seqCanvas.highlightSearchResults( results );\r
}\r
\r
\r
- public void setGraphPanelVisible(boolean b)\r
+ public void setAnnotationVisible(boolean b)\r
{\r
- scorePanelHolder.setVisible(b);\r
- idSpaceFillerPanel.setVisible(b);\r
- RefreshPanels();\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
- scorePanelHolder.setVisible(!wrap);\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
+\r
+ RefreshPanels();\r
\r
- hscroll.setVisible(!wrap);\r
- idSpaceFillerPanel.setVisible(!wrap);\r
- idSpaceFillerPanel1.setVisible(!wrap);\r
}\r
\r
\r
- public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation)\r
+ public void setColourScheme()\r
{\r
- seqPanel.setColourScheme(cs, conservation);\r
- if(overviewPanel!=null)\r
- overviewPanel.updateOverviewImage();\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, 100);\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
+ requestFocus();\r
invalidate();\r
- seqPanel.seqCanvas.paintFlag = true;\r
- idPanel.idCanvas.paintFlag = true;\r
- idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );\r
- setScrollValues(av.getStartRes(), av.getStartSeq());\r
- av.getConsensus(true);\r
- repaint();\r
- validate();\r
- if(overviewPanel!=null)\r
- overviewPanel.updateOverviewImage();\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() /\r
+ (seqPanel.seqCanvas.getWidth() / av.charWidth) + 1;\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
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 = (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth());\r
- vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();\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
hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());\r
vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );\r
- repaint();\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 + (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1));\r
+ av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);\r
}\r
\r
if (evt.getSource() == vscroll)\r
{\r
- int offy = vscroll.getValue();\r
+ int offy = vscroll.getValue();\r
+ if (av.getWrapAlignment())\r
+ {\r
+ av.setStartRes( vscroll.getValue() * av.getChunkWidth());\r
+ }\r
+ else\r
+ {\r
av.setStartSeq(offy);\r
- av.setEndSeq(offy + seqPanel.seqCanvas.getHeight()/av.getCharHeight());\r
+ av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());\r
+ }\r
}\r
\r
\r
if(overviewPanel!=null)\r
overviewPanel.setBoxPosition();\r
\r
- seqPanel.seqCanvas.paintFlag=true;\r
- repaint();\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
-\r
pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());\r
\r
- int pwidth = (int)pf.getImageableWidth();\r
- int pheight = (int)pf.getImageableHeight();\r
- int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();\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
- //BufferedImage printImage = new BufferedImage(pwidth,pheight,BufferedImage.TYPE_INT_RGB);\r
- // Graphics pg = printImage.getGraphics();\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 = (int)((pwidth - idWidth)/av.getCharWidth());\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
//draw Scale\r
pg.translate(idWidth,0);\r
- scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth);\r
+ scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);\r
\r
pg.translate(-idWidth, 30);\r
////////////////\r
Color currentTextColor=null;\r
for(int i=startSeq; i<endSeq; i++)\r
{\r
- if (av.getSelection().contains(av.getAlignment().getSequenceAt(i)))\r
+ if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))\r
{\r
currentColor = Color.gray;\r
currentTextColor = Color.black;\r
\r
pg.setColor(currentColor);\r
pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),\r
- getWidth(),\r
+ idWidth,\r
av.getCharHeight());\r
\r
pg.setColor(currentTextColor);\r
\r
- String string = av.getAlignment().getSequenceAt(i).getDisplayId();\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
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
+ int row = pi*noChunksOnPage;\r
+ pg.setColor(Color.black);\r
+ for(int ypos=2*av.charHeight;\r
+ ypos <= pheight && row*chunkWidth<da.getWidth();\r
+ ypos += chunkHeight, row++ )\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
git://source.jalview.org / jalview.git / blobdiff