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
\r
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener\r
+import com.sun.image.codec.jpeg.*;\r
+import java.io.*;\r
+import java.awt.image.*;\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
+ SecondaryStructurePanel ssPanel;\r
public AlignFrame alignFrame;\r
ScalePanel scalePanel;\r
ScorePanel scorePanel;\r
\r
- public boolean groupEdit = false;\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
+ scalePanel = new ScalePanel(av, this);\r
scorePanel = new ScorePanel(av);\r
+ ssPanel = new SecondaryStructurePanel(av);\r
\r
+ secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);\r
idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
idPanel.addNotify();\r
scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
\r
hscroll.addAdjustmentListener(this);\r
vscroll.addAdjustmentListener(this);\r
- selectAll(false);\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
- }\r
\r
- public int countSelected()\r
- {\r
- return av.getSelection().size();\r
- }\r
+ // hscroll.setFocusable(false);\r
+ // vscroll.setFocusable(false);\r
+ setFocusable(true);\r
\r
- public void selectAll(boolean flag) {\r
- int i = 0;\r
- if (flag) {\r
- while (i < av.getAlignment().getHeight()) {\r
- if (! av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {\r
- av.getSelection().addElement(av.getAlignment().getSequenceAt(i));\r
- }\r
- i++;\r
- }\r
- } else {\r
- av.getSelection().clear();\r
- }\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
+ alignFrame.cut_actionPerformed(null);\r
+ break;\r
+ case KeyEvent.VK_C:\r
+ alignFrame.copy_actionPerformed(null);\r
+ break;\r
+ case KeyEvent.VK_V:\r
+ alignFrame.paste(true);\r
+ break;\r
+ case KeyEvent.VK_A:\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
+ alignFrame.findMenuItem_actionPerformed(null);\r
+ break;\r
+ }\r
+ }\r
+ });\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
public void setGraphPanelVisible(boolean b)\r
{\r
- scorePanelHolder.setVisible(b);\r
idSpaceFillerPanel.setVisible(b);\r
+ scorePanelHolder.setVisible(b);\r
+\r
+ RefreshPanels();\r
+ // bit annoying to call this twice, can you do better?\r
+ RefreshPanels();\r
+ }\r
+\r
+ public void setSecondaryStructureVisible(boolean b)\r
+ {\r
+ secondaryPanelHolder.setVisible(b);\r
RefreshPanels();\r
}\r
\r
public void setWrapAlignment(boolean wrap)\r
{\r
+ scorePanelHolder.setVisible(!wrap);\r
+ scalePanelHolder.setVisible(!wrap);\r
+ secondaryPanelHolder.setVisible(!wrap);\r
\r
- scalePanelHolder.setVisible(!wrap);\r
- scorePanelHolder.setVisible(!wrap);\r
+ hscroll.setVisible(!wrap);\r
\r
- hscroll.setVisible(!wrap);\r
- idSpaceFillerPanel.setVisible(!wrap);\r
- idSpaceFillerPanel1.setVisible(!wrap);\r
+ idSpaceFillerPanel.setVisible(!wrap);\r
+ idSpaceFillerPanel1.setVisible(!wrap);\r
+\r
+ RefreshPanels();\r
\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
- }\r
+ ColourSchemeI cs = av.getGlobalColourScheme();\r
\r
+ if(av.getConservationSelected())\r
+ {\r
\r
- public void RefreshPanels()\r
- {\r
- invalidate();\r
- validate();\r
- idPanel.idCanvas.paintFlag = true;\r
- idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );\r
- seqPanel.seqCanvas.paintFlag = true;\r
- setScrollValues(av.getStartRes(), av.getStartSeq());\r
- av.getConsensus(true);\r
- repaint();\r
+ Alignment al = (Alignment)av.getAlignment();\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3, al.getSequences(), 0,\r
+ al.getWidth() );\r
\r
- if(overviewPanel!=null)\r
- overviewPanel.updateOverviewImage();\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
+ public void RefreshPanels()\r
+ {\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+\r
+ requestFocus();\r
+ invalidate();\r
+ idPanelHolder.setPreferredSize(idPanel.idCanvas.getPreferredSize());\r
+ hscrollFillerPanel.setPreferredSize(new Dimension(idPanel.idCanvas.\r
+ getPreferredSize().width, 12));\r
+ idSpaceFillerPanel1.setPreferredSize(new Dimension(500,\r
+ av.charHeight / 2 + 12));\r
+ scalePanelHolder.setPreferredSize(new Dimension(500,\r
+ av.charHeight / 2 + 12));\r
+ if (av.getWrapAlignment())\r
+ {\r
+ int max = av.alignment.getWidth() /\r
+ (seqPanel.seqCanvas.getWidth() / av.charWidth) + 1;\r
+\r
+ int h = (av.alignment.getHeight() + 2) * av.charHeight;\r
+ vextent = seqPanel.seqCanvas.getHeight() / h;\r
+ vscroll.setValues(0, vextent, 0, max);\r
+ }\r
+ else\r
+\r
+ setScrollValues(av.getStartRes(), av.getStartSeq());\r
+ av.getConsensus(true);\r
+ if (overviewPanel != null)\r
+ overviewPanel.updateOverviewImage();\r
+\r
+ }\r
+ });\r
+\r
+ validate();\r
+ repaint();\r
+ }\r
int hextent = 0;\r
int vextent = 0;\r
\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
+ vscroll.setValue(vscroll.getValue() - 1);\r
+ }\r
+ else\r
+ {\r
+ if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())\r
+ return false;\r
+ vscroll.setValue(vscroll.getValue() + 1);\r
+ }\r
+\r
+ return true;\r
+ }\r
+\r
+ public boolean scrollRight(boolean right)\r
+ {\r
+ if(right)\r
+ {\r
+ if(hscroll.getValue()<1)\r
+ return false;\r
+ hscroll.setValue(hscroll.getValue() - 1);\r
+ }\r
+ else\r
+ {\r
+ if(hextent+hscroll.getValue() >= av.getAlignment().getWidth())\r
+ return false;\r
+ hscroll.setValue(hscroll.getValue() + 1);\r
+ }\r
+\r
+ return true;\r
+ }\r
+\r
+\r
public void setScrollValues(int x, int y)\r
{\r
- hextent = (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth());\r
+ hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();\r
vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();\r
\r
if(hextent+x > av.getAlignment().getWidth())\r
\r
hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());\r
vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );\r
- seqPanel.seqCanvas.paintFlag = true;\r
+\r
+\r
repaint();\r
\r
}\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
-\r
repaint();\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 = (int)idPanel.idCanvas.getLabelWidth().getWidth();\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.alignment.findGroup(av.getAlignment().getSequenceAt(i))==null)\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).getDisplayId();\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
+ pg.setClip(0,0,pwidth-idWidth, pheight);\r
+ seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);\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 = (int)idPanel.idCanvas.getLabelWidth().getWidth();\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
+ pg.drawString(s.getDisplayId(), 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
+ public void makeJPG(int width, int height)\r
+ {\r
+ try\r
+ {\r
+\r
+ BufferedImage bi = new BufferedImage(width, height,\r
+ BufferedImage.TYPE_INT_RGB);\r
+ Graphics pg = bi.getGraphics();\r
\r
+ try\r
+ {\r
+ if (av.getWrapAlignment())\r
+ printWrappedAlignment(pg, width, height, 0);\r
+ else\r
+ printUnwrapped(pg, width, height, 0);\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
+\r
+ javax.swing.JFileChooser chooser = new javax.swing.JFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"));\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle("Create JPG image from alignment");\r
+ chooser.setToolTipText("Save");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+ if (value == javax.swing.JFileChooser.APPROVE_OPTION)\r
+ {\r
+\r
+ FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
+ JPEGImageEncoder jie = JPEGCodec.createJPEGEncoder(out);\r
+ JPEGEncodeParam param = JPEGCodec.getDefaultJPEGEncodeParam(bi);\r
+ param.setQuality(1.0f, true);\r
+\r
+ jie.encode(bi, param);\r
+ out.close();\r
+ }\r
+\r
+ }\r
+ catch (IOException ex)\r
+ {\r
+ System.out.println("ex Writing image ");\r
+ }\r
+ }\r
\r
}\r
+\r
+\r
+\r
git://source.jalview.org / jalview.git / blobdiff