import java.awt.event.*;\r
import java.awt.print.*;\r
\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
OverviewPanel overviewPanel;\r
SeqPanel seqPanel;\r
IdPanel idPanel;\r
+ SecondaryStructurePanel ssPanel;\r
public AlignFrame alignFrame;\r
ScalePanel scalePanel;\r
ScorePanel scorePanel;\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
idPanel = new IdPanel (av, this);\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
addComponentListener(new ComponentAdapter()\r
{\r
- public void componentResized(ComponentEvent evt)\r
+ public void componentResized(ComponentEvent evt)\r
{\r
RefreshPanels();\r
}\r
});\r
+\r
+\r
+ // hscroll.setFocusable(false);\r
+ // vscroll.setFocusable(false);\r
+ setFocusable(true);\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
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
- scalePanelHolder.setVisible(!wrap);\r
- scorePanelHolder.setVisible(!wrap);\r
+ scorePanelHolder.setVisible(!wrap);\r
+ scalePanelHolder.setVisible(!wrap);\r
+ secondaryPanelHolder.setVisible(!wrap);\r
+\r
+ hscroll.setVisible(!wrap);\r
+\r
+ idSpaceFillerPanel.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
av.setGlobalColourScheme( ccs );\r
\r
}\r
- seqPanel.seqCanvas.paintFlag = true;\r
- repaint();\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
- 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
- if(overviewPanel!=null)\r
- overviewPanel.updateOverviewImage();\r
\r
- validate();\r
- repaint();\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
- int hextent = 0;\r
- int vextent = 0;\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
\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
\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 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
//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.alignment.findGroup(av.getAlignment().getSequenceAt(i))==null)\r
{\r
currentColor = Color.gray;\r
currentTextColor = Color.black;\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
git://source.jalview.org / jalview.git / blobdiff