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
\r
public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable\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 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
+ addKeyListener(new KeyAdapter()\r
+ {\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
+ switch(evt.getKeyCode())\r
+ {\r
+ case 27: // escape key\r
+ av.setRubberbandGroup(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
+\r
+ }\r
+\r
+ /* public void doKeyPressed(KeyEvent evt)\r
+ {\r
+\r
+ if (evt.isControlDown() && evt.getKeyChar() == 'f')\r
+ findMenuItem_actionPerformed(null);\r
+ }*/\r
+\r
+ }\r
+ });\r
+\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
}\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
+ 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
public void RefreshPanels()\r
{\r
+ requestFocus();\r
invalidate();\r
- validate();\r
+ seqPanel.seqCanvas.paintFlag = true;\r
idPanel.idCanvas.paintFlag = true;\r
idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );\r
- seqPanel.seqCanvas.paintFlag = true;\r
+\r
+ if(av.getWrapAlignment())\r
+ {\r
+ int max = av.alignment.getWidth()/ (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
- repaint();\r
-\r
if(overviewPanel!=null)\r
overviewPanel.updateOverviewImage();\r
\r
+ validate();\r
+ repaint();\r
+\r
}\r
\r
int hextent = 0;\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
+ // System.out.println(vscroll.getValue()+" "+ av.getChunkWidth());\r
+ // int resSpan = av.alignment.getWidth()/ (seqPanel.seqCanvas.getWidth()/av.charWidth)+1;\r
+ // int h = (av.alignment.getHeight() + 2)*av.charHeight;\r
+ // vextent = seqPanel.seqCanvas.getHeight()/h;\r
+ // vscroll.setValues(0,vextent,0,max);\r
+\r
+\r
+ // av.setStartSeq( );\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
+ seqPanel.seqCanvas.paintFlag=true;\r
repaint();\r
}\r
\r
\r
+\r
public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException\r
{\r
+ if(av.getWrapAlignment())\r
+ {\r
+ return PrintWrappedAlignment(pg, pf, pi);\r
+ }\r
\r
pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());\r
\r
int pheight = (int)pf.getImageableHeight();\r
int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();\r
\r
- //BufferedImage printImage = new BufferedImage(pwidth,pheight,BufferedImage.TYPE_INT_RGB);\r
- // Graphics pg = printImage.getGraphics();\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 = (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
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
// 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
+ class VPanel extends javax.swing.JPanel\r
+ {\r
+ Image image;\r
+ public VPanel(Image i)\r
+ {\r
+ image = i;\r
+ repaint();\r
+ }\r
+ public void paintComponent(Graphics g)\r
+ {\r
+ if(image!=null)\r
+ g.drawImage(image,0,0,this);\r
+ }\r
+\r
+ }\r
+\r
+ public int PrintWrappedAlignment(Graphics pg, PageFormat pf, int pi)\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
+\r
+ if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)\r
+ pwidth = seqPanel.seqCanvas.getWidth() + idWidth;\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 = endy / chunkHeight;\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.NO_SUCH_PAGE;//.PAGE_EXISTS;\r
+\r
+ }\r
}\r
\r
+\r
+\r
git://source.jalview.org / jalview.git / blobdiff