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.io.*;\r
+import java.awt.print.*;\r
\r
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener\r
+public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable\r
{\r
\r
AlignViewport av;\r
OverviewPanel overviewPanel;\r
- public SeqPanel seqPanel;\r
- public IdPanel idPanel;\r
+ SeqPanel seqPanel;\r
+ IdPanel idPanel;\r
+ SecondaryStructurePanel ssPanel;\r
public AlignFrame alignFrame;\r
- public ScalePanel scalePanel;\r
- public ScorePanel scorePanel;\r
-\r
- public boolean groupEdit = false;\r
+ ScalePanel scalePanel;\r
+ ScorePanel scorePanel;\r
\r
public AlignmentPanel(AlignFrame af, AlignViewport av)\r
{\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
-\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
{\r
- // if(!initialising)\r
- RefreshPanels();\r
+ RefreshPanels();\r
}\r
});\r
-\r
}\r
\r
- public int countSelected()\r
- {\r
- return av.getSelection().size();\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
- public void selectAll(boolean flag) {\r
- int i = 0;\r
- if (flag) {\r
- while (i < seqPanel.align.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 OverviewPanel getOverviewPanel()\r
{\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 setColourScheme(jalview.schemes.ColourSchemeI cs)\r
+ public void setSecondaryStructureVisible(boolean b)\r
{\r
- seqPanel.setColourScheme(cs);\r
- if(overviewPanel!=null)\r
- overviewPanel.updateOverviewImage();\r
+ secondaryPanelHolder.setVisible(b);\r
+ RefreshPanels();\r
}\r
\r
+ public void setWrapAlignment(boolean wrap)\r
+ {\r
+ scalePanelHolder.setVisible(!wrap);\r
+ scorePanelHolder.setVisible(!wrap);\r
\r
- public void RefreshPanels()\r
+ hscroll.setVisible(!wrap);\r
+ idSpaceFillerPanel.setVisible(!wrap);\r
+ idSpaceFillerPanel1.setVisible(!wrap);\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
- /* try{\r
- ObjectOutputStream out = new ObjectOutputStream(new FileOutputStream("dump.dat"));\r
- out.writeObject( (jalview.datamodel.Alignment)av.getAlignment() );\r
- }catch(IOException ex){ex.printStackTrace();}*/\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
\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
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
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
if(overviewPanel!=null)\r
overviewPanel.setBoxPosition();\r
\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 idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();\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.scaleCanvas.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.getSelection().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).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
+\r
+\r
+\r
git://source.jalview.org / jalview.git / blobdiff