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
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
seqPanel.seqCanvas.highlightSearchResults( results );\r
\r
// do we need to scroll the panel?\r
- if(av.getStartSeq()>results[0] || av.getEndSeq()<results[0] || av.getStartRes()>results[1] || av.getEndRes()<results[2])\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
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
}\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
+\r
invalidate();\r
- validate();\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
-\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
+\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
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
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
}\r
\r
+\r
+\r
git://source.jalview.org / jalview.git / blobdiff