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.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
+ }\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
}\r
\r
public void highlightSearchResults(int [] results)\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
- 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
if(av.getConservationSelected())\r
{\r
\r
- Alignment al = (Alignment)av.getAlignment();\r
- Conservation c = new Conservation("All",\r
+ Alignment al = (Alignment)av.getAlignment();\r
+ Conservation c = new Conservation("All",\r
ResidueProperties.propHash, 3, al.getSequences(), 0,\r
al.getWidth() );\r
\r
av.setGlobalColourScheme( ccs );\r
\r
}\r
- seqPanel.seqCanvas.paintFlag = true;\r
- repaint();\r
- }\r
- /*\r
- seqCanvas.paintFlag = true;\r
- if (av.getSelection().size() == 0)\r
- {\r
- seqCanvas.globalColorScheme = cs;\r
- for (int i = 0; i < av.alignment.getGroups().size();i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i);\r
- sg.cs = cs;\r
- if(!showConservation\r
- && !(sg.cs instanceof Blosum62ColourScheme)\r
- && sg.cs instanceof ConservationColourScheme)\r
- {\r
- // remove ConservationColouring from existing Conservation group\r
- ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
- sg.cs = ccs.cs;\r
- }\r
- else if(showConservation && !(sg.cs instanceof ConservationColourScheme))\r
- {\r
- // add ConservationColouring to new group\r
- Conservation c = sg.getConservation();\r
- Alignment al = (Alignment) av.getAlignment();\r
- c = new Conservation("All", al.cons,\r
- ResidueProperties.propHash, 3, sg.sequences, 0,\r
- al.getWidth() );\r
- c.calculate();\r
- c.verdict(false, 100);\r
- sg.setConservation(c);\r
- sg.cs = new ConservationColourScheme(sg);\r
- }\r
- }\r
- }\r
- else\r
- {\r
- SequenceGroup sg = av.alignment.findGroup((Sequence)av.sel.sequenceAt(0));\r
-\r
- if( isNewSelection(sg) )\r
- {\r
- sg = av.getAlignment().addGroup();\r
- for (int i=0; i < av.getSelection().size(); i++)\r
- {\r
- av.alignment.removeFromGroup(av.alignment.findGroup( (Sequence) av.\r
- sel.sequenceAt(i)),\r
- (Sequence) av.sel.sequenceAt(i));\r
- av.alignment.addToGroup(sg, (Sequence) av.sel.sequenceAt(i));\r
- }\r
- }\r
-\r
-\r
- sg.cs = cs;\r
-\r
- // Selection is made, we only want to change the conservationColour for selected group\r
- if( showConservation\r
- && !(sg.cs instanceof ConservationColourScheme)\r
- && !(sg.cs instanceof Blosum62ColourScheme))\r
- {\r
- Conservation c = sg.getConservation();\r
- Alignment al = (Alignment) av.getAlignment();\r
-\r
- c = new Conservation("All", al.cons,\r
- ResidueProperties.propHash, 3, sg.sequences, 0,\r
- al.getWidth() );\r
- c.calculate();\r
- c.verdict(false, 100);\r
- sg.setConservation(c);\r
- sg.cs = new ConservationColourScheme(sg);\r
- }\r
- else if( !showConservation && sg.cs instanceof ConservationColourScheme)\r
- {\r
- ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
- sg.cs = ccs.cs;\r
- }\r
- }\r
- repaint();\r
- }\r
\r
- boolean isNewSelection(SequenceGroup sg)\r
- {\r
- if(sg==null)\r
- return true;\r
-\r
- if(sg.getSize()!=av.getSelection().size())\r
- return true;\r
-\r
- for(int i=0; i<sg.getSize(); i++)\r
- if( !av.getSelection().contains( sg.getSequenceAt(i) ))\r
- return true;\r
-\r
- return false;\r
- }\r
-\r
-\r
- public ColourSchemeI getColourScheme()\r
- {\r
- if(av.getSelection().size()>0)\r
- return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;\r
- else\r
- return seqCanvas.globalColorScheme;\r
- }\r
-*/\r
-\r
-/* public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation)\r
- {\r
- seqPanel.setColourScheme(cs, conservation);\r
-\r
- av.setGlobalColourScheme(cs);\r
-\r
- if(overviewPanel!=null)\r
- overviewPanel.updateOverviewImage();\r
+ RefreshPanels();\r
}\r
\r
- void updateResidueView()\r
- {\r
- if (viewport.getSelection().size() == 0)\r
- {\r
- for (int i = 0; i < viewport.alignment.getGroups().size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);\r
- sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );\r
- sg.setDisplayText( viewTextMenuItem.isSelected() );\r
- sg.setColourText( colourTextMenuItem.isSelected() );\r
- }\r
- }\r
- else\r
- {\r
- SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));\r
- if (alignPanel.seqPanel.isNewSelection(sg))\r
- {\r
- sg = viewport.getAlignment().addGroup();\r
- for (int i = 0; i < viewport.getSelection().size(); i++)\r
- {\r
- viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (\r
- Sequence) viewport.sel.sequenceAt(i)),\r
- (Sequence) viewport.sel.sequenceAt(\r
- i));\r
- viewport.alignment.addToGroup(sg,\r
- (Sequence) viewport.sel.sequenceAt(i));\r
- }\r
- }\r
-\r
- sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());\r
- sg.setDisplayText(viewTextMenuItem.isSelected());\r
- sg.setColourText(colourTextMenuItem.isSelected());\r
- }\r
- alignPanel.RefreshPanels();\r
- }*/\r
-\r
-\r
-\r
public void RefreshPanels()\r
{\r
+ requestFocus();\r
invalidate();\r
seqPanel.seqCanvas.paintFlag = true;\r
idPanel.idCanvas.paintFlag = true;\r
idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );\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
- validate();\r
- repaint();\r
if(overviewPanel!=null)\r
overviewPanel.updateOverviewImage();\r
\r
+ validate();\r
+ repaint();\r
+\r
}\r
\r
int hextent = 0;\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
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
}\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
+\r
pg.setColor(Color.white);\r
pg.fillRect(0,0,pwidth, pheight);\r
pg.setFont( av.getFont() );\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
git://source.jalview.org / jalview.git / blobdiff