/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
PCA pca;\r
int top;\r
RotatableCanvas rc;\r
+ AlignmentPanel ap;\r
AlignViewport av;\r
- SequenceI [] seqs;\r
+ AlignmentView seqstrings;\r
+ SequenceI [] seqs;\r
\r
/**\r
* Creates a new PCAPanel object.\r
* @param av DOCUMENT ME!\r
* @param s DOCUMENT ME!\r
*/\r
- public PCAPanel(AlignViewport av)\r
+ public PCAPanel(AlignmentPanel ap)\r
{\r
- this.av = av;\r
+ this.av = ap.av;\r
+ this.ap = ap;\r
\r
boolean sameLength = true;\r
\r
- if ((av.getSelectionGroup() != null) &&\r
- (av.getSelectionGroup().getSize() > 3))\r
+ seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null);\r
+ if(av.getSelectionGroup()==null)\r
{\r
- seqs = new Sequence[av.getSelectionGroup().getSize()];\r
- int length = av.getSelectionGroup().getSequenceAt(0).getLength();\r
- for (int i = 0; i < av.getSelectionGroup().getSize(); i++)\r
- {\r
- seqs[i] = av.getSelectionGroup().getSequenceAt(i);\r
- if(seqs[i].getLength()!=length)\r
- {\r
- sameLength = false;\r
- break;\r
- }\r
- }\r
+ seqs = av.alignment.getSequencesArray();\r
}\r
else\r
{\r
- seqs = new Sequence[av.getAlignment().getHeight()];\r
- int length = av.alignment.getSequenceAt(0).getLength();\r
-\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
- {\r
- seqs[i] = av.getAlignment().getSequenceAt(i);\r
- if(seqs[i].getLength()!=length)\r
- {\r
- sameLength = false;\r
- break;\r
- }\r
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
+ }\r
+ SeqCigar sq[]=seqstrings.getSequences();\r
+ int length = sq[0].getWidth();\r
\r
- }\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ if (sq[i].getWidth() != length)\r
+ {\r
+ sameLength = false;\r
+ break;\r
+ }\r
}\r
\r
if (!sameLength)\r
400, 400);\r
\r
\r
- rc = new RotatableCanvas(av);\r
+\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
+\r
+ rc = new RotatableCanvas(ap);\r
this.getContentPane().add(rc, BorderLayout.CENTER);\r
Thread worker = new Thread(this);\r
worker.start();\r
public void run()\r
{\r
try{\r
- pca = new PCA(seqs);\r
+ pca = new PCA(seqstrings.getSequenceStrings(' '));\r
pca.run();\r
\r
// Now find the component coordinates\r
\r
rc.setPoints(points, pca.getM().rows);\r
rc.repaint();\r
- seqs = null;\r
+\r
+ addKeyListener(rc);\r
+\r
}\r
catch(OutOfMemoryError er)\r
{ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
printer.start();\r
}\r
\r
+ public void originalSeqData_actionPerformed(ActionEvent e)\r
+ {\r
+ // this was cut'n'pasted from the equivalent TreePanel method - we should make this an abstract function of all jalview analysis windows\r
+ if (seqstrings==null)\r
+ {\r
+ jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");\r
+ return;\r
+ }\r
+ // decide if av alignment is sufficiently different to original data to warrant a new window to be created\r
+ // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)\r
+ // or create a selection box around columns in alignment view\r
+ // test Alignment(SeqCigar[])\r
+ Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.\r
+ getGapCharacter());\r
+\r
+\r
+ if (alAndColsel != null && alAndColsel[0]!=null)\r
+ {\r
+ // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);\r
+\r
+ Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);\r
+ Alignment dataset = av.getAlignment().getDataset();\r
+ if (dataset != null)\r
+ {\r
+ al.setDataset(dataset);\r
+ }\r
+\r
+ if (true)\r
+ {\r
+ // make a new frame!\r
+ AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT\r
+);\r
+\r
+ //>>>This is a fix for the moment, until a better solution is found!!<<<\r
+ // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());\r
+\r
+ // af.addSortByOrderMenuItem(ServiceName + " Ordering",\r
+ // msaorder);\r
+\r
+ Desktop.addInternalFrame(af, "Original Data for " + this.title,\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
+ }\r
+ }\r
+ /* CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ cap.appendText(new jalview.util.Format("%-" + 15 + "s").form(\r
+ seqs[i].getName()));\r
+ cap.appendText(" " + seqstrings[i] + "\n");\r
+\r
+ }\r
+\r
+ Desktop.addInternalFrame(cap, "Original Data",\r
+ 400, 400);\r
+ */\r
+ }\r
+\r
+\r
\r
class PCAPrinter extends Thread implements Printable\r
{\r
im.writeImage();\r
}\r
}\r
+\r
+\r
+ public void viewMenu_menuSelected()\r
+ {\r
+ buildAssociatedViewMenu();\r
+ }\r
+\r
+\r
+ void buildAssociatedViewMenu()\r
+ {\r
+ AlignmentPanel [] aps = PaintRefresher.getAssociatedPanels(av.getSequenceSetId());\r
+ if(aps.length==1 && rc.av ==aps[0].av)\r
+ {\r
+ associateViewsMenu.setVisible(false);\r
+ return;\r
+ }\r
+\r
+ associateViewsMenu.setVisible(true);\r
+\r
+ if( (viewMenu.getItem(viewMenu.getItemCount()-2) instanceof JMenuItem))\r
+ {\r
+ viewMenu.insertSeparator(viewMenu.getItemCount()-1);\r
+ }\r
+\r
+ associateViewsMenu.removeAll();\r
+\r
+\r
+ JRadioButtonMenuItem item;\r
+ ButtonGroup buttonGroup = new ButtonGroup();\r
+ int i, iSize = aps.length;\r
+ final PCAPanel thisPCAPanel = this;\r
+ for(i=0; i<iSize; i++)\r
+ {\r
+ final AlignmentPanel ap = aps[i];\r
+ item = new JRadioButtonMenuItem(ap.av.viewName, ap.av==rc.av );\r
+ buttonGroup.add(item);\r
+ item.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ rc.applyToAllViews = false;\r
+ rc.av = ap.av;\r
+ rc.ap = ap;\r
+ PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());\r
+ }\r
+ });\r
+\r
+ associateViewsMenu.add(item);\r
+ }\r
+\r
+ final JRadioButtonMenuItem itemf =\r
+ new JRadioButtonMenuItem("All Views", rc.applyToAllViews);\r
+ buttonGroup.add(itemf);\r
+ itemf.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ rc.applyToAllViews = itemf.isSelected();\r
+ }\r
+ });\r
+ associateViewsMenu.add(itemf);\r
+\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff