RotatableCanvas rc;\r
AlignViewport av;\r
SequenceI [] seqs;\r
+ AlignmentView seqstrings;\r
\r
\r
public PCAPanel(AlignViewport av)\r
}\r
\r
this.av = av;\r
- if (av.getSelectionGroup()!=null && 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
- for (int i = 0; i < av.getSelectionGroup().getSize(); i++)\r
- {\r
- seqs[i] = av.getSelectionGroup().getSequenceAt(i);\r
- }\r
+ seqs = av.alignment.getSequencesArray();\r
}\r
else\r
{\r
- seqs = new Sequence[av.getAlignment().getHeight()];\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
+ }\r
+ SeqCigar sq[]=seqstrings.getSequences();\r
+ int length = sq[0].getWidth();\r
+\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ if (sq[i].getWidth() != length)\r
{\r
- seqs[i] = av.getAlignment().getSequenceAt(i);\r
+ System.out.println("Sequences must be equal length for PCA analysis");\r
+ return;\r
}\r
}\r
\r
+\r
rc = new RotatableCanvas(av);\r
add(rc, BorderLayout.CENTER);\r
\r
*/\r
public void run()\r
{\r
- pca = new PCA(seqs);\r
+ pca = new PCA(seqstrings.getSequenceStrings(' '));\r
pca.run();\r
\r
// Now find the component coordinates\r
\r
public void actionPerformed(ActionEvent evt)\r
{\r
- values_actionPerformed();\r
+ if(evt.getSource()==inputData)\r
+ showOriginalData();\r
+ else\r
+ values_actionPerformed();\r
}\r
\r
public void itemStateChanged(ItemEvent evt)\r
cap.setText(pca.getDetails());\r
}\r
\r
+ void showOriginalData()\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
+ Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);\r
+ AlignFrame af = new AlignFrame(al,\r
+ av.applet,\r
+ "Original Data for PCA",\r
+ false);\r
+\r
+ af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1] );\r
+ }\r
+ }\r
+\r
public void labels_itemStateChanged(ItemEvent itemEvent)\r
{\r
rc.showLabels( labels.getState() );\r
Menu menu2 = new Menu();\r
protected CheckboxMenuItem labels = new CheckboxMenuItem();\r
MenuItem values = new MenuItem();\r
+ MenuItem inputData = new MenuItem();\r
\r
private void jbInit()\r
throws Exception\r
labels.addItemListener(this);\r
values.setLabel("Output Values...");\r
values.addActionListener(this);\r
+ inputData.setLabel("Input Data...");\r
this.add(jPanel2, BorderLayout.SOUTH);\r
jPanel2.add(jLabel1, null);\r
jPanel2.add(xCombobox, null);\r
menuBar1.add(menu2);\r
menu2.add(labels);\r
menu1.add(values);\r
+ menu1.add(inputData);\r
+ inputData.addActionListener(this);\r
}\r
\r
}\r