int top;\r
RotatableCanvas rc;\r
AlignViewport av;\r
- String [] seqstrings;\r
+ AlignmentView seqstrings;\r
SequenceI [] seqs;\r
\r
/**\r
\r
boolean sameLength = true;\r
\r
- seqstrings = av.getViewAsString(true);\r
-\r
- if (av.getSelectionGroup() == null)\r
+ seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null);\r
+ if(av.getSelectionGroup()==null)\r
{\r
seqs = av.alignment.getSequencesArray();\r
}\r
{\r
seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
}\r
-\r
- int length = seqs[0].getLength();\r
+ SeqCigar sq[]=seqstrings.getSequences();\r
+ int length = sq[0].getWidth();\r
\r
for (int i = 0; i < seqs.length; i++)\r
{\r
- if (seqs[i].getLength() != length)\r
+ if (sq[i].getWidth() != length)\r
{\r
sameLength = false;\r
break;\r
public void run()\r
{\r
try{\r
- pca = new PCA(seqstrings);\r
+ pca = new PCA(seqstrings.getSequenceStrings(' '));\r
pca.run();\r
\r
// Now find the component coordinates\r
\r
public void originalSeqData_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- for (int i = 0; i < seqs.length; i++)\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
- cap.appendText(new jalview.util.Format("%-" + 15 + "s").form(\r
- seqs[i].getName()));\r
- cap.appendText(" " + seqstrings[i] + "\n");\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
+\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.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_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
- Desktop.addInternalFrame(cap, "Original Data",\r
- 400, 400);\r
+ }\r
\r
+ Desktop.addInternalFrame(cap, "Original Data",\r
+ 400, 400);\r
+ */\r
}\r
\r
\r