class TreeLoader extends Thread\r
{\r
NewickFile newtree;\r
- jalview.datamodel.CigarArray odata=null;\r
+ jalview.datamodel.AlignmentView odata=null;\r
public TreeLoader(NewickFile newtree)\r
{\r
this.newtree = newtree;\r
public void run()\r
{\r
\r
- if(newtree!=null) {\r
-\r
+ if(newtree!=null)\r
+ {\r
if (odata==null) {\r
tree = new NJTree(av.alignment.getSequencesArray(),\r
newtree);\r
{\r
int start, end;\r
SequenceI [] seqs;\r
- CigarArray seqStrings = av.getViewAsCigars(av.getSelectionGroup()!=null);\r
+ AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);\r
if(av.getSelectionGroup()==null)\r
{\r
start = 0;\r
placeholdersMenu.setState(b);\r
treeCanvas.setMarkPlaceholders(b);\r
}\r
+\r
private void allowOriginalSeqData(boolean b) {\r
originalSeqData.setVisible(b);\r
}\r
\r
public void originalSeqData_actionPerformed(ActionEvent e)\r
{\r
- String originalData = tree.printOriginalSequenceData();\r
- if (originalData!=null) {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- cap.setText(originalData);\r
- Desktop.addInternalFrame(cap, "Original Data",\r
- 400, 400);\r
- } else {\r
- System.err.println("IMPLEMENTATION BUG! originalSeqData is not available.");\r
+ if (!tree.hasOriginalSequenceData())\r
+ {\r
+ jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");\r
+ return;\r
}\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 = tree.seqData.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
}\r
\r
\r