initTreePanel(av, type, pwtype, null);\r
\r
// We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
- showDistances(true);\r
+ // showDistances(true);\r
}\r
\r
/**\r
class TreeLoader extends Thread\r
{\r
NewickFile newtree;\r
-\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
- tree = new NJTree(av.alignment.getSequencesArray(),\r
- newtree);\r
+ if(newtree!=null) {\r
+\r
+ if (odata==null) {\r
+ tree = new NJTree(av.alignment.getSequencesArray(),\r
+ newtree);\r
+ } else {\r
+ tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);\r
+ }\r
+ if (!tree.hasOriginalSequenceData())\r
+ allowOriginalSeqData(false);\r
+ }\r
else\r
{\r
int start, end;\r
SequenceI [] seqs;\r
- String [] seqStrings = null;\r
- if (av.hasHiddenColumns)\r
- {\r
- seqStrings = av.getSelectionAsString();\r
- }\r
-\r
+ AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);\r
if(av.getSelectionGroup()==null)\r
{\r
start = 0;\r
}\r
\r
tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
+ showDistances(true);\r
}\r
\r
\r
tree.reCount(tree.getTopNode());\r
tree.findHeight(tree.getTopNode());\r
treeCanvas.setTree(tree);\r
-\r
treeCanvas.repaint();\r
-\r
av.setCurrentTree(tree);\r
\r
}\r
placeholdersMenu.setState(b);\r
treeCanvas.setMarkPlaceholders(b);\r
}\r
-\r
+ private void allowOriginalSeqData(boolean b) {\r
+ originalSeqData.setVisible(b);\r
+ }\r
\r
\r
\r
\r
public void originalSeqData_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- cap.setText(tree.printOriginalSequenceData());\r
- Desktop.addInternalFrame(cap, "Original Data",\r
- 400, 400);\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
+ // 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