JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);\r
\r
if (reply == JOptionPane.YES_OPTION)\r
- omitHidden = viewport.getSelectionAsString();\r
+ omitHidden = viewport.getViewAsString(false);\r
}\r
\r
String output = new FormatAdapter().formatSequences(\r
format,\r
viewport.alignment.getSequencesArray(),\r
- null);\r
- //viewport.getSelectionAsNewSequence(),\r
- //omitHidden) ;\r
-\r
+ omitHidden);\r
\r
if (output == null)\r
{\r
*/\r
protected void outputText_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- Desktop.addInternalFrame(cap,\r
- "Alignment output - " + e.getActionCommand(), 600,\r
- 500);\r
-\r
-\r
String [] omitHidden = null;\r
\r
if(viewport.hasHiddenColumns)\r
JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);\r
\r
if(reply==JOptionPane.YES_OPTION)\r
- omitHidden = viewport.getSelectionAsString();\r
+ {\r
+ omitHidden = viewport.getViewAsString(false);\r
+ }\r
}\r
\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ Desktop.addInternalFrame(cap,\r
+ "Alignment output - " + e.getActionCommand(), 600,\r
+ 500);\r
+\r
+\r
cap.setText(new FormatAdapter().formatSequences(\r
e.getActionCommand(),\r
- viewport.getSelectionAsNewSequence(),\r
+ viewport.alignment.getSequencesArray(),\r
omitHidden));\r
}\r
\r
\r
if (viewport.hasHiddenColumns)\r
{\r
- omitHidden = viewport.getSelectionAsString();\r
+ omitHidden = viewport.getViewAsString(true);\r
}\r
\r
String output = new FormatAdapter().formatSequences(\r
for(int i=0; i<hc.size(); i++)\r
{\r
int [] region = (int[]) hc.elementAt(i);\r
- af.viewport.hideColumns(region[0], region[1]);\r
+ af.viewport.hideColumns(region[0], region[1]+1);\r
}\r
}\r
\r
\r
\r
\r
-\r
public void showTranslation_actionPerformed(ActionEvent e)\r
{\r
SequenceI [] selection = viewport.getSelectionAsNewSequence();\r
- String [] seqstring = viewport.getSelectionAsString();\r
+ String [] seqstring = viewport.getViewAsString(true);\r
\r
int s, sSize = selection.length;\r
SequenceI [] newSeq = new SequenceI[sSize];\r
\r
\r
/**\r
- * This method returns the visible selected area as text, as\r
+ * This method returns the visible alignment as text, as\r
* seen on the GUI, ie if columns are hidden they will not\r
* be returned in the result.\r
* Use this for calculating trees, PCA, redundancy etc on views\r
* which contain hidden columns.\r
* @return String[]\r
*/\r
- public String [] getSelectionAsString()\r
+ public String [] getViewAsString(boolean selectedRegionOnly)\r
{\r
String [] selection = null;\r
SequenceI [] seqs= null;\r
int i, iSize;\r
int start = 0, end = 0;\r
- if(selectionGroup!=null)\r
+ if(selectedRegionOnly && selectionGroup!=null)\r
{\r
iSize = selectionGroup.getSize(false);\r
seqs = selectionGroup.getSequencesInOrder(alignment);\r
{\r
selection[i] = seqs[i].getSequence(start, end);\r
}\r
-\r
- // System.out.println(seqs[i].getName()+"\t"+ selection[i]);\r
}\r
\r
return selection;\r