import jalview.schemes.*;\r
import jalview.ws.*;\r
import java.awt.dnd.*;\r
-import jalview.biojava.dasobert.eventmodel.*;\r
+import org.biojava.dasobert.eventmodel.*;\r
\r
/**\r
* DOCUMENT ME!\r
Stack redoList = new Stack();\r
private int treeCount = 0;\r
\r
-\r
/**\r
- * Creates a new AlignFrame object.\r
- *\r
- * @param al DOCUMENT ME!\r
+ * new alignment window with hidden columns\r
+ * @param al AlignmentI\r
+ * @param hiddenColumns ColumnSelection or null\r
*/\r
- public AlignFrame(AlignmentI al)\r
- {\r
- viewport = new AlignViewport(al);\r
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns) {\r
+\r
+ viewport = new AlignViewport(al, hiddenColumns);\r
\r
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));\r
\r
\r
}\r
\r
+\r
+ /**\r
+ * Creates a new AlignFrame object.\r
+ *\r
+ * @param al DOCUMENT ME!\r
+ */\r
+ public AlignFrame(AlignmentI al)\r
+ {\r
+ this(al, null);\r
+ }\r
+\r
public AlignViewport getViewport()\r
{\r
return viewport;\r
{\r
alignPanel.seqPanel.seqCanvas.fr.featuresAdded();\r
alignPanel.repaint();\r
- if(featureSettings!=null)\r
- featureSettings.setTableData();\r
}\r
}\r
\r
.setContents(new StringSelection(output), Desktop.instance);\r
\r
Vector hiddenColumns = null;\r
- if(viewport.hasHiddenColumns && viewport.getSelectionGroup()!=null)\r
+ if(viewport.hasHiddenColumns)\r
{\r
hiddenColumns =new Vector();\r
int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
\r
if (newAlignment)\r
{\r
- System.out.println(format +" 2");\r
alignment = new Alignment(sequences);\r
\r
if(Desktop.jalviewClipboard!=null)\r
}\r
else\r
{\r
- System.out.println(format +" 24");\r
alignment = viewport.getAlignment();\r
\r
//!newAlignment\r
AlignFrame af = new AlignFrame(alignment);\r
String newtitle = new String("Copied sequences");\r
\r
- if(Desktop.jalviewClipboard[2]!=null)\r
+ if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)\r
{\r
Vector hc = (Vector)Desktop.jalviewClipboard[2];\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]+1);\r
+ af.viewport.hideColumns(region[0], region[1]);\r
}\r
}\r
\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
+ public void invertColSel_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.invertColumnSelection();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
\r
public void showAllColumns_actionPerformed(ActionEvent e)\r
{\r
- viewport.getColumnSelection().revealAllHiddenColumns(viewport);\r
+ viewport.showAllHiddenColumns();\r
}\r
\r
public void hideSelSequences_actionPerformed(ActionEvent e)\r
}\r
\r
\r
- FeatureSettings featureSettings;\r
+ public FeatureSettings featureSettings;\r
public void featureSettings_actionPerformed(ActionEvent e)\r
{\r
if(featureSettings !=null )\r
return;\r
}\r
\r
+ if(viewport.alignment.getHeight()<2)\r
+ return;\r
+\r
tp = new TreePanel(viewport, type, pwType);\r
}\r
\r
* or just the selected set will be submitted for multiple alignment.\r
*\r
*/\r
- private SequenceI[] gatherSequencesForAlignment()\r
+ private jalview.datamodel.AlignmentView gatherSequencesForAlignment()\r
{\r
// Now, check we have enough sequences\r
- SequenceI[] msa = null;\r
+ AlignmentView msa = null;\r
\r
if ( (viewport.getSelectionGroup() != null) &&\r
(viewport.getSelectionGroup().getSize(false) > 1))\r
{\r
// JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
- SequenceGroup seqs = viewport.getSelectionGroup();\r
+ /*SequenceGroup seqs = viewport.getSelectionGroup();\r
int sz;\r
msa = new SequenceI[sz = seqs.getSize(false)];\r
\r
for (int i = 0; i < sz; i++)\r
{\r
msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
- }\r
+ } */\r
+ msa = viewport.getAlignmentView(true);\r
}\r
else\r
{\r
- Vector seqs = viewport.getAlignment().getSequences();\r
+ /*Vector seqs = viewport.getAlignment().getSequences();\r
\r
if (seqs.size() > 1)\r
{\r
{\r
msa[i] = (SequenceI) seqs.elementAt(i);\r
}\r
- }\r
+ }*/\r
+ msa = viewport.getAlignmentView(false);\r
}\r
return msa;\r
}\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- SequenceI[] msa = gatherSequencesForAlignment();\r
+ AlignmentView msa = gatherSequencesForAlignment();\r
new jalview.ws.MsaWSClient(sh, title, msa,\r
false, true, viewport.getAlignment().getDataset(), af);\r
\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- SequenceI[] msa = gatherSequencesForAlignment();\r
+ AlignmentView msa = gatherSequencesForAlignment();\r
new jalview.ws.MsaWSClient(sh, title, msa,\r
true, true, viewport.getAlignment().getDataset(), af);\r
\r