- else
- {
- ap.av.getAlignment().setSeqrep(sequence);
- }
- }
- refresh();
- }
-
- protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
- {
- if (sequence != null)
- {
- ColumnSelection cs = ap.av.getColumnSelection();
- if (cs == null)
- {
- cs = new ColumnSelection();
- }
- cs.hideInsertionsFor(sequence);
- ap.av.setColumnSelection(cs);
- }
- refresh();
- }
-
- protected void sequenceSelectionDetails_actionPerformed()
- {
- createSequenceDetailsReport(ap.av.getSequenceSelection());
- }
-
- protected void sequenceDetails_actionPerformed()
- {
- createSequenceDetailsReport(new SequenceI[] { sequence });
- }
-
- public void createSequenceDetailsReport(SequenceI[] sequences)
- {
- CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
- StringBuffer contents = new StringBuffer();
- for (SequenceI seq : sequences)
- {
- contents.append("<p><h2>"
- + MessageManager
- .formatMessage(
- "label.create_sequence_details_report_annotation_for",
- new Object[] { seq.getDisplayId(true) })
- + "</h2></p><p>");
- new SequenceAnnotationReport(null)
- .createSequenceAnnotationReport(
- contents,
- seq,
- true,
- true,
- false,
- (ap.getSeqPanel().seqCanvas.fr != null) ? ap
- .getSeqPanel().seqCanvas.fr.getMinMax()
- : null);
- contents.append("</p>");
- }
- cap.setText("<html>" + contents.toString() + "</html>");
-
- Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.sequence_details_for",
- (sequences.length == 1 ? new Object[] { sequences[0]
- .getDisplayId(true) } : new Object[] { MessageManager
- .getString("label.selection") })), 500, 400);
-
- }
-
- protected void showNonconserved_actionPerformed()
- {
- getGroup().setShowNonconserved(displayNonconserved.isSelected());
- refresh();
- }
-
- /**
- * call to refresh view after settings change
- */
- void refresh()
- {
- ap.updateAnnotation();
- ap.paintAlignment(true);
-
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void clustalColour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void zappoColour_actionPerformed()
- {
- getGroup().cs = new ZappoColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void taylorColour_actionPerformed()
- {
- getGroup().cs = new TaylorColourScheme();