alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
+ viewport.initInformationWorker(alignPanel);
displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
followMouseOverFlag.setState(viewport.isFollowHighlight());
viewport.featureSettings.refreshTable();
}
alignPanel.paintAlignment(true, true);
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.getString("label.successfully_added_features_alignment"));
}
return featuresFile;
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.keyboard_editing_mode", new String[]
{ (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
}
else if (source == autoCalculate)
{
- viewport.autoCalculateConsensus = autoCalculate.getState();
+ viewport.setAutoCalculateConsensusAndConservation(autoCalculate.getState());
}
else if (source == sortByTree)
{
{
sortGroupMenuItem_actionPerformed();
}
+ else if (source == sortEValueMenuItem)
+ {
+ sortEValueMenuItem_actionPerformed();
+ }
+ else if (source == sortBitScoreMenuItem)
+ {
+ sortBitScoreMenuItem_actionPerformed();
+ }
else if (source == removeRedundancyMenuItem)
{
removeRedundancyMenuItem_actionPerformed();
// viewport.getColumnSelection().getHiddenColumns()
// != null;
updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null,
- originalSource.getAlignment().getSequences());
+ originalSource.notifyAlignment();
}
/**
// != null;
updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null,
- originalSource.getAlignment().getSequences());
+ originalSource.notifyAlignment();
}
AlignmentViewport getOriginatingSource(CommandI command)
seqs, 0, viewport.getAlignment().getWidth(),
viewport.getAlignment()));
- viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
+ viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
+ // 2019.04.18
viewport.getAlignment().getWidth();
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.notifyAlignment();
}
viewport.setSelectionGroup(null);
viewport.getAlignment().deleteGroup(sg);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.notifyAlignment();
if (viewport.getAlignment().getHeight() < 1)
{
column, al);
}
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.removed_columns", new String[]
{ Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
}
}
- viewport.firePropertyChange("alignment", null, al.getSequences());
+ viewport.notifyAlignment();
}
}
addHistoryItem(removeGapCols);
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.removed_empty_columns", new String[]
{ Integer.valueOf(removeGapCols.getSize()).toString() }));
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
ranges.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null, al.getSequences());
+ viewport.notifyAlignment();
}
ranges.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null, al.getSequences());
+ viewport.notifyAlignment();
}
}
+ public void sortEValueMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByEValue(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
+
+ }
+
+ public void sortBitScoreMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByBitScore(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
+
+ }
+
public void removeRedundancyMenuItem_actionPerformed()
{
new RedundancyPanel(alignPanel);
MenuItem sortGroupMenuItem = new MenuItem();
+ MenuItem sortEValueMenuItem = new MenuItem();
+
+ MenuItem sortBitScoreMenuItem = new MenuItem();
+
MenuItem removeRedundancyMenuItem = new MenuItem();
MenuItem pairwiseAlignmentMenuItem = new MenuItem();
*/
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
- statusBar.setText(MessageManager.getString("label.status_bar"));
+ setStatus(MessageManager.getString("label.status_bar"));
this.add(statusBar, BorderLayout.SOUTH);
}
}
else
{
- new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
+ new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
}
}