import jalview.analysis.TreeBuilder;
import jalview.analysis.scoremodels.PIDModel;
import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.AlignFrameI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import org.jmol.viewer.Viewer;
-public class AlignFrame extends EmbmenuFrame implements ActionListener,
+public class AlignFrame extends EmbmenuFrame implements AlignFrameI,
+ ActionListener,
ItemListener, KeyListener, AlignViewControllerGuiI
{
public AlignViewControllerI avc;
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)
FeaturesFile formatter = new FeaturesFile();
if (format.equalsIgnoreCase("Jalview"))
{
- features = formatter.printJalviewFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols(),
- getDisplayedFeatureGroups(), true);
+ features = formatter.printJalviewFormat(
+ viewport.getAlignment().getSequencesArray(),
+ alignPanel.getFeatureRenderer(), true);
}
else
{
features = formatter.printGffFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols(),
- getDisplayedFeatureGroups(), true);
+ .getSequencesArray(), alignPanel.getFeatureRenderer(), true);
}
if (displayTextbox)
static StringBuffer copiedSequences;
- static Vector<int[]> copiedHiddenColumns;
+ static HiddenColumns copiedHiddenColumns;
protected void copy_actionPerformed()
{
if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
{
- copiedHiddenColumns = new Vector<>(viewport.getAlignment()
- .getHiddenColumns().getHiddenColumnsCopy());
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int[] region : copiedHiddenColumns)
- {
- region[0] = region[0] - hiddenOffset;
- region[1] = region[1] - hiddenOffset;
- }
+ int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
+
+ // create new HiddenColumns object with copy of hidden regions
+ // between startRes and endRes, offset by startRes
+ copiedHiddenColumns = new HiddenColumns(
+ viewport.getAlignment().getHiddenColumns(), hiddenOffset,
+ hiddenCutoff, hiddenOffset);
}
else
{
{
try
{
-
if (copiedSequences == null)
{
return;
}
- StringTokenizer st = new StringTokenizer(copiedSequences.toString());
+ StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
+ "\t");
Vector seqs = new Vector();
while (st.hasMoreElements())
{
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
viewport.applet, newtitle, false);
- if (copiedHiddenColumns != null)
- {
- for (int i = 0; i < copiedHiddenColumns.size(); i++)
- {
- int[] region = copiedHiddenColumns.elementAt(i);
- af.viewport.hideColumns(region[0], region[1]);
- }
- }
+ af.viewport.setHiddenColumns(copiedHiddenColumns);
jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
frameHeight);
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());
column, al);
}
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.removed_columns", new String[]
{ Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
addHistoryItem(removeGapCols);
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.removed_empty_columns", new String[]
{ Integer.valueOf(removeGapCols.getSize()).toString() }));
*/
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);
}
}