import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.util.MessageManager;
-import jalview.util.dialogrunner.RunResponse;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
private Rectangle explodedGeometry;
- String viewName;
+ private String viewName;
/*
* Flag set true on the view that should 'gather' multiple views of the same
ResidueColourScheme.NONE);
}
ColourSchemeI colourScheme = ColourSchemeProperty
- .getColourScheme(alignment, schemeName);
+ .getColourScheme(this, alignment, schemeName);
residueShading = new ResidueShader(colourScheme);
if (colourScheme instanceof UserColourScheme)
{
residueShading.setConsensus(hconsensus);
}
+ setColourAppliesToAllGroups(true);
}
boolean validCharWidth;
*/
if (align != null)
{
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- ssm.registerMappings(align.getCodonFrames());
+ Desktop.getInstance().getStructureSelectionManager()
+ .registerMappings(align.getCodonFrames());
}
/*
List<AlignedCodonFrame> mappings = al.getCodonFrames();
if (mappings != null)
{
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ StructureSelectionManager ssm = Desktop.getInstance()
+ .getStructureSelectionManager();
for (AlignedCodonFrame acf : mappings)
{
if (noReferencesTo(acf))
@Override
public void sendSelection()
{
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
- .sendSelection(new SequenceGroup(getSelectionGroup()),
- new ColumnSelection(getColumnSelection()),
- new HiddenColumns(getAlignment().getHiddenColumns()),
- this);
+ Desktop.getInstance().getStructureSelectionManager().sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()),
+ new HiddenColumns(getAlignment().getHiddenColumns()), this);
}
/**
@Override
public StructureSelectionManager getStructureSelectionManager()
{
- return StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
+ return Desktop.getInstance().getStructureSelectionManager();
}
@Override
return;
}
}
- alignmentDataAdded(toAdd);
+ addDataToAlignment(toAdd);
}
- private void alignmentDataAdded(AlignmentI toAdd)
+ /**
+ * adds sequences to this alignment
+ *
+ * @param toAdd
+ */
+ void addDataToAlignment(AlignmentI toAdd)
{
- /*
- * No mappings, or offer declined - add sequences to this alignment
- */
// TODO: JAL-407 regardless of above - identical sequences (based on ID and
// provenance) should share the same dataset sequence
}
}
- ranges.setEndSeq(getAlignment().getHeight());
+ ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
firePropertyChange("alignment", null, getAlignment().getSequences());
}
final String question = JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.open_split_window?"));
final AlignViewport us = this;
- JvOptionPane.newOptionDialog(Desktop.desktop)
- .response(new RunResponse(1)
+
+ /*
+ * options No, Split Window, New Window correspond to
+ * dialog responses 0, 1, 2 (even though JOptionPane shows them
+ * in reverse order)
+ */
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane())
+ .setResponseHandler(0, new Runnable()
{
@Override
public void run()
{
- us.openLinkedAlignmentAs(al, title, true);
+ addDataToAlignment(al);
}
- }).response(new RunResponse(2)
+ }).setResponseHandler(1, new Runnable()
{
@Override
public void run()
{
- us.openLinkedAlignmentAs(al, title, false);
+ us.openLinkedAlignmentAs(al, title, true);
}
- }).defaultResponse(new Runnable()
+ }).setResponseHandler(2, new Runnable()
{
@Override
public void run()
{
- alignmentDataAdded(al);
+ us.openLinkedAlignmentAs(al, title, false);
}
- }).showDialog(question,
+ });
+ dialog.showDialog(question,
MessageManager.getString("label.open_split_window"),
JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
newAlignFrame.setTitle(title);
- newAlignFrame.statusBar.setText(MessageManager
+ newAlignFrame.setStatus(MessageManager
.formatMessage("label.successfully_loaded_file", new Object[]
{ title }));
}
fr.setTransparency(featureSettings.getTransparency());
}
+
+ public String getViewName()
+ {
+ return viewName;
+ }
+
+ public void setViewName(String viewName)
+ {
+ this.viewName = viewName;
+ }
}