import jalview.schemes.PIDColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.RNAHelicesColourChooser;
-import jalview.schemes.RNAInteractionColourScheme;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.schemes.TaylorColourScheme;
import java.util.StringTokenizer;
import java.util.Vector;
+import org.jmol.viewer.Viewer;
+
public class AlignFrame extends EmbmenuFrame implements ActionListener,
ItemListener, KeyListener, AlignViewControllerGuiI
{
public AlignFrame(AlignmentI al, JalviewLite applet,
String title, boolean embedded, boolean addToDisplay)
{
+ this(al, null, null, applet, title, embedded, addToDisplay);
+ }
+
+ public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+ ColumnSelection columnSelection, JalviewLite applet,
+ String title, boolean embedded)
+ {
+ this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
+ }
+
+ public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+ ColumnSelection columnSelection, JalviewLite applet,
+ String title, boolean embedded, boolean addToDisplay)
+ {
if (applet != null)
{
jalviewServletURL = applet.getParameter("APPLICATION_URL");
}
}
viewport = new AlignViewport(al, applet);
+
+ if (hiddenSeqs != null && hiddenSeqs.length > 0)
+ {
+ viewport.hideSequence(hiddenSeqs);
+ }
+ if (columnSelection != null)
+ {
+ viewport.setColumnSelection(columnSelection);
+ }
+
alignPanel = new AlignmentPanel(this, viewport);
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
: showForSequences);
aa.visible = visible;
}
- alignPanel.validateAnnotationDimensions(false);
+ alignPanel.validateAnnotationDimensions(true);
+ validate();
+ repaint();
}
private void setAnnotationSortOrder(SequenceAnnotationOrder order)
{
changeColour(new PurinePyrimidineColourScheme());
}
- else if (source == RNAInteractionColour)
- {
- changeColour(new RNAInteractionColourScheme());
- }
+ // else if (source == RNAInteractionColour)
+ // {
+ // changeColour(new RNAInteractionColourScheme());
+ // }
else if (source == RNAHelixColour)
{
new RNAHelicesColourChooser(viewport, alignPanel);
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
"label.alignment_output_command", new Object[]
{ e.getActionCommand() }), 600, 500);
- cap.setText(new AppletFormatAdapter().formatSequences(
+
+ FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
+ cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
e.getActionCommand(), viewport.getAlignment(),
viewport.getShowJVSuffix()));
}
MenuItem purinePyrimidineColour = new MenuItem();
- MenuItem RNAInteractionColour = new MenuItem();
+ // MenuItem RNAInteractionColour = new MenuItem();
MenuItem RNAHelixColour = new MenuItem();
purinePyrimidineColour.setLabel(MessageManager
.getString("label.purine_pyrimidine"));
purinePyrimidineColour.addActionListener(this);
- RNAInteractionColour.setLabel(MessageManager
- .getString("label.rna_interaction"));
- RNAInteractionColour.addActionListener(this);
+ // RNAInteractionColour.setLabel(MessageManager
+ // .getString("label.rna_interaction"));
+ // RNAInteractionColour.addActionListener(this);
RNAHelixColour.setLabel(MessageManager
.getString("action.by_rna_helixes"));
RNAHelixColour.addActionListener(this);
public SequenceStructureBinding addStructureViewInstance(
Object jmolviewer, String[] sequenceIds)
{
- org.jmol.api.JmolViewer viewer = null;
+ Viewer viewer = null;
try
{
- viewer = (org.jmol.api.JmolViewer) jmolviewer;
+ viewer = (Viewer) jmolviewer;
} catch (ClassCastException ex)
{
System.err.println("Unsupported viewer object :"
boolean needtoadd = false;
if (toaddpdb != null)
{
- Vector pdbe = toaddpdb.getPDBId();
+ Vector pdbe = toaddpdb.getAllPDBEntries();
PDBEntry pdbentry = null;
if (pdbe != null && pdbe.size() > 0)
{
{
this.splitFrame = sf;
}
+
// may not need this
@Override
public void setShowSeqFeatures(boolean b)