*/
package jalview.appletgui;
-import java.io.*;
import java.net.*;
import java.util.*;
import jalview.datamodel.*;
import jalview.io.*;
import jalview.schemes.*;
+import jalview.structure.StructureSelectionManager;
public class AlignFrame extends EmbmenuFrame implements ActionListener,
ItemListener, KeyListener
annotationPanelMenuItem.setState(viewport.showAnnotation);
displayNonconservedMenuItem.setState(viewport.getShowunconserved());
+ followMouseOverFlag.setState(viewport.getFollowHighlight());
+ showGroupConsensus.setState(viewport.showGroupConsensus);
+ showGroupConservation.setState(viewport.showGroupConservation);
+ showConsensusHistogram.setState(viewport.showConsensusHistogram);
+ showSequenceLogo.setState(viewport.showSequenceLogo);
seqLimits.setState(viewport.showJVSuffix);
alignPanel.idPanel.idCanvas.addKeyListener(this);
alignPanel.scalePanel.addKeyListener(this);
alignPanel.annotationPanel.addKeyListener(this);
+ alignPanel.annotationPanelHolder.addKeyListener(this);
+ alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
+ alignPanel.alabels.addKeyListener(this);
createAlignFrameWindow(embedded, title);
alignPanel.validate();
alignPanel.paintAlignment(true);
featuresFile = new jalview.io.FeaturesFile(file, type)
.parse(viewport.alignment,
alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
- featureLinks, true);
+ featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
} catch (Exception ex)
{
ex.printStackTrace();
{
case 27: // escape key
deselectAllSequenceMenuItem_actionPerformed();
+
+ alignPanel.alabels.cancelDrag();
break;
case KeyEvent.VK_X:
if (evt.isControlDown() || evt.isMetaDown())
{
mouseOverFlag_stateChanged();
}
-
+ else if (evt.getSource() == showGroupConsensus)
+ {
+ showGroupConsensus_actionPerformed();
+ }
+ else if (evt.getSource() == showGroupConservation)
+ {
+ showGroupConservation_actionPerformed();
+ }
+ else if (evt.getSource() == showSequenceLogo)
+ {
+ showSequenceLogo_actionPerformed();
+ }
+ else if (evt.getSource() == showConsensusHistogram)
+ {
+ showConsensusHistogram_actionPerformed();
+ }
+ else if (evt.getSource() == applyAutoAnnotationSettings)
+ {
+ applyAutoAnnotationSettings_actionPerformed();
+ }
alignPanel.paintAlignment(true);
}
viewport.showAllHiddenSeqs();
alignPanel.paintAlignment(true);
}
+ else if (source == showGroupConsensus)
+ {
+ showGroupConsensus_actionPerformed();
+ }
+ else if (source == showGroupConservation)
+ {
+ showGroupConservation_actionPerformed();
+ }
+ else if (source == showSequenceLogo)
+ {
+ showSequenceLogo_actionPerformed();
+ }
+ else if (source == showConsensusHistogram)
+ {
+ showConsensusHistogram_actionPerformed();
+ }
+ else if (source == applyAutoAnnotationSettings)
+ {
+ applyAutoAnnotationSettings_actionPerformed();
+ }
else if (source == featureSettings)
{
new FeatureSettings(alignPanel);
viewport.sendSelection();
}
+ /**
+ * group consensus toggled
+ *
+ */
+ protected void showGroupConsensus_actionPerformed()
+ {
+ viewport.setShowGroupConsensus(showGroupConsensus.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+
+ }
+
+ /**
+ * group conservation toggled.
+ */
+ protected void showGroupConservation_actionPerformed()
+ {
+ viewport.setShowGroupConservation(showGroupConservation.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showConsensusHistogram_actionPerformed()
+ {
+ viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showSequenceLogo_actionPerformed()
+ {
+ viewport.setShowSequenceLogo(showSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ protected void applyAutoAnnotationSettings_actionPerformed()
+ {
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
protected void makeGrpsFromSelection_actionPerformed()
{
if (viewport.getSelectionGroup() != null)
;
}
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
- // alignPanel.updateAnnotation();
+ alignPanel.updateAnnotation();
alignPanel.paintAlignment(true);
}
}
|| (viewport.getSelectionGroup() == null && viewport.alignment
.getHeight() > 1))
{
- final TreePanel tp = new TreePanel(viewport, type, pwType);
+ final TreePanel tp = new TreePanel(alignPanel, type, pwType);
addTreeMenuItem(tp, title);
public void loadTree(jalview.io.NewickFile tree, String treeFile)
{
- TreePanel tp = new TreePanel(viewport, treeFile, "From File - ", tree);
+ TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
addTreeMenuItem(tp, treeFile);
}
};
});
}
-
+ public boolean sortBy(AlignmentOrder alorder, String undoname)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment()
+ .getSequencesArray();
+ if (viewport.applet.debug)
+ {
+ System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
+ }
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
+ if (undoname!=null)
+ {
+ addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
+ }
+ alignPanel.paintAlignment(true);
+ return true;
+ }
protected void documentation_actionPerformed()
{
showURL("http://www.jalview.org/help.html", "HELP");
CheckboxMenuItem seqLimits = new CheckboxMenuItem();
CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
-
+
CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
+ Menu autoAnnMenu=new Menu();
+ CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
+ CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
+ CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
+ CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
+ CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
private void jbInit() throws Exception
{
hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
hideAllSelection.setLabel("Selected Region");
showAllHidden.setLabel("All Sequences and Columns");
+ showGroupConsensus.setLabel("Group Consensus");
+ showGroupConservation.setLabel("Group Conservation");
+ showConsensusHistogram.setLabel("Show Consensus Histogram");
+ showSequenceLogo.setLabel("Show Consensus Logo");
+ applyAutoAnnotationSettings.setLabel("Apply to all groups");
+ applyAutoAnnotationSettings.setState(true);
+ autoAnnMenu.setLabel("Autocalculated Annotation");
+
invertColSel.addActionListener(this);
showColumns.addActionListener(this);
showSeqs.addActionListener(this);
hideAllButSelection.addActionListener(this);
hideAllSelection.addActionListener(this);
showAllHidden.addActionListener(this);
+ showGroupConsensus.addItemListener(this);
+ showGroupConservation.addItemListener(this);
+ showConsensusHistogram.addItemListener(this);
+ showSequenceLogo.addItemListener(this);
+ applyAutoAnnotationSettings.addItemListener(this);
formatMenu.setLabel("Format");
selectMenu.setLabel("Select");
newView.setLabel("New View");
viewMenu.addSeparator();
viewMenu.add(followMouseOverFlag);
viewMenu.add(annotationPanelMenuItem);
+ autoAnnMenu.add(applyAutoAnnotationSettings);
+ autoAnnMenu.add(showConsensusHistogram);
+ autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(showGroupConservation);
+ autoAnnMenu.add(showGroupConsensus);
+ viewMenu.add(autoAnnMenu);
viewMenu.addSeparator();
viewMenu.add(sequenceFeatures);
viewMenu.add(featureSettings);
viewport.applet.getSize().height - embeddedMenu.HEIGHT
- statusBar.HEIGHT);
viewport.applet.add(alignPanel, BorderLayout.CENTER);
+ final AlignFrame me = this;
+ viewport.applet.addFocusListener(new FocusListener()
+ {
+
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ if (me.viewport.applet.currentAlignFrame==me) {
+ me.viewport.applet.currentAlignFrame = null;
+ }}
+
+ @Override
+ public void focusGained(FocusEvent e)
+ {
+ me.viewport.applet.currentAlignFrame = me;
+ }
+ });
viewport.applet.validate();
}
else
return;
}
}
+ if (applet.useXtrnalSviewer)
+ {
+ // register the association(s) and quit, don't create any windows.
+ StructureSelectionManager.getStructureSelectionManager().setMapping(seqs, chains, pdb.getFile(), protocol);
+ return;
+ }
if (applet.isAlignPdbStructures() && applet.jmolAvailable)
{
// can only do alignments with Jmol
git://source.jalview.org / jalview.git / blobdiff