import jalview.api.FeatureSettingsControllerI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
-import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.commands.CommandI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.FileLoader;
+import jalview.io.FileParse;
import jalview.io.FormatAdapter;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileView;
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
+import jalview.io.ScoreMatrixFile;
import jalview.io.TCoffeeScoreFile;
import jalview.jbgui.GAlignFrame;
-import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.NucleotideColourScheme;
-import jalview.schemes.PIDColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.RNAHelicesColourChooser;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.StrandColourScheme;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.UserColourScheme;
-import jalview.schemes.ZappoColourScheme;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
import jalview.ws.jws1.Discoverer;
import java.awt.event.ItemListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.print.PageFormat;
import java.awt.print.PrinterJob;
import javax.swing.JLayeredPane;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JRadioButtonMenuItem;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
* @version $Revision$
*/
public class AlignFrame extends GAlignFrame implements DropTargetListener,
- IProgressIndicator, AlignViewControllerGuiI
+ IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
public static final int DEFAULT_WIDTH = 700;
AlignViewport viewport;
+ ViewportRanges vpRanges;
+
public AlignViewControllerI avc;
List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
* @param height
* height of frame.
*/
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
int width, int height)
{
this(al, hiddenColumns, width, height, null);
* @param sequenceSetId
* (may be null)
*/
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
int width, int height, String sequenceSetId)
{
this(al, hiddenColumns, width, height, sequenceSetId, null);
* @param viewId
* (may be null)
*/
- public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns,
int width, int height, String sequenceSetId, String viewId)
{
setSize(width, height);
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
- ColumnSelection hiddenColumns, int width, int height)
+ HiddenColumns hiddenColumns, int width, int height)
{
setSize(width, height);
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
}
+ vpRanges = viewport.getRanges();
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
{
- BLOSUM62Colour.setEnabled(false);
+ // BLOSUM62Colour.setEnabled(false);
conservationMenuItem.setEnabled(false);
modifyConservation.setEnabled(false);
// PIDColour.setEnabled(false);
sortPairwiseMenuItem_actionPerformed(null);
}
- if (Desktop.desktop != null)
- {
- this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- addServiceListeners();
- setGUINucleotide(viewport.getAlignment().isNucleotide());
- }
-
this.alignPanel.av
.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
- buildTreeMenu();
+ calculateTree.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ openTreePcaDialog();
+ }
+ });
+ buildColourMenu();
+
+ if (Desktop.desktop != null)
+ {
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+ addServiceListeners();
+ setGUINucleotide();
+ }
if (viewport.getWrapAlignment())
{
new String[] { (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
- alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
+ alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
+ .getStartRes();
+ alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
+ .getStartSeq();
}
alignPanel.getSeqPanel().seqCanvas.repaint();
break;
case KeyEvent.VK_PAGE_UP:
if (viewport.getWrapAlignment())
{
- alignPanel.scrollUp(true);
+ vpRanges.scrollUp(true);
}
else
{
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
+ vpRanges.pageUp();
}
break;
case KeyEvent.VK_PAGE_DOWN:
if (viewport.getWrapAlignment())
{
- alignPanel.scrollUp(false);
+ vpRanges.scrollUp(false);
}
else
{
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
+ vpRanges.pageDown();
}
break;
}
/**
* Configure menu items that vary according to whether the alignment is
* nucleotide or protein
- *
- * @param nucleotide
*/
- public void setGUINucleotide(boolean nucleotide)
+ public void setGUINucleotide()
{
+ AlignmentI al = getViewport().getAlignment();
+ boolean nucleotide = al.isNucleotide();
+
showTranslation.setVisible(nucleotide);
showReverse.setVisible(nucleotide);
showReverseComplement.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
- modifyConservation.setEnabled(!nucleotide);
+ modifyConservation.setEnabled(!nucleotide
+ && conservationMenuItem.isSelected());
showGroupConservation.setEnabled(!nucleotide);
- rnahelicesColour.setEnabled(nucleotide);
- nucleotideColour.setEnabled(nucleotide);
- purinePyrimidineColour.setEnabled(nucleotide);
- RNAInteractionColour.setEnabled(nucleotide);
+
showComplementMenuItem.setText(nucleotide ? MessageManager
.getString("label.protein") : MessageManager
.getString("label.nucleotide"));
- setColourSelected(jalview.bin.Cache.getDefault(
- nucleotide ? Preferences.DEFAULT_COLOUR_NUC
- : Preferences.DEFAULT_COLOUR_PROT, "None"));
}
/**
padGapsMenuitem.setSelected(av.isPadGaps());
colourTextMenuItem.setSelected(av.isShowColourText());
abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
+ modifyPID.setEnabled(abovePIDThreshold.isSelected());
conservationMenuItem.setSelected(av.getConservationSelected());
+ modifyConservation.setEnabled(conservationMenuItem.isSelected());
seqLimits.setSelected(av.getShowJVSuffix());
idRightAlign.setSelected(av.isRightAlignIds());
centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
showSequenceLogo.setSelected(av.isShowSequenceLogo());
normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
- setColourSelected(ColourSchemeProperty.getColourName(av
- .getGlobalColourScheme()));
+ ColourMenuHelper.setColourSelected(colourMenu,
+ av.getGlobalColourScheme());
showSeqFeatures.setSelected(av.isShowSequenceFeatures());
hiddenMarkers.setState(av.getShowHiddenMarkers());
autoCalculate.setSelected(av.autoCalculateConsensus);
sortByTree.setSelected(av.sortByTree);
listenToViewSelections.setSelected(av.followSelection);
- rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
- rnahelicesColour
- .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
showProducts.setEnabled(canShowProducts());
setGroovyEnabled(Desktop.getGroovyConsole() != null);
exportData.getAlignment(), // class cast exceptions will
// occur in the distant future
exportData.getOmitHidden(), exportData.getStartEndPostions(),
- f.getCacheSuffixDefault(format),
- viewport.getColumnSelection());
+ f.getCacheSuffixDefault(format), viewport.getAlignment()
+ .getHiddenColumns());
if (output == null)
{
{
FileFormatI format = fileFormat;
cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
- .formatSequences(format,
- exportData.getAlignment(),
+ .formatSequences(format, exportData.getAlignment(),
exportData.getOmitHidden(),
- exportData.getStartEndPostions(),
- viewport.getColumnSelection()));
+ exportData
+ .getStartEndPostions(), viewport
+ .getAlignment().getHiddenColumns()));
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
"label.alignment_output_command",
new Object[] { e.getActionCommand() }), 600, 500);
alignmentToExport = viewport.getAlignment();
}
alignmentStartEnd = alignmentToExport
- .getVisibleStartAndEndIndex(viewport.getColumnSelection()
- .getHiddenColumns());
+ .getVisibleStartAndEndIndex(viewport.getAlignment()
+ .getHiddenColumns()
+ .getHiddenRegions());
AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
omitHidden, alignmentStartEnd, settings);
return ed;
}
String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
- seqs,
- omitHidden, null);
+ seqs, omitHidden, null);
StringSelection ss = new StringSelection(output);
hiddenColumns = new ArrayList<int[]>();
int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
.getSelectionGroup().getEndRes();
- for (int[] region : viewport.getColumnSelection().getHiddenColumns())
+ for (int[] region : viewport.getAlignment().getHiddenColumns()
+ .getHiddenRegions())
{
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
{
{
// propagate alignment changed.
- viewport.setEndSeq(alignment.getHeight());
+ vpRanges.setEndSeq(alignment.getHeight());
if (annotationAdded)
{
// Duplicate sequence annotation in all views.
{
trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
column, viewport.getAlignment());
- viewport.setStartRes(0);
+ vpRanges.setStartRes(0);
}
else
{
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
+ int startRes = seq.findPosition(vpRanges.getStartRes());
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
- viewport.setStartRes(seq.findIndex(startRes) - 1);
+ vpRanges.setStartRes(seq.findIndex(startRes) - 1);
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
+ int startRes = seq.findPosition(vpRanges.getStartRes());
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
viewport.getAlignment()));
- viewport.setStartRes(seq.findIndex(startRes) - 1);
+ vpRanges.setStartRes(seq.findIndex(startRes) - 1);
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
*/
newap.av.replaceMappings(viewport.getAlignment());
+ /*
+ * start up cDNA consensus (if applicable) now mappings are in place
+ */
+ if (newap.av.initComplementConsensus())
+ {
+ newap.refresh(true); // adjust layout of annotations
+ }
+
newap.av.viewName = getNewViewName(viewTitle);
addAlignmentPanel(newap, true);
frame.setContentPane(overview);
Desktop.addInternalFrame(frame, MessageManager.formatMessage(
"label.overview_params", new Object[] { this.getTitle() }),
- frame.getWidth(), frame.getHeight());
+ true, frame.getWidth(), frame.getHeight(), true, true);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
}
@Override
- public void textColour_actionPerformed(ActionEvent e)
+ public void textColour_actionPerformed()
{
new TextColourChooser().chooseColour(alignPanel, null);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
- {
- changeColour(null);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void clustalColour_actionPerformed(ActionEvent e)
- {
- changeColour(new ClustalxColourScheme(viewport.getAlignment(),
- viewport.getHiddenRepSequences()));
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void zappoColour_actionPerformed(ActionEvent e)
- {
- changeColour(new ZappoColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void taylorColour_actionPerformed(ActionEvent e)
- {
- changeColour(new TaylorColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void hydrophobicityColour_actionPerformed(ActionEvent e)
- {
- changeColour(new HydrophobicColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void helixColour_actionPerformed(ActionEvent e)
- {
- changeColour(new HelixColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void strandColour_actionPerformed(ActionEvent e)
- {
- changeColour(new StrandColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void turnColour_actionPerformed(ActionEvent e)
- {
- changeColour(new TurnColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void buriedColour_actionPerformed(ActionEvent e)
- {
- changeColour(new BuriedColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void nucleotideColour_actionPerformed(ActionEvent e)
- {
- changeColour(new NucleotideColourScheme());
- }
-
- @Override
- public void purinePyrimidineColour_actionPerformed(ActionEvent e)
- {
- changeColour(new PurinePyrimidineColourScheme());
- }
-
/*
- * public void covariationColour_actionPerformed(ActionEvent e) {
+ * public void covariationColour_actionPerformed() {
* changeColour(new
* CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
* ()[0])); }
*/
@Override
- public void annotationColour_actionPerformed(ActionEvent e)
+ public void annotationColour_actionPerformed()
{
new AnnotationColourChooser(viewport, alignPanel);
}
new AnnotationColumnChooser(viewport, alignPanel);
}
+ /**
+ * Action on the user checking or unchecking the option to apply the selected
+ * colour scheme to all groups. If unchecked, groups may have their own
+ * independent colour schemes.
+ *
+ * @param selected
+ */
@Override
- public void rnahelicesColour_actionPerformed(ActionEvent e)
+ public void applyToAllGroups_actionPerformed(boolean selected)
{
- new RNAHelicesColourChooser(viewport, alignPanel);
+ viewport.setColourAppliesToAllGroups(selected);
}
/**
- * DOCUMENT ME!
+ * Action on user selecting a colour from the colour menu
*
- * @param e
- * DOCUMENT ME!
+ * @param name
+ * the name (not the menu item label!) of the colour scheme
*/
@Override
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ public void changeColour_actionPerformed(String name)
{
- viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
+ /*
+ * 'User Defined' opens a panel to configure or load a
+ * user-defined colour scheme
+ */
+ if (ResidueColourScheme.USER_DEFINED.equals(name))
+ {
+ new UserDefinedColours(alignPanel);
+ return;
+ }
+
+ /*
+ * otherwise set the chosen colour scheme (or null for 'None')
+ */
+ ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
+ viewport.getAlignment(), viewport.getHiddenRepSequences());
+ changeColour(cs);
}
/**
- * DOCUMENT ME!
+ * Actions on setting or changing the alignment colour scheme
*
* @param cs
- * DOCUMENT ME!
*/
@Override
public void changeColour(ColourSchemeI cs)
{
// TODO: pull up to controller method
-
- if (cs != null)
- {
- // Make sure viewport is up to date w.r.t. any sliders
- if (viewport.getAbovePIDThreshold())
- {
- int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
- viewport.setThreshold(threshold);
- }
-
- if (viewport.getConservationSelected())
- {
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
- cs, "Background"));
- }
- if (cs instanceof TCoffeeColourScheme)
- {
- tcoffeeColour.setEnabled(true);
- tcoffeeColour.setSelected(true);
- }
- }
+ ColourMenuHelper.setColourSelected(colourMenu, cs);
viewport.setGlobalColourScheme(cs);
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Show the PID threshold slider panel
*/
@Override
- protected void modifyPID_actionPerformed(ActionEvent e)
+ protected void modifyPID_actionPerformed()
{
- if (viewport.getAbovePIDThreshold()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
- SliderPanel.showPIDSlider();
- }
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getResidueShading(), alignPanel.getViewName());
+ SliderPanel.showPIDSlider();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Show the Conservation slider panel
*/
@Override
- protected void modifyConservation_actionPerformed(ActionEvent e)
+ protected void modifyConservation_actionPerformed()
{
- if (viewport.getConservationSelected()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setConservationSlider(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
- SliderPanel.showConservationSlider();
- }
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.getResidueShading(), alignPanel.getViewName());
+ SliderPanel.showConservationSlider();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action on selecting or deselecting (Colour) By Conservation
*/
@Override
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ public void conservationMenuItem_actionPerformed(boolean selected)
{
- viewport.setConservationSelected(conservationMenuItem.isSelected());
-
- viewport.setAbovePIDThreshold(false);
- abovePIDThreshold.setSelected(false);
+ modifyConservation.setEnabled(selected);
+ viewport.setConservationSelected(selected);
+ viewport.getResidueShading().setConservationApplied(selected);
changeColour(viewport.getGlobalColourScheme());
-
- modifyConservation_actionPerformed(null);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void abovePIDThreshold_actionPerformed(ActionEvent e)
- {
- viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
-
- conservationMenuItem.setSelected(false);
- viewport.setConservationSelected(false);
-
- changeColour(viewport.getGlobalColourScheme());
-
- modifyPID_actionPerformed(null);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void userDefinedColour_actionPerformed(ActionEvent e)
- {
- if (e.getActionCommand().equals(
- MessageManager.getString("action.user_defined")))
+ if (selected)
{
- new UserDefinedColours(alignPanel, null);
+ modifyConservation_actionPerformed();
}
else
{
- UserColourScheme udc = (UserColourScheme) UserDefinedColours
- .getUserColourSchemes().get(e.getActionCommand());
-
- changeColour(udc);
+ SliderPanel.hideConservationSlider();
}
}
- public void updateUserColourMenu()
+ /**
+ * Action on selecting or deselecting (Colour) Above PID Threshold
+ */
+ @Override
+ public void abovePIDThreshold_actionPerformed(boolean selected)
{
+ modifyPID.setEnabled(selected);
+ viewport.setAbovePIDThreshold(selected);
+ if (!selected)
+ {
+ viewport.getResidueShading().setThreshold(0,
+ viewport.isIgnoreGapsConsensus());
+ }
- Component[] menuItems = colourMenu.getMenuComponents();
- int iSize = menuItems.length;
- for (int i = 0; i < iSize; i++)
+ changeColour(viewport.getGlobalColourScheme());
+ if (selected)
{
- if (menuItems[i].getName() != null
- && menuItems[i].getName().equals("USER_DEFINED"))
- {
- colourMenu.remove(menuItems[i]);
- iSize--;
- }
+ modifyPID_actionPerformed();
}
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+ else
{
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
- .getUserColourSchemes().keys();
-
- while (userColours.hasMoreElements())
- {
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColours.nextElement().toString());
- radioItem.setName("USER_DEFINED");
- radioItem.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Mac
- {
- offerRemoval(radioItem);
- }
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Windows
- {
- offerRemoval(radioItem);
- }
- }
-
- /**
- * @param radioItem
- */
- void offerRemoval(final JRadioButtonMenuItem radioItem)
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JvOptionPane.showInternalConfirmDialog(
- jalview.gui.Desktop.desktop, MessageManager
- .getString("label.remove_from_default_list"),
- MessageManager
- .getString("label.remove_user_defined_colour"),
- JvOptionPane.YES_NO_OPTION);
- if (option == JvOptionPane.YES_OPTION)
- {
- jalview.gui.UserDefinedColours
- .removeColourFromDefaults(radioItem.getText());
- colourMenu.remove(radioItem);
- }
- else
- {
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
- }
- });
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
-
- colourMenu.insert(radioItem, 15);
- colours.add(radioItem);
- }
+ SliderPanel.hidePIDSlider();
}
}
* DOCUMENT ME!
*/
@Override
- public void PIDColour_actionPerformed(ActionEvent e)
- {
- changeColour(new PIDColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)
- {
- changeColour(new Blosum62ColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
- .getAlignment().getSequenceAt(0), null);
+ .getAlignment().getSequenceAt(0));
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void PCAMenuItem_actionPerformed(ActionEvent e)
- {
- if (((viewport.getSelectionGroup() != null)
- && (viewport.getSelectionGroup().getSize() < 4) && (viewport
- .getSelectionGroup().getSize() > 0))
- || (viewport.getAlignment().getHeight() < 4))
- {
- JvOptionPane
- .showInternalMessageDialog(
- this,
- MessageManager
- .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
- MessageManager
- .getString("label.sequence_selection_insufficient"),
- JvOptionPane.WARNING_MESSAGE);
-
- return;
- }
-
- new PCAPanel(alignPanel);
- }
-
@Override
public void autoCalculate_actionPerformed(ActionEvent e)
{
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
- {
- newTreePanel("AV", "PID", "Average distance tree using PID");
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
- {
- newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
- }
-
- /**
- * DOCUMENT ME!
+ * Constructs a tree panel and adds it to the desktop
*
* @param type
- * DOCUMENT ME!
- * @param pwType
- * DOCUMENT ME!
- * @param title
- * DOCUMENT ME!
+ * tree type (NJ or AV)
+ * @param modelName
+ * name of score model used to compute the tree
+ * @param options
+ * parameters for the distance or similarity calculation
*/
- void newTreePanel(String type, String pwType, String title)
+ void newTreePanel(String type, String modelName, SimilarityParamsI options)
{
+ String frameTitle = "";
TreePanel tp;
+ boolean onSelection = false;
if (viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() > 0)
{
- if (viewport.getSelectionGroup().getSize() < 3)
- {
- JvOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.you_need_more_two_sequences_selected_build_tree"),
- MessageManager
- .getString("label.not_enough_sequences"),
- JvOptionPane.WARNING_MESSAGE);
- return;
- }
-
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
return;
}
}
-
- title = title + " on region";
- tp = new TreePanel(alignPanel, type, pwType);
+ onSelection = true;
}
else
{
- // are the visible sequences aligned?
- if (!viewport.getAlignment().isAligned(false))
- {
- JvOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.sequences_must_be_aligned_before_creating_tree"),
- MessageManager
- .getString("label.sequences_not_aligned"),
- JvOptionPane.WARNING_MESSAGE);
-
- return;
- }
-
if (viewport.getAlignment().getHeight() < 2)
{
return;
}
-
- tp = new TreePanel(alignPanel, type, pwType);
}
- title += " from ";
+ tp = new TreePanel(alignPanel, type, modelName, options);
+ frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
+
+ frameTitle += " from ";
if (viewport.viewName != null)
{
- title += viewport.viewName + " of ";
+ frameTitle += viewport.viewName + " of ";
}
- title += this.title;
+ frameTitle += this.title;
- Desktop.addInternalFrame(tp, title, 600, 500);
+ Desktop.addInternalFrame(tp, frameTitle, 600, 500);
}
/**
* call. Listeners are added to remove the menu item when the treePanel is
* closed, and adjust the tree leaf to sequence mapping when the alignment is
* modified.
- *
- * @param treePanel
- * Displayed tree window.
- * @param title
- * SortBy menu item title.
*/
@Override
- public void buildTreeMenu()
+ public void buildTreeSortMenu()
{
- calculateTree.removeAll();
- // build the calculate menu
-
- for (final String type : new String[] { "NJ", "AV" })
- {
- String treecalcnm = MessageManager.getString("label.tree_calc_"
- + type.toLowerCase());
- for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
- {
- JMenuItem tm = new JMenuItem();
- ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
- if (sm.isDNA() == viewport.getAlignment().isNucleotide()
- || sm.isProtein() == !viewport.getAlignment()
- .isNucleotide())
- {
- String smn = MessageManager.getStringOrReturn(
- "label.score_model_", sm.getName());
- final String title = MessageManager.formatMessage(
- "label.treecalc_title", treecalcnm, smn);
- tm.setText(title);//
- tm.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- newTreePanel(type, pwtype, title);
- }
- });
- calculateTree.add(tm);
- }
-
- }
- }
sortByTreeMenu.removeAll();
List<Component> comps = PaintRefresher.components.get(viewport
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- jalview.io.NewickFile fin = null;
+ String filePath = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", filePath);
+ NewickFile fin = null;
try
{
- fin = new NewickFile(choice, DataSourceType.FILE);
- viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
+ fin = new NewickFile(filePath, DataSourceType.FILE);
+ viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
} catch (Exception ex)
{
JvOptionPane
}
}
- @Override
- protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
+ public TreePanel showNewickTree(NewickFile nf, String treeTitle)
{
- changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+ return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
}
- public TreePanel ShowNewickTree(NewickFile nf, String title)
- {
- return ShowNewickTree(nf, title, 600, 500, 4, 5);
- }
-
- public TreePanel ShowNewickTree(NewickFile nf, String title,
- AlignmentView input)
- {
- return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
- }
-
- public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
+ public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
int h, int x, int y)
{
- return ShowNewickTree(nf, title, null, w, h, x, y);
+ return showNewickTree(nf, treeTitle, null, w, h, x, y);
}
/**
- * Add a treeviewer for the tree extracted from a newick file object to the
+ * Add a treeviewer for the tree extracted from a Newick file object to the
* current alignment view
*
* @param nf
* position
* @return TreePanel handle
*/
- public TreePanel ShowNewickTree(NewickFile nf, String title,
+ public TreePanel showNewickTree(NewickFile nf, String treeTitle,
AlignmentView input, int w, int h, int x, int y)
{
TreePanel tp = null;
if (nf.getTree() != null)
{
- tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
+ tp = new TreePanel(alignPanel, nf, treeTitle, input);
tp.setSize(w, h);
tp.setLocation(x, y);
}
- Desktop.addInternalFrame(tp, title, w, h);
+ Desktop.addInternalFrame(tp, treeTitle, w, h);
}
} catch (Exception ex)
{
}
/**
- * Attempt to load a "dropped" file or URL string: First by testing whether
- * it's an Annotation file, then a JNet file, and finally a features file. If
- * all are false then the user may have dropped an alignment file onto this
- * AlignFrame.
+ * Attempt to load a "dropped" file or URL string, by testing in turn for
+ * <ul>
+ * <li>an Annotation file</li>
+ * <li>a JNet file</li>
+ * <li>a features file</li>
+ * <li>else try to interpret as an alignment file</li>
+ * </ul>
*
* @param file
* either a filename or a URL string.
{
if (tcf.annotateAlignment(viewport.getAlignment(), true))
{
- tcoffeeColour.setEnabled(true);
- tcoffeeColour.setSelected(true);
+ buildColourMenu();
changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
statusBar
{
format = new IdentifyFile().identify(file, sourceType);
}
- if (FileFormat.Jnet.equals(format))
+ if (FileFormat.ScoreMatrix == format)
+ {
+ ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
+ sourceType));
+ sm.parse();
+ // todo: i18n this message
+ statusBar
+ .setText(MessageManager.formatMessage(
+ "label.successfully_loaded_matrix",
+ sm.getMatrixName()));
+ }
+ else if (FileFormat.Jnet.equals(format))
{
- JPredFile predictions = new JPredFile(
- file, sourceType);
+ JPredFile predictions = new JPredFile(file, sourceType);
new JnetAnnotationMaker();
JnetAnnotationMaker.add_annotation(predictions,
viewport.getAlignment(), 0, false);
SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
viewport.getAlignment().setSeqrep(repseq);
- ColumnSelection cs = new ColumnSelection();
+ HiddenColumns cs = new HiddenColumns();
cs.hideInsertionsFor(repseq);
- viewport.setColumnSelection(cs);
+ viewport.getAlignment().setHiddenColumns(cs);
isAnnotation = true;
}
// else if (IdentifyFile.FeaturesFile.equals(format))
}
/*
+ * 'focus' any colour slider that is open to the selected viewport
+ */
+ if (viewport.getConservationSelected())
+ {
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.getResidueShading(), alignPanel.getViewName());
+ }
+ else
+ {
+ SliderPanel.hideConservationSlider();
+ }
+ if (viewport.getAbovePIDThreshold())
+ {
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getResidueShading(), alignPanel.getViewName());
+ }
+ else
+ {
+ SliderPanel.hidePIDSlider();
+ }
+
+ /*
* If there is a frame linked to this one in a SplitPane, switch it to the
* same view tab index. No infinite recursion of calls should happen, since
* tabSelectionChanged() should not get invoked on setting the selected
}
AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
.size()]));
- AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
+ GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
cdna.alignAs(alignment);
String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
true,
(actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
}
+
+ /**
+ * Rebuilds the Colour menu, including any user-defined colours which have
+ * been loaded either on startup or during the session
+ */
+ public void buildColourMenu()
+ {
+ colourMenu.removeAll();
+
+ colourMenu.add(applyToAllGroups);
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
+
+ ColourMenuHelper.addMenuItems(colourMenu, this,
+ viewport.getAlignment(), false);
+
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDThreshold);
+ colourMenu.add(modifyPID);
+ colourMenu.add(annotationColour);
+
+ ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
+ ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
+ }
+
+ /**
+ * Open a dialog (if not already open) that allows the user to select and
+ * calculate PCA or Tree analysis
+ */
+ protected void openTreePcaDialog()
+ {
+ if (alignPanel.getCalculationDialog() == null)
+ {
+ new CalculationChooser(AlignFrame.this);
+ }
+ }
}
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