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.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.HtmlSvgOutput;
import jalview.io.TCoffeeScoreFile;
import jalview.jbgui.GAlignFrame;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.schemes.TCoffeeColourScheme;
-import jalview.schemes.UserColourScheme;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.DBRefFetcher;
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 java.beans.PropertyChangeEvent;
import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Vector;
-import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JEditorPane;
import javax.swing.JInternalFrame;
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;
*/
public void setGUINucleotide()
{
- boolean nucleotide = viewport.getAlignment().isNucleotide();
+ 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);
- AlignmentI al = getViewport().getAlignment();
-
- /*
- * enable / disable colour schemes by querying whether they
- * are applicable to the alignment data (for example, peptide or
- * nucleotide specific, or require certain annotation present)
- */
- for (Component menuItem : colourMenu.getMenuComponents())
- {
- if (menuItem instanceof JRadioButtonMenuItem)
- {
- String colourName = ((JRadioButtonMenuItem) menuItem).getName();
- ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(
- colourName, viewport);
- if (cs != null)
- {
- ((JRadioButtonMenuItem) menuItem).setEnabled(cs
- .isApplicableTo(al));
- }
- }
- }
-
showComplementMenuItem.setText(nucleotide ? MessageManager
.getString("label.protein") : MessageManager
.getString("label.nucleotide"));
-
- String selectedColourScheme = Cache.getDefault(
- nucleotide ? Preferences.DEFAULT_COLOUR_NUC
- : Preferences.DEFAULT_COLOUR_PROT,
- ResidueColourScheme.NONE);
- setColourSelected(selectedColourScheme);
}
/**
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());
public void saveAs_actionPerformed(ActionEvent e)
{
String format = currentFileFormat == null ? null : currentFileFormat
- .toString();
+ .getName();
JalviewFileChooser chooser = JalviewFileChooser.forWrite(
Cache.getProperty("LAST_DIRECTORY"), format);
fileName = chooser.getSelectedFile().getPath();
- Cache.setProperty("DEFAULT_FILE_FORMAT",
- currentFileFormat.toString());
+ Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
Cache.setProperty("LAST_DIRECTORY", fileName);
saveAlignment(fileName, currentFileFormat);
}
else
{
- // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
- // {
- // warningMessage("Cannot save file " + fileName + " using format "
- // + format, "Alignment output format not supported");
- // if (!Jalview.isHeadlessMode())
- // {
- // saveAs_actionPerformed(null);
- // }
- // return false;
- // }
-
AlignmentExportData exportData = getAlignmentForExport(format,
viewport, null);
if (exportData.getSettings().isCancelled())
{
try
{
- java.io.PrintWriter out = new java.io.PrintWriter(
- new java.io.FileWriter(file));
+ PrintWriter out = new PrintWriter(new FileWriter(file));
out.print(output);
out.close();
this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format",
- new Object[] { fileName, format }));
+ new Object[] { fileName, format.getName() }));
} catch (Exception ex)
{
success = false;
@Override
protected void outputText_actionPerformed(ActionEvent e)
{
-
- FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
+ FileFormatI fileFormat = FileFormats.getInstance().forName(
+ e.getActionCommand());
AlignmentExportData exportData = getAlignmentForExport(fileFormat,
viewport, null);
if (exportData.getSettings().isCancelled())
{
FileFormatI format = fileFormat;
cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
- .formatSequences(format,
- exportData.getAlignment(),
+ .formatSequences(format, exportData.getAlignment(),
exportData.getOmitHidden(),
exportData.getStartEndPostions(),
viewport.getColumnSelection()));
}
String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
- seqs,
- omitHidden, null);
+ seqs, omitHidden, null);
StringSelection ss = new StringSelection(output);
new TextColourChooser().chooseColour(alignPanel, null);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void noColourmenuItem_actionPerformed()
- {
- changeColour(null);
- }
-
/*
* public void covariationColour_actionPerformed() {
* changeColour(new
* colour scheme to all groups. If unchecked, groups may have their own
* independent colour schemes.
*
+ * @param selected
*/
@Override
- protected void applyToAllGroups_actionPerformed()
+ public void applyToAllGroups_actionPerformed(boolean selected)
{
- viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
+ viewport.setColourAppliesToAllGroups(selected);
}
/**
* @param name
* the name (not the menu item label!) of the colour scheme
*/
+ @Override
public void changeColour_actionPerformed(String name)
{
+ /*
+ * 'User Defined' opens a panel to configure or load a
+ * user-defined colour scheme
+ */
+ if (ResidueColourScheme.USER_DEFINED.equals(name))
+ {
+ new UserDefinedColours(alignPanel, null);
+ return;
+ }
+
+ /*
+ * otherwise set the chosen colour scheme (or null for 'None')
+ */
ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
- viewport);
+ viewport.getAlignment(), viewport.getHiddenRepSequences());
changeColour(cs);
}
// TODO: pull up to controller method
if (cs != null)
{
- setColourSelected(cs.getSchemeName());
- // 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"));
- }
+ ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
}
viewport.setGlobalColourScheme(cs);
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Show the PID threshold slider panel
*/
@Override
protected void modifyPID_actionPerformed()
{
- if (viewport.getAbovePIDThreshold()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
- SliderPanel.showPIDSlider();
- }
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getViewportColourScheme(), alignPanel.getViewName());
+ SliderPanel.showPIDSlider();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Show the Conservation slider panel
*/
@Override
protected void modifyConservation_actionPerformed()
{
- if (viewport.getConservationSelected()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setConservationSlider(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
- SliderPanel.showConservationSlider();
- }
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.getViewportColourScheme(), alignPanel.getViewName());
+ SliderPanel.showConservationSlider();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action on selecting or deselecting (Colour) By Conservation
*/
@Override
- protected void conservationMenuItem_actionPerformed()
+ public void conservationMenuItem_actionPerformed(boolean selected)
{
- viewport.setConservationSelected(conservationMenuItem.isSelected());
-
- viewport.setAbovePIDThreshold(false);
- abovePIDThreshold.setSelected(false);
+ modifyConservation.setEnabled(selected);
+ viewport.setConservationSelected(selected);
+ viewport.getViewportColourScheme().setConservationApplied(selected);
changeColour(viewport.getGlobalColourScheme());
-
- modifyConservation_actionPerformed();
+ if (selected)
+ {
+ modifyConservation_actionPerformed();
+ }
+ else
+ {
+ SliderPanel.hideConservationSlider();
+ }
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action on selecting or deselecting (Colour) Above PID Threshold
*/
@Override
- public void abovePIDThreshold_actionPerformed()
+ public void abovePIDThreshold_actionPerformed(boolean selected)
{
- viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
-
- conservationMenuItem.setSelected(false);
- viewport.setConservationSelected(false);
+ modifyPID.setEnabled(selected);
+ viewport.setAbovePIDThreshold(selected);
+ if (!selected)
+ {
+ viewport.getViewportColourScheme().setThreshold(0,
+ viewport.isIgnoreGapsConsensus());
+ }
changeColour(viewport.getGlobalColourScheme());
-
- modifyPID_actionPerformed();
- }
-
- /**
- * Action on the user selecting the option "User Defined" to create or load a
- * new colour scheme
- *
- * @param e
- */
- @Override
- public void userDefinedColour_actionPerformed(ActionEvent e)
- {
- new UserDefinedColours(alignPanel, null);
+ if (selected)
+ {
+ modifyPID_actionPerformed();
+ }
+ else
+ {
+ SliderPanel.hidePIDSlider();
+ }
}
/**
{
if (tcf.annotateAlignment(viewport.getAlignment(), true))
{
- // tcoffeeColour.setEnabled(true);
- // tcoffeeColour.setSelected(true);
- for (Component menuItem : colourMenu.getMenuComponents())
- {
- if (menuItem instanceof JRadioButtonMenuItem
- && ((JRadioButtonMenuItem) menuItem).getText()
- .equals("T-Coffee Scores"))
- {
- ((JRadioButtonMenuItem) menuItem).setSelected(true);
- }
- }
buildColourMenu();
changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
}
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);
}
/*
+ * 'focus' any colour slider that is open to the selected viewport
+ */
+ if (viewport.getConservationSelected())
+ {
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.getViewportColourScheme(), alignPanel.getViewName());
+ }
+ else
+ {
+ SliderPanel.hideConservationSlider();
+ }
+ if (viewport.getAbovePIDThreshold())
+ {
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getViewportColourScheme(), 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
{
colourMenu.removeAll();
- /*
- * ButtonGroup groups those items whose
- * selection is mutually exclusive
- */
- ButtonGroup colours = new ButtonGroup();
-
colourMenu.add(applyToAllGroups);
colourMenu.add(textColour);
colourMenu.addSeparator();
- colourMenu.add(noColourmenuItem);
- colours.add(noColourmenuItem);
-
- /*
- * scan registered colour schemes (built-in or user-defined
- * and add them to the menu (in the order they were added)
- */
- Iterable<ColourSchemeI> colourSchemes = ColourSchemes.getInstance()
- .getColourSchemes();
- for (ColourSchemeI scheme : colourSchemes)
- {
- /*
- * button text is i18n'd but the name is the canonical name of
- * the colour scheme (inspected in changeColour_actionPerformed)
- */
- final String name = scheme.getSchemeName();
- String label = MessageManager.getString("label.colourScheme_"
- + name.toLowerCase().replace(" ", "_"));
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(label);
- radioItem.setName(name);
- if (scheme instanceof UserColourScheme)
- {
- /*
- * user-defined colour scheme loaded on startup or during the
- * Jalview session; right-click on this offers the option to
- * remove it as a colour choice
- */
- radioItem.setText(((UserColourScheme) scheme).getName());
- radioItem.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Mac
- {
- offerRemoval();
- }
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Windows
- {
- offerRemoval();
- }
- }
-
- void offerRemoval()
- {
- ActionListener al = radioItem.getActionListeners()[0];
- radioItem.removeActionListener(al);
- int option = JvOptionPane.showInternalConfirmDialog(
- 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)
- {
- UserDefinedColours.removeColourFromDefaults(radioItem
- .getName());
- ColourSchemes.getInstance().removeColourScheme(
- radioItem.getName());
- colourMenu.remove(radioItem);
- }
- else
- {
- radioItem.addActionListener(al);
- }
- }
- });
- }
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- changeColour_actionPerformed(name);
- }
- });
- colourMenu.add(radioItem);
- colours.add(radioItem);
- }
- colourMenu.add(userDefinedColour);
- colours.add(userDefinedColour);
+ ColourMenuHelper.addMenuItems(colourMenu, this,
+ viewport.getAlignment(), false);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
- setColourSelected(Cache.getDefault(Preferences.DEFAULT_COLOUR,
- ResidueColourScheme.NONE));
+ ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
+ String schemeName = colourScheme == null ? null : colourScheme
+ .getSchemeName();
- setGUINucleotide();
+ ColourMenuHelper.setColourSelected(colourMenu, schemeName);
}
}
git://source.jalview.org / jalview.git / blobdiff