X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=266cbcb4c79792b46fbff69ea03f2be9d81247c0;hb=400b50efffaa43ae2c3b4d3f653bf8215c5d1edc;hp=468791388fdf7d31f31561e7d755edc4923dd849;hpb=94379c810f9115b8564ee7bac46ed119218d5fd2;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 4687913..266cbcb 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -59,6 +59,7 @@ 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; @@ -66,6 +67,7 @@ import jalview.io.BioJsHTMLOutput; 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; @@ -78,12 +80,10 @@ import jalview.io.NewickFile; 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; @@ -114,12 +114,13 @@ import java.awt.event.ItemEvent; 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; @@ -129,14 +130,12 @@ import java.util.Hashtable; 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; @@ -147,7 +146,7 @@ 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; @@ -839,46 +838,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ 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); } /** @@ -904,7 +877,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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()); @@ -930,8 +905,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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()); @@ -1125,7 +1100,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void saveAs_actionPerformed(ActionEvent e) { String format = currentFileFormat == null ? null : currentFileFormat - .toString(); + .getName(); JalviewFileChooser chooser = JalviewFileChooser.forWrite( Cache.getProperty("LAST_DIRECTORY"), format); @@ -1159,8 +1134,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); @@ -1190,17 +1164,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } 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()) @@ -1225,15 +1188,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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; @@ -1278,8 +1240,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @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()) @@ -1292,8 +1254,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { FileFormatI format = fileFormat; cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) - .formatSequences(format, - exportData.getAlignment(), + .formatSequences(format, exportData.getAlignment(), exportData.getOmitHidden(), exportData.getStartEndPostions(), viewport.getColumnSelection())); @@ -1884,8 +1845,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } String output = new FormatAdapter().formatSequences(FileFormat.Fasta, - seqs, - omitHidden, null); + seqs, omitHidden, null); StringSelection ss = new StringSelection(output); @@ -3315,18 +3275,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new TextColourChooser().chooseColour(alignPanel, null); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - protected void noColourmenuItem_actionPerformed() - { - changeColour(null); - } - /* * public void covariationColour_actionPerformed() { * changeColour(new @@ -3350,11 +3298,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * colour scheme to all groups. If unchecked, groups may have their own * independent colour schemes. * + * @param selected */ @Override - protected void applyToAllGroups_actionPerformed() + protected void applyToAllGroups_actionPerformed(boolean selected) { - viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); + viewport.setColourAppliesToAllGroups(selected); } /** @@ -3363,10 +3312,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @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); } @@ -3381,20 +3344,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // 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); @@ -3403,89 +3353,66 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * 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(), "Background"); + 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(), "Background"); + SliderPanel.showConservationSlider(); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Action on selecting or deselecting (Colour) By Conservation */ @Override - protected void conservationMenuItem_actionPerformed() + protected 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); 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(); + } } /** @@ -4787,17 +4714,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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; @@ -4842,8 +4758,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } 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); @@ -5737,102 +5652,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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 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); @@ -5841,10 +5666,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); } }