X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=941052de099e9c6bbf2a81d88fe4b2d9d01a011e;hb=09d9063e70931a6cb75d16b230f5cd0665f0f340;hp=d625f785d7d0237d3b5690ec37b4ac0b2c6fbb41;hpb=e80a27f6eb12a788bbc78347a760e795ad8bd8c6;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index d625f78..941052d 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -24,7 +24,7 @@ import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentAnnotationUtils; import jalview.analysis.AlignmentUtils; import jalview.analysis.Conservation; -import jalview.bin.Cache; +import jalview.bin.JalviewLite; import jalview.commands.ChangeCaseCommand; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; @@ -35,14 +35,20 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; import jalview.io.SequenceAnnotationReport; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; import jalview.schemes.ClustalxColourScheme; +import jalview.schemes.CollectionColourScheme; +import jalview.schemes.CollectionColourSchemeI; import jalview.schemes.HelixColourScheme; import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.JalviewColourScheme; import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; +import jalview.schemes.PurinePyrimidineColourScheme; import jalview.schemes.StrandColourScheme; import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; @@ -64,6 +70,7 @@ import java.util.Collections; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; +import java.util.SortedMap; import java.util.TreeMap; import java.util.Vector; @@ -74,33 +81,37 @@ public class APopupMenu extends java.awt.PopupMenu implements MenuItem editGroupName = new MenuItem(); - protected MenuItem clustalColour = new MenuItem(); + CheckboxMenuItem noColour = new CheckboxMenuItem(); - protected MenuItem zappoColour = new MenuItem(); + protected CheckboxMenuItem clustalColour = new CheckboxMenuItem(); - protected MenuItem taylorColour = new MenuItem(); + protected CheckboxMenuItem zappoColour = new CheckboxMenuItem(); - protected MenuItem hydrophobicityColour = new MenuItem(); + protected CheckboxMenuItem taylorColour = new CheckboxMenuItem(); - protected MenuItem helixColour = new MenuItem(); + protected CheckboxMenuItem hydrophobicityColour = new CheckboxMenuItem(); - protected MenuItem strandColour = new MenuItem(); + protected CheckboxMenuItem helixColour = new CheckboxMenuItem(); - protected MenuItem turnColour = new MenuItem(); + protected CheckboxMenuItem strandColour = new CheckboxMenuItem(); - protected MenuItem buriedColour = new MenuItem(); + protected CheckboxMenuItem turnColour = new CheckboxMenuItem(); - protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem(); + protected CheckboxMenuItem buriedColour = new CheckboxMenuItem(); - protected MenuItem userDefinedColour = new MenuItem(); + protected CheckboxMenuItem PIDColour = new CheckboxMenuItem(); - protected MenuItem PIDColour = new MenuItem(); + protected CheckboxMenuItem BLOSUM62Colour = new CheckboxMenuItem(); - protected MenuItem BLOSUM62Colour = new MenuItem(); + CheckboxMenuItem nucleotideColour = new CheckboxMenuItem(); - MenuItem noColourmenuItem = new MenuItem(); + CheckboxMenuItem purinePyrimidineColour = new CheckboxMenuItem(); - protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + protected MenuItem userDefinedColour = new MenuItem(); + + protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem(); + + protected CheckboxMenuItem conservationColour = new CheckboxMenuItem(); final AlignmentPanel ap; @@ -108,8 +119,6 @@ public class APopupMenu extends java.awt.PopupMenu implements MenuItem createGroupMenuItem = new MenuItem(); - MenuItem nucleotideMenuItem = new MenuItem(); - Menu colourMenu = new Menu(); CheckboxMenuItem showBoxes = new CheckboxMenuItem(); @@ -214,10 +223,9 @@ public class APopupMenu extends java.awt.PopupMenu implements e.printStackTrace(); } - for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) + for (String ff : FileFormat.getWritableFormats(true)) { - MenuItem item = new MenuItem( - jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); + MenuItem item = new MenuItem(ff); item.addActionListener(this); outputmenu.add(item); @@ -243,8 +251,13 @@ public class APopupMenu extends java.awt.PopupMenu implements { menu1.setLabel(MessageManager.getString("action.edit_group")); groupMenu.remove(createGroupMenuItem); + if (sg.cs != null) + { + abovePIDColour.setState(sg.cs.getThreshold() > 0); + conservationColour.setState(sg.cs.conservationApplied()); + } } - + setSelectedColour(sg.cs); } else { @@ -302,6 +315,36 @@ public class APopupMenu extends java.awt.PopupMenu implements } /** + * Select the menu item (if any) matching the current colour scheme. This + * works by matching the menu item name (not display text) to the canonical + * name of the colour scheme. + * + * @param cs + */ + protected void setSelectedColour(CollectionColourSchemeI cs) + { + if (cs == null || cs.getColourScheme() == null) + { + noColour.setState(true); + } + else + { + String name = cs.getColourScheme().getSchemeName(); + for (int i = 0; i < colourMenu.getItemCount(); i++) + { + MenuItem item = colourMenu.getItem(i); + if (item instanceof CheckboxMenuItem) + { + if (name.equals(item.getName())) + { + ((CheckboxMenuItem) item).setState(true); + } + } + } + } + } + + /** * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided. * * @param seq @@ -320,13 +363,14 @@ public class APopupMenu extends java.awt.PopupMenu implements urlLink = new UrlLink(link); } catch (Exception foo) { - Cache.log.error("Exception for URLLink '" + link + "'", foo); + System.err.println("Exception for URLLink '" + link + "': " + + foo.getMessage()); continue; } if (!urlLink.isValid()) { - Cache.log.error(urlLink.getInvalidMessage()); + System.err.println(urlLink.getInvalidMessage()); continue; } @@ -335,17 +379,25 @@ public class APopupMenu extends java.awt.PopupMenu implements addshowLinks(linkMenu, linkset.values()); + // disable link menu if there are no valid entries if (linkMenu.getItemCount() > 0) { - if (seq != null) - { - seqMenu.add(linkMenu); - } - else - { - add(linkMenu); - } + linkMenu.setEnabled(true); + } + else + { + linkMenu.setEnabled(false); + } + + if (seq != null) + { + seqMenu.add(linkMenu); + } + else + { + add(linkMenu); } + } private void addshowLinks(Menu linkMenu, Collection> linkset) @@ -402,7 +454,7 @@ public class APopupMenu extends java.awt.PopupMenu implements * Temporary store to hold distinct calcId / type pairs for the tooltip. * Using TreeMap means calcIds are shown in alphabetical order. */ - Map tipEntries = new TreeMap(); + SortedMap tipEntries = new TreeMap(); final Map> candidates = new LinkedHashMap>(); AlignmentI al = this.ap.av.getAlignment(); AlignmentUtils.findAddableReferenceAnnotations(forSequences, @@ -487,38 +539,28 @@ public class APopupMenu extends java.awt.PopupMenu implements linkMenu.add(item); } + /** + * Actions on selecting / unselecting a checkbox menu item + */ @Override public void itemStateChanged(ItemEvent evt) { - if (evt.getSource() == abovePIDColour) - { - abovePIDColour_itemStateChanged(); - } - else if (evt.getSource() == showColourText) - { - showColourText_itemStateChanged(); - } - else if (evt.getSource() == showText) + Object source = evt.getSource(); + if (source == noColour) { - showText_itemStateChanged(); + noColourmenuItem_actionPerformed(); } - else if (evt.getSource() == showBoxes) + else if (source == clustalColour) { - showBoxes_itemStateChanged(); + clustalColour_actionPerformed(); } - else if (evt.getSource() == displayNonconserved) + else if (source == BLOSUM62Colour) { - this.showNonconserved_itemStateChanged(); + BLOSUM62Colour_actionPerformed(); } - } - - @Override - public void actionPerformed(ActionEvent evt) - { - Object source = evt.getSource(); - if (source == clustalColour) + else if (evt.getSource() == PIDColour) { - clustalColour_actionPerformed(); + PIDColour_actionPerformed(); } else if (source == zappoColour) { @@ -548,30 +590,50 @@ public class APopupMenu extends java.awt.PopupMenu implements { buriedColour_actionPerformed(); } - else if (source == nucleotideMenuItem) + else if (source == nucleotideColour) { nucleotideMenuItem_actionPerformed(); } - - else if (source == userDefinedColour) + else if (source == purinePyrimidineColour) { - userDefinedColour_actionPerformed(); + purinePyrimidineColour_actionPerformed(); } - else if (source == PIDColour) + else if (source == abovePIDColour) { - PIDColour_actionPerformed(); + abovePIDColour_itemStateChanged(); } - else if (source == BLOSUM62Colour) + else if (source == conservationColour) { - BLOSUM62Colour_actionPerformed(); + conservationMenuItem_itemStateChanged(); } - else if (source == noColourmenuItem) + else if (source == showColourText) { - noColourmenuItem_actionPerformed(); + showColourText_itemStateChanged(); } - else if (source == conservationMenuItem) + else if (source == showText) { - conservationMenuItem_itemStateChanged(); + showText_itemStateChanged(); + } + else if (source == showBoxes) + { + showBoxes_itemStateChanged(); + } + else if (source == displayNonconserved) + { + this.showNonconserved_itemStateChanged(); + } + } + + /** + * Actions on clicking a menu item + */ + @Override + public void actionPerformed(ActionEvent evt) + { + Object source = evt.getSource(); + if (source == userDefinedColour) + { + userDefinedColour_actionPerformed(); } else if (source == unGroupMenuItem) { @@ -767,15 +829,16 @@ public class APopupMenu extends java.awt.PopupMenu implements Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( + JalviewLite.addFrame(frame, MessageManager.formatMessage( "label.selection_output_command", new Object[] { e.getActionCommand() }), 600, 500); // JBPNote: getSelectionAsNewSequence behaviour has changed - this method // now returns a full copy of sequence data // TODO consider using getSequenceSelection instead here - cap.setText(new jalview.io.AppletFormatAdapter().formatSequences( - e.getActionCommand(), ap.av.getShowJVSuffix(), ap, true)); + FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand()); + cap.setText(new AppletFormatAdapter().formatSequences(fileFormat, + ap.av.getShowJVSuffix(), ap, true)); } @@ -794,7 +857,7 @@ public class APopupMenu extends java.awt.PopupMenu implements CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame); - StringBuffer contents = new StringBuffer(); + StringBuilder contents = new StringBuilder(128); for (SequenceI seq : sequences) { contents.append(MessageManager.formatMessage( @@ -805,7 +868,6 @@ public class APopupMenu extends java.awt.PopupMenu implements seq, true, true, - false, (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr .getMinMax() : null); contents.append("

"); @@ -836,19 +898,20 @@ public class APopupMenu extends java.awt.PopupMenu implements void addPDB() { - if (seq.getAllPDBEntries() != null) + Vector pdbs = seq.getAllPDBEntries(); + if (pdbs != null&& !pdbs.isEmpty()) { - PDBEntry entry = seq.getAllPDBEntries().firstElement(); + PDBEntry entry = pdbs.firstElement(); if (ap.av.applet.jmolAvailable) { new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq }, - null, ap, AppletFormatAdapter.URL); + null, ap, DataSourceType.URL); } else { new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null, - ap, AppletFormatAdapter.URL); + ap, DataSourceType.URL); } } @@ -879,11 +942,6 @@ public class APopupMenu extends java.awt.PopupMenu implements .getString("action.create_group")); createGroupMenuItem.addActionListener(this); - nucleotideMenuItem.setLabel(MessageManager - .getString("label.nucleotide")); - nucleotideMenuItem.addActionListener(this); - conservationMenuItem.addItemListener(this); - abovePIDColour.addItemListener(this); colourMenu.setLabel(MessageManager.getString("label.group_colour")); showBoxes.setLabel(MessageManager.getString("action.boxes")); showBoxes.setState(true); @@ -892,7 +950,7 @@ public class APopupMenu extends java.awt.PopupMenu implements sequenceDetails.addActionListener(this); selSeqDetails.addActionListener(this); displayNonconserved.setLabel(MessageManager - .getString("label.show_non_conversed")); + .getString("label.show_non_conserved")); displayNonconserved.setState(false); displayNonconserved.addItemListener(this); showText.setLabel(MessageManager.getString("action.text")); @@ -924,7 +982,7 @@ public class APopupMenu extends java.awt.PopupMenu implements groupMenu.add(unGroupMenuItem); groupMenu.add(menu1); - colourMenu.add(noColourmenuItem); + colourMenu.add(noColour); colourMenu.add(clustalColour); colourMenu.add(BLOSUM62Colour); colourMenu.add(PIDColour); @@ -935,48 +993,80 @@ public class APopupMenu extends java.awt.PopupMenu implements colourMenu.add(strandColour); colourMenu.add(turnColour); colourMenu.add(buriedColour); - colourMenu.add(nucleotideMenuItem); + colourMenu.add(nucleotideColour); + colourMenu.add(purinePyrimidineColour); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); colourMenu.add(abovePIDColour); - colourMenu.add(conservationMenuItem); + colourMenu.add(conservationColour); - noColourmenuItem.setLabel(MessageManager.getString("label.none")); - noColourmenuItem.addActionListener(this); + noColour.setLabel(MessageManager.getString("label.none")); + noColour.addItemListener(this); + /* + * setName allows setSelectedColour to do its thing + */ clustalColour.setLabel(MessageManager - .getString("label.clustalx_colours")); - clustalColour.addActionListener(this); - zappoColour.setLabel(MessageManager.getString("label.zappo")); - zappoColour.addActionListener(this); - taylorColour.setLabel(MessageManager.getString("label.taylor")); - taylorColour.addActionListener(this); + .getString("label.colourScheme_clustal")); + clustalColour.setName(JalviewColourScheme.Clustal.toString()); + clustalColour.addItemListener(this); + BLOSUM62Colour.setLabel(MessageManager + .getString("label.colourScheme_blosum62")); + BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString()); + BLOSUM62Colour.addItemListener(this); + PIDColour.setLabel(MessageManager + .getString("label.colourScheme_%_identity")); + PIDColour.setName(JalviewColourScheme.PID.toString()); + PIDColour.addItemListener(this); + zappoColour.setLabel(MessageManager + .getString("label.colourScheme_zappo")); + zappoColour.setName(JalviewColourScheme.Zappo.toString()); + zappoColour.addItemListener(this); + taylorColour.setLabel(MessageManager + .getString("label.colourScheme_taylor")); + taylorColour.setName(JalviewColourScheme.Taylor.toString()); + taylorColour.addItemListener(this); hydrophobicityColour.setLabel(MessageManager - .getString("label.hydrophobicity")); - hydrophobicityColour.addActionListener(this); - helixColour - .setLabel(MessageManager.getString("label.helix_propensity")); - helixColour.addActionListener(this); + .getString("label.colourScheme_hydrophobic")); + hydrophobicityColour + .setName(JalviewColourScheme.Hydrophobic.toString()); + hydrophobicityColour.addItemListener(this); + helixColour.setLabel(MessageManager + .getString("label.colourScheme_helix_propensity")); + helixColour.setName(JalviewColourScheme.Helix.toString()); + helixColour.addItemListener(this); strandColour.setLabel(MessageManager - .getString("label.strand_propensity")); - strandColour.addActionListener(this); - turnColour.setLabel(MessageManager.getString("label.turn_propensity")); - turnColour.addActionListener(this); - buriedColour.setLabel(MessageManager.getString("label.buried_index")); - buriedColour.addActionListener(this); - abovePIDColour.setLabel(MessageManager - .getString("label.above_identity_percentage")); + .getString("label.colourScheme_strand_propensity")); + strandColour.setName(JalviewColourScheme.Strand.toString()); + strandColour.addItemListener(this); + turnColour.setLabel(MessageManager + .getString("label.colourScheme_turn_propensity")); + turnColour.setName(JalviewColourScheme.Turn.toString()); + turnColour.addItemListener(this); + buriedColour.setLabel(MessageManager + .getString("label.colourScheme_buried_index")); + buriedColour.setName(JalviewColourScheme.Buried.toString()); + buriedColour.addItemListener(this); + nucleotideColour.setLabel(MessageManager + .getString("label.colourScheme_nucleotide")); + nucleotideColour.setName(JalviewColourScheme.Nucleotide.toString()); + nucleotideColour.addItemListener(this); + purinePyrimidineColour.setLabel(MessageManager + .getString("label.colourScheme_purine/pyrimidine")); + purinePyrimidineColour.setName(JalviewColourScheme.PurinePyrimidine + .toString()); + purinePyrimidineColour.addItemListener(this); userDefinedColour.setLabel(MessageManager .getString("action.user_defined")); userDefinedColour.addActionListener(this); - PIDColour.setLabel(MessageManager - .getString("label.percentage_identity")); - PIDColour.addActionListener(this); - BLOSUM62Colour.setLabel("BLOSUM62"); - BLOSUM62Colour.addActionListener(this); - conservationMenuItem.setLabel(MessageManager + + abovePIDColour.setLabel(MessageManager + .getString("label.above_identity_threshold")); + abovePIDColour.addItemListener(this); + conservationColour.setLabel(MessageManager .getString("label.conservation")); + conservationColour.addItemListener(this); editMenu.add(copy); copy.addActionListener(this); @@ -1026,55 +1116,63 @@ public class APopupMenu extends java.awt.PopupMenu implements protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()); + sg.cs = new CollectionColourScheme(new ClustalxColourScheme(sg, + ap.av.getHiddenRepSequences())); refresh(); } protected void zappoColour_actionPerformed() { - getGroup().cs = new ZappoColourScheme(); + getGroup().cs = new CollectionColourScheme(new ZappoColourScheme()); refresh(); } protected void taylorColour_actionPerformed() { - getGroup().cs = new TaylorColourScheme(); + getGroup().cs = new CollectionColourScheme(new TaylorColourScheme()); refresh(); } protected void hydrophobicityColour_actionPerformed() { - getGroup().cs = new HydrophobicColourScheme(); + getGroup().cs = new CollectionColourScheme(new HydrophobicColourScheme()); refresh(); } protected void helixColour_actionPerformed() { - getGroup().cs = new HelixColourScheme(); + getGroup().cs = new CollectionColourScheme(new HelixColourScheme()); refresh(); } protected void strandColour_actionPerformed() { - getGroup().cs = new StrandColourScheme(); + getGroup().cs = new CollectionColourScheme(new StrandColourScheme()); refresh(); } protected void turnColour_actionPerformed() { - getGroup().cs = new TurnColourScheme(); + getGroup().cs = new CollectionColourScheme(new TurnColourScheme()); refresh(); } protected void buriedColour_actionPerformed() { - getGroup().cs = new BuriedColourScheme(); + getGroup().cs = new CollectionColourScheme(new BuriedColourScheme()); refresh(); } public void nucleotideMenuItem_actionPerformed() { - getGroup().cs = new NucleotideColourScheme(); + getGroup().cs = new CollectionColourScheme(new NucleotideColourScheme()); + refresh(); + } + + public void purinePyrimidineColour_actionPerformed() + { + getGroup().cs = new CollectionColourScheme( + new PurinePyrimidineColourScheme()); refresh(); } @@ -1116,7 +1214,7 @@ public class APopupMenu extends java.awt.PopupMenu implements protected void PIDColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new PIDColourScheme(); + sg.cs = new CollectionColourScheme(new PIDColourScheme()); sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); refresh(); @@ -1126,7 +1224,7 @@ public class APopupMenu extends java.awt.PopupMenu implements { SequenceGroup sg = getGroup(); - sg.cs = new Blosum62ColourScheme(); + sg.cs = new CollectionColourScheme(new Blosum62ColourScheme()); sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); @@ -1148,12 +1246,14 @@ public class APopupMenu extends java.awt.PopupMenu implements return; } - if (conservationMenuItem.getState()) + if (conservationColour.getState()) { - sg.cs.setConservation(Conservation.calculateConservation("Group", sg + Conservation conservation = Conservation.calculateConservation( + "Group", sg .getSequences(ap.av.getHiddenRepSequences()), 0, ap.av .getAlignment().getWidth(), false, ap.av.getConsPercGaps(), - false)); + false); + sg.getGroupColourScheme().setConservation(conservation); SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); SliderPanel.showConservationSlider(); }