X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=86610a2f16697d0fde5a2ec58f810401ecf9f435;hb=fb548a8458941602b0b8b45da5aaf60206e10ec2;hp=8f7a15bb32d7ce8b789b2635ffd799eb7cca27b5;hpb=95ebbef7b78bf266a8252bd479510be3c80cd234;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 8f7a15b..86610a2 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -39,13 +39,17 @@ import jalview.io.DataSourceType; import jalview.io.FileFormatI; import jalview.io.FileFormats; import jalview.io.SequenceAnnotationReport; +import jalview.renderer.ResidueShader; +import jalview.renderer.ResidueShaderI; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; import jalview.schemes.ClustalxColourScheme; 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; @@ -61,12 +65,14 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; +import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; 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; @@ -77,33 +83,43 @@ 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 CheckboxMenuItem PIDColour = new CheckboxMenuItem(); + + protected CheckboxMenuItem BLOSUM62Colour = new CheckboxMenuItem(); + + CheckboxMenuItem nucleotideColour = new CheckboxMenuItem(); + + CheckboxMenuItem purinePyrimidineColour = new CheckboxMenuItem(); protected MenuItem userDefinedColour = new MenuItem(); - protected MenuItem PIDColour = new MenuItem(); + protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem(); - protected MenuItem BLOSUM62Colour = new MenuItem(); + MenuItem modifyPID = new MenuItem(); - MenuItem noColourmenuItem = new MenuItem(); + protected CheckboxMenuItem conservationColour = new CheckboxMenuItem(); - protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + MenuItem modifyConservation = new MenuItem(); + + MenuItem noColourmenuItem = new MenuItem(); final AlignmentPanel ap; @@ -111,8 +127,6 @@ public class APopupMenu extends java.awt.PopupMenu implements MenuItem createGroupMenuItem = new MenuItem(); - MenuItem nucleotideMenuItem = new MenuItem(); - Menu colourMenu = new Menu(); CheckboxMenuItem showBoxes = new CheckboxMenuItem(); @@ -197,7 +211,7 @@ public class APopupMenu extends java.awt.PopupMenu implements Menu menu1 = new Menu(); public APopupMenu(AlignmentPanel apanel, final SequenceI seq, - Vector links) + List links) { // ///////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -230,6 +244,24 @@ public class APopupMenu extends java.awt.PopupMenu implements SequenceGroup sg = ap.av.getSelectionGroup(); if (sg != null && sg.getSize() > 0) { + if (sg.isNucleotide()) + { + conservationColour.setEnabled(false); + clustalColour.setEnabled(false); + BLOSUM62Colour.setEnabled(false); + zappoColour.setEnabled(false); + taylorColour.setEnabled(false); + hydrophobicityColour.setEnabled(false); + helixColour.setEnabled(false); + strandColour.setEnabled(false); + turnColour.setEnabled(false); + buriedColour.setEnabled(false); + } + else + { + purinePyrimidineColour.setEnabled(false); + nucleotideColour.setEnabled(false); + } editGroupName.setLabel(MessageManager.formatMessage( "label.name_param", new Object[] { sg.getName() })); showText.setState(sg.getDisplayText()); @@ -248,9 +280,12 @@ public class APopupMenu extends java.awt.PopupMenu implements if (sg.cs != null) { abovePIDColour.setState(sg.cs.getThreshold() > 0); - conservationMenuItem.setState(sg.cs.conservationApplied()); + conservationColour.setState(sg.cs.conservationApplied()); + modifyPID.setEnabled(abovePIDColour.getState()); + modifyConservation.setEnabled(conservationColour.getState()); } } + setSelectedColour(sg.cs); } else { @@ -308,6 +343,36 @@ 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(ResidueShaderI 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 @@ -417,7 +482,7 @@ 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, @@ -502,43 +567,28 @@ 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) { Object source = evt.getSource(); - if (source == abovePIDColour) - { - abovePIDColour_itemStateChanged(); - } - else if (source == conservationMenuItem) + if (source == noColour) { - conservationMenuItem_itemStateChanged(); - } - else if (source == showColourText) - { - showColourText_itemStateChanged(); - } - else if (source == showText) - { - showText_itemStateChanged(); + noColourmenuItem_actionPerformed(); } - else if (source == showBoxes) + else if (source == clustalColour) { - showBoxes_itemStateChanged(); + clustalColour_actionPerformed(); } - else if (source == 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) { @@ -568,26 +618,58 @@ 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 == showText) + { + 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 == modifyConservation) + { + conservationMenuItem_itemStateChanged(); + } + else if (source == modifyPID) + { + abovePIDColour_itemStateChanged(); } else if (source == unGroupMenuItem) { @@ -738,9 +820,9 @@ public class APopupMenu extends java.awt.PopupMenu implements return; } - int rsize = 0, gSize = sg.getSize(); - SequenceI[] rseqs, seqs = new SequenceI[gSize]; - SequenceFeature[] tfeatures, features = new SequenceFeature[gSize]; + int gSize = sg.getSize(); + List seqs = new ArrayList(); + List features = new ArrayList(); for (int i = 0; i < gSize; i++) { @@ -748,26 +830,21 @@ public class APopupMenu extends java.awt.PopupMenu implements int end = sg.findEndRes(sg.getSequenceAt(i)); if (start <= end) { - seqs[rsize] = sg.getSequenceAt(i); - features[rsize] = new SequenceFeature(null, null, null, start, - end, "Jalview"); - rsize++; + seqs.add(sg.getSequenceAt(i)); + features.add(new SequenceFeature(null, null, null, start, end, + "Jalview")); } } - rseqs = new SequenceI[rsize]; - tfeatures = new SequenceFeature[rsize]; - System.arraycopy(seqs, 0, rseqs, 0, rsize); - System.arraycopy(features, 0, tfeatures, 0, rsize); - features = tfeatures; - seqs = rseqs; - - if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, - features, true, ap)) + + if (!seqs.isEmpty()) { - ap.alignFrame.sequenceFeatures.setState(true); - ap.av.setShowSequenceFeatures(true); - ; - ap.highlightSearchResults(null); + if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, + features, true, ap)) + { + ap.alignFrame.sequenceFeatures.setState(true); + ap.av.setShowSequenceFeatures(true); + ap.highlightSearchResults(null); + } } } else @@ -854,14 +931,14 @@ public class APopupMenu extends java.awt.PopupMenu implements void addPDB() { Vector pdbs = seq.getAllPDBEntries(); - if (pdbs != null&& !pdbs.isEmpty()) + if (pdbs != null && !pdbs.isEmpty()) { PDBEntry entry = pdbs.firstElement(); if (ap.av.applet.jmolAvailable) { - new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq }, - null, ap, DataSourceType.URL); + new AppletJmol(entry, new SequenceI[] { seq }, null, ap, + DataSourceType.URL); } else { @@ -877,7 +954,7 @@ public class APopupMenu extends java.awt.PopupMenu implements cap.setPDBImport(seq); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( + JalviewLite.addFrame(frame, MessageManager.formatMessage( "label.paste_pdb_file_for_sequence", new Object[] { seq.getName() }), 400, 300); } @@ -897,11 +974,8 @@ 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); + modifyPID.setEnabled(abovePIDColour.getState()); + modifyConservation.setEnabled(conservationColour.getState()); colourMenu.setLabel(MessageManager.getString("label.group_colour")); showBoxes.setLabel(MessageManager.getString("action.boxes")); showBoxes.setState(true); @@ -910,7 +984,7 @@ 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")); @@ -942,7 +1016,7 @@ 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); @@ -953,48 +1027,91 @@ 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(conservationColour); + colourMenu.add(modifyConservation); colourMenu.add(abovePIDColour); - colourMenu.add(conservationMenuItem); + colourMenu.add(modifyPID); - 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")); + + abovePIDColour.setLabel(MessageManager + .getString("label.above_identity_threshold")); + abovePIDColour.addItemListener(this); + modifyPID.setLabel(MessageManager + .getString("label.modify_identity_threshold")); + modifyPID.addActionListener(this); + conservationColour.setLabel(MessageManager + .getString("action.by_conservation")); + conservationColour.addItemListener(this); + modifyConservation.setLabel(MessageManager + .getString("label.modify_conservation_threshold")); + modifyConservation.addActionListener(this); + PIDColour.addActionListener(this); - BLOSUM62Colour.setLabel("BLOSUM62"); BLOSUM62Colour.addActionListener(this); - conservationMenuItem.setLabel(MessageManager - .getString("label.conservation")); editMenu.add(copy); copy.addActionListener(this); @@ -1044,55 +1161,63 @@ 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 ResidueShader(new ClustalxColourScheme(sg, + ap.av.getHiddenRepSequences())); refresh(); } protected void zappoColour_actionPerformed() { - getGroup().cs = new ZappoColourScheme(); + getGroup().cs = new ResidueShader(new ZappoColourScheme()); refresh(); } protected void taylorColour_actionPerformed() { - getGroup().cs = new TaylorColourScheme(); + getGroup().cs = new ResidueShader(new TaylorColourScheme()); refresh(); } protected void hydrophobicityColour_actionPerformed() { - getGroup().cs = new HydrophobicColourScheme(); + getGroup().cs = new ResidueShader(new HydrophobicColourScheme()); refresh(); } protected void helixColour_actionPerformed() { - getGroup().cs = new HelixColourScheme(); + getGroup().cs = new ResidueShader(new HelixColourScheme()); refresh(); } protected void strandColour_actionPerformed() { - getGroup().cs = new StrandColourScheme(); + getGroup().cs = new ResidueShader(new StrandColourScheme()); refresh(); } protected void turnColour_actionPerformed() { - getGroup().cs = new TurnColourScheme(); + getGroup().cs = new ResidueShader(new TurnColourScheme()); refresh(); } protected void buriedColour_actionPerformed() { - getGroup().cs = new BuriedColourScheme(); + getGroup().cs = new ResidueShader(new BuriedColourScheme()); refresh(); } public void nucleotideMenuItem_actionPerformed() { - getGroup().cs = new NucleotideColourScheme(); + getGroup().cs = new ResidueShader(new NucleotideColourScheme()); + refresh(); + } + + public void purinePyrimidineColour_actionPerformed() + { + getGroup().cs = new ResidueShader( + new PurinePyrimidineColourScheme()); refresh(); } @@ -1119,11 +1244,11 @@ public class APopupMenu extends java.awt.PopupMenu implements else // remove PIDColouring { + SliderPanel.hidePIDSlider(); sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); } - + modifyPID.setEnabled(abovePIDColour.getState()); refresh(); - } protected void userDefinedColour_actionPerformed() @@ -1134,7 +1259,7 @@ public class APopupMenu extends java.awt.PopupMenu implements protected void PIDColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new PIDColourScheme(); + sg.cs = new ResidueShader(new PIDColourScheme()); sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); refresh(); @@ -1144,7 +1269,7 @@ public class APopupMenu extends java.awt.PopupMenu implements { SequenceGroup sg = getGroup(); - sg.cs = new Blosum62ColourScheme(); + sg.cs = new ResidueShader(new Blosum62ColourScheme()); sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); @@ -1166,21 +1291,24 @@ 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(); } else // remove ConservationColouring { + SliderPanel.hideConservationSlider(); sg.cs.setConservation(null); } - + modifyConservation.setEnabled(conservationColour.getState()); refresh(); }