X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=46bd4fd37730ed5cf4a75f48fecc0544d7859049;hb=a57976ba40e1abe6d7c1940386e1a25419ef9c9d;hp=897c78c5499e8945fb6d29234c23b288e2180137;hpb=5abd8cc59e692171861a337e189faaa26dcfff16;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 897c78c..46bd4fd 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -39,10 +39,11 @@ 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.ColourSchemeI; import jalview.schemes.HelixColourScheme; import jalview.schemes.HydrophobicColourScheme; import jalview.schemes.JalviewColourScheme; @@ -64,6 +65,7 @@ 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; @@ -74,8 +76,8 @@ import java.util.SortedMap; import java.util.TreeMap; import java.util.Vector; -public class APopupMenu extends java.awt.PopupMenu implements - ActionListener, ItemListener +public class APopupMenu extends java.awt.PopupMenu + implements ActionListener, ItemListener { Menu groupMenu = new Menu(); @@ -209,7 +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 @@ -242,8 +244,27 @@ public class APopupMenu extends java.awt.PopupMenu implements SequenceGroup sg = ap.av.getSelectionGroup(); if (sg != null && sg.getSize() > 0) { - editGroupName.setLabel(MessageManager.formatMessage( - "label.name_param", new Object[] { sg.getName() })); + 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()); showColourText.setState(sg.getColourText()); showBoxes.setState(sg.getDisplayBoxes()); @@ -284,17 +305,18 @@ public class APopupMenu extends java.awt.PopupMenu implements seqMenu.setLabel(seq.getName()); if (seq == ap.av.getAlignment().getSeqrep()) { - makeReferenceSeq.setLabel(MessageManager - .getString("action.unmark_as_reference"));// Unmark - // representative"); + makeReferenceSeq.setLabel( + MessageManager.getString("action.unmark_as_reference"));// Unmark + // representative"); } else { - makeReferenceSeq.setLabel(MessageManager - .getString("action.set_as_reference")); // ); + makeReferenceSeq.setLabel( + MessageManager.getString("action.set_as_reference")); // ); } - repGroup.setLabel(MessageManager.formatMessage( - "label.represent_group_with", new Object[] { seq.getName() })); + repGroup.setLabel(MessageManager + .formatMessage("label.represent_group_with", new Object[] + { seq.getName() })); } else { @@ -329,20 +351,21 @@ public class APopupMenu extends java.awt.PopupMenu implements * * @param cs */ - protected void setSelectedColour(ColourSchemeI cs) + protected void setSelectedColour(ResidueShaderI cs) { - if (cs == null) + 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 (cs.getSchemeName().equals(item.getName())) + if (name.equals(item.getName())) { ((CheckboxMenuItem) item).setState(true); } @@ -360,7 +383,7 @@ public class APopupMenu extends java.awt.PopupMenu implements void addFeatureLinks(final SequenceI seq, List links) { Menu linkMenu = new Menu(MessageManager.getString("action.link")); - Map> linkset = new LinkedHashMap>(); + Map> linkset = new LinkedHashMap<>(); for (String link : links) { @@ -425,8 +448,9 @@ public class APopupMenu extends java.awt.PopupMenu implements /* * First for the currently selected sequence (if there is one): */ - final List selectedSequence = (seq == null ? Collections - . emptyList() : Arrays.asList(seq)); + final List selectedSequence = (seq == null + ? Collections. emptyList() + : Arrays.asList(seq)); buildAnnotationTypesMenus(seqShowAnnotationsMenu, seqHideAnnotationsMenu, selectedSequence); configureReferenceAnnotationsMenu(seqAddReferenceAnnotations, @@ -435,9 +459,9 @@ public class APopupMenu extends java.awt.PopupMenu implements /* * and repeat for the current selection group (if there is one): */ - final List selectedGroup = (ap.av.getSelectionGroup() == null ? Collections - . emptyList() : ap.av.getSelectionGroup() - .getSequences()); + final List selectedGroup = (ap.av.getSelectionGroup() == null + ? Collections. emptyList() + : ap.av.getSelectionGroup().getSequences()); buildAnnotationTypesMenus(groupShowAnnotationsMenu, groupHideAnnotationsMenu, selectedGroup); configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, @@ -461,11 +485,11 @@ 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. */ - SortedMap tipEntries = new TreeMap(); - final Map> candidates = new LinkedHashMap>(); + SortedMap tipEntries = new TreeMap<>(); + final Map> candidates = new LinkedHashMap<>(); AlignmentI al = this.ap.av.getAlignment(); - AlignmentUtils.findAddableReferenceAnnotations(forSequences, - tipEntries, candidates, al); + AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries, + candidates, al); if (!candidates.isEmpty()) { StringBuilder tooltip = new StringBuilder(64); @@ -565,7 +589,7 @@ public class APopupMenu extends java.awt.PopupMenu implements { BLOSUM62Colour_actionPerformed(); } - else if (source == PIDColour) + else if (evt.getSource() == PIDColour) { PIDColour_actionPerformed(); } @@ -730,9 +754,10 @@ public class APopupMenu extends java.awt.PopupMenu implements seq = sg.getSequenceAt(0); } - EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString( - sg.getStartRes(), sg.getEndRes() + 1), null, - "Edit Sequence ", null, + EditNameDialog dialog = new EditNameDialog( + seq.getSequenceAsString(sg.getStartRes(), + sg.getEndRes() + 1), + null, "Edit Sequence ", null, ap.alignFrame, "Edit Sequence", 500, 100, true); @@ -740,16 +765,16 @@ public class APopupMenu extends java.awt.PopupMenu implements { EditCommand editCommand = new EditCommand( MessageManager.getString("label.edit_sequences"), - Action.REPLACE, dialog.getName().replace(' ', - ap.av.getGapCharacter()), + Action.REPLACE, + dialog.getName().replace(' ', ap.av.getGapCharacter()), sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); ap.alignFrame.addHistoryItem(editCommand); - ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() - .getSequences()); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); } } } @@ -786,8 +811,8 @@ public class APopupMenu extends java.awt.PopupMenu implements ap.alignFrame.addHistoryItem(caseCommand); - ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() - .getSequences()); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); } } @@ -799,9 +824,9 @@ 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++) { @@ -809,26 +834,22 @@ 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, 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.av.setSearchResults(null); // clear highlighting + ap.repaint(); // draw new/amended features + } } } else @@ -844,15 +865,15 @@ public class APopupMenu extends java.awt.PopupMenu implements Frame frame = new Frame(); frame.add(cap); - JalviewLite.addFrame(frame, MessageManager.formatMessage( - "label.selection_output_command", - new Object[] { e.getActionCommand() }), 600, 500); + 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 - FileFormatI fileFormat = FileFormats.getInstance().forName( - e.getActionCommand()); + FileFormatI fileFormat = FileFormats.getInstance() + .forName(e.getActionCommand()); cap.setText(new AppletFormatAdapter().formatSequences(fileFormat, ap.av.getShowJVSuffix(), ap, true)); @@ -876,25 +897,26 @@ public class APopupMenu extends java.awt.PopupMenu implements StringBuilder contents = new StringBuilder(128); for (SequenceI seq : sequences) { - contents.append(MessageManager.formatMessage( - "label.annotation_for_displayid", - new Object[] { seq.getDisplayId(true) })); + contents.append(MessageManager + .formatMessage("label.annotation_for_displayid", new Object[] + { seq.getDisplayId(true) })); new SequenceAnnotationReport(null).createSequenceAnnotationReport( - contents, - seq, - true, - true, - (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr - .getMinMax() : null); + contents, seq, true, true, + (ap.seqPanel.seqCanvas.fr != null) + ? ap.seqPanel.seqCanvas.fr.getMinMax() + : null); contents.append("

"); } Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for " - + (sequences.length == 1 ? sequences[0].getDisplayId(true) - : "Selection"), 600, 500); - cap.setText(MessageManager.formatMessage("label.html_content", - new Object[] { contents.toString() })); + jalview.bin.JalviewLite.addFrame(frame, + "Sequence Details for " + (sequences.length == 1 + ? sequences[0].getDisplayId(true) + : "Selection"), + 600, 500); + cap.setText( + MessageManager.formatMessage("label.html_content", new Object[] + { contents.toString() })); } void editName() @@ -908,7 +930,7 @@ public class APopupMenu extends java.awt.PopupMenu implements { seq.setName(dialog.getName()); seq.setDescription(dialog.getDescription()); - ap.paintAlignment(false); + ap.paintAlignment(false, false); } } @@ -926,21 +948,22 @@ public class APopupMenu extends java.awt.PopupMenu implements } else { - new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null, - ap, DataSourceType.URL); + new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null, ap, + DataSourceType.URL); } } else { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, + ap.alignFrame); cap.setText(MessageManager.getString("label.paste_pdb_file")); cap.setPDBImport(seq); Frame frame = new Frame(); frame.add(cap); JalviewLite.addFrame(frame, MessageManager.formatMessage( - "label.paste_pdb_file_for_sequence", - new Object[] { seq.getName() }), 400, 300); + "label.paste_pdb_file_for_sequence", new Object[] + { seq.getName() }), 400, 300); } } @@ -950,12 +973,12 @@ public class APopupMenu extends java.awt.PopupMenu implements sequenceFeature.addActionListener(this); editGroupName.addActionListener(this); - unGroupMenuItem.setLabel(MessageManager - .getString("action.remove_group")); + unGroupMenuItem + .setLabel(MessageManager.getString("action.remove_group")); unGroupMenuItem.addActionListener(this); - createGroupMenuItem.setLabel(MessageManager - .getString("action.create_group")); + createGroupMenuItem + .setLabel(MessageManager.getString("action.create_group")); createGroupMenuItem.addActionListener(this); modifyPID.setEnabled(abovePIDColour.getState()); @@ -967,8 +990,8 @@ public class APopupMenu extends java.awt.PopupMenu implements sequenceName.addActionListener(this); sequenceDetails.addActionListener(this); selSeqDetails.addActionListener(this); - displayNonconserved.setLabel(MessageManager - .getString("label.show_non_conserved")); + displayNonconserved + .setLabel(MessageManager.getString("label.show_non_conserved")); displayNonconserved.setState(false); displayNonconserved.addItemListener(this); showText.setLabel(MessageManager.getString("action.text")); @@ -979,8 +1002,9 @@ public class APopupMenu extends java.awt.PopupMenu implements seqMenu.setLabel(MessageManager.getString("label.sequence")); pdb.setLabel(MessageManager.getString("label.view_pdb_structure")); hideSeqs.setLabel(MessageManager.getString("action.hide_sequences")); - repGroup.setLabel(MessageManager.formatMessage( - "label.represent_group_with", new Object[] { "" })); + repGroup.setLabel(MessageManager + .formatMessage("label.represent_group_with", new Object[] + { "" })); revealAll.setLabel(MessageManager.getString("action.reveal_all")); revealSeq.setLabel(MessageManager.getString("action.reveal_sequences")); menu1.setLabel(MessageManager.getString("label.group:")); @@ -1026,28 +1050,28 @@ public class APopupMenu extends java.awt.PopupMenu implements /* * setName allows setSelectedColour to do its thing */ - clustalColour.setLabel(MessageManager - .getString("label.colourScheme_clustal")); + clustalColour.setLabel( + MessageManager.getString("label.colourScheme_clustal")); clustalColour.setName(JalviewColourScheme.Clustal.toString()); clustalColour.addItemListener(this); - BLOSUM62Colour.setLabel(MessageManager - .getString("label.colourScheme_blosum62")); + BLOSUM62Colour.setLabel( + MessageManager.getString("label.colourScheme_blosum62")); BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString()); BLOSUM62Colour.addItemListener(this); - PIDColour.setLabel(MessageManager - .getString("label.colourScheme_%_identity")); + PIDColour.setLabel( + MessageManager.getString("label.colourScheme_%_identity")); PIDColour.setName(JalviewColourScheme.PID.toString()); PIDColour.addItemListener(this); - zappoColour.setLabel(MessageManager - .getString("label.colourScheme_zappo")); + zappoColour + .setLabel(MessageManager.getString("label.colourScheme_zappo")); zappoColour.setName(JalviewColourScheme.Zappo.toString()); zappoColour.addItemListener(this); - taylorColour.setLabel(MessageManager - .getString("label.colourScheme_taylor")); + taylorColour.setLabel( + MessageManager.getString("label.colourScheme_taylor")); taylorColour.setName(JalviewColourScheme.Taylor.toString()); taylorColour.addItemListener(this); - hydrophobicityColour.setLabel(MessageManager - .getString("label.colourScheme_hydrophobic")); + hydrophobicityColour.setLabel( + MessageManager.getString("label.colourScheme_hydrophobic")); hydrophobicityColour .setName(JalviewColourScheme.Hydrophobic.toString()); hydrophobicityColour.addItemListener(this); @@ -1059,36 +1083,36 @@ public class APopupMenu extends java.awt.PopupMenu implements .getString("label.colourScheme_strand_propensity")); strandColour.setName(JalviewColourScheme.Strand.toString()); strandColour.addItemListener(this); - turnColour.setLabel(MessageManager - .getString("label.colourScheme_turn_propensity")); + 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.setLabel( + MessageManager.getString("label.colourScheme_buried_index")); buriedColour.setName(JalviewColourScheme.Buried.toString()); buriedColour.addItemListener(this); - nucleotideColour.setLabel(MessageManager - .getString("label.colourScheme_nucleotide")); + 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 + .setName(JalviewColourScheme.PurinePyrimidine.toString()); purinePyrimidineColour.addItemListener(this); - userDefinedColour.setLabel(MessageManager - .getString("action.user_defined")); + userDefinedColour + .setLabel(MessageManager.getString("action.user_defined")); userDefinedColour.addActionListener(this); - abovePIDColour.setLabel(MessageManager - .getString("label.above_identity_threshold")); + abovePIDColour.setLabel( + MessageManager.getString("label.above_identity_threshold")); abovePIDColour.addItemListener(this); - modifyPID.setLabel(MessageManager - .getString("label.modify_identity_threshold")); + modifyPID.setLabel( + MessageManager.getString("label.modify_identity_threshold")); modifyPID.addActionListener(this); - conservationColour.setLabel(MessageManager - .getString("action.by_conservation")); + conservationColour + .setLabel(MessageManager.getString("action.by_conservation")); conservationColour.addItemListener(this); modifyConservation.setLabel(MessageManager .getString("label.modify_conservation_threshold")); @@ -1139,67 +1163,68 @@ public class APopupMenu extends java.awt.PopupMenu implements void refresh() { - ap.paintAlignment(true); + ap.paintAlignment(true, true); } 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 PurinePyrimidineColourScheme(); + getGroup().cs = new ResidueShader(new PurinePyrimidineColourScheme()); refresh(); } @@ -1213,10 +1238,11 @@ public class APopupMenu extends java.awt.PopupMenu implements if (abovePIDColour.getState()) { - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av - .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); - int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() - .getName()); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), 0, + ap.av.getAlignment().getWidth())); + int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, + getGroup().getName()); sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus()); @@ -1241,9 +1267,10 @@ public class APopupMenu extends java.awt.PopupMenu implements protected void PIDColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av - .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); + sg.cs = new ResidueShader(new PIDColourScheme()); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), 0, + ap.av.getAlignment().getWidth())); refresh(); } @@ -1251,10 +1278,11 @@ 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())); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), 0, + ap.av.getAlignment().getWidth())); refresh(); } @@ -1275,10 +1303,11 @@ public class APopupMenu extends java.awt.PopupMenu implements if (conservationColour.getState()) { - sg.cs.setConservation(Conservation.calculateConservation("Group", sg - .getSequences(ap.av.getHiddenRepSequences()), 0, ap.av - .getAlignment().getWidth(), false, ap.av.getConsPercGaps(), - false)); + Conservation conservation = Conservation.calculateConservation( + "Group", sg.getSequences(ap.av.getHiddenRepSequences()), 0, + ap.av.getAlignment().getWidth(), false, + ap.av.getConsPercGaps(), false); + sg.getGroupColourScheme().setConservation(conservation); SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); SliderPanel.showConservationSlider(); } @@ -1310,7 +1339,7 @@ public class APopupMenu extends java.awt.PopupMenu implements SequenceGroup sg = ap.av.getSelectionGroup(); ap.av.getAlignment().deleteGroup(sg); ap.av.setSelectionGroup(null); - ap.paintAlignment(true); + ap.paintAlignment(true, true); } void createGroupMenuItem_actionPerformed() @@ -1392,9 +1421,11 @@ public class APopupMenu extends java.awt.PopupMenu implements showMenu.removeAll(); hideMenu.removeAll(); - final List all = Arrays.asList(new String[] { MessageManager - .getString("label.all") }); - addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true); + final List all = Arrays + .asList(new String[] + { MessageManager.getString("label.all") }); + addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, + true); addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true, false); showMenu.addSeparator(); @@ -1409,8 +1440,8 @@ public class APopupMenu extends java.awt.PopupMenu implements * the insertion order, which is the order of the annotations on the * alignment. */ - Map>> shownTypes = new LinkedHashMap>>(); - Map>> hiddenTypes = new LinkedHashMap>>(); + Map>> shownTypes = new LinkedHashMap<>(); + Map>> hiddenTypes = new LinkedHashMap<>(); AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes, AlignmentAnnotationUtils.asList(annotations), forSequences);