X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=897c78c5499e8945fb6d29234c23b288e2180137;hb=5abd8cc59e692171861a337e189faaa26dcfff16;hp=c30fdad070889b67bfac15c76cf2ca41a5e36b6a;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index c30fdad..897c78c 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -24,25 +24,31 @@ import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentAnnotationUtils; import jalview.analysis.AlignmentUtils; import jalview.analysis.Conservation; +import jalview.bin.JalviewLite; import jalview.commands.ChangeCaseCommand; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; -import jalview.datamodel.DBRefEntry; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.SequenceAnnotationReport; 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; import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; +import jalview.schemes.PurinePyrimidineColourScheme; import jalview.schemes.StrandColourScheme; import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; @@ -59,10 +65,12 @@ import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; 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; @@ -73,33 +81,43 @@ 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(); + + MenuItem modifyConservation = new MenuItem(); - protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + MenuItem noColourmenuItem = new MenuItem(); final AlignmentPanel ap; @@ -107,8 +125,6 @@ public class APopupMenu extends java.awt.PopupMenu implements MenuItem createGroupMenuItem = new MenuItem(); - MenuItem nucleotideMenuItem = new MenuItem(); - Menu colourMenu = new Menu(); CheckboxMenuItem showBoxes = new CheckboxMenuItem(); @@ -213,10 +229,9 @@ 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 : FileFormats.getInstance().getWritableFormats(true)) { - MenuItem item = new MenuItem( - jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); + MenuItem item = new MenuItem(ff); item.addActionListener(this); outputmenu.add(item); @@ -242,8 +257,15 @@ 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()); + modifyPID.setEnabled(abovePIDColour.getState()); + modifyConservation.setEnabled(conservationColour.getState()); + } } - + setSelectedColour(sg.cs); } else { @@ -253,122 +275,9 @@ public class APopupMenu extends java.awt.PopupMenu implements if (links != null && links.size() > 0) { - Menu linkMenu = new Menu(MessageManager.getString("action.link")); - for (int i = 0; i < links.size(); i++) - { - String link = links.elementAt(i); - UrlLink urlLink = new UrlLink(link); - if (!urlLink.isValid()) - { - System.err.println(urlLink.getInvalidMessage()); - continue; - } - final String target = urlLink.getTarget(); // link.substring(0, - // link.indexOf("|")); - final String label = urlLink.getLabel(); - if (seq != null && urlLink.isDynamic()) - { - - // collect matching db-refs - DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs( - seq.getDBRefs(), new String[] { target }); - // collect id string too - String id = seq.getName(); - String descr = seq.getDescription(); - if (descr != null && descr.length() < 1) - { - descr = null; - } - if (dbr != null) - { - for (int r = 0; r < dbr.length; r++) - { - if (id != null && dbr[r].getAccessionId().equals(id)) - { - // suppress duplicate link creation for the bare sequence ID - // string with this link - id = null; - } - // create Bare ID link for this RUL - String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), - true); - if (urls != null) - { - for (int u = 0; u < urls.length; u += 2) - { - addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]); - } - } - } - } - if (id != null) - { - // create Bare ID link for this RUL - String[] urls = urlLink.makeUrls(id, true); - if (urls != null) - { - for (int u = 0; u < urls.length; u += 2) - { - addshowLink(linkMenu, label, urls[u + 1]); - } - } - // addshowLink(linkMenu, target, url_pref + id + url_suff); - } - // Now construct URLs from description but only try to do it for regex - // URL links - if (descr != null && urlLink.getRegexReplace() != null) - { - // create link for this URL from description only if regex matches - String[] urls = urlLink.makeUrls(descr, true); - if (urls != null) - { - for (int u = 0; u < urls.length; u += 2) - { - addshowLink(linkMenu, label, urls[u + 1]); - } - } - } - } - else - { - addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1)); - } - /* - * final String url; - * - * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID - * string and any matching database reference accessions String url_pref - * = link.substring(link.indexOf("|") + 1, - * link.indexOf("$SEQUENCE_ID$")); - * - * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13); - * // collect matching db-refs DBRefEntry[] dbr = - * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new - * String[]{target}); // collect id string too String id = - * seq.getName(); if (id.indexOf("|") > -1) { id = - * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int - * r=0;r 0) - { - if (seq != null) - { - seqMenu.add(linkMenu); - } - else - { - add(linkMenu); - } - } + addFeatureLinks(seq, links); } + // TODO: add group link menu entry here if (seq != null) { @@ -414,6 +323,100 @@ 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(ColourSchemeI cs) + { + if (cs == null) + { + noColour.setState(true); + } + else + { + for (int i = 0; i < colourMenu.getItemCount(); i++) + { + MenuItem item = colourMenu.getItem(i); + if (item instanceof CheckboxMenuItem) + { + if (cs.getSchemeName().equals(item.getName())) + { + ((CheckboxMenuItem) item).setState(true); + } + } + } + } + } + + /** + * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided. + * + * @param seq + * @param links + */ + void addFeatureLinks(final SequenceI seq, List links) + { + Menu linkMenu = new Menu(MessageManager.getString("action.link")); + Map> linkset = new LinkedHashMap>(); + + for (String link : links) + { + UrlLink urlLink = null; + try + { + urlLink = new UrlLink(link); + } catch (Exception foo) + { + System.err.println("Exception for URLLink '" + link + "': " + + foo.getMessage()); + continue; + } + + if (!urlLink.isValid()) + { + System.err.println(urlLink.getInvalidMessage()); + continue; + } + + urlLink.createLinksFromSeq(seq, linkset); + } + + addshowLinks(linkMenu, linkset.values()); + + // disable link menu if there are no valid entries + if (linkMenu.getItemCount() > 0) + { + linkMenu.setEnabled(true); + } + else + { + linkMenu.setEnabled(false); + } + + if (seq != null) + { + seqMenu.add(linkMenu); + } + else + { + add(linkMenu); + } + + } + + private void addshowLinks(Menu linkMenu, Collection> linkset) + { + for (List linkstrset : linkset) + { + // split linkstr into label and url + addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3)); + } + } + + /** * Build menus for annotation types that may be shown or hidden, and for * 'reference annotations' that may be added to the alignment. */ @@ -458,7 +461,7 @@ 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, @@ -543,38 +546,28 @@ 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 (source == PIDColour) { - clustalColour_actionPerformed(); + PIDColour_actionPerformed(); } else if (source == zappoColour) { @@ -604,31 +597,59 @@ 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 == conservationMenuItem) + else if (source == modifyConservation) { conservationMenuItem_itemStateChanged(); } + else if (source == modifyPID) + { + abovePIDColour_itemStateChanged(); + } else if (source == unGroupMenuItem) { unGroupMenuItem_actionPerformed(); @@ -823,15 +844,17 @@ 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)); + FileFormatI fileFormat = FileFormats.getInstance().forName( + e.getActionCommand()); + cap.setText(new AppletFormatAdapter().formatSequences(fileFormat, + ap.av.getShowJVSuffix(), ap, true)); } @@ -850,7 +873,7 @@ 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( @@ -861,7 +884,6 @@ 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("

"); @@ -892,19 +914,20 @@ 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); + new AppletJmol(entry, new SequenceI[] { seq }, null, ap, + DataSourceType.URL); } else { new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null, - ap, AppletFormatAdapter.URL); + ap, DataSourceType.URL); } } @@ -915,7 +938,7 @@ 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); } @@ -935,11 +958,8 @@ 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); @@ -948,7 +968,7 @@ 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")); @@ -980,7 +1000,7 @@ 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); @@ -991,48 +1011,91 @@ 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); @@ -1134,6 +1197,12 @@ public class APopupMenu extends java.awt.PopupMenu implements refresh(); } + public void purinePyrimidineColour_actionPerformed() + { + getGroup().cs = new PurinePyrimidineColourScheme(); + refresh(); + } + protected void abovePIDColour_itemStateChanged() { SequenceGroup sg = getGroup(); @@ -1157,11 +1226,11 @@ 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() @@ -1204,22 +1273,22 @@ public class APopupMenu extends java.awt.PopupMenu implements return; } - if (conservationMenuItem.getState()) + if (conservationColour.getState()) { - - sg.cs.setConservation(Conservation.calculateConservation("Group", 3, - sg.getSequences(ap.av.getHiddenRepSequences()), 0, ap.av - .getAlignment().getWidth(), false, ap.av - .getConsPercGaps(), false)); + sg.cs.setConservation(Conservation.calculateConservation("Group", sg + .getSequences(ap.av.getHiddenRepSequences()), 0, ap.av + .getAlignment().getWidth(), false, ap.av.getConsPercGaps(), + false)); SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); SliderPanel.showConservationSlider(); } else // remove ConservationColouring { + SliderPanel.hideConservationSlider(); sg.cs.setConservation(null); } - + modifyConservation.setEnabled(conservationColour.getState()); refresh(); }