X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=b860a36a416452c9fbad13661f93327dd8af876f;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=30f2e7f195ddee7e40f414454f385185cc15062b;hpb=c86442e455c858f4a092fbb2e9394faa3e161a89;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 30f2e7f..b860a36 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -20,30 +20,55 @@ */ package jalview.appletgui; +import java.awt.CheckboxMenuItem; +import java.awt.Frame; +import java.awt.Menu; +import java.awt.MenuItem; +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; + 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.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.ResidueProperties; +import jalview.schemes.PurinePyrimidineColourScheme; import jalview.schemes.StrandColourScheme; import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; @@ -51,58 +76,50 @@ import jalview.schemes.ZappoColourScheme; import jalview.util.MessageManager; import jalview.util.UrlLink; -import java.awt.CheckboxMenuItem; -import java.awt.Frame; -import java.awt.Menu; -import java.awt.MenuItem; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.util.Arrays; -import java.util.Collections; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Map; -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 { - private static final String ALL_ANNOTATIONS = "All"; - Menu groupMenu = new Menu(); 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; @@ -110,8 +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(); @@ -181,7 +196,7 @@ public class APopupMenu extends java.awt.PopupMenu implements MessageManager.getString("label.sequence_details")); MenuItem makeReferenceSeq = new MenuItem(); - + SequenceI seq; MenuItem revealAll = new MenuItem(); @@ -196,7 +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 @@ -216,10 +231,9 @@ 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); @@ -230,8 +244,26 @@ 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[] + 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()); @@ -246,8 +278,15 @@ 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 { @@ -257,140 +296,26 @@ 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.getDBRef(), 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) { 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[] + repGroup.setLabel(MessageManager + .formatMessage("label.represent_group_with", new Object[] { seq.getName() })); } else @@ -420,6 +345,101 @@ 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 + * @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. */ @@ -428,8 +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, @@ -438,9 +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, @@ -464,11 +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. */ - Map 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); @@ -540,6 +561,7 @@ public class APopupMenu extends java.awt.PopupMenu implements MenuItem item = new MenuItem(label); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ap.alignFrame.showURL(url, target); @@ -548,36 +570,28 @@ 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(); } - } - - 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) { @@ -607,31 +621,59 @@ 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(); } - else if (source == conservationMenuItem) + } + + /** + * 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) { unGroupMenuItem_actionPerformed(); @@ -712,25 +754,27 @@ 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); if (dialog.accept) { - EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"), - Action.REPLACE, dialog.getName().replace(' ', - ap.av.getGapCharacter()), + EditCommand editCommand = new EditCommand( + MessageManager.getString("label.edit_sequences"), + 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()); } } } @@ -767,8 +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()); } } @@ -780,9 +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++) { @@ -790,25 +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 @@ -824,15 +865,17 @@ public class APopupMenu extends java.awt.PopupMenu implements Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( - "label.selection_output_command", new Object[] + 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)); } @@ -843,8 +886,7 @@ public class APopupMenu extends java.awt.PopupMenu implements protected void showSequenceDetails() { - createSequenceDetailsReport(new SequenceI[] - { seq }); + createSequenceDetailsReport(new SequenceI[] { seq }); } public void createSequenceDetailsReport(SequenceI[] sequences) @@ -852,30 +894,25 @@ 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( - "label.annotation_for_displayid", new Object[] + contents.append(MessageManager + .formatMessage("label.annotation_for_displayid", new Object[] { seq.getDisplayId(true) })); - new SequenceAnnotationReport(null) - .createSequenceAnnotationReport( - contents, - seq, - true, - true, - false, - (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax() - : null); + new SequenceAnnotationReport(false).createSequenceAnnotationReport( + contents, seq, true, true, ap.seqPanel.seqCanvas.fr); 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[] + 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() })); } @@ -890,36 +927,38 @@ public class APopupMenu extends java.awt.PopupMenu implements { seq.setName(dialog.getName()); seq.setDescription(dialog.getDescription()); - ap.paintAlignment(false); + ap.paintAlignment(false, false); } } 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); + new mc_view.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); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( + JalviewLite.addFrame(frame, MessageManager.formatMessage( "label.paste_pdb_file_for_sequence", new Object[] { seq.getName() }), 400, 300); } @@ -931,19 +970,16 @@ 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); - 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); @@ -951,8 +987,8 @@ public class APopupMenu extends java.awt.PopupMenu implements sequenceName.addActionListener(this); sequenceDetails.addActionListener(this); selSeqDetails.addActionListener(this); - displayNonconserved.setLabel(MessageManager - .getString("label.show_non_conversed")); + displayNonconserved + .setLabel(MessageManager.getString("label.show_non_conserved")); displayNonconserved.setState(false); displayNonconserved.addItemListener(this); showText.setLabel(MessageManager.getString("action.text")); @@ -963,12 +999,12 @@ 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") + ":"); + menu1.setLabel(MessageManager.getString("label.group:")); add(groupMenu); this.add(seqMenu); this.add(hideSeqs); @@ -985,7 +1021,7 @@ 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); @@ -996,41 +1032,91 @@ 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); - - noColourmenuItem.setLabel(MessageManager.getString("label.none")); - noColourmenuItem.addActionListener(this); - - 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); - hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity")); - hydrophobicityColour.addActionListener(this); - helixColour.setLabel(MessageManager.getString("label.helix_propensity")); - helixColour.addActionListener(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")); - - userDefinedColour.setLabel(MessageManager.getString("action.user_defined")); + colourMenu.add(modifyPID); + + noColour.setLabel(MessageManager.getString("label.none")); + noColour.addItemListener(this); + + /* + * setName allows setSelectedColour to do its thing + */ + clustalColour.setLabel( + MessageManager.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.colourScheme_hydrophobic")); + hydrophobicityColour + .setName(JalviewColourScheme.Hydrophobic.toString()); + hydrophobicityColour.addItemListener(this); + helixColour.setLabel( + MessageManager.getString("label.colourScheme_helixpropensity")); + helixColour.setName(JalviewColourScheme.Helix.toString()); + helixColour.addItemListener(this); + strandColour.setLabel(MessageManager + .getString("label.colourScheme_strandpropensity")); + strandColour.setName(JalviewColourScheme.Strand.toString()); + strandColour.addItemListener(this); + turnColour.setLabel( + MessageManager.getString("label.colourScheme_turnpropensity")); + turnColour.setName(JalviewColourScheme.Turn.toString()); + turnColour.addItemListener(this); + buriedColour.setLabel( + MessageManager.getString("label.colourScheme_buriedindex")); + 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); @@ -1074,61 +1160,68 @@ 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 ResidueShader(new PurinePyrimidineColourScheme()); refresh(); } @@ -1142,10 +1235,11 @@ 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()); @@ -1155,11 +1249,11 @@ 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() @@ -1170,9 +1264,10 @@ 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(); } @@ -1180,10 +1275,11 @@ 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(); } @@ -1202,22 +1298,23 @@ public class APopupMenu extends java.awt.PopupMenu implements return; } - if (conservationMenuItem.getState()) + if (conservationColour.getState()) { - - sg.cs.setConservation(Conservation.calculateConservation("Group", - ResidueProperties.propHash, 3, 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(); } else // remove ConservationColouring { + SliderPanel.hideConservationSlider(); sg.cs.setConservation(null); } - + modifyConservation.setEnabled(conservationColour.getState()); refresh(); } @@ -1239,7 +1336,7 @@ 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() @@ -1259,6 +1356,7 @@ public class APopupMenu extends java.awt.PopupMenu implements getGroup().setDisplayText(showText.getState()); refresh(); } + public void makeReferenceSeq_actionPerformed() { if (!ap.av.getAlignment().hasSeqrep()) @@ -1296,36 +1394,7 @@ public class APopupMenu extends java.awt.PopupMenu implements void hideSequences(boolean representGroup) { - SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg == null || sg.getSize() < 1) - { - ap.av.hideSequence(new SequenceI[] - { seq }); - return; - } - - ap.av.setSelectionGroup(null); - - if (representGroup) - { - ap.av.hideRepSequences(seq, sg); - - return; - } - - int gsize = sg.getSize(); - SequenceI[] hseqs; - - hseqs = new SequenceI[gsize]; - - int index = 0; - for (int i = 0; i < gsize; i++) - { - hseqs[index++] = sg.getSequenceAt(i); - } - - ap.av.hideSequence(hseqs); - ap.av.sendSelection(); + ap.av.hideSequences(seq, representGroup); } /** @@ -1348,47 +1417,48 @@ public class APopupMenu extends java.awt.PopupMenu implements { showMenu.removeAll(); hideMenu.removeAll(); - - final List all = Arrays.asList(ALL_ANNOTATIONS); - 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(); hideMenu.addSeparator(); - + final AlignmentAnnotation[] annotations = ap.getAlignment() .getAlignmentAnnotation(); - + /* * Find shown/hidden annotations types, distinguished by source (calcId), * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in * the insertion order, which is the order of the annotations on the * alignment. */ - Map>> shownTypes = new LinkedHashMap>>(); - Map>> hiddenTypes = new LinkedHashMap>>(); - AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, - hiddenTypes, - AlignmentAnnotationUtils.asList(annotations), - forSequences); - + Map>> shownTypes = new LinkedHashMap<>(); + Map>> hiddenTypes = new LinkedHashMap<>(); + AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes, + AlignmentAnnotationUtils.asList(annotations), forSequences); + for (String calcId : hiddenTypes.keySet()) { for (List type : hiddenTypes.get(calcId)) { - addAnnotationTypeToShowHide(showMenu, forSequences, - calcId, type, false, true); + addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type, + false, true); } } // grey out 'show annotations' if none are hidden showMenu.setEnabled(!hiddenTypes.isEmpty()); - + for (String calcId : shownTypes.keySet()) { for (List type : shownTypes.get(calcId)) { - addAnnotationTypeToShowHide(hideMenu, forSequences, - calcId, type, false, false); + addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type, + false, false); } } // grey out 'hide annotations' if none are shown @@ -1425,8 +1495,8 @@ public class APopupMenu extends java.awt.PopupMenu implements @Override public void actionPerformed(ActionEvent e) { - AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types, - forSequences, allTypes, actionIsShow); + AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), + types, forSequences, allTypes, actionIsShow); refresh(); } });