X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=aa3cad49ba9e45d6976f869e4e11d6d399854603;hb=bb90751010ab798f54dabddb8cfb6f51e847072c;hp=7d238a0601827b8dbb15d77ab1894228f91ed987;hpb=3f3c6c3a2b99fee2e726d18302af1b3320331212;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 7d238a0..aa3cad4 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -24,6 +24,7 @@ import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentAnnotationUtils; import jalview.analysis.AlignmentUtils; import jalview.analysis.Conservation; +import jalview.bin.Cache; import jalview.commands.ChangeCaseCommand; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; @@ -48,7 +49,6 @@ import jalview.schemes.HydrophobicColourScheme; import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; -import jalview.schemes.ResidueProperties; import jalview.schemes.StrandColourScheme; import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; @@ -63,6 +63,7 @@ import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.Arrays; +import java.util.Collection; import java.util.Collections; import java.util.Hashtable; import java.util.LinkedHashMap; @@ -88,10 +89,6 @@ import javax.swing.JRadioButtonMenuItem; */ public class PopupMenu extends JPopupMenu { - private static final String ALL_ANNOTATIONS = "All"; - - private static final String COMMA = ","; - JMenu groupMenu = new JMenu(); JMenuItem groupName = new JMenuItem(); @@ -137,7 +134,7 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceDetails = new JMenuItem(); JMenuItem sequenceSelDetails = new JMenuItem(); - + JMenuItem makeReferenceSeq = new JMenuItem(); JMenuItem chooseAnnotations = new JMenuItem(); @@ -176,12 +173,6 @@ public class PopupMenu extends JPopupMenu JMenu pdbMenu = new JMenu(); - JMenuItem pdbFromFile = new JMenuItem(); - - JMenuItem enterPDB = new JMenuItem(); - - JMenuItem discoverPDB = new JMenuItem(); - JMenu outputMenu = new JMenu(); JMenu seqShowAnnotationsMenu = new JMenu(); @@ -204,7 +195,7 @@ public class PopupMenu extends JPopupMenu JMenu jMenu1 = new JMenu(); - JMenuItem proteinStructureMenu = new JMenuItem(); + JMenuItem pdbStructureDialog = new JMenuItem(); JMenu rnaStructureMenu = new JMenu(); @@ -222,7 +213,7 @@ public class PopupMenu extends JPopupMenu * @param seq * DOCUMENT ME! */ - public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links) + public PopupMenu(final AlignmentPanel ap, Sequence seq, List links) { this(ap, seq, links, null); } @@ -235,7 +226,7 @@ public class PopupMenu extends JPopupMenu * @param groupLinks */ public PopupMenu(final AlignmentPanel ap, final SequenceI seq, - Vector links, Vector groupLinks) + List links, List groupLinks) { // ///////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -317,75 +308,86 @@ public class PopupMenu extends JPopupMenu sequenceMenu.setText(sequence.getName()); if (seq == ap.av.getAlignment().getSeqrep()) { - makeReferenceSeq.setText("Unmark representative"); - } else { - makeReferenceSeq.setText("Mark as representative"); + makeReferenceSeq.setText(MessageManager + .getString("action.unmark_as_reference")); + } + else + { + makeReferenceSeq.setText(MessageManager + .getString("action.set_as_reference")); } - if (ap.av.getAlignment().isNucleotide() == false) + if (!ap.av.getAlignment().isNucleotide()) { remove(rnaStructureMenu); } - - if (ap.av.getAlignment().isNucleotide() == true) + else { - AlignmentAnnotation[] aa = ap.av.getAlignment() + int origCount = rnaStructureMenu.getItemCount(); + /* + * add menu items to 2D-render any alignment or sequence secondary + * structure annotation + */ + AlignmentAnnotation[] aas = ap.av.getAlignment() .getAlignmentAnnotation(); - for (int i = 0; aa != null && i < aa.length; i++) + if (aas != null) { - if (aa[i].isValidStruc() && aa[i].sequenceRef == null) + for (final AlignmentAnnotation aa : aas) { - final String rnastruc = aa[i].getRNAStruc(); - final String structureLine = aa[i].label + " (alignment)"; - menuItem = new JMenuItem(); - menuItem.setText(MessageManager.formatMessage( - "label.2d_rna_structure_line", new Object[] - { structureLine })); - menuItem.addActionListener(new java.awt.event.ActionListener() + if (aa.isValidStruc() && aa.sequenceRef == null) { - @Override - public void actionPerformed(ActionEvent e) + /* + * valid alignment RNA secondary structure annotation + */ + menuItem = new JMenuItem(); + menuItem.setText(MessageManager.formatMessage( + "label.2d_rna_structure_line", + new Object[] { aa.label })); + menuItem.addActionListener(new java.awt.event.ActionListener() { - new AppVarna(structureLine, seq, seq.getSequenceAsString(), - rnastruc, seq.getName(), ap); - System.out.println("end"); - } - }); - rnaStructureMenu.add(menuItem); + @Override + public void actionPerformed(ActionEvent e) + { + new AppVarna(seq, aa, ap); + } + }); + rnaStructureMenu.add(menuItem); + } } } - if (seq.getAnnotation() != null) { - AlignmentAnnotation seqAnno[] = seq.getAnnotation(); - for (int i = 0; i < seqAnno.length; i++) + AlignmentAnnotation seqAnns[] = seq.getAnnotation(); + for (final AlignmentAnnotation aa : seqAnns) { - if (seqAnno[i].isValidStruc()) + if (aa.isValidStruc()) { - final String rnastruc = seqAnno[i].getRNAStruc(); - + /* + * valid sequence RNA secondary structure annotation + */ // TODO: make rnastrucF a bit more nice menuItem = new JMenuItem(); menuItem.setText(MessageManager.formatMessage( - "label.2d_rna_sequence_name", new Object[] - { seq.getName() })); + "label.2d_rna_sequence_name", + new Object[] { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { // TODO: VARNA does'nt print gaps in the sequence - - new AppVarna(seq.getName() + " structure", seq, seq - .getSequenceAsString(), rnastruc, seq.getName(), - ap); + new AppVarna(seq, aa, ap); } }); rnaStructureMenu.add(menuItem); } } } + if (rnaStructureMenu.getItemCount() == origCount) + { + remove(rnaStructureMenu); + } } menuItem = new JMenuItem( @@ -404,8 +406,8 @@ public class PopupMenu extends JPopupMenu && ap.av.getSelectionGroup().getSize() > 1) { menuItem = new JMenuItem(MessageManager.formatMessage( - "label.represent_group_with", new Object[] - { seq.getName() })); + "label.represent_group_with", + new Object[] { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { @Override @@ -472,9 +474,6 @@ public class PopupMenu extends JPopupMenu if (sg != null && sg.getSize() > 0) { - groupName.setText(MessageManager.formatMessage("label.name_param", - new Object[] - { sg.getName() })); groupName.setText(MessageManager .getString("label.edit_name_and_description_current_group")); @@ -554,7 +553,7 @@ public class PopupMenu extends JPopupMenu SequenceI sqass = null; for (SequenceI sq : ap.av.getSequenceSelection()) { - Vector pes = sq.getDatasetSequence().getPDBId(); + Vector pes = sq.getDatasetSequence().getAllPDBEntries(); if (pes != null && pes.size() > 0) { reppdb.put(pes.get(0).getId(), pes.get(0)); @@ -598,133 +597,62 @@ public class PopupMenu extends JPopupMenu if (seq == null) { sequenceMenu.setVisible(false); - proteinStructureMenu.setVisible(false); + pdbStructureDialog.setVisible(false); rnaStructureMenu.setVisible(false); } if (links != null && links.size() > 0) { + addFeatureLinks(seq, links); + } + } - JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); - Vector linkset = new Vector(); - for (int i = 0; i < links.size(); i++) - { - String link = links.elementAt(i).toString(); - UrlLink urlLink = null; - try - { - urlLink = new UrlLink(link); - } catch (Exception foo) - { - jalview.bin.Cache.log.error("Exception for URLLink '" + link - + "'", foo); - continue; - } - ; - if (!urlLink.isValid()) - { - jalview.bin.Cache.log.error(urlLink.getInvalidMessage()); - continue; - } - final String label = urlLink.getLabel(); - if (seq != null && urlLink.isDynamic()) - { - - // collect matching db-refs - DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs( - seq.getDBRef(), new String[] - { urlLink.getTarget() }); - // collect id string too - String id = seq.getName(); - String descr = seq.getDescription(); - if (descr != null && descr.length() < 1) - { - descr = null; - } + /** + * 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) + { + JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); + Map linkset = new LinkedHashMap(); - 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) - { - if (!linkset.contains(urls[u] + "|" + urls[u + 1])) - { - linkset.addElement(urls[u] + "|" + urls[u + 1]); - 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) - { - if (!linkset.contains(urls[u] + "|" + urls[u + 1])) - { - linkset.addElement(urls[u] + "|" + urls[u + 1]); - addshowLink(linkMenu, label, urls[u + 1]); - } - } - } - } - // Create urls from description but only for URL links which are regex - // links - if (descr != null && urlLink.getRegexReplace() != null) - { - // create link for this URL from description where regex matches - String[] urls = urlLink.makeUrls(descr, true); - if (urls != null) - { - for (int u = 0; u < urls.length; u += 2) - { - if (!linkset.contains(urls[u] + "|" + urls[u + 1])) - { - linkset.addElement(urls[u] + "|" + urls[u + 1]); - addshowLink(linkMenu, label, urls[u + 1]); - } - } - } - } - } - else - { - if (!linkset.contains(label + "|" + urlLink.getUrl_prefix())) - { - linkset.addElement(label + "|" + urlLink.getUrl_prefix()); - // Add a non-dynamic link - addshowLink(linkMenu, label, urlLink.getUrl_prefix()); - } - } - } - if (sequence != null) + for (String link : links) + { + UrlLink urlLink = null; + try + { + urlLink = new UrlLink(link); + } catch (Exception foo) { - sequenceMenu.add(linkMenu); + Cache.log.error("Exception for URLLink '" + link + "'", foo); + continue; } - else + + if (!urlLink.isValid()) { - add(linkMenu); + Cache.log.error(urlLink.getInvalidMessage()); + continue; } + + urlLink.createLinksFromSeq(seq, linkset); + } + + addshowLinks(linkMenu, linkset.values()); + + if (sequence != null) + { + sequenceMenu.add(linkMenu); + } + else + { + add(linkMenu); } } + + /** * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus. * "All" is added first, followed by a separator. Then add any annotation @@ -746,7 +674,8 @@ public class PopupMenu extends JPopupMenu showMenu.removeAll(); hideMenu.removeAll(); - final List all = Arrays.asList(ALL_ANNOTATIONS); + final List all = Arrays.asList(new String[] { MessageManager + .getString("label.all") }); addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true); addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true, false); @@ -764,17 +693,15 @@ public class PopupMenu extends JPopupMenu */ Map>> shownTypes = new LinkedHashMap>>(); Map>> hiddenTypes = new LinkedHashMap>>(); - AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, - hiddenTypes, - AlignmentAnnotationUtils.asList(annotations), - forSequences); + 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 @@ -784,8 +711,8 @@ public class PopupMenu extends JPopupMenu { 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 @@ -846,15 +773,15 @@ public class PopupMenu extends JPopupMenu @Override public void actionPerformed(ActionEvent e) { - AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types, - forSequences, allTypes, actionIsShow); + AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), + types, forSequences, allTypes, actionIsShow); refresh(); } }); showOrHideMenu.add(item); } - private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks) + private void buildGroupURLMenu(SequenceGroup sg, List groupLinks) { // TODO: usability: thread off the generation of group url content so root @@ -863,19 +790,15 @@ public class PopupMenu extends JPopupMenu // ID/regex match URLs groupLinksMenu = new JMenu( MessageManager.getString("action.group_link")); - JMenu[] linkMenus = new JMenu[] - { null, new JMenu(MessageManager.getString("action.ids")), + // three types of url that might be created. + JMenu[] linkMenus = new JMenu[] { null, + new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")), - new JMenu(MessageManager.getString("action.ids_sequences")) }; // three - // types - // of url - // that - // might - // be - // created. + new JMenu(MessageManager.getString("action.ids_sequences")) }; + SequenceI[] seqs = ap.av.getSelectionAsNewSequence(); String[][] idandseqs = GroupUrlLink.formStrings(seqs); - Hashtable commonDbrefs = new Hashtable(); + Hashtable commonDbrefs = new Hashtable(); for (int sq = 0; sq < seqs.length; sq++) { @@ -889,18 +812,17 @@ public class PopupMenu extends JPopupMenu { sqi = sqi.getDatasetSequence(); } - DBRefEntry[] dbr = sqi.getDBRef(); + DBRefEntry[] dbr = sqi.getDBRefs(); if (dbr != null && dbr.length > 0) { for (int d = 0; d < dbr.length; d++) { String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(); - Object[] sarray = (Object[]) commonDbrefs.get(src); + Object[] sarray = commonDbrefs.get(src); if (sarray == null) { sarray = new Object[2]; - sarray[0] = new int[] - { 0 }; + sarray[0] = new int[] { 0 }; sarray[1] = new String[seqs.length]; commonDbrefs.put(src, sarray); @@ -921,30 +843,28 @@ public class PopupMenu extends JPopupMenu // now create group links for all distinct ID/sequence sets. boolean addMenu = false; // indicates if there are any group links to give // to user - for (int i = 0; i < groupLinks.size(); i++) + for (String link : groupLinks) { - String link = groupLinks.elementAt(i).toString(); GroupUrlLink urlLink = null; try { urlLink = new GroupUrlLink(link); } catch (Exception foo) { - jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link - + "'", foo); + Cache.log.error("Exception for GroupURLLink '" + link + "'", foo); continue; } ; if (!urlLink.isValid()) { - jalview.bin.Cache.log.error(urlLink.getInvalidMessage()); + Cache.log.error(urlLink.getInvalidMessage()); continue; } final String label = urlLink.getLabel(); boolean usingNames = false; // Now see which parts of the group apply for this URL String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget()); - Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase()); + Object[] idset = commonDbrefs.get(ltarget.toUpperCase()); String[] seqstr, ids; // input to makeUrl if (idset != null) { @@ -1007,6 +927,15 @@ public class PopupMenu extends JPopupMenu } } + private void addshowLinks(JMenu linkMenu, Collection linkset) + { + for (String[] linkstrset : linkset) + { + // split linkstr into label and url + addshowLink(linkMenu, linkstrset[1], linkstrset[3]); + } + } + /** * add a show URL menu item to the given linkMenu * @@ -1020,8 +949,7 @@ public class PopupMenu extends JPopupMenu { JMenuItem item = new JMenuItem(label); item.setToolTipText(MessageManager.formatMessage( - "label.open_url_param", new Object[] - { url })); + "label.open_url_param", new Object[] { url })); item.addActionListener(new java.awt.event.ActionListener() { @Override @@ -1060,11 +988,10 @@ public class PopupMenu extends JPopupMenu JMenuItem item = new JMenuItem(label); item.setToolTipText(MessageManager.formatMessage( "label.open_url_seqs_param", - new Object[] - { urlgenerator.getUrl_prefix(), + new Object[] { urlgenerator.getUrl_prefix(), urlgenerator.getNumberInvolved(urlstub) })); // TODO: put in info about what is being sent. - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1078,7 +1005,7 @@ public class PopupMenu extends JPopupMenu try { showLink(urlgenerator.constructFrom(urlstub)); - } catch (UrlStringTooLongException e) + } catch (UrlStringTooLongException e2) { } } @@ -1098,7 +1025,6 @@ public class PopupMenu extends JPopupMenu */ private void jbInit() throws Exception { - groupMenu.setText(MessageManager.getString("label.group")); groupMenu.setText(MessageManager.getString("label.selection")); groupName.setText(MessageManager.getString("label.name")); groupName.addActionListener(new java.awt.event.ActionListener() @@ -1121,7 +1047,7 @@ public class PopupMenu extends JPopupMenu } }); chooseAnnotations.setText(MessageManager - .getString("label.choose_annotations") + "..."); + .getString("action.choose_annotations")); chooseAnnotations.addActionListener(new java.awt.event.ActionListener() { @Override @@ -1131,7 +1057,7 @@ public class PopupMenu extends JPopupMenu } }); sequenceDetails.setText(MessageManager - .getString("label.sequence_details") + "..."); + .getString("label.sequence_details")); sequenceDetails.addActionListener(new java.awt.event.ActionListener() { @Override @@ -1141,7 +1067,7 @@ public class PopupMenu extends JPopupMenu } }); sequenceSelDetails.setText(MessageManager - .getString("label.sequence_details") + "..."); + .getString("label.sequence_details")); sequenceSelDetails .addActionListener(new java.awt.event.ActionListener() { @@ -1280,36 +1206,6 @@ public class PopupMenu extends JPopupMenu changeCase(e); } }); - pdbMenu.setText(MessageManager - .getString("label.associate_structure_with_sequence")); - pdbFromFile.setText(MessageManager.getString("label.from_file")); - pdbFromFile.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - pdbFromFile_actionPerformed(); - } - }); - - enterPDB.setText(MessageManager.getString("label.enter_pdb_id")); - enterPDB.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - enterPDB_actionPerformed(); - } - }); - discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids")); - discoverPDB.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - discoverPDB_actionPerformed(); - } - }); outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "..."); seqShowAnnotationsMenu.setText(MessageManager @@ -1340,15 +1236,14 @@ public class PopupMenu extends JPopupMenu } }); jMenu1.setText(MessageManager.getString("label.group")); - proteinStructureMenu.setText(MessageManager - .getString("label.view_protein_structure")); - proteinStructureMenu.addActionListener(new ActionListener() + pdbStructureDialog.setText(MessageManager + .getString("label.show_pdbstruct_dialog")); + pdbStructureDialog.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { - SequenceI[] selectedSeqs = new SequenceI[] - { sequence }; + SequenceI[] selectedSeqs = new SequenceI[] { sequence }; if (ap.av.getSelectionGroup() != null) { selectedSeqs = ap.av.getSequenceSelection(); @@ -1375,15 +1270,16 @@ public class PopupMenu extends JPopupMenu .getString("label.mark_as_representative")); makeReferenceSeq.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent actionEvent) { makeReferenceSeq_actionPerformed(actionEvent); - + } }); - hideInsertions.setText(MessageManager.getString("label.hide_insertions")); + hideInsertions.setText(MessageManager + .getString("label.hide_insertions")); hideInsertions.addActionListener(new ActionListener() { @@ -1403,8 +1299,8 @@ public class PopupMenu extends JPopupMenu add(groupMenu); add(sequenceMenu); add(rnaStructureMenu); - add(proteinStructureMenu); - if (sequence!=null) + add(pdbStructureDialog); + if (sequence != null) { add(hideInsertions); } @@ -1479,13 +1375,10 @@ public class PopupMenu extends JPopupMenu editMenu.add(upperCase); editMenu.add(lowerCase); editMenu.add(toggle); - pdbMenu.add(pdbFromFile); // JBPNote: These shouldn't be added here - should appear in a generic // 'apply web service to this sequence menu' // pdbMenu.add(RNAFold); // pdbMenu.add(ContraFold); - pdbMenu.add(enterPDB); - pdbMenu.add(discoverPDB); jMenu1.add(groupName); jMenu1.add(colourMenu); jMenu1.add(showBoxes); @@ -1662,8 +1555,8 @@ public class PopupMenu extends JPopupMenu * @param menuItem * @param forSequences */ - protected void configureReferenceAnnotationsMenu( - JMenuItem menuItem, List forSequences) + protected void configureReferenceAnnotationsMenu(JMenuItem menuItem, + List forSequences) { menuItem.setEnabled(false); @@ -1759,6 +1652,7 @@ public class PopupMenu extends JPopupMenu } refresh(); } + protected void sequenceSelectionDetails_actionPerformed() { createSequenceDetailsReport(ap.av.getSequenceSelection()); @@ -1766,8 +1660,7 @@ public class PopupMenu extends JPopupMenu protected void sequenceDetails_actionPerformed() { - createSequenceDetailsReport(new SequenceI[] - { sequence }); + createSequenceDetailsReport(new SequenceI[] { sequence }); } public void createSequenceDetailsReport(SequenceI[] sequences) @@ -1780,8 +1673,8 @@ public class PopupMenu extends JPopupMenu + MessageManager .formatMessage( "label.create_sequence_details_report_annotation_for", - new Object[] - { seq.getDisplayId(true) }) + "

"); + new Object[] { seq.getDisplayId(true) }) + + "

"); new SequenceAnnotationReport(null) .createSequenceAnnotationReport( contents, @@ -1790,8 +1683,7 @@ public class PopupMenu extends JPopupMenu true, false, (ap.getSeqPanel().seqCanvas.fr != null) ? ap - .getSeqPanel().seqCanvas.fr - .getMinMax() + .getSeqPanel().seqCanvas.fr.getMinMax() : null); contents.append("

"); } @@ -1799,9 +1691,9 @@ public class PopupMenu extends JPopupMenu Desktop.addInternalFrame(cap, MessageManager.formatMessage( "label.sequence_details_for", - (sequences.length == 1 ? new Object[] - { sequences[0].getDisplayId(true) } : new Object[] - { MessageManager.getString("label.selection") })), 500, 400); + (sequences.length == 1 ? new Object[] { sequences[0] + .getDisplayId(true) } : new Object[] { MessageManager + .getString("label.selection") })), 500, 400); } @@ -2077,9 +1969,8 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { // JBPNote: Conservation name shouldn't be i18n translated - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.getSequences(ap.av - .getHiddenRepSequences()), sg.getStartRes(), + Conservation c = new Conservation("Group", 3, sg.getSequences(ap.av + .getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); @@ -2304,29 +2195,7 @@ public class PopupMenu extends JPopupMenu void hideSequences(boolean representGroup) { - SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg == null || sg.getSize() < 1) - { - ap.av.hideSequence(new SequenceI[] - { sequence }); - return; - } - - ap.av.setSelectionGroup(null); - - if (representGroup) - { - ap.av.hideRepSequences(sequence, sg); - - return; - } - - int gsize = sg.getSize(); - SequenceI[] hseqs = sg.getSequences().toArray(new SequenceI[gsize]); - - ap.av.hideSequence(hseqs); - // refresh(); TODO: ? needed ? - ap.av.sendSelection(); + ap.av.hideSequences(sequence, representGroup); } public void copy_actionPerformed() @@ -2347,8 +2216,7 @@ public class PopupMenu extends JPopupMenu if (sg != null) { List startEnd = ap.av.getVisibleRegionBoundaries( - sg.getStartRes(), - sg.getEndRes() + 1); + sg.getStartRes(), sg.getEndRes() + 1); String description; int caseChange; @@ -2386,8 +2254,8 @@ public class PopupMenu extends JPopupMenu CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", new Object[] - { e.getActionCommand() }), 600, 500); + "label.alignment_output_command", + new Object[] { e.getActionCommand() }), 600, 500); String[] omitHidden = null; @@ -2399,67 +2267,6 @@ public class PopupMenu extends JPopupMenu ap, true)); } - public void pdbFromFile_actionPerformed() - { - jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager.formatMessage( - "label.select_pdb_file_for", new Object[] - { sequence.getDisplayId(false) })); - chooser.setToolTipText(MessageManager.formatMessage( - "label.load_pdb_file_associate_with_sequence", new Object[] - { sequence.getDisplayId(false) })); - - int value = chooser.showOpenDialog(null); - - if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) - { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, - jalview.io.AppletFormatAdapter.FILE, sequence, true, - Desktop.instance); - } - - } - - - public void enterPDB_actionPerformed() - { - String id = JOptionPane.showInternalInputDialog(Desktop.desktop, - MessageManager.getString("label.enter_pdb_id"), - MessageManager.getString("label.enter_pdb_id"), - JOptionPane.QUESTION_MESSAGE); - - if (id != null && id.length() > 0) - { - PDBEntry entry = new PDBEntry(); - entry.setId(id.toUpperCase()); - sequence.getDatasetSequence().addPDBId(entry); - } - } - - public void discoverPDB_actionPerformed() - { - - final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[] - { sequence } - : ap.av.getSequenceSelection()); - Thread discpdb = new Thread(new Runnable() - { - @Override - public void run() - { - - new jalview.ws.DBRefFetcher(sequences, ap.alignFrame) - .fetchDBRefs(false); - } - - }); - discpdb.start(); - } - public void sequenceFeature_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup();