X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=9b206bd96e6652f9d983c4824728e50b127f7fb4;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=72313beb455f586ab8944ad97d01fb2aa34e7f52;hpb=7d76e402efd4e04e179bc9bb264551bc2d3df936;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 72313be..9b206bd 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -22,6 +22,7 @@ package jalview.gui; import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentAnnotationUtils; +import jalview.analysis.AlignmentUtils; import jalview.analysis.Conservation; import jalview.commands.ChangeCaseCommand; import jalview.commands.EditCommand; @@ -61,9 +62,7 @@ import jalview.util.UrlLink; import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.util.ArrayList; import java.util.Arrays; -import java.util.Collection; import java.util.Collections; import java.util.Hashtable; import java.util.LinkedHashMap; @@ -125,9 +124,6 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); - // protected JRadioButtonMenuItem covariationColour = new - // JRadioButtonMenuItem(); - JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); @@ -141,7 +137,7 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceDetails = new JMenuItem(); JMenuItem sequenceSelDetails = new JMenuItem(); - + JMenuItem makeReferenceSeq = new JMenuItem(); JMenuItem chooseAnnotations = new JMenuItem(); @@ -182,12 +178,6 @@ public class PopupMenu extends JPopupMenu JMenuItem pdbFromFile = new JMenuItem(); - // JBPNote: Commented these out - Should add these services via the web - // services menu system. - // JMenuItem ContraFold = new JMenuItem(); - - // JMenuItem RNAFold = new JMenuItem(); - JMenuItem enterPDB = new JMenuItem(); JMenuItem discoverPDB = new JMenuItem(); @@ -198,13 +188,15 @@ public class PopupMenu extends JPopupMenu JMenu seqHideAnnotationsMenu = new JMenu(); - JMenuItem seqAddReferenceAnnotations = new JMenuItem(); + JMenuItem seqAddReferenceAnnotations = new JMenuItem( + MessageManager.getString("label.add_reference_annotations")); JMenu groupShowAnnotationsMenu = new JMenu(); JMenu groupHideAnnotationsMenu = new JMenu(); - JMenuItem groupAddReferenceAnnotations = new JMenuItem(); + JMenuItem groupAddReferenceAnnotations = new JMenuItem( + MessageManager.getString("label.add_reference_annotations")); JMenuItem sequenceFeature = new JMenuItem(); @@ -212,15 +204,12 @@ public class PopupMenu extends JPopupMenu JMenu jMenu1 = new JMenu(); - JMenuItem structureMenu = new JMenuItem(); + JMenuItem pdbStructureDialog = new JMenuItem(); - JMenu viewStructureMenu = new JMenu(); + JMenu rnaStructureMenu = new JMenu(); - // JMenu colStructureMenu = new JMenu(); JMenuItem editSequence = new JMenuItem(); - // JMenuItem annotationMenuItem = new JMenuItem(); - JMenu groupLinksMenu; JMenuItem hideInsertions = new JMenuItem(); @@ -273,7 +262,6 @@ public class PopupMenu extends JPopupMenu colours.add(BLOSUM62Colour); colours.add(purinePyrimidineColour); colours.add(RNAInteractionColour); - // colours.add(covariationColour); for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) { @@ -329,128 +317,86 @@ 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")); } - - if (seq.getDatasetSequence().getPDBId() != null - && seq.getDatasetSequence().getPDBId().size() > 0) + else { - java.util.Enumeration e = seq.getDatasetSequence().getPDBId() - .elements(); - - while (e.hasMoreElements()) - { - final PDBEntry pdb = (PDBEntry) e.nextElement(); - - menuItem = new JMenuItem(); - menuItem.setText(pdb.getId()); - menuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - // TODO re JAL-860: optionally open dialog or provide a menu entry - // allowing user to open just one structure per sequence - // new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] - // { pdb })[0], null, ap); - new StructureViewer(ap.getStructureSelectionManager()) - .viewStructures(pdb, - ap.av.collateForPDB(new PDBEntry[] - { pdb })[0], null, ap); - } - }); - viewStructureMenu.add(menuItem); - - /* - * menuItem = new JMenuItem(); menuItem.setText(pdb.getId()); - * menuItem.addActionListener(new java.awt.event.ActionListener() { - * public void actionPerformed(ActionEvent e) { - * colourByStructure(pdb.getId()); } }); - * colStructureMenu.add(menuItem); - */ - } + makeReferenceSeq.setText(MessageManager + .getString("action.set_as_reference")); } - else + + if (!ap.av.getAlignment().isNucleotide()) { - if (ap.av.getAlignment().isNucleotide() == false) - { - structureMenu.remove(viewStructureMenu); - } - // structureMenu.remove(colStructureMenu); + 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 String[] - { 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() { - // // System.out.println("1:"+structureLine); - // System.out.println("1:sname" + seq.getName()); - // System.out.println("2:seq" + seq); - // - // // System.out.println("3:"+seq.getSequenceAsString()); - // System.out.println("3:strucseq" + rnastruc); - // // System.out.println("4:struc"+seq.getRNA()); - // System.out.println("5:name" + seq.getName()); - // System.out.println("6:ap" + ap); - new AppVarna(structureLine, seq, seq.getSequenceAsString(), - rnastruc, seq.getName(), ap); - // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), - // seq.getName(), ap); - System.out.println("end"); - } - }); - viewStructureMenu.add(menuItem); + @Override + public void actionPerformed(ActionEvent e) + { + new AppVarna(seq, aa, ap); + } + }); + rnaStructureMenu.add(menuItem); + } } } - // SequenceFeatures[] test = seq.getSequenceFeatures(); - 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 String[] - { 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); } }); - viewStructureMenu.add(menuItem); + rnaStructureMenu.add(menuItem); } } } + if (rnaStructureMenu.getItemCount() == origCount) + { + remove(rnaStructureMenu); + } } menuItem = new JMenuItem( @@ -469,8 +415,8 @@ public class PopupMenu extends JPopupMenu && ap.av.getSelectionGroup().getSize() > 1) { menuItem = new JMenuItem(MessageManager.formatMessage( - "label.represent_group_with", new String[] - { seq.getName() })); + "label.represent_group_with", + new Object[] { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { @Override @@ -538,8 +484,7 @@ public class PopupMenu extends JPopupMenu if (sg != null && sg.getSize() > 0) { groupName.setText(MessageManager.formatMessage("label.name_param", - new String[] - { sg.getName() })); + new Object[] { sg.getName() })); groupName.setText(MessageManager .getString("label.edit_name_and_description_current_group")); @@ -619,7 +564,7 @@ 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)); @@ -639,50 +584,6 @@ public class PopupMenu extends JPopupMenu new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray( new PDBEntry[reppdb.size()]); final JMenuItem gpdbview, rpdbview; - // if (pdbe.size() == 1) - // { - // structureMenu.add(gpdbview = new JMenuItem(MessageManager - // .formatMessage("label.view_structure_for", new String[] - // { sqass.getDisplayId(false) }))); - // } - // else - // { - // structureMenu.add(gpdbview = new JMenuItem(MessageManager - // .formatMessage("label.view_all_structures", new String[] - // { new Integer(pdbe.size()).toString() }))); - // } - // gpdbview.setToolTipText(MessageManager - // .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment")); - // gpdbview.addActionListener(new ActionListener() - // { - // - // @Override - // public void actionPerformed(ActionEvent e) - // { - // new StructureViewer(ap.getStructureSelectionManager()) - // .viewStructures(ap, pe, ap.av.collateForPDB(pe)); - // } - // }); - // if (reppdb.size() > 1 && reppdb.size() < pdbe.size()) - // { - // structureMenu.add(rpdbview = new JMenuItem(MessageManager - // .formatMessage( - // "label.view_all_representative_structures", - // new String[] - // { new Integer(reppdb.size()).toString() }))); - // rpdbview.setToolTipText(MessageManager - // .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment")); - // rpdbview.addActionListener(new ActionListener() - // { - // - // @Override - // public void actionPerformed(ActionEvent e) - // { - // new StructureViewer(ap.getStructureSelectionManager()) - // .viewStructures(ap, pr, ap.av.collateForPDB(pr)); - // } - // }); - // } } } else @@ -707,7 +608,8 @@ public class PopupMenu extends JPopupMenu if (seq == null) { sequenceMenu.setVisible(false); - structureMenu.setVisible(false); + pdbStructureDialog.setVisible(false); + rnaStructureMenu.setVisible(false); } if (links != null && links.size() > 0) @@ -740,8 +642,7 @@ public class PopupMenu extends JPopupMenu // collect matching db-refs DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs( - seq.getDBRef(), new String[] - { urlLink.getTarget() }); + seq.getDBRef(), new String[] { urlLink.getTarget() }); // collect id string too String id = seq.getName(); String descr = seq.getDescription(); @@ -872,17 +773,15 @@ 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 @@ -892,8 +791,8 @@ 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 @@ -946,7 +845,7 @@ public class PopupMenu extends JPopupMenu final boolean actionIsShow) { String label = types.toString(); // [a, b, c] - label = label.substring(1, label.length() - 1); + label = label.substring(1, label.length() - 1); // a, b, c final JMenuItem item = new JMenuItem(label); item.setToolTipText(calcId); item.addActionListener(new java.awt.event.ActionListener() @@ -954,41 +853,14 @@ public class PopupMenu extends JPopupMenu @Override public void actionPerformed(ActionEvent e) { - showHideAnnotation_actionPerformed(types, forSequences, allTypes, - actionIsShow); + AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), + types, forSequences, allTypes, actionIsShow); + refresh(); } }); showOrHideMenu.add(item); } - /** - * Action on selecting a list of annotation type (or the 'all types' values) - * to show or hide for the specified sequences. - * - * @param types - * @param forSequences - * @param anyType - * @param doShow - */ - protected void showHideAnnotation_actionPerformed( - Collection types, List forSequences, - boolean anyType, boolean doShow) - { - for (AlignmentAnnotation aa : ap.getAlignment() - .getAlignmentAnnotation()) - { - if (anyType || types.contains(aa.label)) - { - if ((aa.sequenceRef != null) - && forSequences.contains(aa.sequenceRef)) - { - aa.visible = doShow; - } - } - } - refresh(); - } - private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks) { @@ -998,8 +870,8 @@ 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")), + 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 @@ -1034,8 +906,7 @@ public class PopupMenu extends JPopupMenu 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); @@ -1116,8 +987,6 @@ public class PopupMenu extends JPopupMenu if (urlset != null) { int type = urlLink.getGroupURLType() & 3; - // System.out.println(urlLink.getGroupURLType() - // +" "+((String[])urlset[3])[0]); // first two bits ofurlLink type bitfield are sequenceids and sequences // TODO: FUTURE: ensure the groupURL menu structure can be generalised addshowLink(linkMenus[type], label @@ -1157,8 +1026,7 @@ public class PopupMenu extends JPopupMenu { JMenuItem item = new JMenuItem(label); item.setToolTipText(MessageManager.formatMessage( - "label.open_url_param", new String[] - { url })); + "label.open_url_param", new Object[] { url })); item.addActionListener(new java.awt.event.ActionListener() { @Override @@ -1197,8 +1065,7 @@ 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() @@ -1258,7 +1125,7 @@ public class PopupMenu extends JPopupMenu } }); chooseAnnotations.setText(MessageManager - .getString("label.choose_annotations") + "..."); + .getString("action.choose_annotations")); chooseAnnotations.addActionListener(new java.awt.event.ActionListener() { @Override @@ -1268,7 +1135,7 @@ public class PopupMenu extends JPopupMenu } }); sequenceDetails.setText(MessageManager - .getString("label.sequence_details") + "..."); + .getString("label.sequence_details")); sequenceDetails.addActionListener(new java.awt.event.ActionListener() { @Override @@ -1278,7 +1145,7 @@ public class PopupMenu extends JPopupMenu } }); sequenceSelDetails.setText(MessageManager - .getString("label.sequence_details") + "..."); + .getString("label.sequence_details")); sequenceSelDetails .addActionListener(new java.awt.event.ActionListener() { @@ -1428,32 +1295,7 @@ public class PopupMenu extends JPopupMenu pdbFromFile_actionPerformed(); } }); - // RNAFold.setText("From RNA Fold with predict2D"); - // RNAFold.addActionListener(new ActionListener() - // { - // public void actionPerformed(ActionEvent e) - // { - // try { - // RNAFold_actionPerformed(); - // } catch (Exception e1) { - // // TODO Auto-generated catch block - // e1.printStackTrace(); - // } - // } - // }); - // ContraFold.setText("From Contra Fold with predict2D"); - // ContraFold.addActionListener(new ActionListener() - // { - // public void actionPerformed(ActionEvent e) - // { - // try { - // ContraFold_actionPerformed(); - // } catch (Exception e1) { - // // TODO Auto-generated catch block - // e1.printStackTrace(); - // } - // } - // }); + enterPDB.setText(MessageManager.getString("label.enter_pdb_id")); enterPDB.addActionListener(new ActionListener() { @@ -1502,19 +1344,25 @@ public class PopupMenu extends JPopupMenu } }); jMenu1.setText(MessageManager.getString("label.group")); - // structureMenu.setText(MessageManager.getString("label.structure")); - structureMenu.setText(MessageManager.getString("label.view_structure")); - structureMenu.addActionListener(new ActionListener() + pdbStructureDialog.setText(MessageManager + .getString("label.show_pdbstruct_dialog")); + pdbStructureDialog.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { - new StructureChooser(ap, sequence); + SequenceI[] selectedSeqs = new SequenceI[] { sequence }; + if (ap.av.getSelectionGroup() != null) + { + selectedSeqs = ap.av.getSequenceSelection(); + } + new StructureChooser(selectedSeqs, sequence, ap); } }); - viewStructureMenu.setText(MessageManager - .getString("label.view_structure")); + rnaStructureMenu.setText(MessageManager + .getString("label.view_rna_structure")); + // colStructureMenu.setText("Colour By Structure"); editSequence.setText(MessageManager.getString("label.edit_sequence") + "..."); @@ -1530,15 +1378,16 @@ 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() { @@ -1557,8 +1406,9 @@ public class PopupMenu extends JPopupMenu groupMenu.add(sequenceSelDetails); add(groupMenu); add(sequenceMenu); - add(structureMenu); - if (sequence!=null) + add(rnaStructureMenu); + add(pdbStructureDialog); + if (sequence != null) { add(hideInsertions); } @@ -1600,10 +1450,8 @@ public class PopupMenu extends JPopupMenu if (ap.getAlignment().isNucleotide()) { // JBPNote - commented since the colourscheme isn't functional - // colourMenu.add(RNAInteractionColour); colourMenu.add(purinePyrimidineColour); } - // colourMenu.add(covariationColour); colourMenu.add(userDefinedColour); if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) @@ -1629,7 +1477,6 @@ public class PopupMenu extends JPopupMenu colourMenu.addSeparator(); colourMenu.add(abovePIDColour); colourMenu.add(conservationMenuItem); - // colourMenu.add(annotationMenuItem); editMenu.add(copy); editMenu.add(cut); editMenu.add(editSequence); @@ -1650,9 +1497,6 @@ public class PopupMenu extends JPopupMenu jMenu1.add(showColourText); jMenu1.add(outline); jMenu1.add(displayNonconserved); - // structureMenu.add(pdbMenu); - // structureMenu.add(viewStructureMenu); - // structureMenu.add(colStructureMenu); noColourmenuItem.setText(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -1822,71 +1666,25 @@ public class PopupMenu extends JPopupMenu * @param menuItem * @param forSequences */ - protected void configureReferenceAnnotationsMenu( - JMenuItem menuItem, List forSequences) + protected void configureReferenceAnnotationsMenu(JMenuItem menuItem, + List forSequences) { - menuItem.setText(MessageManager - .getString("label.add_reference_annotations")); menuItem.setEnabled(false); - if (forSequences == null) - { - return; - } /* * Temporary store to hold distinct calcId / type pairs for the tooltip. * Using TreeMap means calcIds are shown in alphabetical order. */ Map tipEntries = new TreeMap(); - StringBuilder tooltip = new StringBuilder(64); - tooltip.append(MessageManager.getString("label.add_annotations_for")); - - /* - * For each sequence selected in the alignment, make a list of any - * annotations on the underlying dataset sequence which are not already on - * the alignment. - * - * Build a map of { alignmentSequence, } - */ - AlignmentI al = this.ap.av.getAlignment(); final Map> candidates = new LinkedHashMap>(); - for (SequenceI seq : forSequences) - { - SequenceI dataset = seq.getDatasetSequence(); - if (dataset == null) - { - continue; - } - AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation(); - if (datasetAnnotations == null) - { - continue; - } - final List result = new ArrayList(); - for (AlignmentAnnotation dsann : datasetAnnotations) - { - /* - * Find matching annotations on the alignment. - */ - final Iterable matchedAlignmentAnnotations = al - .findAnnotations(seq, dsann.getCalcId(), - dsann.label); - if (!matchedAlignmentAnnotations.iterator().hasNext()) - { - result.add(dsann); - tipEntries.put(dsann.getCalcId(), dsann.label); - } - } - /* - * Save any addable annotations for this sequence - */ - if (!result.isEmpty()) - { - candidates.put(seq, result); - } - } + AlignmentI al = this.ap.av.getAlignment(); + AlignmentUtils.findAddableReferenceAnnotations(forSequences, + tipEntries, candidates, al); if (!candidates.isEmpty()) { + StringBuilder tooltip = new StringBuilder(64); + tooltip.append(MessageManager.getString("label.add_annotations_for")); + /* * Found annotations that could be added. Enable the menu item, and * configure its tooltip and action. @@ -1921,40 +1719,10 @@ public class PopupMenu extends JPopupMenu protected void addReferenceAnnotations_actionPerformed( Map> candidates) { - /* - * Add annotations at the top of the annotation, in the same order as their - * related sequences. - */ - for (SequenceI seq : candidates.keySet()) - { - for (AlignmentAnnotation ann : candidates.get(seq)) - { - AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann); - int startRes = 0; - int endRes = ann.annotations.length; - final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup(); - if (selectionGroup != null) - { - startRes = selectionGroup.getStartRes(); - endRes = selectionGroup.getEndRes(); - } - copyAnn.restrict(startRes, endRes); - - /* - * Add to the sequence (sets copyAnn.datasetSequence), unless the - * original annotation is already on the sequence. - */ - if (!seq.hasAnnotation(ann)) - { - seq.addAlignmentAnnotation(copyAnn); - } - // adjust for gaps - copyAnn.adjustForAlignment(); - // add to the alignment and set visible - this.ap.getAlignment().addAnnotation(copyAnn); - copyAnn.visible = true; - } - } + final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup(); + final AlignmentI alignment = this.ap.getAlignment(); + AlignmentUtils.addReferenceAnnotations(candidates, alignment, + selectionGroup); refresh(); } @@ -1995,6 +1763,7 @@ public class PopupMenu extends JPopupMenu } refresh(); } + protected void sequenceSelectionDetails_actionPerformed() { createSequenceDetailsReport(ap.av.getSequenceSelection()); @@ -2002,8 +1771,7 @@ public class PopupMenu extends JPopupMenu protected void sequenceDetails_actionPerformed() { - createSequenceDetailsReport(new SequenceI[] - { sequence }); + createSequenceDetailsReport(new SequenceI[] { sequence }); } public void createSequenceDetailsReport(SequenceI[] sequences) @@ -2016,8 +1784,8 @@ public class PopupMenu extends JPopupMenu + MessageManager .formatMessage( "label.create_sequence_details_report_annotation_for", - new String[] - { seq.getDisplayId(true) }) + "

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

"); new SequenceAnnotationReport(null) .createSequenceAnnotationReport( contents, @@ -2026,8 +1794,7 @@ public class PopupMenu extends JPopupMenu true, false, (ap.getSeqPanel().seqCanvas.fr != null) ? ap - .getSeqPanel().seqCanvas.fr - .getMinMax() + .getSeqPanel().seqCanvas.fr.getMinMax() : null); contents.append("

"); } @@ -2035,9 +1802,9 @@ 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); } @@ -2200,14 +1967,14 @@ public class PopupMenu extends JPopupMenu int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); - sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); + sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus()); SliderPanel.showPIDSlider(); } else // remove PIDColouring { - sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); + sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); } refresh(); @@ -2543,8 +2310,7 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = ap.av.getSelectionGroup(); if (sg == null || sg.getSize() < 1) { - ap.av.hideSequence(new SequenceI[] - { sequence }); + ap.av.hideSequence(new SequenceI[] { sequence }); return; } @@ -2558,15 +2324,7 @@ public class PopupMenu extends JPopupMenu } 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); - } + SequenceI[] hseqs = sg.getSequences().toArray(new SequenceI[gsize]); ap.av.hideSequence(hseqs); // refresh(); TODO: ? needed ? @@ -2590,8 +2348,8 @@ public class PopupMenu extends JPopupMenu if (sg != null) { - int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(), - sg.getEndRes() + 1); + List startEnd = ap.av.getVisibleRegionBoundaries( + sg.getStartRes(), sg.getEndRes() + 1); String description; int caseChange; @@ -2629,8 +2387,8 @@ public class PopupMenu extends JPopupMenu CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", new String[] - { e.getActionCommand() }), 600, 500); + "label.alignment_output_command", + new Object[] { e.getActionCommand() }), 600, 500); String[] omitHidden = null; @@ -2638,8 +2396,8 @@ public class PopupMenu extends JPopupMenu // or we simply trust the user wants // wysiwig behaviour - cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), - ap.av, true)); + cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(), + ap, true)); } public void pdbFromFile_actionPerformed() @@ -2648,11 +2406,11 @@ public class PopupMenu extends JPopupMenu jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); chooser.setDialogTitle(MessageManager.formatMessage( - "label.select_pdb_file_for", new String[] - { sequence.getDisplayId(false) })); + "label.select_pdb_file_for", + new Object[] { sequence.getDisplayId(false) })); chooser.setToolTipText(MessageManager.formatMessage( - "label.load_pdb_file_associate_with_sequence", new String[] - { sequence.getDisplayId(false) })); + "label.load_pdb_file_associate_with_sequence", + new Object[] { sequence.getDisplayId(false) })); int value = chooser.showOpenDialog(null); @@ -2667,18 +2425,6 @@ public class PopupMenu extends JPopupMenu } - // JBNote: commented out - these won't be instantiated here...! - // public void RNAFold_actionPerformed() throws Exception - // { - // Predict2D P2D = new Predict2D(); - // P2D.getStructure2DFromRNAFold("toto"); - // } - // - // public void ContraFold_actionPerformed() throws Exception - // { - // Predict2D P2D = new Predict2D(); - // P2D.getStructure2DFromContraFold("toto"); - // } public void enterPDB_actionPerformed() { String id = JOptionPane.showInternalInputDialog(Desktop.desktop,