X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=766d44b9cd7ba5c57bdbdcd8dd39bbfee05dcbd0;hb=adb62c0d58c02d19e4d6611c3df211f27b930f06;hp=6042ab89e1a35cf8231407c1e65714bc226c0e13;hpb=ab4788fa5cf6a8a7f7089d8d222a3be8ddb7a13b;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 6042ab8..766d44b 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,12 +20,39 @@ */ package jalview.gui; +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; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; +import java.util.Vector; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JColorChooser; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JPopupMenu; +import javax.swing.JRadioButtonMenuItem; + import jalview.analysis.AAFrequency; +import jalview.analysis.AlignmentAnnotationUtils; import jalview.analysis.Conservation; import jalview.commands.ChangeCaseCommand; import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; +import jalview.datamodel.ColumnSelection; import jalview.datamodel.DBRefEntry; import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; @@ -34,7 +61,6 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.FormatAdapter; import jalview.io.SequenceAnnotationReport; -import jalview.renderer.AnnotationRenderer; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; @@ -55,28 +81,6 @@ import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; 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.BitSet; -import java.util.Collection; -import java.util.Hashtable; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Map; -import java.util.Vector; - -import javax.swing.ButtonGroup; -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JColorChooser; -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JOptionPane; -import javax.swing.JPopupMenu; -import javax.swing.JRadioButtonMenuItem; - /** * DOCUMENT ME! * @@ -121,9 +125,6 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); - // protected JRadioButtonMenuItem covariationColour = new - // JRadioButtonMenuItem(); - JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); @@ -137,6 +138,8 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceDetails = new JMenuItem(); JMenuItem sequenceSelDetails = new JMenuItem(); + + JMenuItem makeReferenceSeq = new JMenuItem(); JMenuItem chooseAnnotations = new JMenuItem(); @@ -176,21 +179,23 @@ 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(); JMenu outputMenu = new JMenu(); - JMenu showAnnotationsMenu = new JMenu(); + JMenu seqShowAnnotationsMenu = new JMenu(); + + JMenu seqHideAnnotationsMenu = new JMenu(); + + JMenuItem seqAddReferenceAnnotations = new JMenuItem(); + + JMenu groupShowAnnotationsMenu = new JMenu(); + + JMenu groupHideAnnotationsMenu = new JMenu(); - JMenu hideAnnotationsMenu = new JMenu(); + JMenuItem groupAddReferenceAnnotations = new JMenuItem(); JMenuItem sequenceFeature = new JMenuItem(); @@ -198,17 +203,16 @@ public class PopupMenu extends JPopupMenu JMenu jMenu1 = new JMenu(); - JMenu structureMenu = new JMenu(); + JMenuItem structureMenu = new JMenuItem(); JMenu viewStructureMenu = new JMenu(); - // JMenu colStructureMenu = new JMenu(); JMenuItem editSequence = new JMenuItem(); - // JMenuItem annotationMenuItem = new JMenuItem(); - JMenu groupLinksMenu; + JMenuItem hideInsertions = new JMenuItem(); + /** * Creates a new PopupMenu object. * @@ -257,7 +261,6 @@ 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++) { @@ -277,9 +280,27 @@ public class PopupMenu extends JPopupMenu } /* - * Build menus for annotation types that may be shown or hidden. + * Build menus for annotation types that may be shown or hidden, and for + * 'reference annotations' that may be added to the alignment. First for the + * currently selected sequence (if there is one): + */ + final List selectedSequence = (seq == null ? Collections + . emptyList() : Arrays.asList(seq)); + buildAnnotationTypesMenus(seqShowAnnotationsMenu, + seqHideAnnotationsMenu, selectedSequence); + configureReferenceAnnotationsMenu(seqAddReferenceAnnotations, + selectedSequence); + + /* + * And repeat for the current selection group (if there is one): */ - buildAnnotationTypesMenus(); + final List selectedGroup = (ap.av.getSelectionGroup() == null ? Collections + . emptyList() : ap.av.getSelectionGroup() + .getSequences()); + buildAnnotationTypesMenus(groupShowAnnotationsMenu, + groupHideAnnotationsMenu, selectedGroup); + configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, + selectedGroup); try { @@ -293,6 +314,12 @@ public class PopupMenu extends JPopupMenu if (seq != null) { sequenceMenu.setText(sequence.getName()); + if (seq == ap.av.getAlignment().getSeqrep()) + { + makeReferenceSeq.setText("Unmark representative"); + } else { + makeReferenceSeq.setText("Mark as representative"); + } if (seq.getDatasetSequence().getPDBId() != null && seq.getDatasetSequence().getPDBId().size() > 0) @@ -306,8 +333,9 @@ public class PopupMenu extends JPopupMenu menuItem = new JMenuItem(); menuItem.setText(pdb.getId()); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO re JAL-860: optionally open dialog or provide a menu entry @@ -337,42 +365,28 @@ public class PopupMenu extends JPopupMenu { structureMenu.remove(viewStructureMenu); } - // structureMenu.remove(colStructureMenu); } - if (ap.av.getAlignment().isNucleotide() == true) { AlignmentAnnotation[] aa = ap.av.getAlignment() .getAlignmentAnnotation(); - for (int i = 0; i < aa.length; i++) + for (int i = 0; aa != null && i < aa.length; i++) { - if (aa[i].getRNAStruc() != null) + if (aa[i].isValidStruc() && aa[i].sequenceRef == null) { final String rnastruc = aa[i].getRNAStruc(); - final String structureLine = aa[i].label; + final String structureLine = aa[i].label + " (alignment)"; menuItem = new JMenuItem(); menuItem.setText(MessageManager.formatMessage( - "label.2d_rna_structure_line", new String[] + "label.2d_rna_structure_line", new Object[] { structureLine })); menuItem.addActionListener(new java.awt.event.ActionListener() - { @Override public void actionPerformed(ActionEvent e) { - // 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"); } }); @@ -380,21 +394,20 @@ public class PopupMenu extends JPopupMenu } } - // SequenceFeatures[] test = seq.getSequenceFeatures(); if (seq.getAnnotation() != null) { AlignmentAnnotation seqAnno[] = seq.getAnnotation(); for (int i = 0; i < seqAnno.length; i++) { - if (seqAnno[i].getRNAStruc() != null) + if (seqAnno[i].isValidStruc()) { final String rnastruc = seqAnno[i].getRNAStruc(); // TODO: make rnastrucF a bit more nice menuItem = new JMenuItem(); menuItem.setText(MessageManager.formatMessage( - "label.2d_rna_sequence_name", new String[] + "label.2d_rna_sequence_name", new Object[] { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { @@ -412,7 +425,6 @@ public class PopupMenu extends JPopupMenu } } } - } menuItem = new JMenuItem( @@ -431,7 +443,7 @@ public class PopupMenu extends JPopupMenu && ap.av.getSelectionGroup().getSize() > 1) { menuItem = new JMenuItem(MessageManager.formatMessage( - "label.represent_group_with", new String[] + "label.represent_group_with", new Object[] { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { @@ -500,7 +512,7 @@ public class PopupMenu extends JPopupMenu if (sg != null && sg.getSize() > 0) { groupName.setText(MessageManager.formatMessage("label.name_param", - new String[] + new Object[] { sg.getName() })); groupName.setText(MessageManager .getString("label.edit_name_and_description_current_group")); @@ -601,50 +613,6 @@ 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 @@ -796,9 +764,10 @@ public class PopupMenu extends JPopupMenu } /** - * Add annotation types to a 'Show annotations' or 'Hide annotations' menu. + * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus. * "All" is added first, followed by a separator. Then add any annotation - * types associated with the current selection. + * types associated with the current selection. Separate menus are built for + * the selected sequence group (if any), and the selected sequence. *

* Some annotation rows are always rendered together - these can be identified * by a common graphGroup property > -1. Only one of each group will be marked @@ -806,168 +775,82 @@ public class PopupMenu extends JPopupMenu * composite type name, e.g. *

* IUPredWS (Long), IUPredWS (Short) + * + * @param seq */ - protected void buildAnnotationTypesMenus() + protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu, + List forSequences) { - showAnnotationsMenu.removeAll(); - hideAnnotationsMenu.removeAll(); + showMenu.removeAll(); + hideMenu.removeAll(); + final List all = Arrays.asList(ALL_ANNOTATIONS); - addAnnotationTypeToShowHide(showAnnotationsMenu, - all, true, - true); - addAnnotationTypeToShowHide(hideAnnotationsMenu, all, true, + addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true); + addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true, false); - showAnnotationsMenu.addSeparator(); - hideAnnotationsMenu.addSeparator(); + showMenu.addSeparator(); + hideMenu.addSeparator(); final AlignmentAnnotation[] annotations = ap.getAlignment() .getAlignmentAnnotation(); - BitSet visibleGraphGroups = PopupMenu - .getVisibleLineGraphGroups(annotations); - - List> shownTypes = new ArrayList>(); - List> hiddenTypes = new ArrayList>(); - PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes, - visibleGraphGroups, annotations, ap.av.getSelectionGroup()); - - for (List types : hiddenTypes) - { - addAnnotationTypeToShowHide(showAnnotationsMenu, types, false, true); - } - - for (List types : shownTypes) - { - addAnnotationTypeToShowHide(hideAnnotationsMenu, types, false, false); - } - } - /** - * Helper method to populate lists of annotation types for the Show/Hide - * Annotations menus. If sequenceGroup is not null, this is restricted to - * annotations which are associated with sequences in the selection group. - *

- * If an annotation row is currently visible, its type (label) is added (once - * only per type), to the shownTypes list. If it is currently hidden, it is - * added to the hiddenTypesList. - *

- * For rows that belong to a line graph group, so are always rendered - * together: - *

    - *
  • Treat all rows in the group as visible, if at least one of them is
    • - *
  • Build a comma-separated label with all the types that belong to the - * group
    • - *
- * - * @param shownTypes - * @param hiddenTypes - * @param visibleGraphGroups - * @param annotations - * @param sequenceGroup - */ - public static void getAnnotationTypesForShowHide( - List> shownTypes, List> hiddenTypes, - BitSet visibleGraphGroups, - AlignmentAnnotation[] annotations, SequenceGroup sequenceGroup) - { - // lookup table, key = graph group, value = list of types in the group - Map> groupLabels = new LinkedHashMap>(); - - List addedToShown = new ArrayList(); - List addedToHidden = new ArrayList(); + /* + * 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); - for (AlignmentAnnotation aa : annotations) + for (String calcId : hiddenTypes.keySet()) { - - if (sequenceGroup == null - || (aa.sequenceRef != null && sequenceGroup.getSequences() - .contains(aa.sequenceRef))) + for (List type : hiddenTypes.get(calcId)) { - /* - * Build a 'composite label' for types in line graph groups. - */ - final List labelAsList = new ArrayList(); - labelAsList.add(aa.label); - if (aa.graph == AlignmentAnnotation.LINE_GRAPH - && aa.graphGroup > -1) - { - if (groupLabels.containsKey(aa.graphGroup)) - { - if (!groupLabels.get(aa.graphGroup).contains(aa.label)) - { - groupLabels.get(aa.graphGroup).add(aa.label); - } - } - else - { - groupLabels.put(aa.graphGroup, labelAsList); - } - } - else if (aa.visible && !addedToShown.contains(aa.label)) - { - shownTypes.add(labelAsList); - addedToShown.add(aa.label); - } - else - { - if (!aa.visible && !addedToHidden.contains(aa.label)) - { - hiddenTypes.add(labelAsList); - addedToHidden.add(aa.label); - } - } + addAnnotationTypeToShowHide(showMenu, forSequences, + calcId, type, false, true); } } - /* - * finally add the 'composite group labels' to the appropriate lists, - * depending on whether the group is identified as visible or hidden - */ - for (int group : groupLabels.keySet()) + // grey out 'show annotations' if none are hidden + showMenu.setEnabled(!hiddenTypes.isEmpty()); + + for (String calcId : shownTypes.keySet()) { - final List groupLabel = groupLabels.get(group); - if (visibleGraphGroups.get(group)) - { - if (!shownTypes.contains(groupLabel)) - { - shownTypes.add(groupLabel); - } - } - else if (!hiddenTypes.contains(groupLabel)) + for (List type : shownTypes.get(calcId)) { - hiddenTypes.add(groupLabel); + addAnnotationTypeToShowHide(hideMenu, forSequences, + calcId, type, false, false); } } + // grey out 'hide annotations' if none are shown + hideMenu.setEnabled(!shownTypes.isEmpty()); } /** - * Returns a BitSet (possibly empty) of those graphGroups for line graph - * annotations, which have at least one member annotation row marked visible. - * The logic is that only one row in the group is marked visible, but when it - * is drawn, so are all the other rows in the same group. - *

- * This lookup set allows us to check whether rows marked not visible are in - * fact shown. + * Returns a list of sequences - either the current selection group (if there + * is one), else the specified single sequence. * - * @see AnnotationRenderer#drawComponent - * @param annotations + * @param seq * @return */ - public static BitSet getVisibleLineGraphGroups( - AlignmentAnnotation[] annotations) + protected List getSequenceScope(SequenceI seq) { - // todo move to a utility class - BitSet result = new BitSet(); - for (AlignmentAnnotation ann : annotations) + List forSequences = null; + final SequenceGroup selectionGroup = ap.av.getSelectionGroup(); + if (selectionGroup != null && selectionGroup.getSize() > 0) { - if (ann.graph == AlignmentAnnotation.LINE_GRAPH && ann.visible) - { - int gg = ann.graphGroup; - if (gg > -1) - { - result.set(gg); - } - } + forSequences = selectionGroup.getSequences(); + } + else + { + forSequences = seq == null ? Collections. emptyList() + : Arrays.asList(seq); } - return result; + return forSequences; } /** @@ -976,6 +859,9 @@ public class PopupMenu extends JPopupMenu * * @param showOrHideMenu * the menu to add to + * @param forSequences + * the sequences whose annotations may be shown or hidden + * @param calcId * @param types * the label to add * @param allTypes @@ -985,18 +871,21 @@ public class PopupMenu extends JPopupMenu * type, else hide */ protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu, - final Collection types, final boolean allTypes, + final List forSequences, String calcId, + final List types, final boolean allTypes, final boolean actionIsShow) { String label = types.toString(); // [a, b, c] label = label.substring(1, label.length() - 1); final JMenuItem item = new JMenuItem(label); + item.setToolTipText(calcId); item.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) { - showHideAnnotation_actionPerformed(types, allTypes, actionIsShow); + showHideAnnotation_actionPerformed(types, forSequences, allTypes, + actionIsShow); } }); showOrHideMenu.add(item); @@ -1004,14 +893,15 @@ public class PopupMenu extends JPopupMenu /** * Action on selecting a list of annotation type (or the 'all types' values) - * to show or hide for the selection. + * to show or hide for the specified sequences. * * @param types + * @param forSequences * @param anyType * @param doShow */ protected void showHideAnnotation_actionPerformed( - Collection types, + Collection types, List forSequences, boolean anyType, boolean doShow) { for (AlignmentAnnotation aa : ap.getAlignment() @@ -1020,8 +910,7 @@ public class PopupMenu extends JPopupMenu if (anyType || types.contains(aa.label)) { if ((aa.sequenceRef != null) - && ap.av.getSelectionGroup().getSequences() - .contains(aa.sequenceRef)) + && forSequences.contains(aa.sequenceRef)) { aa.visible = doShow; } @@ -1157,8 +1046,6 @@ 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 @@ -1198,7 +1085,7 @@ public class PopupMenu extends JPopupMenu { JMenuItem item = new JMenuItem(label); item.setToolTipText(MessageManager.formatMessage( - "label.open_url_param", new String[] + "label.open_url_param", new Object[] { url })); item.addActionListener(new java.awt.event.ActionListener() { @@ -1469,32 +1356,7 @@ 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() { @@ -1515,9 +1377,13 @@ public class PopupMenu extends JPopupMenu }); outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "..."); - showAnnotationsMenu.setText(MessageManager + seqShowAnnotationsMenu.setText(MessageManager + .getString("label.show_annotations")); + seqHideAnnotationsMenu.setText(MessageManager + .getString("label.hide_annotations")); + groupShowAnnotationsMenu.setText(MessageManager .getString("label.show_annotations")); - hideAnnotationsMenu.setText(MessageManager + groupHideAnnotationsMenu.setText(MessageManager .getString("label.hide_annotations")); sequenceFeature.setText(MessageManager .getString("label.create_sequence_feature")); @@ -1539,7 +1405,22 @@ 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() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + 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")); // colStructureMenu.setText("Colour By Structure"); @@ -1553,7 +1434,28 @@ public class PopupMenu extends JPopupMenu editSequence_actionPerformed(actionEvent); } }); + makeReferenceSeq.setText(MessageManager + .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.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hideInsertions_actionPerformed(e); + } + }); /* * annotationMenuItem.setText("By Annotation"); * annotationMenuItem.addActionListener(new ActionListener() { public void @@ -1563,10 +1465,24 @@ public class PopupMenu extends JPopupMenu groupMenu.add(sequenceSelDetails); add(groupMenu); add(sequenceMenu); - this.add(structureMenu); + add(structureMenu); + if (sequence!=null) + { + add(hideInsertions); + } + // annotations configuration panel suppressed for now // groupMenu.add(chooseAnnotations); - groupMenu.add(showAnnotationsMenu); - groupMenu.add(hideAnnotationsMenu); + + /* + * Add show/hide annotations to the Sequence menu, and to the Selection menu + * (if a selection group is in force). + */ + sequenceMenu.add(seqShowAnnotationsMenu); + sequenceMenu.add(seqHideAnnotationsMenu); + sequenceMenu.add(seqAddReferenceAnnotations); + groupMenu.add(groupShowAnnotationsMenu); + groupMenu.add(groupHideAnnotationsMenu); + groupMenu.add(groupAddReferenceAnnotations); groupMenu.add(editMenu); groupMenu.add(outputMenu); groupMenu.add(sequenceFeature); @@ -1575,6 +1491,7 @@ public class PopupMenu extends JPopupMenu groupMenu.add(jMenu1); sequenceMenu.add(sequenceName); sequenceMenu.add(sequenceDetails); + sequenceMenu.add(makeReferenceSeq); colourMenu.add(textColour); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); @@ -1591,10 +1508,8 @@ 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) @@ -1620,7 +1535,6 @@ 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); @@ -1641,9 +1555,6 @@ 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() { @@ -1800,6 +1711,192 @@ public class PopupMenu extends JPopupMenu }); } + /** + * Check for any annotations on the underlying dataset sequences (for the + * current selection group) which are not 'on the alignment'.If any are found, + * enable the option to add them to the alignment. The criteria for 'on the + * alignment' is finding an alignment annotation on the alignment, matched on + * calcId, label and sequenceRef. + * + * A tooltip is also constructed that displays the source (calcId) and type + * (label) of the annotations that can be added. + * + * @param menuItem + * @param 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); + } + } + if (!candidates.isEmpty()) + { + /* + * Found annotations that could be added. Enable the menu item, and + * configure its tooltip and action. + */ + menuItem.setEnabled(true); + for (String calcId : tipEntries.keySet()) + { + tooltip.append("
" + calcId + "/" + tipEntries.get(calcId)); + } + String tooltipText = JvSwingUtils.wrapTooltip(true, + tooltip.toString()); + menuItem.setToolTipText(tooltipText); + + menuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + addReferenceAnnotations_actionPerformed(candidates); + } + }); + } + } + + /** + * Add annotations to the sequences and to the alignment. + * + * @param candidates + * a map whose keys are sequences on the alignment, and values a list + * of annotations to add to each sequence + */ + 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; + } + } + refresh(); + } + + protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent) + { + if (!ap.av.getAlignment().hasSeqrep()) + { + // initialise the display flags so the user sees something happen + ap.av.setDisplayReferenceSeq(true); + ap.av.setColourByReferenceSeq(true); + ap.av.getAlignment().setSeqrep(sequence); + } + else + { + if (ap.av.getAlignment().getSeqrep() == sequence) + { + ap.av.getAlignment().setSeqrep(null); + } + else + { + ap.av.getAlignment().setSeqrep(sequence); + } + } + refresh(); + } + + protected void hideInsertions_actionPerformed(ActionEvent actionEvent) + { + if (sequence != null) + { + ColumnSelection cs = ap.av.getColumnSelection(); + if (cs == null) + { + cs = new ColumnSelection(); + } + cs.hideInsertionsFor(sequence); + ap.av.setColumnSelection(cs); + } + refresh(); + } protected void sequenceSelectionDetails_actionPerformed() { createSequenceDetailsReport(ap.av.getSequenceSelection()); @@ -1821,7 +1918,7 @@ public class PopupMenu extends JPopupMenu + MessageManager .formatMessage( "label.create_sequence_details_report_annotation_for", - new String[] + new Object[] { seq.getDisplayId(true) }) + "

"); new SequenceAnnotationReport(null) .createSequenceAnnotationReport( @@ -1830,16 +1927,18 @@ public class PopupMenu extends JPopupMenu true, true, false, - (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax + (ap.getSeqPanel().seqCanvas.fr != null) ? ap + .getSeqPanel().seqCanvas.fr + .getMinMax() : null); contents.append("

"); } cap.setText("" + contents.toString() + ""); - Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage( - "label.sequece_details_for", - (sequences.length == 1 ? new String[] - { sequences[0].getDisplayId(true) } : new String[] + 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); } @@ -2003,14 +2102,14 @@ 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(); @@ -2361,15 +2460,7 @@ 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 ? @@ -2393,7 +2484,8 @@ public class PopupMenu extends JPopupMenu if (sg != null) { - int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(), + List startEnd = ap.av.getVisibleRegionBoundaries( + sg.getStartRes(), sg.getEndRes() + 1); String description; @@ -2432,7 +2524,7 @@ public class PopupMenu extends JPopupMenu CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", new String[] + "label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); String[] omitHidden = null; @@ -2451,10 +2543,10 @@ 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[] + "label.select_pdb_file_for", new Object[] { sequence.getDisplayId(false) })); chooser.setToolTipText(MessageManager.formatMessage( - "label.load_pdb_file_associate_with_sequence", new String[] + "label.load_pdb_file_associate_with_sequence", new Object[] { sequence.getDisplayId(false) })); int value = chooser.showOpenDialog(null); @@ -2464,23 +2556,13 @@ public class PopupMenu extends JPopupMenu String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, - jalview.io.AppletFormatAdapter.FILE, sequence, true); + jalview.io.AppletFormatAdapter.FILE, sequence, true, + Desktop.instance); } } - // 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, @@ -2546,7 +2628,7 @@ public class PopupMenu extends JPopupMenu System.arraycopy(features, 0, tfeatures, 0, rsize); features = tfeatures; seqs = rseqs; - if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, + if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, true, ap)) { ap.alignFrame.setShowSeqFeatures(true); @@ -2589,7 +2671,9 @@ public class PopupMenu extends JPopupMenu if (sg != null) { if (sequence == null) + { sequence = sg.getSequenceAt(0); + } EditNameDialog dialog = new EditNameDialog( sequence.getSequenceAsString(sg.getStartRes(), @@ -2602,7 +2686,7 @@ public class PopupMenu extends JPopupMenu { EditCommand editCommand = new EditCommand( MessageManager.getString("label.edit_sequences"), - EditCommand.REPLACE, dialog.getName().replace(' ', + Action.REPLACE, dialog.getName().replace(' ', ap.av.getGapCharacter()), sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());