X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=ad3d6af347997305f9483e80c07b1b5dbf1e490d;hb=e373651097c72eb6c9ca6009fb70d47341e8f405;hp=78c159257dda91e618202bc33c82dff99af1a652;hpb=2e7da637a195ff484f92a333675284f071657cd6;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 78c1592..ad3d6af 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 +20,38 @@ */ package jalview.gui; +import java.awt.Color; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.util.Arrays; +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.AlignmentUtils; 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 +60,6 @@ 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 +80,6 @@ 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.HashMap; -import java.util.Hashtable; -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 +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(); @@ -137,6 +137,8 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceDetails = new JMenuItem(); JMenuItem sequenceSelDetails = new JMenuItem(); + + JMenuItem makeReferenceSeq = new JMenuItem(); JMenuItem chooseAnnotations = new JMenuItem(); @@ -176,23 +178,25 @@ 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(); - JMenu hideAnnotationsMenu = new JMenu(); + JMenuItem seqAddReferenceAnnotations = new JMenuItem( + MessageManager.getString("label.add_reference_annotations")); - JMenuItem addDatasequenceAnnotations = new JMenuItem(); + JMenu groupShowAnnotationsMenu = new JMenu(); + + JMenu groupHideAnnotationsMenu = new JMenu(); + + JMenuItem groupAddReferenceAnnotations = new JMenuItem( + MessageManager.getString("label.add_reference_annotations")); JMenuItem sequenceFeature = new JMenuItem(); @@ -200,17 +204,16 @@ public class PopupMenu extends JPopupMenu JMenu jMenu1 = new JMenu(); - JMenu structureMenu = new JMenu(); + JMenuItem proteinStructureMenu = 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(); + /** * Creates a new PopupMenu object. * @@ -259,7 +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++) { @@ -279,9 +281,27 @@ 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): */ - buildAnnotationTypesMenus(); + 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): + */ + final List selectedGroup = (ap.av.getSelectionGroup() == null ? Collections + . emptyList() : ap.av.getSelectionGroup() + .getSequences()); + buildAnnotationTypesMenus(groupShowAnnotationsMenu, + groupHideAnnotationsMenu, selectedGroup); + configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, + selectedGroup); try { @@ -295,107 +315,65 @@ public class PopupMenu extends JPopupMenu if (seq != null) { sequenceMenu.setText(sequence.getName()); - - if (seq.getDatasetSequence().getPDBId() != null - && seq.getDatasetSequence().getPDBId().size() > 0) + if (seq == ap.av.getAlignment().getSeqrep()) { - 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("Unmark representative"); + } else { + makeReferenceSeq.setText("Mark as representative"); } - 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() + /* + * add menu items to 2D-render any alignment or sequence secondary + * structure annotation + */ + AlignmentAnnotation[] aas = ap.av.getAlignment() .getAlignmentAnnotation(); - for (int i = 0; i < aa.length; i++) + if (aas != null) { - if (aa[i].getRNAStruc() != null) + for (final AlignmentAnnotation aa : aas) { - final String rnastruc = aa[i].getRNAStruc(); - final String structureLine = aa[i].label; - 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].getRNAStruc() != null) + 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[] + "label.2d_rna_sequence_name", new Object[] { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { @@ -403,17 +381,13 @@ public class PopupMenu extends JPopupMenu 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); } } } - } menuItem = new JMenuItem( @@ -432,7 +406,7 @@ 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() { @@ -501,7 +475,7 @@ 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")); @@ -602,50 +576,6 @@ 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 @@ -670,7 +600,8 @@ public class PopupMenu extends JPopupMenu if (seq == null) { sequenceMenu.setVisible(false); - structureMenu.setVisible(false); + proteinStructureMenu.setVisible(false); + rnaStructureMenu.setVisible(false); } if (links != null && links.size() > 0) @@ -797,9 +728,10 @@ 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 @@ -807,230 +739,82 @@ 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) { - final SequenceGroup selectionGroup = ap.av.getSelectionGroup(); - if (selectionGroup == null) - { - // this menu option is only for a selection - return; - } + showMenu.removeAll(); + hideMenu.removeAll(); - showAnnotationsMenu.removeAll(); - hideAnnotationsMenu.removeAll(); final List all = Arrays.asList(ALL_ANNOTATIONS); - addAnnotationTypeToShowHide(showAnnotationsMenu, "", all, true, true); - addAnnotationTypeToShowHide(hideAnnotationsMenu, "", all, true, false); - showAnnotationsMenu.addSeparator(); - hideAnnotationsMenu.addSeparator(); + addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true); + addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true, + false); + showMenu.addSeparator(); + hideMenu.addSeparator(); final AlignmentAnnotation[] annotations = ap.getAlignment() .getAlignmentAnnotation(); - BitSet visibleGraphGroups = PopupMenu - .getVisibleLineGraphGroups(annotations); /* * Find shown/hidden annotations types, distinguished by source (calcId), - * and grouped by graphGroup. + * 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 HashMap>>(); - Map>> hiddenTypes = new HashMap>>(); - PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes, - visibleGraphGroups, annotations, selectionGroup); + Map>> shownTypes = new LinkedHashMap>>(); + Map>> hiddenTypes = new LinkedHashMap>>(); + AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, + hiddenTypes, + AlignmentAnnotationUtils.asList(annotations), + forSequences); for (String calcId : hiddenTypes.keySet()) { for (List type : hiddenTypes.get(calcId)) { - addAnnotationTypeToShowHide(showAnnotationsMenu, calcId, type, - false, true); + addAnnotationTypeToShowHide(showMenu, forSequences, + calcId, type, false, true); } } + // grey out 'show annotations' if none are hidden + showMenu.setEnabled(!hiddenTypes.isEmpty()); for (String calcId : shownTypes.keySet()) { for (List type : shownTypes.get(calcId)) { - addAnnotationTypeToShowHide(hideAnnotationsMenu, calcId, type, - false, false); + addAnnotationTypeToShowHide(hideMenu, forSequences, + calcId, type, false, false); } } + // grey out 'hide annotations' if none are shown + hideMenu.setEnabled(!shownTypes.isEmpty()); } /** - * 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
    • - *
+ * Returns a list of sequences - either the current selection group (if there + * is one), else the specified single sequence. * - * @param shownTypes - * a map, keyed by calcId (annotation source), whose entries are the - * lists of annotation types found for the calcId; each annotation - * type in turn may be a list (in the case of grouped annotations) - * @param hiddenTypes - * a map, similar to shownTypes, but for hidden annotation types - * @param visibleGraphGroups - * a lookup keyed by graphGroup identifier - * @param annotations - * the annotations on the alignment to scan - * @param sequenceGroup - * the sequence group to restrict search to + * @param seq + * @return */ - public static void getAnnotationTypesForShowHide( - Map>> shownTypes, - Map>> hiddenTypes, - BitSet visibleGraphGroups, AlignmentAnnotation[] annotations, - SequenceGroup sequenceGroup) + protected List getSequenceScope(SequenceI seq) { - /* - * Build a lookup, by calcId (annotation source), of all annotation types in - * each graph group. - */ - Map>> groupLabels = new HashMap>>(); - - // trackers for which calcId!label combinations we have dealt with - List addedToShown = new ArrayList(); - List addedToHidden = new ArrayList(); - - for (AlignmentAnnotation aa : annotations) - { - - if (sequenceGroup == null - || (aa.sequenceRef != null && sequenceGroup.getSequences() - .contains(aa.sequenceRef))) - { - String calcId = aa.getCalcId(); - - /* - * Build a 'composite label' for types in line graph groups. - */ - final List labelAsList = new ArrayList(); - final String displayLabel = aa.label; - labelAsList.add(displayLabel); - if (aa.graph == AlignmentAnnotation.LINE_GRAPH - && aa.graphGroup > -1) - { - if (!groupLabels.containsKey(calcId)) - { - groupLabels.put(calcId, new HashMap>()); - } - Map> groupLabelsForCalcId = groupLabels - .get(calcId); - if (groupLabelsForCalcId.containsKey(aa.graphGroup)) - { - if (!groupLabelsForCalcId.get(aa.graphGroup).contains( - displayLabel)) - { - groupLabelsForCalcId.get(aa.graphGroup).add(displayLabel); - } - } - else - { - groupLabelsForCalcId.put(aa.graphGroup, labelAsList); - } - } - else - /* - * 'Simple case' - not a grouped annotation type - list of one label - * only - */ - { - String rememberAs = calcId + "!" + displayLabel; - if (aa.visible && !addedToShown.contains(rememberAs)) - { - if (!shownTypes.containsKey(calcId)) - { - shownTypes.put(calcId, new ArrayList>()); - } - shownTypes.get(calcId).add(labelAsList); - addedToShown.add(rememberAs); - } - else - { - if (!aa.visible && !addedToHidden.contains(rememberAs)) - { - if (!hiddenTypes.containsKey(calcId)) - { - hiddenTypes.put(calcId, new ArrayList>()); - } - hiddenTypes.get(calcId).add(labelAsList); - addedToHidden.add(rememberAs); - } - } - } - } - } - /* - * finally add the 'composite group labels' to the appropriate lists, - * depending on whether the group is identified as visible or hidden - */ - for (String calcId : groupLabels.keySet()) + List forSequences = null; + final SequenceGroup selectionGroup = ap.av.getSelectionGroup(); + if (selectionGroup != null && selectionGroup.getSize() > 0) { - for (int group : groupLabels.get(calcId).keySet()) - { - final List groupLabel = groupLabels.get(calcId).get(group); - if (visibleGraphGroups.get(group)) - { - if (!shownTypes.containsKey(calcId)) - { - shownTypes.put(calcId, new ArrayList>()); - } - shownTypes.get(calcId).add(groupLabel); - } - else - { - if (!hiddenTypes.containsKey(calcId)) - { - hiddenTypes.put(calcId, new ArrayList>()); - } - hiddenTypes.get(calcId).add(groupLabel); - } - } + forSequences = selectionGroup.getSequences(); } - } - - /** - * 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. - * - * @see AnnotationRenderer#drawComponent - * @param annotations - * @return - */ - public static BitSet getVisibleLineGraphGroups( - AlignmentAnnotation[] annotations) - { - // todo move to a utility class - BitSet result = new BitSet(); - for (AlignmentAnnotation ann : annotations) + else { - if (ann.graph == AlignmentAnnotation.LINE_GRAPH && ann.visible) - { - int gg = ann.graphGroup; - if (gg > -1) - { - result.set(gg); - } - } + forSequences = seq == null ? Collections. emptyList() + : Arrays.asList(seq); } - return result; + return forSequences; } /** @@ -1039,6 +823,8 @@ 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 @@ -1049,11 +835,12 @@ public class PopupMenu extends JPopupMenu * type, else hide */ protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu, - String calcId, final List 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); + 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() @@ -1061,42 +848,14 @@ public class PopupMenu extends JPopupMenu @Override public void actionPerformed(ActionEvent e) { - showHideAnnotation_actionPerformed(types, 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 selection. - * - * @param types - * @param anyType - * @param doShow - */ - protected void showHideAnnotation_actionPerformed( - Collection types, boolean anyType, boolean doShow) - { - for (AlignmentAnnotation aa : ap.getAlignment() - .getAlignmentAnnotation()) - { - // TODO: select by calcId (source of annotation) as well as label - // e.g. by refactoring of buildAnnotationTypeMenus to as - // to construct the actionPerformed methods as the calcId/labels are found - if (anyType || types.contains(aa.label)) - { - if ((aa.sequenceRef != null) - && ap.av.getSelectionGroup().getSequences() - .contains(aa.sequenceRef)) - { - aa.visible = doShow; - } - } - } - refresh(); - } - private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks) { @@ -1224,8 +983,6 @@ 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 @@ -1265,7 +1022,7 @@ 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() { @@ -1536,32 +1293,7 @@ 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() { @@ -1582,11 +1314,14 @@ public class PopupMenu extends JPopupMenu }); outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "..."); - showAnnotationsMenu.setText(MessageManager + seqShowAnnotationsMenu.setText(MessageManager .getString("label.show_annotations")); - hideAnnotationsMenu.setText(MessageManager + seqHideAnnotationsMenu.setText(MessageManager + .getString("label.hide_annotations")); + groupShowAnnotationsMenu.setText(MessageManager + .getString("label.show_annotations")); + groupHideAnnotationsMenu.setText(MessageManager .getString("label.hide_annotations")); - configureReferenceAnnotationsMenu(); sequenceFeature.setText(MessageManager .getString("label.create_sequence_feature")); sequenceFeature.addActionListener(new ActionListener() @@ -1607,9 +1342,26 @@ public class PopupMenu extends JPopupMenu } }); jMenu1.setText(MessageManager.getString("label.group")); - structureMenu.setText(MessageManager.getString("label.structure")); - viewStructureMenu.setText(MessageManager - .getString("label.view_structure")); + proteinStructureMenu.setText(MessageManager + .getString("label.view_protein_structure")); + proteinStructureMenu.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); + } + }); + + rnaStructureMenu.setText(MessageManager + .getString("label.view_rna_structure")); + // colStructureMenu.setText("Colour By Structure"); editSequence.setText(MessageManager.getString("label.edit_sequence") + "..."); @@ -1621,7 +1373,28 @@ 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 @@ -1631,11 +1404,25 @@ public class PopupMenu extends JPopupMenu groupMenu.add(sequenceSelDetails); add(groupMenu); add(sequenceMenu); - this.add(structureMenu); + add(rnaStructureMenu); + add(proteinStructureMenu); + if (sequence!=null) + { + add(hideInsertions); + } + // annotations configuration panel suppressed for now // groupMenu.add(chooseAnnotations); - groupMenu.add(showAnnotationsMenu); - groupMenu.add(hideAnnotationsMenu); - groupMenu.add(addDatasequenceAnnotations); + + /* + * 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); @@ -1644,6 +1431,7 @@ 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); @@ -1660,10 +1448,8 @@ 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) @@ -1689,7 +1475,6 @@ 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); @@ -1710,9 +1495,6 @@ 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() { @@ -1871,89 +1653,50 @@ 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, + * 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 annotation that matches on - * sequenceRef.datasetSequence, calcId and label. + * 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() + protected void configureReferenceAnnotationsMenu( + JMenuItem menuItem, List forSequences) { - addDatasequenceAnnotations.setText(MessageManager - .getString("label.add_reference_annotations")); - addDatasequenceAnnotations.setEnabled(false); - - /* - * Temporary store so we can write distinct calcId / type pairs on the - * tooltip. - */ - Map tipEntries = new HashMap(); - StringBuilder tooltip = new StringBuilder(64); - tooltip.append(MessageManager.getString("label.add_annotations_for")); - - // this menu option only applies for a Selection - if (this.ap.av.getSelectionGroup() == null) - { - return; - } + menuItem.setEnabled(false); /* - * For each sequence selected in the alignment, make a list of any - * annotations on the underlying dataset sequence which are not already on - * the sequence in the alignment. - * - * Build a map of { alignmentSequence, } + * Temporary store to hold distinct calcId / type pairs for the tooltip. + * Using TreeMap means calcIds are shown in alphabetical order. */ - final Map> candidates = new HashMap>(); - for (SequenceI seq : this.ap.av.getSelectionGroup().getSequences()) - { - 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) - { - /* - * If the sequence has no annotation that matches this one, then add - * this one to the results list. - */ - if (seq.getAlignmentAnnotations(dsann.getCalcId(), dsann.label) - .isEmpty()) - { - result.add(dsann); - tipEntries.put(dsann.getCalcId(), dsann.label); - } - } - /* - * Save any addable annotations for this sequence - */ - if (!result.isEmpty()) - { - candidates.put(seq, result); - } - } + Map tipEntries = new TreeMap(); + final Map> candidates = new LinkedHashMap>(); + 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. */ - addDatasequenceAnnotations.setEnabled(true); + menuItem.setEnabled(true); for (String calcId : tipEntries.keySet()) { tooltip.append("
" + calcId + "/" + tipEntries.get(calcId)); } String tooltipText = JvSwingUtils.wrapTooltip(true, tooltip.toString()); - addDatasequenceAnnotations.setToolTipText(tooltipText); + menuItem.setToolTipText(tooltipText); - addDatasequenceAnnotations.addActionListener(new ActionListener() + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1974,33 +1717,50 @@ public class PopupMenu extends JPopupMenu protected void addReferenceAnnotations_actionPerformed( Map> candidates) { - for (SequenceI seq : candidates.keySet()) + final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup(); + final AlignmentI alignment = this.ap.getAlignment(); + AlignmentUtils.addReferenceAnnotations(candidates, alignment, + selectionGroup); + 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 { - for (AlignmentAnnotation ann : candidates.get(seq)) + if (ap.av.getAlignment().getSeqrep() == sequence) { - 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 correct copyAnn.datasetSequence) - seq.addAlignmentAnnotation(copyAnn); - // adjust for gaps - copyAnn.adjustForAlignment(); - // add to the alignment and set visible - this.ap.getAlignment().addAnnotation(copyAnn); - copyAnn.visible = true; + 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()); @@ -2022,7 +1782,7 @@ 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( @@ -2031,16 +1791,18 @@ 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); } @@ -2204,14 +1966,14 @@ 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(); @@ -2562,15 +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 ? @@ -2594,7 +2348,8 @@ 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; @@ -2633,7 +2388,7 @@ 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; @@ -2642,8 +2397,8 @@ 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() @@ -2652,10 +2407,10 @@ 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); @@ -2665,23 +2420,13 @@ 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, @@ -2747,7 +2492,7 @@ 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); @@ -2790,7 +2535,9 @@ public class PopupMenu extends JPopupMenu if (sg != null) { if (sequence == null) + { sequence = sg.getSequenceAt(0); + } EditNameDialog dialog = new EditNameDialog( sequence.getSequenceAsString(sg.getStartRes(), @@ -2803,7 +2550,7 @@ 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());