X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=b574dddd50d0fe7d608473cf31b800bf8d129080;hb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;hp=3ea689fdba5fd1dc131601f116aaa32e0f2b8b18;hpb=2273eba5668e5340354da60fed329c6c716cc439;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 3ea689f..b574ddd 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. * @@ -22,7 +22,9 @@ package jalview.gui; import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentAnnotationUtils; +import jalview.analysis.AlignmentUtils; import jalview.analysis.Conservation; +import jalview.bin.Cache; import jalview.commands.ChangeCaseCommand; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; @@ -30,28 +32,20 @@ import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; import jalview.datamodel.DBRefEntry; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; -import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.gui.ColourMenuHelper.ColourChangeListener; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FormatAdapter; import jalview.io.SequenceAnnotationReport; -import jalview.schemes.AnnotationColourGradient; import jalview.schemes.Blosum62ColourScheme; -import jalview.schemes.BuriedColourScheme; -import jalview.schemes.ClustalxColourScheme; -import jalview.schemes.HelixColourScheme; -import jalview.schemes.HydrophobicColourScheme; -import jalview.schemes.NucleotideColourScheme; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemes; import jalview.schemes.PIDColourScheme; -import jalview.schemes.PurinePyrimidineColourScheme; -import jalview.schemes.ResidueProperties; -import jalview.schemes.StrandColourScheme; -import jalview.schemes.TaylorColourScheme; -import jalview.schemes.TurnColourScheme; -import jalview.schemes.UserColourScheme; -import jalview.schemes.ZappoColourScheme; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; @@ -62,23 +56,22 @@ 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.Collections; import java.util.Hashtable; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; +import java.util.SortedMap; import java.util.TreeMap; import java.util.Vector; -import 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! @@ -86,51 +79,20 @@ import javax.swing.JRadioButtonMenuItem; * @author $author$ * @version $Revision: 1.118 $ */ -public class PopupMenu extends JPopupMenu +public class PopupMenu extends JPopupMenu implements ColourChangeListener { - private static final String ALL_ANNOTATIONS = "All"; - - private static final String COMMA = ","; - JMenu groupMenu = new JMenu(); JMenuItem groupName = new JMenuItem(); - protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); - protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem(); - protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); - - // protected JRadioButtonMenuItem covariationColour = new - // JRadioButtonMenuItem(); - - JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); + protected JMenuItem modifyPID = new JMenuItem(); protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + protected JMenuItem modifyConservation = new JMenuItem(); + AlignmentPanel ap; JMenu sequenceMenu = new JMenu(); @@ -141,6 +103,8 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceSelDetails = new JMenuItem(); + JMenuItem makeReferenceSeq = new JMenuItem(); + JMenuItem chooseAnnotations = new JMenuItem(); SequenceI sequence; @@ -151,8 +115,6 @@ public class PopupMenu extends JPopupMenu JMenuItem outline = new JMenuItem(); - JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); - JMenu colourMenu = new JMenu(); JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); @@ -177,31 +139,21 @@ public class PopupMenu extends JPopupMenu JMenu pdbMenu = new JMenu(); - 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 seqShowAnnotationsMenu = new JMenu(); 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(); @@ -209,39 +161,45 @@ public class PopupMenu extends JPopupMenu JMenu jMenu1 = new JMenu(); - JMenu structureMenu = new JMenu(); + 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(); + /** * Creates a new PopupMenu object. * * @param ap - * DOCUMENT ME! * @param seq - * DOCUMENT ME! + * @param features + * non-positional features (for seq not null), or positional features + * at residue (for seq equal to null) */ - public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links) + public PopupMenu(final AlignmentPanel ap, SequenceI seq, + List features) { - this(ap, seq, links, null); + this(ap, seq, features, null); } /** + * Constructor * - * @param ap + * @param alignPanel * @param seq - * @param links + * the sequence under the cursor if in the Id panel, null if in the + * sequence panel + * @param features + * non-positional features if in the Id panel, features at the + * clicked residue if in the sequence panel * @param groupLinks */ - public PopupMenu(final AlignmentPanel ap, final SequenceI seq, - Vector links, Vector groupLinks) + public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq, + List features, List groupLinks) { // ///////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -249,33 +207,14 @@ public class PopupMenu extends JPopupMenu // // If from the IDPanel, we must display the sequence menu // //////////////////////////////////////////////////////// - this.ap = ap; + this.ap = alignPanel; sequence = seq; - ButtonGroup colours = new ButtonGroup(); - colours.add(noColourmenuItem); - colours.add(clustalColour); - colours.add(zappoColour); - colours.add(taylorColour); - colours.add(hydrophobicityColour); - colours.add(helixColour); - colours.add(strandColour); - colours.add(turnColour); - colours.add(buriedColour); - colours.add(abovePIDColour); - colours.add(userDefinedColour); - colours.add(PIDColour); - colours.add(BLOSUM62Colour); - colours.add(purinePyrimidineColour); - colours.add(RNAInteractionColour); - // colours.add(covariationColour); - - for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) - { - JMenuItem item = new JMenuItem( - jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]); - - item.addActionListener(new java.awt.event.ActionListener() + for (String ff : FileFormats.getInstance().getWritableFormats(true)) + { + JMenuItem item = new JMenuItem(ff); + + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -292,8 +231,9 @@ public class PopupMenu extends JPopupMenu * '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)); + final List selectedSequence = (seq == null + ? Collections. emptyList() + : Arrays.asList(seq)); buildAnnotationTypesMenus(seqShowAnnotationsMenu, seqHideAnnotationsMenu, selectedSequence); configureReferenceAnnotationsMenu(seqAddReferenceAnnotations, @@ -302,9 +242,9 @@ public class PopupMenu extends JPopupMenu /* * And repeat for the current selection group (if there is one): */ - final List selectedGroup = (ap.av.getSelectionGroup() == null ? Collections - . emptyList() : ap.av.getSelectionGroup() - .getSequences()); + final List selectedGroup = (alignPanel.av.getSelectionGroup() == null + ? Collections. emptyList() + : alignPanel.av.getSelectionGroup().getSequences()); buildAnnotationTypesMenus(groupShowAnnotationsMenu, groupHideAnnotationsMenu, selectedGroup); configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, @@ -322,131 +262,93 @@ public class PopupMenu extends JPopupMenu if (seq != null) { sequenceMenu.setText(sequence.getName()); - - if (seq.getDatasetSequence().getPDBId() != null - && seq.getDatasetSequence().getPDBId().size() > 0) + if (seq == alignPanel.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( + MessageManager.getString("action.unmark_as_reference")); } else { - if (ap.av.getAlignment().isNucleotide() == false) - { - structureMenu.remove(viewStructureMenu); - } - // structureMenu.remove(colStructureMenu); + makeReferenceSeq.setText( + MessageManager.getString("action.set_as_reference")); } - if (ap.av.getAlignment().isNucleotide() == true) + if (!alignPanel.av.getAlignment().isNucleotide()) + { + remove(rnaStructureMenu); + } + 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 = alignPanel.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 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, alignPanel); + } + }); + 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[] + "label.2d_rna_sequence_name", new Object[] { seq.getName() })); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new 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, alignPanel); } }); - viewStructureMenu.add(menuItem); + rnaStructureMenu.add(menuItem); } } } - + if (rnaStructureMenu.getItemCount() == origCount) + { + remove(rnaStructureMenu); + } } menuItem = new JMenuItem( MessageManager.getString("action.hide_sequences")); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -456,13 +358,13 @@ public class PopupMenu extends JPopupMenu }); add(menuItem); - if (ap.av.getSelectionGroup() != null - && ap.av.getSelectionGroup().getSize() > 1) + if (alignPanel.av.getSelectionGroup() != null + && alignPanel.av.getSelectionGroup().getSize() > 1) { - menuItem = new JMenuItem(MessageManager.formatMessage( - "label.represent_group_with", new String[] + menuItem = new JMenuItem(MessageManager + .formatMessage("label.represent_group_with", new Object[] { seq.getName() })); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -473,12 +375,12 @@ public class PopupMenu extends JPopupMenu sequenceMenu.add(menuItem); } - if (ap.av.hasHiddenRows()) + if (alignPanel.av.hasHiddenRows()) { - final int index = ap.av.getAlignment().findIndex(seq); + final int index = alignPanel.av.getAlignment().findIndex(seq); - if (ap.av.adjustForHiddenSeqs(index) - - ap.av.adjustForHiddenSeqs(index - 1) > 1) + if (alignPanel.av.adjustForHiddenSeqs(index) + - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1) { menuItem = new JMenuItem( MessageManager.getString("action.reveal_sequences")); @@ -487,10 +389,10 @@ public class PopupMenu extends JPopupMenu @Override public void actionPerformed(ActionEvent e) { - ap.av.showSequence(index); - if (ap.overviewPanel != null) + alignPanel.av.showSequence(index); + if (alignPanel.overviewPanel != null) { - ap.overviewPanel.updateOverviewImage(); + alignPanel.overviewPanel.updateOverviewImage(); } } }); @@ -499,7 +401,7 @@ public class PopupMenu extends JPopupMenu } } // for the case when no sequences are even visible - if (ap.av.hasHiddenRows()) + if (alignPanel.av.hasHiddenRows()) { { menuItem = new JMenuItem( @@ -509,93 +411,45 @@ public class PopupMenu extends JPopupMenu @Override public void actionPerformed(ActionEvent e) { - ap.av.showAllHiddenSeqs(); - if (ap.overviewPanel != null) + alignPanel.av.showAllHiddenSeqs(); + if (alignPanel.overviewPanel != null) { - ap.overviewPanel.updateOverviewImage(); + alignPanel.overviewPanel.updateOverviewImage(); } } }); add(menuItem); } - } - SequenceGroup sg = ap.av.getSelectionGroup(); - boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment() - .getGroups().contains(sg) : false; + SequenceGroup sg = alignPanel.av.getSelectionGroup(); + boolean isDefinedGroup = (sg != null) + ? alignPanel.av.getAlignment().getGroups().contains(sg) + : false; if (sg != null && sg.getSize() > 0) { - groupName.setText(MessageManager.formatMessage("label.name_param", - new String[] - { sg.getName() })); groupName.setText(MessageManager .getString("label.edit_name_and_description_current_group")); - if (sg.cs instanceof ZappoColourScheme) - { - zappoColour.setSelected(true); - } - else if (sg.cs instanceof TaylorColourScheme) - { - taylorColour.setSelected(true); - } - else if (sg.cs instanceof PIDColourScheme) - { - PIDColour.setSelected(true); - } - else if (sg.cs instanceof Blosum62ColourScheme) - { - BLOSUM62Colour.setSelected(true); - } - else if (sg.cs instanceof UserColourScheme) - { - userDefinedColour.setSelected(true); - } - else if (sg.cs instanceof HydrophobicColourScheme) - { - hydrophobicityColour.setSelected(true); - } - else if (sg.cs instanceof HelixColourScheme) - { - helixColour.setSelected(true); - } - else if (sg.cs instanceof StrandColourScheme) - { - strandColour.setSelected(true); - } - else if (sg.cs instanceof TurnColourScheme) - { - turnColour.setSelected(true); - } - else if (sg.cs instanceof BuriedColourScheme) - { - buriedColour.setSelected(true); - } - else if (sg.cs instanceof ClustalxColourScheme) - { - clustalColour.setSelected(true); - } - else if (sg.cs instanceof PurinePyrimidineColourScheme) - { - purinePyrimidineColour.setSelected(true); - } + ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme()); - /* - * else if (sg.cs instanceof CovariationColourScheme) { - * covariationColour.setSelected(true); } - */ - else - { - noColourmenuItem.setSelected(true); - } + conservationMenuItem.setEnabled(!sg.isNucleotide()); - if (sg.cs != null && sg.cs.conservationApplied()) + if (sg.cs != null) { - conservationMenuItem.setSelected(true); + if (sg.cs.conservationApplied()) + { + conservationMenuItem.setSelected(true); + } + if (sg.cs.getThreshold() > 0) + { + abovePIDColour.setSelected(true); + } } + modifyConservation.setEnabled(conservationMenuItem.isSelected()); + modifyPID.setEnabled(abovePIDColour.isSelected()); displayNonconserved.setSelected(sg.getShowNonconserved()); showText.setSelected(sg.getDisplayText()); showColourText.setSelected(sg.getColourText()); @@ -606,11 +460,12 @@ public class PopupMenu extends JPopupMenu buildGroupURLMenu(sg, groupLinks); } // Add a 'show all structures' for the current selection - Hashtable pdbe = new Hashtable(), reppdb = new Hashtable(); + Hashtable pdbe = new Hashtable<>(), reppdb = new Hashtable<>(); + SequenceI sqass = null; - for (SequenceI sq : ap.av.getSequenceSelection()) + for (SequenceI sq : alignPanel.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)); @@ -626,54 +481,10 @@ public class PopupMenu extends JPopupMenu } if (pdbe.size() > 0) { - final PDBEntry[] pe = pdbe.values().toArray( - new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray( - new PDBEntry[reppdb.size()]); + final PDBEntry[] pe = pdbe.values() + .toArray(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 @@ -698,121 +509,142 @@ public class PopupMenu extends JPopupMenu if (seq == null) { sequenceMenu.setVisible(false); - structureMenu.setVisible(false); + pdbStructureDialog.setVisible(false); + rnaStructureMenu.setVisible(false); + } + + addLinks(seq, features); + + if (seq == null) + { + addFeatureDetails(features); } + } - if (links != null && links.size() > 0) + /** + * Add a link to show feature details for each sequence feature + * + * @param features + */ + protected void addFeatureDetails(List features) + { + if (features.isEmpty()) { + return; + } + JMenu details = new JMenu( + MessageManager.getString("label.feature_details")); + add(details); - JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); - Vector linkset = new Vector(); - for (int i = 0; i < links.size(); i++) + for (final SequenceFeature sf : features) + { + int start = sf.getBegin(); + int end = sf.getEnd(); + String desc = null; + if (start == end) { - String link = links.elementAt(i).toString(); - UrlLink urlLink = null; - try - { - urlLink = new UrlLink(link); - } catch (Exception foo) - { - jalview.bin.Cache.log.error("Exception for URLLink '" + link - + "'", foo); - continue; - } - ; - if (!urlLink.isValid()) + desc = String.format("%s %d", sf.getType(), start); + } + else + { + desc = String.format("%s %d-%d", sf.getType(), start, end); + } + if (sf.getFeatureGroup() != null) + { + desc = desc + " (" + sf.getFeatureGroup() + ")"; + } + JMenuItem item = new JMenuItem(desc); + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) { - jalview.bin.Cache.log.error(urlLink.getInvalidMessage()); - continue; + showFeatureDetails(sf); } - final String label = urlLink.getLabel(); - if (seq != null && urlLink.isDynamic()) - { + }); + details.add(item); + } + } - // collect matching db-refs - DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs( - seq.getDBRef(), new String[] - { urlLink.getTarget() }); - // collect id string too - String id = seq.getName(); - String descr = seq.getDescription(); - if (descr != null && descr.length() < 1) - { - descr = null; - } + /** + * Opens a panel showing a text report of feature dteails + * + * @param sf + */ + protected void showFeatureDetails(SequenceFeature sf) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setText(sf.getDetailsReport()); + Desktop.addInternalFrame(cap, + MessageManager.getString("label.feature_details"), 500, 500); + } - if (dbr != null) - { - for (int r = 0; r < dbr.length; r++) - { - if (id != null && dbr[r].getAccessionId().equals(id)) - { - // suppress duplicate link creation for the bare sequence ID - // string with this link - id = null; - } - // create Bare ID link for this RUL - String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), - true); - if (urls != null) - { - for (int u = 0; u < urls.length; u += 2) - { - if (!linkset.contains(urls[u] + "|" + urls[u + 1])) - { - linkset.addElement(urls[u] + "|" + urls[u + 1]); - addshowLink(linkMenu, label + "|" + urls[u], - urls[u + 1]); - } - } - } - } - } - if (id != null) - { - // create Bare ID link for this RUL - String[] urls = urlLink.makeUrls(id, true); - if (urls != null) - { - for (int u = 0; u < urls.length; u += 2) - { - if (!linkset.contains(urls[u] + "|" + urls[u + 1])) - { - linkset.addElement(urls[u] + "|" + urls[u + 1]); - addshowLink(linkMenu, label, urls[u + 1]); - } - } - } - } - // Create urls from description but only for URL links which are regex - // links - if (descr != null && urlLink.getRegexReplace() != null) - { - // create link for this URL from description where regex matches - String[] urls = urlLink.makeUrls(descr, true); - if (urls != null) - { - for (int u = 0; u < urls.length; u += 2) - { - if (!linkset.contains(urls[u] + "|" + urls[u + 1])) - { - linkset.addElement(urls[u] + "|" + urls[u + 1]); - addshowLink(linkMenu, label, urls[u + 1]); - } - } - } - } - } - else + /** + * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided. + * When seq is not null, these are links for the sequence id, which may be to + * external web sites for the sequence accession, and/or links embedded in + * non-positional features. When seq is null, only links embedded in the + * provided features are added. + * + * @param seq + * @param features + */ + void addLinks(final SequenceI seq, List features) + { + JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); + + List nlinks = null; + if (seq != null) + { + nlinks = Preferences.sequenceUrlLinks.getLinksForMenu(); + } + else + { + nlinks = new ArrayList<>(); + } + + if (features != null) + { + for (SequenceFeature sf : features) + { + if (sf.links != null) { - if (!linkset.contains(label + "|" + urlLink.getUrl_prefix())) + for (String link : sf.links) { - linkset.addElement(label + "|" + urlLink.getUrl_prefix()); - // Add a non-dynamic link - addshowLink(linkMenu, label, urlLink.getUrl_prefix()); + nlinks.add(link); } } } + } + + Map> linkset = new LinkedHashMap<>(); + + for (String link : nlinks) + { + UrlLink urlLink = null; + try + { + urlLink = new UrlLink(link); + } catch (Exception foo) + { + Cache.log.error("Exception for URLLink '" + link + "'", foo); + continue; + } + + if (!urlLink.isValid()) + { + Cache.log.error(urlLink.getInvalidMessage()); + continue; + } + + urlLink.createLinksFromSeq(seq, linkset); + } + + addshowLinks(linkMenu, linkset.values()); + + // only add link menu if it has entries + if (linkMenu.getItemCount() > 0) + { if (sequence != null) { sequenceMenu.add(linkMenu); @@ -845,8 +677,11 @@ public class PopupMenu extends JPopupMenu showMenu.removeAll(); hideMenu.removeAll(); - final List all = Arrays.asList(ALL_ANNOTATIONS); - addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true); + final List all = Arrays + .asList(new String[] + { MessageManager.getString("label.all") }); + addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, + true); addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true, false); showMenu.addSeparator(); @@ -861,19 +696,17 @@ public class PopupMenu extends JPopupMenu * the insertion order, which is the order of the annotations on the * alignment. */ - Map>> shownTypes = new LinkedHashMap>>(); - Map>> hiddenTypes = new LinkedHashMap>>(); - AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, - hiddenTypes, - AlignmentAnnotationUtils.asList(annotations), - forSequences); + Map>> shownTypes = new LinkedHashMap<>(); + Map>> hiddenTypes = new LinkedHashMap<>(); + AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes, + AlignmentAnnotationUtils.asList(annotations), forSequences); for (String calcId : hiddenTypes.keySet()) { for (List type : hiddenTypes.get(calcId)) { - addAnnotationTypeToShowHide(showMenu, forSequences, - calcId, type, false, true); + addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type, + false, true); } } // grey out 'show annotations' if none are hidden @@ -883,8 +716,8 @@ 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 @@ -937,50 +770,23 @@ 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() + item.addActionListener(new ActionListener() { @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) + private void buildGroupURLMenu(SequenceGroup sg, List groupLinks) { // TODO: usability: thread off the generation of group url content so root @@ -989,24 +795,20 @@ public class PopupMenu extends JPopupMenu // ID/regex match URLs groupLinksMenu = new JMenu( MessageManager.getString("action.group_link")); - JMenu[] linkMenus = new JMenu[] - { null, new JMenu(MessageManager.getString("action.ids")), + // three types of url that might be created. + JMenu[] linkMenus = new JMenu[] { null, + new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")), - new JMenu(MessageManager.getString("action.ids_sequences")) }; // three - // types - // of url - // that - // might - // be - // created. + new JMenu(MessageManager.getString("action.ids_sequences")) }; + SequenceI[] seqs = ap.av.getSelectionAsNewSequence(); String[][] idandseqs = GroupUrlLink.formStrings(seqs); - Hashtable commonDbrefs = new Hashtable(); + Hashtable commonDbrefs = new Hashtable<>(); for (int sq = 0; sq < seqs.length; sq++) { - int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq] - .findPosition(sg.getEndRes()); + int start = seqs[sq].findPosition(sg.getStartRes()), + end = seqs[sq].findPosition(sg.getEndRes()); // just collect ids from dataset sequence // TODO: check if IDs collected from selecton group intersects with the // current selection, too @@ -1015,18 +817,17 @@ public class PopupMenu extends JPopupMenu { sqi = sqi.getDatasetSequence(); } - DBRefEntry[] dbr = sqi.getDBRef(); + DBRefEntry[] dbr = sqi.getDBRefs(); if (dbr != null && dbr.length > 0) { for (int d = 0; d < dbr.length; d++) { String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(); - Object[] sarray = (Object[]) commonDbrefs.get(src); + Object[] sarray = commonDbrefs.get(src); if (sarray == null) { sarray = new Object[2]; - sarray[0] = new int[] - { 0 }; + sarray[0] = new int[] { 0 }; sarray[1] = new String[seqs.length]; commonDbrefs.put(src, sarray); @@ -1034,8 +835,8 @@ public class PopupMenu extends JPopupMenu if (((String[]) sarray[1])[sq] == null) { - if (!dbr[d].hasMap() - || (dbr[d].getMap().locateMappedRange(start, end) != null)) + if (!dbr[d].hasMap() || (dbr[d].getMap() + .locateMappedRange(start, end) != null)) { ((String[]) sarray[1])[sq] = dbr[d].getAccessionId(); ((int[]) sarray[0])[0]++; @@ -1047,30 +848,28 @@ public class PopupMenu extends JPopupMenu // now create group links for all distinct ID/sequence sets. boolean addMenu = false; // indicates if there are any group links to give // to user - for (int i = 0; i < groupLinks.size(); i++) + for (String link : groupLinks) { - String link = groupLinks.elementAt(i).toString(); GroupUrlLink urlLink = null; try { urlLink = new GroupUrlLink(link); } catch (Exception foo) { - jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link - + "'", foo); + Cache.log.error("Exception for GroupURLLink '" + link + "'", foo); continue; } ; if (!urlLink.isValid()) { - jalview.bin.Cache.log.error(urlLink.getInvalidMessage()); + Cache.log.error(urlLink.getInvalidMessage()); continue; } final String label = urlLink.getLabel(); boolean usingNames = false; // Now see which parts of the group apply for this URL String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget()); - Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase()); + Object[] idset = commonDbrefs.get(ltarget.toUpperCase()); String[] seqstr, ids; // input to makeUrl if (idset != null) { @@ -1107,13 +906,12 @@ 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 - + (((type & 1) == 1) ? ("(" - + (usingNames ? "Names" : ltarget) + ")") : ""), + addshowLink(linkMenus[type], + label + (((type & 1) == 1) + ? ("(" + (usingNames ? "Names" : ltarget) + ")") + : ""), urlLink, urlset); addMenu = true; } @@ -1135,6 +933,16 @@ public class PopupMenu extends JPopupMenu } } + private void addshowLinks(JMenu linkMenu, + Collection> linkset) + { + for (List linkstrset : linkset) + { + // split linkstr into label and url + addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3)); + } + } + /** * add a show URL menu item to the given linkMenu * @@ -1147,10 +955,10 @@ public class PopupMenu extends JPopupMenu private void addshowLink(JMenu linkMenu, String label, final String url) { JMenuItem item = new JMenuItem(label); - item.setToolTipText(MessageManager.formatMessage( - "label.open_url_param", new String[] + item.setToolTipText(MessageManager.formatMessage("label.open_url_param", + new Object[] { url })); - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1186,13 +994,12 @@ public class PopupMenu extends JPopupMenu final GroupUrlLink urlgenerator, final Object[] urlstub) { JMenuItem item = new JMenuItem(label); - item.setToolTipText(MessageManager.formatMessage( - "label.open_url_seqs_param", - new Object[] + item.setToolTipText(MessageManager + .formatMessage("label.open_url_seqs_param", new Object[] { urlgenerator.getUrl_prefix(), urlgenerator.getNumberInvolved(urlstub) })); // TODO: put in info about what is being sent. - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1206,7 +1013,7 @@ public class PopupMenu extends JPopupMenu try { showLink(urlgenerator.constructFrom(urlstub)); - } catch (UrlStringTooLongException e) + } catch (UrlStringTooLongException e2) { } } @@ -1226,10 +1033,9 @@ public class PopupMenu extends JPopupMenu */ private void jbInit() throws Exception { - groupMenu.setText(MessageManager.getString("label.group")); groupMenu.setText(MessageManager.getString("label.selection")); groupName.setText(MessageManager.getString("label.name")); - groupName.addActionListener(new java.awt.event.ActionListener() + groupName.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1238,9 +1044,9 @@ public class PopupMenu extends JPopupMenu } }); sequenceMenu.setText(MessageManager.getString("label.sequence")); - sequenceName.setText(MessageManager - .getString("label.edit_name_description")); - sequenceName.addActionListener(new java.awt.event.ActionListener() + sequenceName.setText( + MessageManager.getString("label.edit_name_description")); + sequenceName.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1248,9 +1054,9 @@ public class PopupMenu extends JPopupMenu sequenceName_actionPerformed(); } }); - chooseAnnotations.setText(MessageManager - .getString("label.choose_annotations") + "..."); - chooseAnnotations.addActionListener(new java.awt.event.ActionListener() + chooseAnnotations + .setText(MessageManager.getString("action.choose_annotations")); + chooseAnnotations.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1258,9 +1064,9 @@ public class PopupMenu extends JPopupMenu chooseAnnotations_actionPerformed(e); } }); - sequenceDetails.setText(MessageManager - .getString("label.sequence_details") + "..."); - sequenceDetails.addActionListener(new java.awt.event.ActionListener() + sequenceDetails + .setText(MessageManager.getString("label.sequence_details")); + sequenceDetails.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1268,21 +1074,20 @@ public class PopupMenu extends JPopupMenu sequenceDetails_actionPerformed(); } }); - sequenceSelDetails.setText(MessageManager - .getString("label.sequence_details") + "..."); sequenceSelDetails - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - sequenceSelectionDetails_actionPerformed(); - } - }); - PIDColour.setFocusPainted(false); + .setText(MessageManager.getString("label.sequence_details")); + sequenceSelDetails.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sequenceSelectionDetails_actionPerformed(); + } + }); + unGroupMenuItem .setText(MessageManager.getString("action.remove_group")); - unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + unGroupMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1290,38 +1095,26 @@ public class PopupMenu extends JPopupMenu unGroupMenuItem_actionPerformed(); } }); - createGroupMenuItem.setText(MessageManager - .getString("action.create_group")); createGroupMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - createGroupMenuItem_actionPerformed(); - } - }); - - outline.setText(MessageManager.getString("action.border_colour")); - outline.addActionListener(new java.awt.event.ActionListener() + .setText(MessageManager.getString("action.create_group")); + createGroupMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - outline_actionPerformed(); + createGroupMenuItem_actionPerformed(); } }); - nucleotideMenuItem - .setText(MessageManager.getString("label.nucleotide")); - nucleotideMenuItem.addActionListener(new ActionListener() + + outline.setText(MessageManager.getString("action.border_colour")); + outline.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - nucleotideMenuItem_actionPerformed(); + outline_actionPerformed(); } }); - colourMenu.setText(MessageManager.getString("label.group_colour")); showBoxes.setText(MessageManager.getString("action.boxes")); showBoxes.setState(true); showBoxes.addActionListener(new ActionListener() @@ -1351,8 +1144,8 @@ public class PopupMenu extends JPopupMenu showColourText_actionPerformed(); } }); - displayNonconserved.setText(MessageManager - .getString("label.show_non_conversed")); + displayNonconserved + .setText(MessageManager.getString("label.show_non_conserved")); displayNonconserved.setState(true); displayNonconserved.addActionListener(new ActionListener() { @@ -1408,116 +1201,90 @@ public class PopupMenu extends JPopupMenu changeCase(e); } }); - pdbMenu.setText(MessageManager - .getString("label.associate_structure_with_sequence")); - pdbFromFile.setText(MessageManager.getString("label.from_file")); - pdbFromFile.addActionListener(new ActionListener() + outputMenu.setText( + MessageManager.getString("label.out_to_textbox") + "..."); + seqShowAnnotationsMenu + .setText(MessageManager.getString("label.show_annotations")); + seqHideAnnotationsMenu + .setText(MessageManager.getString("label.hide_annotations")); + groupShowAnnotationsMenu + .setText(MessageManager.getString("label.show_annotations")); + groupHideAnnotationsMenu + .setText(MessageManager.getString("label.hide_annotations")); + sequenceFeature.setText( + MessageManager.getString("label.create_sequence_feature")); + sequenceFeature.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - pdbFromFile_actionPerformed(); + sequenceFeature_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() + jMenu1.setText(MessageManager.getString("label.group")); + pdbStructureDialog.setText( + MessageManager.getString("label.show_pdbstruct_dialog")); + pdbStructureDialog.addActionListener(new ActionListener() { @Override - public void actionPerformed(ActionEvent e) + public void actionPerformed(ActionEvent actionEvent) { - enterPDB_actionPerformed(); + SequenceI[] selectedSeqs = new SequenceI[] { sequence }; + if (ap.av.getSelectionGroup() != null) + { + selectedSeqs = ap.av.getSequenceSelection(); + } + new StructureChooser(selectedSeqs, sequence, ap); } }); - discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids")); - discoverPDB.addActionListener(new ActionListener() + + rnaStructureMenu + .setText(MessageManager.getString("label.view_rna_structure")); + + // colStructureMenu.setText("Colour By Structure"); + editSequence.setText( + MessageManager.getString("label.edit_sequence") + "..."); + editSequence.addActionListener(new ActionListener() { @Override - public void actionPerformed(ActionEvent e) + public void actionPerformed(ActionEvent actionEvent) { - discoverPDB_actionPerformed(); + editSequence_actionPerformed(actionEvent); } }); - outputMenu.setText(MessageManager.getString("label.out_to_textbox") - + "..."); - seqShowAnnotationsMenu.setText(MessageManager - .getString("label.show_annotations")); - seqHideAnnotationsMenu.setText(MessageManager - .getString("label.hide_annotations")); - groupShowAnnotationsMenu.setText(MessageManager - .getString("label.show_annotations")); - groupHideAnnotationsMenu.setText(MessageManager - .getString("label.hide_annotations")); - sequenceFeature.setText(MessageManager - .getString("label.create_sequence_feature")); - sequenceFeature.addActionListener(new ActionListener() + makeReferenceSeq.setText( + MessageManager.getString("label.mark_as_representative")); + makeReferenceSeq.addActionListener(new ActionListener() { + @Override - public void actionPerformed(ActionEvent e) + public void actionPerformed(ActionEvent actionEvent) { - sequenceFeature_actionPerformed(); + makeReferenceSeq_actionPerformed(actionEvent); + } }); - textColour.setText(MessageManager.getString("label.text_colour")); - textColour.addActionListener(new ActionListener() + hideInsertions + .setText(MessageManager.getString("label.hide_insertions")); + hideInsertions.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - textColour_actionPerformed(); - } - }); - jMenu1.setText(MessageManager.getString("label.group")); - structureMenu.setText(MessageManager.getString("label.structure")); - viewStructureMenu.setText(MessageManager - .getString("label.view_structure")); - // colStructureMenu.setText("Colour By Structure"); - editSequence.setText(MessageManager.getString("label.edit_sequence") - + "..."); - editSequence.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - editSequence_actionPerformed(actionEvent); + hideInsertions_actionPerformed(e); } }); - /* - * annotationMenuItem.setText("By Annotation"); - * annotationMenuItem.addActionListener(new ActionListener() { public void - * actionPerformed(ActionEvent actionEvent) { - * annotationMenuItem_actionPerformed(actionEvent); } }); - */ groupMenu.add(sequenceSelDetails); add(groupMenu); add(sequenceMenu); - this.add(structureMenu); + add(rnaStructureMenu); + add(pdbStructureDialog); + if (sequence != null) + { + add(hideInsertions); + } // annotations configuration panel suppressed for now // groupMenu.add(chooseAnnotations); @@ -1539,65 +1306,21 @@ public class PopupMenu extends JPopupMenu groupMenu.add(jMenu1); sequenceMenu.add(sequenceName); sequenceMenu.add(sequenceDetails); - colourMenu.add(textColour); - colourMenu.add(noColourmenuItem); - colourMenu.add(clustalColour); - colourMenu.add(BLOSUM62Colour); - colourMenu.add(PIDColour); - colourMenu.add(zappoColour); - colourMenu.add(taylorColour); - colourMenu.add(hydrophobicityColour); - colourMenu.add(helixColour); - colourMenu.add(strandColour); - colourMenu.add(turnColour); - colourMenu.add(buriedColour); - colourMenu.add(nucleotideMenuItem); - 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) - { - java.util.Enumeration userColours = jalview.gui.UserDefinedColours - .getUserColourSchemes().keys(); + sequenceMenu.add(makeReferenceSeq); - while (userColours.hasMoreElements()) - { - JMenuItem item = new JMenuItem(userColours.nextElement().toString()); - item.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - colourMenu.add(item); - } - } + initColourMenu(); + buildColourMenu(); - colourMenu.addSeparator(); - colourMenu.add(abovePIDColour); - colourMenu.add(conservationMenuItem); - // colourMenu.add(annotationMenuItem); editMenu.add(copy); editMenu.add(cut); editMenu.add(editSequence); editMenu.add(upperCase); editMenu.add(lowerCase); editMenu.add(toggle); - pdbMenu.add(pdbFromFile); // JBPNote: These shouldn't be added here - should appear in a generic // 'apply web service to this sequence menu' // pdbMenu.add(RNAFold); // pdbMenu.add(ContraFold); - pdbMenu.add(enterPDB); - pdbMenu.add(discoverPDB); jMenu1.add(groupName); jMenu1.add(colourMenu); jMenu1.add(showBoxes); @@ -1605,163 +1328,118 @@ 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() - { - @Override - public void actionPerformed(ActionEvent e) - { - noColourmenuItem_actionPerformed(); - } - }); + } - clustalColour.setText(MessageManager - .getString("label.clustalx_colours")); - clustalColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - clustalColour_actionPerformed(); - } - }); - zappoColour.setText(MessageManager.getString("label.zappo")); - zappoColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - zappoColour_actionPerformed(); - } - }); - taylorColour.setText(MessageManager.getString("label.taylor")); - taylorColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - taylorColour_actionPerformed(); - } - }); - hydrophobicityColour.setText(MessageManager - .getString("label.hydrophobicity")); - hydrophobicityColour - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(); - } - }); - helixColour.setText(MessageManager.getString("label.helix_propensity")); - helixColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - helixColour_actionPerformed(); - } - }); - strandColour.setText(MessageManager - .getString("label.strand_propensity")); - strandColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - strandColour_actionPerformed(); - } - }); - turnColour.setText(MessageManager.getString("label.turn_propensity")); - turnColour.addActionListener(new java.awt.event.ActionListener() + /** + * Constructs the entries for the colour menu + */ + protected void initColourMenu() + { + colourMenu.setText(MessageManager.getString("label.group_colour")); + textColour.setText(MessageManager.getString("label.text_colour")); + textColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - turnColour_actionPerformed(); + textColour_actionPerformed(); } }); - buriedColour.setText(MessageManager.getString("label.buried_index")); - buriedColour.addActionListener(new java.awt.event.ActionListener() + + abovePIDColour.setText( + MessageManager.getString("label.above_identity_threshold")); + abovePIDColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - buriedColour_actionPerformed(); + abovePIDColour_actionPerformed(abovePIDColour.isSelected()); } }); - abovePIDColour.setText(MessageManager - .getString("label.above_identity_percentage")); - abovePIDColour.addActionListener(new java.awt.event.ActionListener() + + modifyPID.setText( + MessageManager.getString("label.modify_identity_threshold")); + modifyPID.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - abovePIDColour_actionPerformed(); + modifyPID_actionPerformed(); } }); - userDefinedColour.setText(MessageManager - .getString("action.user_defined")); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() + + conservationMenuItem + .setText(MessageManager.getString("action.by_conservation")); + conservationMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - userDefinedColour_actionPerformed(e); + conservationMenuItem_actionPerformed( + conservationMenuItem.isSelected()); } }); - PIDColour - .setText(MessageManager.getString("label.percentage_identity")); - PIDColour.addActionListener(new java.awt.event.ActionListener() + + modifyConservation.setText(MessageManager + .getString("label.modify_conservation_threshold")); + modifyConservation.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - PIDColour_actionPerformed(); + modifyConservation_actionPerformed(); } }); - BLOSUM62Colour.setText(MessageManager.getString("label.blosum62")); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() + } + + /** + * Builds the group colour sub-menu, including any user-defined colours which + * were loaded at startup or during the Jalview session + */ + protected void buildColourMenu() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null) { - @Override - public void actionPerformed(ActionEvent e) - { - BLOSUM62Colour_actionPerformed(); - } - }); - purinePyrimidineColour.setText(MessageManager - .getString("label.purine_pyrimidine")); - purinePyrimidineColour - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - purinePyrimidineColour_actionPerformed(); - } - }); + /* + * popup menu with no sequence group scope + */ + return; + } + colourMenu.removeAll(); + colourMenu.add(textColour); + colourMenu.addSeparator(); - /* - * covariationColour.addActionListener(new java.awt.event.ActionListener() { - * public void actionPerformed(ActionEvent e) { - * covariationColour_actionPerformed(); } }); - */ + ColourMenuHelper.addMenuItems(colourMenu, this, sg, false); - conservationMenuItem.setText(MessageManager - .getString("label.conservation")); - conservationMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - conservationMenuItem_actionPerformed(); - } - }); + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDColour); + colourMenu.add(modifyPID); + } + + protected void modifyConservation_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs != null) + { + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); + SliderPanel.showConservationSlider(); + } + } + + protected void modifyPID_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs != null) + { + // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() + // .getName()); + // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus()); + SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName()); + SliderPanel.showPIDSlider(); + } } /** @@ -1777,71 +1455,25 @@ 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, } - */ + SortedMap tipEntries = new TreeMap<>(); + final Map> candidates = new LinkedHashMap<>(); 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); - } - } + 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. @@ -1876,40 +1508,91 @@ 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()) + 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); + ap.av.getAlignment().setSeqrep(null); + } + else + { + ap.av.getAlignment().setSeqrep(sequence); + } + } + refresh(); + } - /* - * Add to the sequence (sets copyAnn.datasetSequence), unless the - * original annotation is already on the sequence. - */ - if (!seq.hasAnnotation(ann)) + protected void hideInsertions_actionPerformed(ActionEvent actionEvent) + { + + HiddenColumns hidden = new HiddenColumns(); + BitSet inserts = new BitSet(), mask = new BitSet(); + + // set mask to preserve existing hidden columns outside selected group + if (ap.av.hasHiddenColumns()) + { + ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask); + } + + boolean markedPopup = false; + // mark inserts in current selection + if (ap.av.getSelectionGroup() != null) + { + // mark just the columns in the selection group to be hidden + inserts.set(ap.av.getSelectionGroup().getStartRes(), + ap.av.getSelectionGroup().getEndRes() + 1); + + // and clear that part of the mask + mask.andNot(inserts); + + // now clear columns without gaps + for (SequenceI sq : ap.av.getSelectionGroup().getSequences()) + { + if (sq == sequence) { - seq.addAlignmentAnnotation(copyAnn); + markedPopup = true; } - // adjust for gaps - copyAnn.adjustForAlignment(); - // add to the alignment and set visible - this.ap.getAlignment().addAnnotation(copyAnn); - copyAnn.visible = true; + inserts.and(sq.getInsertionsAsBits()); } } + else + { + // initially, mark all columns to be hidden + inserts.set(0, ap.av.getAlignment().getWidth()); + + // and clear out old hidden regions completely + mask.clear(); + } + + // now mark for sequence under popup if we haven't already done it + if (!markedPopup && sequence != null) + { + inserts.and(sequence.getInsertionsAsBits()); + } + + // finally, preserve hidden regions outside selection + inserts.or(mask); + + // and set hidden columns accordingly + hidden.hideMarkedBits(inserts); + + ap.av.getAlignment().setHiddenColumns(hidden); refresh(); } @@ -1920,42 +1603,36 @@ public class PopupMenu extends JPopupMenu protected void sequenceDetails_actionPerformed() { - createSequenceDetailsReport(new SequenceI[] - { sequence }); + createSequenceDetailsReport(new SequenceI[] { sequence }); } public void createSequenceDetailsReport(SequenceI[] sequences) { CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); - StringBuffer contents = new StringBuffer(); + StringBuilder contents = new StringBuilder(128); for (SequenceI seq : sequences) { - contents.append("

" - + MessageManager - .formatMessage( - "label.create_sequence_details_report_annotation_for", - new String[] - { seq.getDisplayId(true) }) + "

"); - new SequenceAnnotationReport(null) - .createSequenceAnnotationReport( - contents, - seq, - true, - true, - false, - (ap.getSeqPanel().seqCanvas.fr != null) ? ap - .getSeqPanel().seqCanvas.fr - .getMinMax() - : null); + contents.append("

" + MessageManager.formatMessage( + "label.create_sequence_details_report_annotation_for", + new Object[] + { seq.getDisplayId(true) }) + "

"); + new SequenceAnnotationReport(null).createSequenceAnnotationReport( + contents, seq, true, true, + (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[] - { MessageManager.getString("label.selection") })), 500, 400); + 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); } @@ -1971,126 +1648,13 @@ public class PopupMenu extends JPopupMenu void refresh() { ap.updateAnnotation(); - ap.paintAlignment(true); + // removed paintAlignment(true) here: + // updateAnnotation calls paintAlignment already, so don't need to call + // again PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void clustalColour_actionPerformed() - { - SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void zappoColour_actionPerformed() - { - getGroup().cs = new ZappoColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void taylorColour_actionPerformed() - { - getGroup().cs = new TaylorColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void hydrophobicityColour_actionPerformed() - { - getGroup().cs = new HydrophobicColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void helixColour_actionPerformed() - { - getGroup().cs = new HelixColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void strandColour_actionPerformed() - { - getGroup().cs = new StrandColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void turnColour_actionPerformed() - { - getGroup().cs = new TurnColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void buriedColour_actionPerformed() - { - getGroup().cs = new BuriedColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - public void nucleotideMenuItem_actionPerformed() - { - getGroup().cs = new NucleotideColourScheme(); - refresh(); - } - - protected void purinePyrimidineColour_actionPerformed() - { - getGroup().cs = new PurinePyrimidineColourScheme(); - refresh(); - } - /* * protected void covariationColour_actionPerformed() { getGroup().cs = new * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } @@ -2098,10 +1662,12 @@ public class PopupMenu extends JPopupMenu /** * DOCUMENT ME! * + * @param selected + * * @param e * DOCUMENT ME! */ - protected void abovePIDColour_actionPerformed() + public void abovePIDColour_actionPerformed(boolean selected) { SequenceGroup sg = getGroup(); if (sg.cs == null) @@ -2109,49 +1675,27 @@ public class PopupMenu extends JPopupMenu return; } - if (abovePIDColour.isSelected()) + if (selected) { sg.cs.setConsensus(AAFrequency.calculate( sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1)); - int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() - .getName()); + int threshold = SliderPanel.setPIDSliderSource(ap, + sg.getGroupColourScheme(), 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()); - } - - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void userDefinedColour_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - - if (e.getSource().equals(userDefinedColour)) - { - new UserDefinedColours(ap, sg); + sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); + SliderPanel.hidePIDSlider(); } - else - { - UserColourScheme udc = (UserColourScheme) UserDefinedColours - .getUserColourSchemes().get(e.getActionCommand()); + modifyPID.setEnabled(selected); - sg.cs = udc; - } refresh(); } @@ -2173,54 +1717,7 @@ public class PopupMenu extends JPopupMenu * @param e * DOCUMENT ME! */ - protected void PIDColour_actionPerformed() - { - SequenceGroup sg = getGroup(); - sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.getHiddenRepSequences()), - sg.getStartRes(), sg.getEndRes() + 1)); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void BLOSUM62Colour_actionPerformed() - { - SequenceGroup sg = getGroup(); - - sg.cs = new Blosum62ColourScheme(); - - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.getHiddenRepSequences()), - sg.getStartRes(), sg.getEndRes() + 1)); - - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void noColourmenuItem_actionPerformed() - { - getGroup().cs = null; - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void conservationMenuItem_actionPerformed() + public void conservationMenuItem_actionPerformed(boolean selected) { SequenceGroup sg = getGroup(); if (sg.cs == null) @@ -2228,45 +1725,28 @@ public class PopupMenu extends JPopupMenu return; } - if (conservationMenuItem.isSelected()) + if (selected) { // JBPNote: Conservation name shouldn't be i18n translated Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.getSequences(ap.av - .getHiddenRepSequences()), sg.getStartRes(), - sg.getEndRes() + 1); + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); c.verdict(false, ap.av.getConsPercGaps()); - sg.cs.setConservation(c); - SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); + SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(), + sg.getName()); SliderPanel.showConservationSlider(); } else // remove ConservationColouring { sg.cs.setConservation(null); + SliderPanel.hideConservationSlider(); } - - refresh(); - } - - public void annotationMenuItem_actionPerformed(ActionEvent actionEvent) - { - SequenceGroup sg = getGroup(); - if (sg == null) - { - return; - } - - AnnotationColourGradient acg = new AnnotationColourGradient( - sequence.getAnnotation()[0], null, - AnnotationColourGradient.NO_THRESHOLD); - - acg.setPredefinedColours(true); - sg.cs = acg; + modifyConservation.setEnabled(selected); refresh(); } @@ -2282,8 +1762,8 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = getGroup(); EditNameDialog dialog = new EditNameDialog(sg.getName(), - sg.getDescription(), " " - + MessageManager.getString("label.group_name") + " ", + sg.getDescription(), + " " + MessageManager.getString("label.group_name") + " ", MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"), ap.alignFrame); @@ -2328,8 +1808,8 @@ public class PopupMenu extends JPopupMenu " " + MessageManager.getString("label.sequence_name") + " ", MessageManager.getString("label.sequence_description") + " ", - MessageManager - .getString("label.edit_sequence_name_description"), + MessageManager.getString( + "label.edit_sequence_name_description"), ap.alignFrame); if (!dialog.accept) @@ -2341,14 +1821,12 @@ public class PopupMenu extends JPopupMenu { if (dialog.getName().indexOf(" ") > -1) { - JOptionPane - .showMessageDialog( - ap, - MessageManager - .getString("label.spaces_converted_to_backslashes"), - MessageManager - .getString("label.no_spaces_allowed_sequence_name"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(ap, + MessageManager + .getString("label.spaces_converted_to_backslashes"), + MessageManager + .getString("label.no_spaces_allowed_sequence_name"), + JvOptionPane.WARNING_MESSAGE); } sequence.setName(dialog.getName().replace(' ', '_')); @@ -2357,8 +1835,8 @@ public class PopupMenu extends JPopupMenu sequence.setDescription(dialog.getDescription()); - ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() - .getSequences()); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); } @@ -2447,10 +1925,10 @@ public class PopupMenu extends JPopupMenu jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } @@ -2458,37 +1936,7 @@ public class PopupMenu extends JPopupMenu void hideSequences(boolean representGroup) { - SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg == null || sg.getSize() < 1) - { - ap.av.hideSequence(new SequenceI[] - { sequence }); - return; - } - - ap.av.setSelectionGroup(null); - - if (representGroup) - { - ap.av.hideRepSequences(sequence, sg); - - return; - } - - int gsize = sg.getSize(); - SequenceI[] hseqs; - - hseqs = new SequenceI[gsize]; - - int index = 0; - for (int i = 0; i < gsize; i++) - { - hseqs[index++] = sg.getSequenceAt(i); - } - - ap.av.hideSequence(hseqs); - // refresh(); TODO: ? needed ? - ap.av.sendSelection(); + ap.av.hideSequences(sequence, representGroup); } public void copy_actionPerformed() @@ -2508,8 +1956,8 @@ 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; @@ -2536,8 +1984,8 @@ public class PopupMenu extends JPopupMenu ap.alignFrame.addHistoryItem(caseCommand); - ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() - .getSequences()); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); } } @@ -2546,8 +1994,8 @@ public class PopupMenu extends JPopupMenu { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", new String[] + Desktop.addInternalFrame(cap, MessageManager + .formatMessage("label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); String[] omitHidden = null; @@ -2556,80 +2004,10 @@ public class PopupMenu extends JPopupMenu // or we simply trust the user wants // wysiwig behaviour - cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), - ap.av, true)); - } - - public void pdbFromFile_actionPerformed() - { - jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager.formatMessage( - "label.select_pdb_file_for", new String[] - { sequence.getDisplayId(false) })); - chooser.setToolTipText(MessageManager.formatMessage( - "label.load_pdb_file_associate_with_sequence", new String[] - { sequence.getDisplayId(false) })); - - int value = chooser.showOpenDialog(null); - - if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) - { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, - jalview.io.AppletFormatAdapter.FILE, sequence, true, - Desktop.instance); - } - - } - - // 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, - MessageManager.getString("label.enter_pdb_id"), - MessageManager.getString("label.enter_pdb_id"), - JOptionPane.QUESTION_MESSAGE); - - if (id != null && id.length() > 0) - { - PDBEntry entry = new PDBEntry(); - entry.setId(id.toUpperCase()); - sequence.getDatasetSequence().addPDBId(entry); - } - } - - public void discoverPDB_actionPerformed() - { - - final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[] - { sequence } - : ap.av.getSequenceSelection()); - Thread discpdb = new Thread(new Runnable() - { - @Override - public void run() - { - - new jalview.ws.DBRefFetcher(sequences, ap.alignFrame) - .fetchDBRefs(false); - } - - }); - discpdb.start(); + FileFormatI fileFormat = FileFormats.getInstance() + .forName(e.getActionCommand()); + cap.setText( + new FormatAdapter(ap).formatSequences(fileFormat, ap, true)); } public void sequenceFeature_actionPerformed() @@ -2640,33 +2018,37 @@ public class PopupMenu extends JPopupMenu return; } - int rsize = 0, gSize = sg.getSize(); - SequenceI[] rseqs, seqs = new SequenceI[gSize]; - SequenceFeature[] tfeatures, features = new SequenceFeature[gSize]; + List seqs = new ArrayList<>(); + List features = new ArrayList<>(); + /* + * assemble dataset sequences, and template new sequence features, + * for the amend features dialog + */ + int gSize = sg.getSize(); for (int i = 0; i < gSize; i++) { int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); int end = sg.findEndRes(sg.getSequenceAt(i)); if (start <= end) { - seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence(); - features[rsize] = new SequenceFeature(null, null, null, start, end, - "Jalview"); - rsize++; + seqs.add(sg.getSequenceAt(i).getDatasetSequence()); + features.add(new SequenceFeature(null, null, start, end, null)); } } - rseqs = new SequenceI[rsize]; - tfeatures = new SequenceFeature[rsize]; - System.arraycopy(seqs, 0, rseqs, 0, rsize); - System.arraycopy(features, 0, tfeatures, 0, rsize); - features = tfeatures; - seqs = rseqs; - if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, - features, true, ap)) - { - ap.alignFrame.setShowSeqFeatures(true); - ap.highlightSearchResults(null); + + /* + * an entirely gapped region will generate empty lists of sequence / features + */ + if (!seqs.isEmpty()) + { + if (ap.getSeqPanel().seqCanvas.getFeatureRenderer() + .amendFeatures(seqs, features, true, ap)) + { + ap.alignFrame.setShowSeqFeatures(true); + ap.av.setSearchResults(null); // clear highlighting + ap.repaint(); // draw new/amended features + } } } @@ -2711,8 +2093,8 @@ public class PopupMenu extends JPopupMenu EditNameDialog dialog = new EditNameDialog( sequence.getSequenceAsString(sg.getStartRes(), - sg.getEndRes() + 1), null, - MessageManager.getString("label.edit_sequence"), null, + sg.getEndRes() + 1), + null, MessageManager.getString("label.edit_sequence"), null, MessageManager.getString("label.edit_sequence"), ap.alignFrame); @@ -2720,17 +2102,45 @@ public class PopupMenu extends JPopupMenu { EditCommand editCommand = new EditCommand( MessageManager.getString("label.edit_sequences"), - Action.REPLACE, dialog.getName().replace(' ', - ap.av.getGapCharacter()), + Action.REPLACE, + dialog.getName().replace(' ', ap.av.getGapCharacter()), sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); ap.alignFrame.addHistoryItem(editCommand); - ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() - .getSequences()); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); } } } + /** + * Action on user selecting an item from the colour menu (that does not have + * its bespoke action handler) + * + * @return + */ + @Override + public void changeColour_actionPerformed(String colourSchemeName) + { + SequenceGroup sg = getGroup(); + /* + * switch to the chosen colour scheme (or null for None) + */ + ColourSchemeI colourScheme = ColourSchemes.getInstance() + .getColourScheme(colourSchemeName, sg, + ap.av.getHiddenRepSequences()); + sg.setColourScheme(colourScheme); + if (colourScheme instanceof Blosum62ColourScheme + || colourScheme instanceof PIDColourScheme) + { + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); + } + + refresh(); + } + }