X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=ad3d6af347997305f9483e80c07b1b5dbf1e490d;hb=e373651097c72eb6c9ca6009fb70d47341e8f405;hp=c2bee834e169f2f0d3aa0207d41ac846156fc210;hpb=4935082f08648ab92743e14e5e2dfefa3e0dcd4d;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index c2bee83..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. * @@ -20,8 +20,30 @@ */ 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; @@ -29,6 +51,7 @@ 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; @@ -57,29 +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.Collection; -import java.util.Collections; -import java.util.Hashtable; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Map; -import java.util.TreeMap; -import java.util.Vector; - -import javax.swing.ButtonGroup; -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JColorChooser; -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JOptionPane; -import javax.swing.JPopupMenu; -import javax.swing.JRadioButtonMenuItem; - /** * DOCUMENT ME! * @@ -124,9 +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(); @@ -140,6 +137,8 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceDetails = new JMenuItem(); JMenuItem sequenceSelDetails = new JMenuItem(); + + JMenuItem makeReferenceSeq = new JMenuItem(); JMenuItem chooseAnnotations = new JMenuItem(); @@ -179,12 +178,6 @@ public class PopupMenu extends JPopupMenu JMenuItem pdbFromFile = new JMenuItem(); - // JBPNote: Commented these out - Should add these services via the web - // services menu system. - // JMenuItem ContraFold = new JMenuItem(); - - // JMenuItem RNAFold = new JMenuItem(); - JMenuItem enterPDB = new JMenuItem(); JMenuItem discoverPDB = new JMenuItem(); @@ -195,13 +188,15 @@ public class PopupMenu extends JPopupMenu JMenu seqHideAnnotationsMenu = new JMenu(); - JMenuItem seqAddReferenceAnnotations = new JMenuItem(); + JMenuItem seqAddReferenceAnnotations = new JMenuItem( + MessageManager.getString("label.add_reference_annotations")); JMenu groupShowAnnotationsMenu = new JMenu(); JMenu groupHideAnnotationsMenu = new JMenu(); - JMenuItem groupAddReferenceAnnotations = new JMenuItem(); + JMenuItem groupAddReferenceAnnotations = new JMenuItem( + MessageManager.getString("label.add_reference_annotations")); JMenuItem sequenceFeature = new JMenuItem(); @@ -209,17 +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. * @@ -268,7 +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++) { @@ -322,108 +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; aa != null && i < aa.length; i++) + if (aas != null) { - if (aa[i].isValidStruc() && aa[i].sequenceRef == null) + for (final AlignmentAnnotation aa : aas) { - final String rnastruc = aa[i].getRNAStruc(); - final String structureLine = aa[i].label + " (alignment)"; - menuItem = new JMenuItem(); - menuItem.setText(MessageManager.formatMessage( - "label.2d_rna_structure_line", new String[] - { structureLine })); - menuItem.addActionListener(new java.awt.event.ActionListener() + if (aa.isValidStruc() && aa.sequenceRef == null) { - @Override - public void actionPerformed(ActionEvent e) + /* + * valid alignment RNA secondary structure annotation + */ + menuItem = new JMenuItem(); + menuItem.setText(MessageManager.formatMessage( + "label.2d_rna_structure_line", new Object[] + { aa.label })); + menuItem.addActionListener(new java.awt.event.ActionListener() { - // // System.out.println("1:"+structureLine); - // System.out.println("1:sname" + seq.getName()); - // System.out.println("2:seq" + seq); - // - // // System.out.println("3:"+seq.getSequenceAsString()); - // System.out.println("3:strucseq" + rnastruc); - // // System.out.println("4:struc"+seq.getRNA()); - // System.out.println("5:name" + seq.getName()); - // System.out.println("6:ap" + ap); - new AppVarna(structureLine, seq, seq.getSequenceAsString(), - rnastruc, seq.getName(), ap); - // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), - // seq.getName(), ap); - System.out.println("end"); - } - }); - viewStructureMenu.add(menuItem); + @Override + public void actionPerformed(ActionEvent e) + { + new AppVarna(seq, aa, ap); + } + }); + rnaStructureMenu.add(menuItem); + } } } - // SequenceFeatures[] test = seq.getSequenceFeatures(); - if (seq.getAnnotation() != null) { - AlignmentAnnotation seqAnno[] = seq.getAnnotation(); - for (int i = 0; i < seqAnno.length; i++) + AlignmentAnnotation seqAnns[] = seq.getAnnotation(); + for (final AlignmentAnnotation aa : seqAnns) { - if (seqAnno[i].isValidStruc()) + if (aa.isValidStruc()) { - final String rnastruc = seqAnno[i].getRNAStruc(); - + /* + * valid sequence RNA secondary structure annotation + */ // TODO: make rnastrucF a bit more nice menuItem = new JMenuItem(); menuItem.setText(MessageManager.formatMessage( - "label.2d_rna_sequence_name", new String[] + "label.2d_rna_sequence_name", new Object[] { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { @@ -431,17 +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( @@ -460,7 +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() { @@ -529,7 +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")); @@ -630,50 +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 @@ -698,7 +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) @@ -937,7 +840,7 @@ public class PopupMenu extends JPopupMenu final boolean actionIsShow) { String label = types.toString(); // [a, b, c] - label = label.substring(1, label.length() - 1); + label = label.substring(1, label.length() - 1); // a, b, c final JMenuItem item = new JMenuItem(label); item.setToolTipText(calcId); item.addActionListener(new java.awt.event.ActionListener() @@ -945,41 +848,14 @@ public class PopupMenu extends JPopupMenu @Override public void actionPerformed(ActionEvent e) { - showHideAnnotation_actionPerformed(types, forSequences, allTypes, - actionIsShow); + AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types, + forSequences, allTypes, actionIsShow); + refresh(); } }); showOrHideMenu.add(item); } - /** - * Action on selecting a list of annotation type (or the 'all types' values) - * to show or hide for the specified sequences. - * - * @param types - * @param forSequences - * @param anyType - * @param doShow - */ - protected void showHideAnnotation_actionPerformed( - Collection types, List forSequences, - boolean anyType, boolean doShow) - { - for (AlignmentAnnotation aa : ap.getAlignment() - .getAlignmentAnnotation()) - { - if (anyType || types.contains(aa.label)) - { - if ((aa.sequenceRef != null) - && forSequences.contains(aa.sequenceRef)) - { - aa.visible = doShow; - } - } - } - refresh(); - } - private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks) { @@ -1107,8 +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 @@ -1148,7 +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() { @@ -1419,32 +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() { @@ -1493,9 +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") + "..."); @@ -1507,7 +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 @@ -1517,7 +1404,12 @@ 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); @@ -1539,6 +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); @@ -1555,10 +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) @@ -1584,7 +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); @@ -1605,9 +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() { @@ -1780,68 +1667,22 @@ public class PopupMenu extends JPopupMenu protected void configureReferenceAnnotationsMenu( JMenuItem menuItem, List forSequences) { - menuItem.setText(MessageManager - .getString("label.add_reference_annotations")); menuItem.setEnabled(false); - if (forSequences == null) - { - return; - } /* * Temporary store to hold distinct calcId / type pairs for the tooltip. * Using TreeMap means calcIds are shown in alphabetical order. */ Map tipEntries = new TreeMap(); - StringBuilder tooltip = new StringBuilder(64); - tooltip.append(MessageManager.getString("label.add_annotations_for")); - - /* - * For each sequence selected in the alignment, make a list of any - * annotations on the underlying dataset sequence which are not already on - * the alignment. - * - * Build a map of { alignmentSequence, } - */ - AlignmentI al = this.ap.av.getAlignment(); final Map> candidates = new LinkedHashMap>(); - for (SequenceI seq : forSequences) - { - SequenceI dataset = seq.getDatasetSequence(); - if (dataset == null) - { - continue; - } - AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation(); - if (datasetAnnotations == null) - { - continue; - } - final List result = new ArrayList(); - for (AlignmentAnnotation dsann : datasetAnnotations) - { - /* - * Find matching annotations on the alignment. - */ - final Iterable matchedAlignmentAnnotations = al - .findAnnotations(seq, dsann.getCalcId(), - dsann.label); - if (!matchedAlignmentAnnotations.iterator().hasNext()) - { - result.add(dsann); - tipEntries.put(dsann.getCalcId(), dsann.label); - } - } - /* - * Save any addable annotations for this sequence - */ - if (!result.isEmpty()) - { - candidates.put(seq, result); - } - } + AlignmentI al = this.ap.av.getAlignment(); + AlignmentUtils.findAddableReferenceAnnotations(forSequences, + tipEntries, candidates, al); if (!candidates.isEmpty()) { + StringBuilder tooltip = new StringBuilder(64); + tooltip.append(MessageManager.getString("label.add_annotations_for")); + /* * Found annotations that could be added. Enable the menu item, and * configure its tooltip and action. @@ -1876,43 +1717,50 @@ 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()) { - for (AlignmentAnnotation ann : candidates.get(seq)) + // initialise the display flags so the user sees something happen + ap.av.setDisplayReferenceSeq(true); + ap.av.setColourByReferenceSeq(true); + ap.av.getAlignment().setSeqrep(sequence); + } + else + { + if (ap.av.getAlignment().getSeqrep() == sequence) { - AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann); - int startRes = 0; - int endRes = ann.annotations.length; - final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup(); - if (selectionGroup != null) - { - startRes = selectionGroup.getStartRes(); - endRes = selectionGroup.getEndRes(); - } - copyAnn.restrict(startRes, endRes); - - /* - * Add to the sequence (sets copyAnn.datasetSequence), unless the - * original annotation is already on the sequence. - */ - if (!seq.hasAnnotation(ann)) - { - seq.addAlignmentAnnotation(copyAnn); - } - // adjust for gaps - copyAnn.adjustForAlignment(); - // add to the alignment and set visible - this.ap.getAlignment().addAnnotation(copyAnn); - copyAnn.visible = true; + 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()); @@ -1934,7 +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( @@ -1943,16 +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); } @@ -2116,14 +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(); @@ -2474,15 +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 ? @@ -2506,7 +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; @@ -2545,7 +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; @@ -2554,8 +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() @@ -2564,10 +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); @@ -2583,18 +2426,7 @@ public class PopupMenu extends JPopupMenu } - // JBNote: commented out - these won't be instantiated here...! - // public void RNAFold_actionPerformed() throws Exception - // { - // Predict2D P2D = new Predict2D(); - // P2D.getStructure2DFromRNAFold("toto"); - // } - // - // public void ContraFold_actionPerformed() throws Exception - // { - // Predict2D P2D = new Predict2D(); - // P2D.getStructure2DFromContraFold("toto"); - // } + public void enterPDB_actionPerformed() { String id = JOptionPane.showInternalInputDialog(Desktop.desktop, @@ -2660,7 +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);