X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=c51653d63556f87c84ed95312cb9479412dae86e;hb=452e24303ecf7861ff827c19fcd0fdaa1d288ea1;hp=1fa9f7cf37cbaaa5ad10a27af1fa0e3a77506426;hpb=61f35f2177eb22c3d42cafda13db82d4e904b9f0;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java old mode 100755 new mode 100644 index 1fa9f7c..c51653d --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.appletgui; @@ -27,8 +26,10 @@ import jalview.analysis.*; import jalview.commands.*; import jalview.datamodel.*; import jalview.schemes.*; +import jalview.util.MessageManager; import jalview.util.UrlLink; import jalview.io.AppletFormatAdapter; +import jalview.io.SequenceAnnotationReport; public class APopupMenu extends java.awt.PopupMenu implements ActionListener, ItemListener @@ -69,6 +70,8 @@ public class APopupMenu extends java.awt.PopupMenu implements MenuItem unGroupMenuItem = new MenuItem(); + MenuItem createGroupMenuItem = new MenuItem(); + MenuItem nucleotideMenuItem = new MenuItem(); Menu colourMenu = new Menu(); @@ -79,17 +82,19 @@ public class APopupMenu extends java.awt.PopupMenu implements CheckboxMenuItem showColourText = new CheckboxMenuItem(); - Menu editMenu = new Menu("Edit"); + CheckboxMenuItem displayNonconserved = new CheckboxMenuItem(); + + Menu editMenu = new Menu(MessageManager.getString("action.edit")); - MenuItem copy = new MenuItem("Copy (Jalview Only)"); + MenuItem copy = new MenuItem(MessageManager.getString("label.jalview_copy")); - MenuItem cut = new MenuItem("Cut (Jalview Only)"); + MenuItem cut = new MenuItem(MessageManager.getString("label.jalview_cut")); - MenuItem toUpper = new MenuItem("To Upper Case"); + MenuItem toUpper = new MenuItem(MessageManager.getString("label.to_upper_case")); - MenuItem toLower = new MenuItem("To Lower Case"); + MenuItem toLower = new MenuItem(MessageManager.getString("label.to_lower_case")); - MenuItem toggleCase = new MenuItem("Toggle Case"); + MenuItem toggleCase = new MenuItem(MessageManager.getString("label.toggle_case")); Menu outputmenu = new Menu(); @@ -101,16 +106,27 @@ public class APopupMenu extends java.awt.PopupMenu implements MenuItem repGroup = new MenuItem(); - MenuItem sequenceName = new MenuItem("Edit Name/Description"); + MenuItem sequenceName = new MenuItem(MessageManager.getString("label.edit_name_description")); + + MenuItem sequenceFeature = new MenuItem(MessageManager.getString("label.create_sequence_feature")); + + MenuItem editSequence = new MenuItem(MessageManager.getString("label.edit_sequence")); - MenuItem sequenceFeature = new MenuItem("Create Sequence Feature"); + MenuItem sequenceDetails = new MenuItem(MessageManager.getString("label.sequence_details") + "..."); - MenuItem editSequence = new MenuItem("Edit Sequence"); + MenuItem selSeqDetails = new MenuItem(MessageManager.getString("label.sequence_details") + "..."); Sequence seq; MenuItem revealAll = new MenuItem(); + MenuItem revealSeq = new MenuItem(); + + /** + * index of sequence to be revealed + */ + int revealSeq_index = -1; + Menu menu1 = new Menu(); public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links) @@ -146,13 +162,18 @@ public class APopupMenu extends java.awt.PopupMenu implements if (sg != null && sg.getSize() > 0) { - editGroupName.setLabel(sg.getName()); + editGroupName.setLabel(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()})); showText.setState(sg.getDisplayText()); showColourText.setState(sg.getColourText()); showBoxes.setState(sg.getDisplayBoxes()); - if (!ap.av.alignment.getGroups().contains(sg)) + displayNonconserved.setState(sg.getShowNonconserved()); + if (!ap.av.getAlignment().getGroups().contains(sg)) { + menu1.setLabel(MessageManager.getString("action.edit_new_group")); groupMenu.remove(unGroupMenuItem); + } else { + menu1.setLabel(MessageManager.getString("action.edit_group")); + groupMenu.remove(createGroupMenuItem); } } @@ -164,7 +185,7 @@ public class APopupMenu extends java.awt.PopupMenu implements if (links != null && links.size() > 0) { - Menu linkMenu = new Menu("Link"); + Menu linkMenu = new Menu(MessageManager.getString("action.link")); String link; for (int i = 0; i < links.size(); i++) { @@ -176,19 +197,19 @@ public class APopupMenu extends java.awt.PopupMenu implements continue; } final String target = urlLink.getTarget(); // link.substring(0, - // link.indexOf("|")); + // link.indexOf("|")); final String label = urlLink.getLabel(); - if (urlLink.isDynamic()) + if (seq != null && urlLink.isDynamic()) { // collect matching db-refs - DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq - .getDBRef(), new String[] - { target }); + DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs( + seq.getDBRef(), new String[] + { target }); // collect id string too String id = seq.getName(); String descr = seq.getDescription(); - if (descr!=null && descr.length()<1) + if (descr != null && descr.length() < 1) { descr = null; } @@ -227,21 +248,20 @@ public class APopupMenu extends java.awt.PopupMenu implements } // addshowLink(linkMenu, target, url_pref + id + url_suff); } - // TODO: introduce applet parameter option to dis/en/able URl generation from description - // hard-disable the construction of URLs from regexes that match the description -// if (descr != null) -// { -// // create link for this URL from description where regex matches -// String[] urls = urlLink.makeUrls(descr, false); -// if (urls != null) -// { -// for (int u = 0; u < urls.length; u += 2) -// { -// addshowLink(linkMenu, label, urls[u + 1]); -// } -// } -// // addshowLink(linkMenu, target, url_pref + id + url_suff); -// } + // Now construct URLs from description but only try to do it for regex + // URL links + if (descr != null && urlLink.getRegexReplace() != null) + { + // create link for this URL from description only if regex matches + String[] urls = urlLink.makeUrls(descr, true); + if (urls != null) + { + for (int u = 0; u < urls.length; u += 2) + { + addshowLink(linkMenu, label, urls[u + 1]); + } + } + } } else { @@ -251,11 +271,12 @@ public class APopupMenu extends java.awt.PopupMenu implements * final String url; * * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID - * string and any matching database reference accessions String url_pref = - * link.substring(link.indexOf("|") + 1, link.indexOf("$SEQUENCE_ID$")); + * string and any matching database reference accessions String url_pref + * = link.substring(link.indexOf("|") + 1, + * link.indexOf("$SEQUENCE_ID$")); * * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13); - * // collect matching db-refs DBRefEntry[] dbr = + * // collect matching db-refs DBRefEntry[] dbr = * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new * String[]{target}); // collect id string too String id = * seq.getName(); if (id.indexOf("|") > -1) { id = @@ -270,29 +291,47 @@ public class APopupMenu extends java.awt.PopupMenu implements * link.substring(link.lastIndexOf("|")+1)); } */ } - - if (seq != null) - { - seqMenu.add(linkMenu); - } - else + if (linkMenu.getItemCount() > 0) { - add(linkMenu); + if (seq != null) + { + seqMenu.add(linkMenu); + } + else + { + add(linkMenu); + } } } + // TODO: add group link menu entry here if (seq != null) { seqMenu.setLabel(seq.getName()); - repGroup.setLabel("Represent Group with " + seq.getName()); + repGroup.setLabel(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()})); } else { remove(seqMenu); } - if (!ap.av.hasHiddenRows) + if (!ap.av.hasHiddenRows()) { remove(revealAll); + remove(revealSeq); + } + else + { + final int index = ap.av.getAlignment().findIndex(seq); + + if (ap.av.adjustForHiddenSeqs(index) + - ap.av.adjustForHiddenSeqs(index - 1) > 1) + { + revealSeq_index = index; + } + else + { + remove(revealSeq); + } } } @@ -300,10 +339,10 @@ public class APopupMenu extends java.awt.PopupMenu implements * add a show URL menu item to the given linkMenu * * @param linkMenu - * @param target - - * menu label string - * @param url - - * url to open + * @param target + * - menu label string + * @param url + * - url to open */ private void addshowLink(Menu linkMenu, final String target, final String url) @@ -315,12 +354,12 @@ public class APopupMenu extends java.awt.PopupMenu implements * add a show URL menu item to the given linkMenu * * @param linkMenu - * @param target - - * URL target window - * @param label - - * menu label string - * @param url - - * url to open + * @param target + * - URL target window + * @param label + * - menu label string + * @param url + * - url to open */ private void addshowLink(Menu linkMenu, final String target, final String label, final String url) @@ -354,6 +393,10 @@ public class APopupMenu extends java.awt.PopupMenu implements { showBoxes_itemStateChanged(); } + else if (evt.getSource() == displayNonconserved) + { + this.showNonconserved_itemStateChanged(); + } } public void actionPerformed(ActionEvent evt) @@ -421,10 +464,23 @@ public class APopupMenu extends java.awt.PopupMenu implements unGroupMenuItem_actionPerformed(); } + else if (source == createGroupMenuItem) + { + createGroupMenuItem_actionPerformed(); + } + else if (source == sequenceName) { editName(); } + else if (source == sequenceDetails) + { + showSequenceDetails(); + } + else if (source == selSeqDetails) + { + showSequenceSelectionDetails(); + } else if (source == pdb) { addPDB(); @@ -437,6 +493,10 @@ public class APopupMenu extends java.awt.PopupMenu implements { hideSequences(true); } + else if (source == revealSeq) + { + ap.av.showSequence(revealSeq_index); + } else if (source == revealAll) { ap.av.showAllHiddenSeqs(); @@ -483,9 +543,10 @@ public class APopupMenu extends java.awt.PopupMenu implements { EditCommand editCommand = new EditCommand("Edit Sequences", EditCommand.REPLACE, dialog.getName().replace(' ', - ap.av.getGapCharacter()), sg - .getSequencesAsArray(ap.av.hiddenRepSequences), - sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment); + ap.av.getGapCharacter()), + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1, + ap.av.getAlignment()); ap.alignFrame.addHistoryItem(editCommand); @@ -500,44 +561,8 @@ public class APopupMenu extends java.awt.PopupMenu implements Vector regions = new Vector(); if (sg != null) { - int start = sg.getStartRes(); - int end = sg.getEndRes() + 1; - - do - { - if (ap.av.hasHiddenColumns) - { - if (start == 0) - { - start = ap.av.colSel.adjustForHiddenColumns(start); - } - - end = ap.av.colSel.getHiddenBoundaryRight(start); - if (start == end) - { - end = sg.getEndRes() + 1; - } - if (end > sg.getEndRes()) - { - end = sg.getEndRes() + 1; - } - } - - regions.addElement(new int[] - { start, end }); - - if (ap.av.hasHiddenColumns) - { - start = ap.av.colSel.adjustForHiddenColumns(end); - start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1; - } - } while (end < sg.getEndRes()); - - int[][] startEnd = new int[regions.size()][2]; - for (int i = 0; i < regions.size(); i++) - { - startEnd[i] = (int[]) regions.elementAt(i); - } + int[][] startEnd = ap.av.getVisibleRegionBoundaries( + sg.getStartRes(), sg.getEndRes() + 1); String description; int caseChange; @@ -559,8 +584,8 @@ public class APopupMenu extends java.awt.PopupMenu implements } ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, - sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, - caseChange); + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); @@ -577,18 +602,28 @@ public class APopupMenu extends java.awt.PopupMenu implements return; } - int gSize = sg.getSize(); - SequenceI[] seqs = new SequenceI[gSize]; - SequenceFeature[] features = new SequenceFeature[gSize]; + int rsize = 0, gSize = sg.getSize(); + SequenceI[] rseqs, seqs = new SequenceI[gSize]; + SequenceFeature[] tfeatures, features = new SequenceFeature[gSize]; for (int i = 0; i < gSize; i++) { - seqs[i] = sg.getSequenceAt(i); int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); int end = sg.findEndRes(sg.getSequenceAt(i)); - features[i] = new SequenceFeature(null, null, null, start, end, - "Jalview"); + if (start <= end) + { + seqs[rsize] = sg.getSequenceAt(i); + features[rsize] = new SequenceFeature(null, null, null, start, + end, "Jalview"); + rsize++; + } } + 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.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, true, ap)) @@ -611,19 +646,62 @@ public class APopupMenu extends java.awt.PopupMenu implements Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Selection output - " - + e.getActionCommand(), 600, 500); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.formatMessage("label.selection_output_command", new String[]{e.getActionCommand()}),600, 500); + // JBPNote: getSelectionAsNewSequence behaviour has changed - this method + // now returns a full copy of sequence data + // TODO consider using getSequenceSelection instead here + + cap.setText(new jalview.io.AppletFormatAdapter().formatSequences( + e.getActionCommand(), + new Alignment(ap.av.getSelectionAsNewSequence()), + ap.av.showJVSuffix)); + + } + + protected void showSequenceSelectionDetails() + { + createSequenceDetailsReport(ap.av.getSequenceSelection()); + } + + protected void showSequenceDetails() + { + createSequenceDetailsReport(new SequenceI[] + { seq }); + } + + public void createSequenceDetailsReport(SequenceI[] sequences) + { - cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(e - .getActionCommand(), new Alignment(ap.av - .getSelectionAsNewSequence()), ap.av.showJVSuffix)); + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame); + StringBuffer contents = new StringBuffer(); + for (SequenceI seq : sequences) + { + contents.append(MessageManager.formatMessage("label.annotation_for_displayid",new String[]{seq.getDisplayId(true)})); + new SequenceAnnotationReport(null) + .createSequenceAnnotationReport( + contents, + seq, + true, + true, + false, + (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax + : null); + contents.append("

"); + } + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for " + + (sequences.length == 1 ? sequences[0].getDisplayId(true) + : "Selection"), 600, 500); + cap.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()})); } void editName() { - EditNameDialog dialog = new EditNameDialog(seq.getName(), seq - .getDescription(), " Sequence Name", + EditNameDialog dialog = new EditNameDialog(seq.getName(), + seq.getDescription(), " Sequence Name", "Sequence Description", ap.alignFrame, "Edit Sequence Name / Description", 500, 100, true); @@ -652,53 +730,64 @@ public class APopupMenu extends java.awt.PopupMenu implements else { CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); - cap.setText("Paste your PDB file here."); + cap.setText(MessageManager.getString("label.paste_pdb_file")); cap.setPDBImport(seq); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.formatMessage("label.paste_pdb_file_for_sequence", new String[]{seq.getName()}), 400, 300); } } private void jbInit() throws Exception { - groupMenu.setLabel("Group"); - groupMenu.setLabel("Selection"); + groupMenu.setLabel(MessageManager.getString("label.selection")); sequenceFeature.addActionListener(this); editGroupName.addActionListener(this); - unGroupMenuItem.setLabel("Remove Group"); + unGroupMenuItem.setLabel(MessageManager.getString("action.remove_group")); unGroupMenuItem.addActionListener(this); - nucleotideMenuItem.setLabel("Nucleotide"); + createGroupMenuItem.setLabel(MessageManager.getString("action.create_group")); + createGroupMenuItem.addActionListener(this); + + nucleotideMenuItem.setLabel(MessageManager.getString("label.nucleotide")); nucleotideMenuItem.addActionListener(this); conservationMenuItem.addItemListener(this); abovePIDColour.addItemListener(this); - colourMenu.setLabel("Group Colour"); - showBoxes.setLabel("Boxes"); + colourMenu.setLabel(MessageManager.getString("label.group_colour")); + showBoxes.setLabel(MessageManager.getString("label.boxes")); showBoxes.setState(true); showBoxes.addItemListener(this); sequenceName.addActionListener(this); - - showText.setLabel("Text"); + sequenceDetails.addActionListener(this); + selSeqDetails.addActionListener(this); + displayNonconserved.setLabel(MessageManager.getString("label.show_non_conversed")); + displayNonconserved.setState(false); + displayNonconserved.addItemListener(this); + showText.setLabel(MessageManager.getString("label.text")); showText.addItemListener(this); - showColourText.setLabel("Colour Text"); + showColourText.setLabel(MessageManager.getString("label.colour_text")); showColourText.addItemListener(this); - outputmenu.setLabel("Output to Textbox..."); - seqMenu.setLabel("Sequence"); - pdb.setLabel("View PDB Structure"); - hideSeqs.setLabel("Hide Sequences"); - repGroup.setLabel("Represent Group with"); - revealAll.setLabel("Reveal All"); - menu1.setLabel("Group"); + outputmenu.setLabel(MessageManager.getString("label.out_to_textbox")); + seqMenu.setLabel(MessageManager.getString("label.sequence")); + pdb.setLabel(MessageManager.getString("label.view_pdb_structure")); + hideSeqs.setLabel(MessageManager.getString("action.hide_sequences")); + repGroup.setLabel(MessageManager.getString("label.represent_group_with")); + revealAll.setLabel(MessageManager.getString("action.reveal_all")); + revealSeq.setLabel(MessageManager.getString("action.reveal_sequences")); + menu1.setLabel(MessageManager.getString("label.group")); add(groupMenu); this.add(seqMenu); this.add(hideSeqs); + this.add(revealSeq); this.add(revealAll); - groupMenu.add(editGroupName); + // groupMenu.add(selSeqDetails); groupMenu.add(editMenu); groupMenu.add(outputmenu); groupMenu.add(sequenceFeature); + groupMenu.add(createGroupMenuItem); + groupMenu.add(unGroupMenuItem); groupMenu.add(menu1); colourMenu.add(noColourmenuItem); @@ -761,18 +850,25 @@ public class APopupMenu extends java.awt.PopupMenu implements toLower.addActionListener(this); editMenu.add(toggleCase); seqMenu.add(sequenceName); - seqMenu.add(pdb); + // seqMenu.add(sequenceDetails); + + if (!ap.av.applet.useXtrnalSviewer) + { + seqMenu.add(pdb); + } seqMenu.add(repGroup); - menu1.add(unGroupMenuItem); + menu1.add(editGroupName); menu1.add(colourMenu); menu1.add(showBoxes); menu1.add(showText); menu1.add(showColourText); + menu1.add(displayNonconserved); toggleCase.addActionListener(this); pdb.addActionListener(this); hideSeqs.addActionListener(this); repGroup.addActionListener(this); revealAll.addActionListener(this); + revealSeq.addActionListener(this); } void refresh() @@ -783,9 +879,7 @@ public class APopupMenu extends java.awt.PopupMenu implements protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg - .getSequences(ap.av.hiddenRepSequences), ap.av.alignment - .getWidth()); + sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()); refresh(); } @@ -847,9 +941,8 @@ public class APopupMenu extends java.awt.PopupMenu implements if (abovePIDColour.getState()) { - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment - .getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av + .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); @@ -877,9 +970,8 @@ public class APopupMenu extends java.awt.PopupMenu implements { SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment - .getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av + .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); refresh(); } @@ -889,9 +981,8 @@ public class APopupMenu extends java.awt.PopupMenu implements sg.cs = new Blosum62ColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment - .getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av + .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth())); refresh(); } @@ -913,16 +1004,10 @@ public class APopupMenu extends java.awt.PopupMenu implements if (conservationMenuItem.getState()) { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg - .getSequences(ap.av.hiddenRepSequences), 0, - ap.av.alignment.getWidth()); - - c.calculate(); - c.verdict(false, ap.av.ConsPercGaps); - - sg.cs.setConservation(c); - + sg.cs.setConservation(Conservation.calculateConservation("Group", + ResidueProperties.propHash, 3, sg.getSequences(ap.av + .getHiddenRepSequences()), 0, ap.av.getAlignment() + .getWidth(), false, ap.av.getConsPercGaps(), false)); SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); SliderPanel.showConservationSlider(); } @@ -942,7 +1027,7 @@ public class APopupMenu extends java.awt.PopupMenu implements // this method won't add a new group if it already exists if (sg != null) { - ap.av.alignment.addGroup(sg); + ap.av.getAlignment().addGroup(sg); } return sg; @@ -951,11 +1036,17 @@ public class APopupMenu extends java.awt.PopupMenu implements void unGroupMenuItem_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); - ap.av.alignment.deleteGroup(sg); + ap.av.getAlignment().deleteGroup(sg); ap.av.setSelectionGroup(null); ap.paintAlignment(true); } + void createGroupMenuItem_actionPerformed() + { + getGroup(); // implicitly create group + refresh(); + } + public void showColourText_itemStateChanged() { getGroup().setColourText(showColourText.getState()); @@ -968,6 +1059,12 @@ public class APopupMenu extends java.awt.PopupMenu implements refresh(); } + public void showNonconserved_itemStateChanged() + { + getGroup().setShowNonconserved(this.displayNonconserved.getState()); + refresh(); + } + public void showBoxes_itemStateChanged() { getGroup().setDisplayBoxes(showBoxes.getState()); @@ -1005,6 +1102,7 @@ public class APopupMenu extends java.awt.PopupMenu implements } ap.av.hideSequence(hseqs); + ap.av.sendSelection(); } }