X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=7d953d42e56d93142ddd72819b8abf4354c65c1e;hb=fca189f1ddefa155881dedeeb0f21c1cd0905e74;hp=457638a2f3ad147bee4e007db8a5c73691900d56;hpb=298ac6df4e5542ba4d5aa635831537e8dd887084;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java old mode 100755 new mode 100644 index 457638a..7d953d4 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,20 +1,20 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * - * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; @@ -22,22 +22,24 @@ import java.util.*; import java.awt.*; import java.awt.event.*; + import javax.swing.*; -import MCview.*; import jalview.analysis.*; import jalview.commands.*; import jalview.datamodel.*; import jalview.io.*; import jalview.schemes.*; import jalview.util.GroupUrlLink; +import jalview.util.GroupUrlLink.UrlStringTooLongException; +import jalview.util.MessageManager; import jalview.util.UrlLink; /** * DOCUMENT ME! * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.118 $ */ public class PopupMenu extends JPopupMenu { @@ -69,6 +71,12 @@ public class PopupMenu extends JPopupMenu 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 JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); @@ -79,8 +87,12 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceName = new JMenuItem(); - Sequence sequence; + JMenuItem sequenceDetails = new JMenuItem(); + + JMenuItem sequenceSelDetails = new JMenuItem(); + SequenceI sequence; + JMenuItem createGroupMenuItem = new JMenuItem(); JMenuItem unGroupMenuItem = new JMenuItem(); JMenuItem outline = new JMenuItem(); @@ -112,7 +124,11 @@ 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(); @@ -140,14 +156,15 @@ public class PopupMenu extends JPopupMenu * Creates a new PopupMenu object. * * @param ap - * DOCUMENT ME! + * DOCUMENT ME! * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ - public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links) + public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links) { this(ap, seq, links, null); } + /** * * @param ap @@ -155,7 +172,8 @@ public class PopupMenu extends JPopupMenu * @param links * @param groupLinks */ - public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links, Vector groupLinks) + public PopupMenu(final AlignmentPanel ap, final SequenceI seq, + Vector links, Vector groupLinks) { // ///////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -180,6 +198,9 @@ public class PopupMenu extends JPopupMenu 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++) { @@ -205,11 +226,11 @@ public class PopupMenu extends JPopupMenu e.printStackTrace(); } + JMenuItem menuItem; if (seq != null) { sequenceMenu.setText(sequence.getName()); - JMenuItem menuItem; if (seq.getDatasetSequence().getPDBId() != null && seq.getDatasetSequence().getPDBId().size() > 0) { @@ -226,33 +247,13 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - Vector seqs = new Vector(); - for (int i = 0; i < ap.av.alignment.getHeight(); i++) - { - Vector pdbs = ap.av.alignment.getSequenceAt(i) - .getDatasetSequence().getPDBId(); - if (pdbs == null) - continue; - - for (int p = 0; p < pdbs.size(); p++) - { - PDBEntry p1 = (PDBEntry) pdbs.elementAt(p); - if (p1.getId().equals(pdb.getId())) - { - if (!seqs.contains(ap.av.alignment.getSequenceAt(i))) - seqs.addElement(ap.av.alignment.getSequenceAt(i)); - - continue; - } - } - } - - SequenceI[] seqs2 = new SequenceI[seqs.size()]; - seqs.toArray(seqs2); - - new AppJmol(pdb, seqs2, null, ap); + // 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 PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE); } + }); viewStructureMenu.add(menuItem); @@ -267,11 +268,82 @@ public class PopupMenu extends JPopupMenu } else { - structureMenu.remove(viewStructureMenu); + if (ap.av.getAlignment().isNucleotide() == false) + { + structureMenu.remove(viewStructureMenu); + } // structureMenu.remove(colStructureMenu); } - menuItem = new JMenuItem("Hide Sequences"); + if (ap.av.getAlignment().isNucleotide() == true) + { + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + for (int i = 0; i < aa.length; i++) + { + if (aa[i].getRNAStruc() != null) + { + final String rnastruc = aa[i].getRNAStruc(); + final String structureLine = aa[i].label; + menuItem = new JMenuItem(); + menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine})); + menuItem.addActionListener(new java.awt.event.ActionListener() + + { + public void actionPerformed(ActionEvent e) + { + //System.out.println("1:"+structureLine); + System.out.println("1:sname"+seq.getName()); + System.out.println("2:seq"+seq); + + //System.out.println("3:"+seq.getSequenceAsString()); + System.out.println("3:strucseq"+rnastruc); + //System.out.println("4:struc"+seq.getRNA()); + System.out.println("5:name"+seq.getName()); + System.out.println("6:ap"+ap); + new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq + .getName(), ap); + //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap); + System.out.println("end"); + } + }); + viewStructureMenu.add(menuItem); + } + } + + // SequenceFeatures[] test = seq.getSequenceFeatures(); + + if (seq.getAnnotation() != null) + { + AlignmentAnnotation seqAnno[] = seq.getAnnotation(); + for (int i = 0; i < seqAnno.length; i++) + { + if (seqAnno[i].getRNAStruc() != null) + { + final String rnastruc = seqAnno[i].getRNAStruc(); + + // TODO: make rnastrucF a bit more nice + menuItem = new JMenuItem(); + menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()})); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + 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); + } + }); + viewStructureMenu.add(menuItem); + } + } + } + + } + + menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences")); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -284,7 +356,7 @@ public class PopupMenu extends JPopupMenu if (ap.av.getSelectionGroup() != null && ap.av.getSelectionGroup().getSize() > 1) { - menuItem = new JMenuItem("Represent Group with " + seq.getName()); + menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()})); menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -295,14 +367,14 @@ public class PopupMenu extends JPopupMenu sequenceMenu.add(menuItem); } - if (ap.av.hasHiddenRows) + if (ap.av.hasHiddenRows()) { - final int index = ap.av.alignment.findIndex(seq); + final int index = ap.av.getAlignment().findIndex(seq); if (ap.av.adjustForHiddenSeqs(index) - ap.av.adjustForHiddenSeqs(index - 1) > 1) { - menuItem = new JMenuItem("Reveal Sequences"); + menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences")); menuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -316,8 +388,13 @@ public class PopupMenu extends JPopupMenu }); add(menuItem); } - - menuItem = new JMenuItem("Reveal All"); + } + } + // for the case when no sequences are even visible + if (ap.av.hasHiddenRows()) + { + { + menuItem = new JMenuItem(MessageManager.getString("action.reveal_all")); menuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -336,10 +413,12 @@ public class PopupMenu extends JPopupMenu } SequenceGroup sg = ap.av.getSelectionGroup(); + boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false; - if (sg != null) - { - groupName.setText(sg.getName()); + 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) { @@ -385,6 +464,16 @@ public class PopupMenu extends JPopupMenu { clustalColour.setSelected(true); } + else if (sg.cs instanceof PurinePyrimidineColourScheme) + { + purinePyrimidineColour.setSelected(true); + } + + + /* + * else if (sg.cs instanceof CovariationColourScheme) { + * covariationColour.setSelected(true); } + */ else { noColourmenuItem.setSelected(true); @@ -394,14 +483,74 @@ public class PopupMenu extends JPopupMenu { conservationMenuItem.setSelected(true); } - displayNonconserved.setSelected(sg.getShowunconserved()); + displayNonconserved.setSelected(sg.getShowNonconserved()); showText.setSelected(sg.getDisplayText()); showColourText.setSelected(sg.getColourText()); showBoxes.setSelected(sg.getDisplayBoxes()); // add any groupURLs to the groupURL submenu and make it visible - if (groupLinks!=null && groupLinks.size()>0) { + if (groupLinks != null && groupLinks.size() > 0) + { buildGroupURLMenu(sg, groupLinks); } + // Add a 'show all structures' for the current selection + Hashtable pdbe = new Hashtable(),reppdb=new Hashtable(); + SequenceI sqass = null; + for (SequenceI sq : ap.av.getSequenceSelection()) + { + Vector pes = (Vector) sq.getDatasetSequence() + .getPDBId(); + if (pes != null) + { + reppdb.put(pes.get(0).getId(),pes.get(0)); + for (PDBEntry pe : pes) + { + pdbe.put(pe.getId(), pe); + if (sqass == null) + { + sqass = sq; + } + } + } + } + if (pdbe.size() > 0) + { + 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 AppJmol(ap, pe, ap.av.collateForPDB(pe)); + } + }); + if (reppdb.size()>1 && reppdb.size() 0) { - - JMenu linkMenu = new JMenu("Link"); + + JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); Vector linkset = new Vector(); for (int i = 0; i < links.size(); i++) { @@ -445,17 +600,17 @@ public class PopupMenu extends JPopupMenu continue; } 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[] - { urlLink.getTarget() }); + 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) + if (descr != null && descr.length() < 1) { descr = null; } @@ -477,10 +632,11 @@ public class PopupMenu extends JPopupMenu { for (int u = 0; u < urls.length; u += 2) { - if (!linkset.contains(urls[u]+"|"+urls[u+1])) + if (!linkset.contains(urls[u] + "|" + urls[u + 1])) { - linkset.addElement(urls[u]+"|"+urls[u+1]); - addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]); + linkset.addElement(urls[u] + "|" + urls[u + 1]); + addshowLink(linkMenu, label + "|" + urls[u], + urls[u + 1]); } } } @@ -494,16 +650,17 @@ public class PopupMenu extends JPopupMenu { for (int u = 0; u < urls.length; u += 2) { - if (!linkset.contains(urls[u]+"|"+urls[u+1])) + if (!linkset.contains(urls[u] + "|" + urls[u + 1])) { - linkset.addElement(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 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); @@ -511,9 +668,9 @@ public class PopupMenu extends JPopupMenu { for (int u = 0; u < urls.length; u += 2) { - if (!linkset.contains(urls[u]+"|"+urls[u+1])) + if (!linkset.contains(urls[u] + "|" + urls[u + 1])) { - linkset.addElement(urls[u]+"|"+urls[u+1]); + linkset.addElement(urls[u] + "|" + urls[u + 1]); addshowLink(linkMenu, label, urls[u + 1]); } } @@ -522,9 +679,9 @@ public class PopupMenu extends JPopupMenu } else { - if (!linkset.contains(label+"|"+urlLink.getUrl_prefix())) + if (!linkset.contains(label + "|" + urlLink.getUrl_prefix())) { - linkset.addElement(label+"|"+urlLink.getUrl_prefix()); + linkset.addElement(label + "|" + urlLink.getUrl_prefix()); // Add a non-dynamic link addshowLink(linkMenu, label, urlLink.getUrl_prefix()); } @@ -540,119 +697,150 @@ public class PopupMenu extends JPopupMenu } } } - + private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks) { - - // TODO: usability: thread off the generation of group url content so root menu appears asap + + // TODO: usability: thread off the generation of group url content so root + // menu appears asap // sequence only URLs // ID/regex match URLs - groupLinksMenu = new JMenu("Group Link"); - JMenu[] linkMenus = new JMenu[] { null, new JMenu("IDS"), new JMenu("Sequences"), new JMenu("IDS and Sequences")}; // three types of url that might be created. - SequenceI[] seqs = ap.av.getSelectionAsNewSequence(); + groupLinksMenu = new JMenu(MessageManager.getString("action.group_link")); + 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. + SequenceI[] seqs = ap.av.getSelectionAsNewSequence(); String[][] idandseqs = GroupUrlLink.formStrings(seqs); Hashtable commonDbrefs = new Hashtable(); - for (int sq = 0; sq0) + if (dbr != null && dbr.length > 0) { - for (int d=0;d0) + if (linkMenus[m] != null + && linkMenus[m].getMenuComponentCount() > 0) { groupLinksMenu.add(linkMenus[m]); } } - + groupMenu.add(groupLinksMenu); } } @@ -661,15 +849,15 @@ public class PopupMenu extends JPopupMenu * add a show URL menu item to the given linkMenu * * @param linkMenu - * @param label - - * menu label string - * @param url - - * url to open + * @param label + * - menu label string + * @param url + * - url to open */ private void addshowLink(JMenu linkMenu, String label, final String url) { JMenuItem item = new JMenuItem(label); - item.setToolTipText("open URL: " + url); + item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url})); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -690,16 +878,57 @@ public class PopupMenu extends JPopupMenu } /** + * add a late bound groupURL item to the given linkMenu + * + * @param linkMenu + * @param label + * - menu label string + * @param urlgenerator + * GroupURLLink used to generate URL + * @param urlstub + * Object array returned from the makeUrlStubs function. + */ + private void addshowLink(JMenu linkMenu, String label, + final GroupUrlLink urlgenerator, final Object[] urlstub) + { + JMenuItem item = new JMenuItem(label); + 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() + { + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + public void run() + { + try + { + showLink(urlgenerator.constructFrom(urlstub)); + } catch (UrlStringTooLongException e) + { + } + } + + }).start(); + } + }); + + linkMenu.add(item); + } + + /** * DOCUMENT ME! * * @throws Exception - * DOCUMENT ME! + * DOCUMENT ME! */ private void jbInit() throws Exception { - groupMenu.setText("Group"); - groupMenu.setText("Selection"); - groupName.setText("Name"); + 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() { public void actionPerformed(ActionEvent e) @@ -707,8 +936,8 @@ public class PopupMenu extends JPopupMenu groupName_actionPerformed(); } }); - sequenceMenu.setText("Sequence"); - sequenceName.setText("Edit Name/Description"); + sequenceMenu.setText(MessageManager.getString("label.sequence")); + sequenceName.setText(MessageManager.getString("label.edit_name_description")); sequenceName.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -716,8 +945,25 @@ public class PopupMenu extends JPopupMenu sequenceName_actionPerformed(); } }); + sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "..."); + sequenceDetails.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceDetails_actionPerformed(); + } + }); + sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "..."); + sequenceSelDetails + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceSelectionDetails_actionPerformed(); + } + }); PIDColour.setFocusPainted(false); - unGroupMenuItem.setText("Remove Group"); + unGroupMenuItem.setText(MessageManager.getString("action.remove_group")); unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -725,8 +971,16 @@ public class PopupMenu extends JPopupMenu unGroupMenuItem_actionPerformed(); } }); + createGroupMenuItem.setText(MessageManager.getString("action.create_group")); + createGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + createGroupMenuItem_actionPerformed(); + } + }); - outline.setText("Border colour"); + outline.setText(MessageManager.getString("action.border_colour")); outline.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -734,7 +988,7 @@ public class PopupMenu extends JPopupMenu outline_actionPerformed(); } }); - nucleotideMenuItem.setText("Nucleotide"); + nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide")); nucleotideMenuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -742,8 +996,8 @@ public class PopupMenu extends JPopupMenu nucleotideMenuItem_actionPerformed(); } }); - colourMenu.setText("Group Colour"); - showBoxes.setText("Boxes"); + colourMenu.setText(MessageManager.getString("label.group_colour")); + showBoxes.setText(MessageManager.getString("action.boxes")); showBoxes.setState(true); showBoxes.addActionListener(new ActionListener() { @@ -752,7 +1006,7 @@ public class PopupMenu extends JPopupMenu showBoxes_actionPerformed(); } }); - showText.setText("Text"); + showText.setText(MessageManager.getString("action.text")); showText.setState(true); showText.addActionListener(new ActionListener() { @@ -761,7 +1015,7 @@ public class PopupMenu extends JPopupMenu showText_actionPerformed(); } }); - showColourText.setText("Colour Text"); + showColourText.setText(MessageManager.getString("label.colour_text")); showColourText.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -769,7 +1023,7 @@ public class PopupMenu extends JPopupMenu showColourText_actionPerformed(); } }); - displayNonconserved.setText("Show Nonconserved"); + displayNonconserved.setText(MessageManager.getString("label.show_non_conversed")); displayNonconserved.setState(true); displayNonconserved.addActionListener(new ActionListener() { @@ -778,8 +1032,8 @@ public class PopupMenu extends JPopupMenu showNonconserved_actionPerformed(); } }); - editMenu.setText("Edit"); - cut.setText("Cut"); + editMenu.setText(MessageManager.getString("action.edit")); + cut.setText(MessageManager.getString("action.cut")); cut.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -787,7 +1041,7 @@ public class PopupMenu extends JPopupMenu cut_actionPerformed(); } }); - upperCase.setText("To Upper Case"); + upperCase.setText(MessageManager.getString("label.to_upper_case")); upperCase.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -795,7 +1049,7 @@ public class PopupMenu extends JPopupMenu changeCase(e); } }); - copy.setText("Copy"); + copy.setText(MessageManager.getString("action.copy")); copy.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -803,7 +1057,7 @@ public class PopupMenu extends JPopupMenu copy_actionPerformed(); } }); - lowerCase.setText("To Lower Case"); + lowerCase.setText(MessageManager.getString("label.to_lower_case")); lowerCase.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -811,7 +1065,7 @@ public class PopupMenu extends JPopupMenu changeCase(e); } }); - toggle.setText("Toggle Case"); + toggle.setText(MessageManager.getString("label.toggle_case")); toggle.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -819,8 +1073,8 @@ public class PopupMenu extends JPopupMenu changeCase(e); } }); - pdbMenu.setText("Associate Structure with Sequence"); - pdbFromFile.setText("From File"); + pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence")); + pdbFromFile.setText(MessageManager.getString("label.from_file")); pdbFromFile.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -828,7 +1082,33 @@ public class PopupMenu extends JPopupMenu pdbFromFile_actionPerformed(); } }); - enterPDB.setText("Enter PDB Id"); +// 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() { public void actionPerformed(ActionEvent e) @@ -836,7 +1116,7 @@ public class PopupMenu extends JPopupMenu enterPDB_actionPerformed(); } }); - discoverPDB.setText("Discover PDB ids"); + discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids")); discoverPDB.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -844,8 +1124,8 @@ public class PopupMenu extends JPopupMenu discoverPDB_actionPerformed(); } }); - outputMenu.setText("Output to Textbox..."); - sequenceFeature.setText("Create Sequence Feature"); + outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "..."); + sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature")); sequenceFeature.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -853,7 +1133,7 @@ public class PopupMenu extends JPopupMenu sequenceFeature_actionPerformed(); } }); - textColour.setText("Text Colour"); + textColour.setText(MessageManager.getString("label.text_colour")); textColour.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -861,11 +1141,11 @@ public class PopupMenu extends JPopupMenu textColour_actionPerformed(); } }); - jMenu1.setText("Group"); - structureMenu.setText("Structure"); - viewStructureMenu.setText("View Structure"); + 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("Edit Sequence..."); + editSequence.setText(MessageManager.getString("label.edit_sequence") + "..."); editSequence.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent actionEvent) @@ -873,22 +1153,25 @@ public class PopupMenu extends JPopupMenu editSequence_actionPerformed(actionEvent); } }); + /* * 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); groupMenu.add(editMenu); groupMenu.add(outputMenu); groupMenu.add(sequenceFeature); + groupMenu.add(createGroupMenuItem); + groupMenu.add(unGroupMenuItem); groupMenu.add(jMenu1); sequenceMenu.add(sequenceName); + sequenceMenu.add(sequenceDetails); colourMenu.add(textColour); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); @@ -902,6 +1185,12 @@ public class PopupMenu extends JPopupMenu 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) @@ -934,10 +1223,12 @@ public class PopupMenu extends JPopupMenu 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(unGroupMenuItem); jMenu1.add(colourMenu); jMenu1.add(showBoxes); jMenu1.add(showText); @@ -947,7 +1238,7 @@ public class PopupMenu extends JPopupMenu structureMenu.add(pdbMenu); structureMenu.add(viewStructureMenu); // structureMenu.add(colStructureMenu); - noColourmenuItem.setText("None"); + noColourmenuItem.setText(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -956,7 +1247,7 @@ public class PopupMenu extends JPopupMenu } }); - clustalColour.setText("Clustalx colours"); + clustalColour.setText(MessageManager.getString("label.clustalx_colours")); clustalColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -964,7 +1255,7 @@ public class PopupMenu extends JPopupMenu clustalColour_actionPerformed(); } }); - zappoColour.setText("Zappo"); + zappoColour.setText(MessageManager.getString("label.zappo")); zappoColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -972,7 +1263,7 @@ public class PopupMenu extends JPopupMenu zappoColour_actionPerformed(); } }); - taylorColour.setText("Taylor"); + taylorColour.setText(MessageManager.getString("label.taylor")); taylorColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -980,7 +1271,7 @@ public class PopupMenu extends JPopupMenu taylorColour_actionPerformed(); } }); - hydrophobicityColour.setText("Hydrophobicity"); + hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity")); hydrophobicityColour .addActionListener(new java.awt.event.ActionListener() { @@ -989,7 +1280,7 @@ public class PopupMenu extends JPopupMenu hydrophobicityColour_actionPerformed(); } }); - helixColour.setText("Helix propensity"); + helixColour.setText(MessageManager.getString("label.helix_propensity")); helixColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -997,7 +1288,7 @@ public class PopupMenu extends JPopupMenu helixColour_actionPerformed(); } }); - strandColour.setText("Strand propensity"); + strandColour.setText(MessageManager.getString("label.strand_propensity")); strandColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1005,7 +1296,7 @@ public class PopupMenu extends JPopupMenu strandColour_actionPerformed(); } }); - turnColour.setText("Turn propensity"); + turnColour.setText(MessageManager.getString("label.turn_propensity")); turnColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1013,7 +1304,7 @@ public class PopupMenu extends JPopupMenu turnColour_actionPerformed(); } }); - buriedColour.setText("Buried Index"); + buriedColour.setText(MessageManager.getString("label.buried_index")); buriedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1021,7 +1312,7 @@ public class PopupMenu extends JPopupMenu buriedColour_actionPerformed(); } }); - abovePIDColour.setText("Above % Identity"); + abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage")); abovePIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1029,7 +1320,7 @@ public class PopupMenu extends JPopupMenu abovePIDColour_actionPerformed(); } }); - userDefinedColour.setText("User Defined..."); + userDefinedColour.setText(MessageManager.getString("action.user_defined")); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1037,7 +1328,7 @@ public class PopupMenu extends JPopupMenu userDefinedColour_actionPerformed(e); } }); - PIDColour.setText("Percentage Identity"); + PIDColour.setText(MessageManager.getString("label.percentage_identity")); PIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1045,7 +1336,7 @@ public class PopupMenu extends JPopupMenu PIDColour_actionPerformed(); } }); - BLOSUM62Colour.setText("BLOSUM62"); + BLOSUM62Colour.setText(MessageManager.getString("label.blosum62")); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1053,7 +1344,24 @@ public class PopupMenu extends JPopupMenu BLOSUM62Colour_actionPerformed(); } }); - conservationMenuItem.setText("Conservation"); + purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine")); + purinePyrimidineColour + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + purinePyrimidineColour_actionPerformed(); + } + }); + + + /* + * covariationColour.addActionListener(new java.awt.event.ActionListener() { + * public void actionPerformed(ActionEvent e) { + * covariationColour_actionPerformed(); } }); + */ + + conservationMenuItem.setText(MessageManager.getString("label.conservation")); conservationMenuItem .addActionListener(new java.awt.event.ActionListener() { @@ -1064,9 +1372,46 @@ public class PopupMenu extends JPopupMenu }); } + protected void sequenceSelectionDetails_actionPerformed() + { + createSequenceDetailsReport(ap.av.getSequenceSelection()); + } + + protected void sequenceDetails_actionPerformed() + { + createSequenceDetailsReport(new SequenceI[] + { sequence }); + } + + public void createSequenceDetailsReport(SequenceI[] sequences) + { + CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); + StringBuffer contents = new StringBuffer(); + 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.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax + : 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); + + } + protected void showNonconserved_actionPerformed() { - getGroup().setShowunconserved(displayNonconserved.isSelected()); + getGroup().setShowNonconserved(displayNonconserved.isSelected()); refresh(); } @@ -1085,14 +1430,12 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ 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(); } @@ -1100,7 +1443,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void zappoColour_actionPerformed() { @@ -1112,7 +1455,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void taylorColour_actionPerformed() { @@ -1124,7 +1467,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void hydrophobicityColour_actionPerformed() { @@ -1136,7 +1479,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void helixColour_actionPerformed() { @@ -1148,7 +1491,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void strandColour_actionPerformed() { @@ -1160,7 +1503,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void turnColour_actionPerformed() { @@ -1172,7 +1515,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void buriedColour_actionPerformed() { @@ -1184,7 +1527,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void nucleotideMenuItem_actionPerformed() { @@ -1192,11 +1535,22 @@ public class PopupMenu extends JPopupMenu refresh(); } + protected void purinePyrimidineColour_actionPerformed() + { + getGroup().cs = new PurinePyrimidineColourScheme(); + refresh(); + } + + + /* + * protected void covariationColour_actionPerformed() { getGroup().cs = new + * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } + */ /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void abovePIDColour_actionPerformed() { @@ -1208,9 +1562,9 @@ public class PopupMenu extends JPopupMenu if (abovePIDColour.isSelected()) { - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg - .getEndRes() + 1)); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); @@ -1232,13 +1586,13 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void userDefinedColour_actionPerformed(ActionEvent e) { SequenceGroup sg = getGroup(); - if (e.getActionCommand().equals("User Defined...")) + if (e.getSource().equals(userDefinedColour)) { new UserDefinedColours(ap, sg); } @@ -1256,15 +1610,15 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void PIDColour_actionPerformed() { SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg - .getEndRes() + 1)); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } @@ -1272,7 +1626,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void BLOSUM62Colour_actionPerformed() { @@ -1280,9 +1634,9 @@ public class PopupMenu extends JPopupMenu sg.cs = new Blosum62ColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg - .getEndRes() + 1)); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); refresh(); } @@ -1291,7 +1645,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void noColourmenuItem_actionPerformed() { @@ -1303,7 +1657,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void conservationMenuItem_actionPerformed() { @@ -1315,13 +1669,14 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { + // JBPNote: Conservation name shouldn't be i18n translated Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg - .getSequences(ap.av.hiddenRepSequences), sg - .getStartRes(), sg.getEndRes() + 1); + ResidueProperties.propHash, 3, sg.getSequences(ap.av + .getHiddenRepSequences()), sg.getStartRes(), + sg.getEndRes() + 1); c.calculate(); - c.verdict(false, ap.av.ConsPercGaps); + c.verdict(false, ap.av.getConsPercGaps()); sg.cs.setConservation(c); @@ -1345,11 +1700,11 @@ public class PopupMenu extends JPopupMenu return; } - AnnotationColourGradient acg = new AnnotationColourGradient(sequence - .getAnnotation()[0], null, + AnnotationColourGradient acg = new AnnotationColourGradient( + sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD); - acg.predefinedColours = true; + acg.setPredefinedColours(true); sg.cs = acg; refresh(); @@ -1359,15 +1714,16 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void groupName_actionPerformed() { SequenceGroup sg = getGroup(); - EditNameDialog dialog = new EditNameDialog(sg.getName(), sg - .getDescription(), " Group Name ", "Group Description ", - "Edit Group Name/Description"); + EditNameDialog dialog = new EditNameDialog(sg.getName(), + sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ", + MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"), + ap.alignFrame); if (!dialog.accept) { @@ -1376,12 +1732,13 @@ public class PopupMenu extends JPopupMenu sg.setName(dialog.getName()); sg.setDescription(dialog.getDescription()); + refresh(); } /** - * DOCUMENT ME! + * Get selection group - adding it to the alignment if necessary. * - * @return DOCUMENT ME! + * @return sequence group to operate on */ SequenceGroup getGroup() { @@ -1389,7 +1746,7 @@ public class PopupMenu extends JPopupMenu // 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; @@ -1399,13 +1756,14 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ void sequenceName_actionPerformed() { - EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence - .getDescription(), " Sequence Name ", - "Sequence Description ", "Edit Sequence Name/Description"); + EditNameDialog dialog = new EditNameDialog(sequence.getName(), + sequence.getDescription(), " " + MessageManager.getString("label.sequence_name") + " ", + MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"), + ap.alignFrame); if (!dialog.accept) { @@ -1417,8 +1775,8 @@ public class PopupMenu extends JPopupMenu if (dialog.getName().indexOf(" ") > -1) { JOptionPane.showMessageDialog(ap, - "Spaces have been converted to \"_\"", - "No spaces allowed in Sequence Name", + MessageManager.getString("label.spaces_converted_to_backslashes"), + MessageManager.getString("label.no_spaces_allowed_sequence_name"), JOptionPane.WARNING_MESSAGE); } @@ -1437,26 +1795,31 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ void unGroupMenuItem_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); - ap.av.alignment.deleteGroup(sg); + ap.av.getAlignment().deleteGroup(sg); ap.av.setSelectionGroup(null); refresh(); } + void createGroupMenuItem_actionPerformed() + { + getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this + refresh(); + } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void outline_actionPerformed() { SequenceGroup sg = getGroup(); - Color col = JColorChooser.showDialog(this, "Select Outline Colour", + Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"), Color.BLUE); if (col != null) @@ -1471,7 +1834,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void showBoxes_actionPerformed() { @@ -1483,7 +1846,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void showText_actionPerformed() { @@ -1495,7 +1858,7 @@ public class PopupMenu extends JPopupMenu * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void showColourText_actionPerformed() { @@ -1513,9 +1876,8 @@ public class PopupMenu extends JPopupMenu JOptionPane .showInternalMessageDialog( Desktop.desktop, - "Unixers: Couldn't find default web browser." - + "\nAdd the full path to your browser in Preferences.", - "Web browser not found", JOptionPane.WARNING_MESSAGE); + MessageManager.getString("label.web_browser_not_found_unix"), + MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } @@ -1552,6 +1914,7 @@ public class PopupMenu extends JPopupMenu } ap.av.hideSequence(hseqs); + // refresh(); TODO: ? needed ? ap.av.sendSelection(); } @@ -1580,23 +1943,23 @@ public class PopupMenu extends JPopupMenu if (source == toggle) { - description = "Toggle Case"; + description = MessageManager.getString("label.toggle_case"); caseChange = ChangeCaseCommand.TOGGLE_CASE; } else if (source == upperCase) { - description = "To Upper Case"; + description = MessageManager.getString("label.to_upper_case"); caseChange = ChangeCaseCommand.TO_UPPER; } else { - description = "To Lower Case"; + description = MessageManager.getString("label.to_lower_case"); caseChange = ChangeCaseCommand.TO_LOWER; } - ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg - .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, - caseChange); + ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); @@ -1610,23 +1973,27 @@ public class PopupMenu extends JPopupMenu { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - Desktop.addInternalFrame(cap, "Alignment output - " - + e.getActionCommand(), 600, 500); + Desktop.addInternalFrame(cap, + MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500); String[] omitHidden = null; System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens - // or we simply trust the user wants - // wysiwig behaviour + // or we simply trust the user wants + // wysiwig behaviour SequenceGroup sg = ap.av.getSelectionGroup(); ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection()); omitHidden = ap.av.getViewAsString(true); Alignment oal = new Alignment(ap.av.getSequenceSelection()); - AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation(); - for (int i = 0; i < nala.length; i++) + AlignmentAnnotation[] nala = ap.av.getAlignment() + .getAlignmentAnnotation(); + if (nala != null) { - AlignmentAnnotation na = nala[i]; - oal.addAnnotation(na); + for (int i = 0; i < nala.length; i++) + { + AlignmentAnnotation na = nala[i]; + oal.addAnnotation(na); + } } cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), oal, omitHidden, csel, sg)); @@ -1638,55 +2005,36 @@ public class PopupMenu extends JPopupMenu jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Select a PDB file"); - chooser.setToolTipText("Load a PDB file"); + 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[]{new Integer(sequence.getDisplayId(false)).toString()})); int value = chooser.showOpenDialog(null); if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) { - PDBEntry entry = new PDBEntry(); String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - try - { - MCview.PDBfile pdbfile = new MCview.PDBfile(choice, - jalview.io.AppletFormatAdapter.FILE); - - if (pdbfile.id == null) - { - String reply = JOptionPane - .showInternalInputDialog( - Desktop.desktop, - "Couldn't find a PDB id in the file supplied." - + "Please enter an Id to identify this structure.", - "No PDB Id in File", JOptionPane.QUESTION_MESSAGE); - if (reply == null) - { - return; - } - - entry.setId(reply); - } - else - { - entry.setId(pdbfile.id); - } - } catch (java.io.IOException ex) - { - ex.printStackTrace(); - } - - entry.setFile(choice); - sequence.getDatasetSequence().addPDBId(entry); + new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, + jalview.io.AppletFormatAdapter.FILE, sequence, true); } } - + // 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, - "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE); + MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE); if (id != null && id.length() > 0) { @@ -1699,9 +2047,9 @@ public class PopupMenu extends JPopupMenu public void discoverPDB_actionPerformed() { - final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[] + final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[] { sequence } - : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment)); + : ap.av.getSequenceSelection()); Thread discpdb = new Thread(new Runnable() { public void run() @@ -1723,25 +2071,25 @@ public class PopupMenu extends JPopupMenu return; } - int rsize=0,gSize = sg.getSize(); - SequenceI[] rseqs,seqs = new SequenceI[gSize]; - SequenceFeature[] tfeatures,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++) { int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); int end = sg.findEndRes(sg.getSequenceAt(i)); - if (start<=end) + if (start <= end) { seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence(); features[rsize] = new SequenceFeature(null, null, null, start, end, - "Jalview"); + "Jalview"); rsize++; } } rseqs = new SequenceI[rsize]; tfeatures = new SequenceFeature[rsize]; - System.arraycopy(seqs,0,rseqs, 0, rsize); + System.arraycopy(seqs, 0, rseqs, 0, rsize); System.arraycopy(features, 0, tfeatures, 0, rsize); features = tfeatures; seqs = rseqs; @@ -1764,17 +2112,16 @@ public class PopupMenu extends JPopupMenu public void colourByStructure(String pdbid) { - Annotation[] anots = jalview.structure.StructureSelectionManager - .getStructureSelectionManager().colourSequenceFromStructure( - sequence, pdbid); + Annotation[] anots = ap.av.getStructureSelectionManager() + .colourSequenceFromStructure(sequence, pdbid); AlignmentAnnotation an = new AlignmentAnnotation("Structure", "Coloured by " + pdbid, anots); - ap.av.alignment.addAnnotation(an); + ap.av.getAlignment().addAnnotation(an); an.createSequenceMapping(sequence, 0, true); // an.adjustForAlignment(); - ap.av.alignment.setAnnotationIndex(an, 0); + ap.av.getAlignment().setAnnotationIndex(an, 0); ap.adjustAnnotationHeight(); @@ -1791,17 +2138,18 @@ public class PopupMenu extends JPopupMenu if (sequence == null) sequence = (Sequence) sg.getSequenceAt(0); - EditNameDialog dialog = new EditNameDialog(sequence - .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1), - null, "Edit Sequence ", null, "Edit Sequence"); + EditNameDialog dialog = new EditNameDialog( + sequence.getSequenceAsString(sg.getStartRes(), + sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null, + MessageManager.getString("label.edit_sequence"), ap.alignFrame); if (dialog.accept) { - EditCommand editCommand = new EditCommand("Edit Sequences", + EditCommand editCommand = new EditCommand(MessageManager.getString("label.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);