-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- */
-package jalview.gui;
-
-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.UrlLink;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class PopupMenu extends JPopupMenu
-{
- JMenu groupMenu = new JMenu();
-
- JMenuItem groupName = new JMenuItem();
-
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-
- protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
-
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
-
- protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
-
- AlignmentPanel ap;
-
- JMenu sequenceMenu = new JMenu();
-
- JMenuItem sequenceName = new JMenuItem();
-
- Sequence sequence;
-
- JMenuItem unGroupMenuItem = new JMenuItem();
-
- JMenuItem outline = new JMenuItem();
-
- JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
-
- JMenu colourMenu = new JMenu();
-
- JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
-
- JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
-
- JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
-
- JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
-
- JMenu editMenu = new JMenu();
-
- JMenuItem cut = new JMenuItem();
-
- JMenuItem copy = new JMenuItem();
-
- JMenuItem upperCase = new JMenuItem();
-
- JMenuItem lowerCase = new JMenuItem();
-
- JMenuItem toggle = new JMenuItem();
-
- JMenu pdbMenu = new JMenu();
-
- JMenuItem pdbFromFile = new JMenuItem();
-
- JMenuItem enterPDB = new JMenuItem();
-
- JMenuItem discoverPDB = new JMenuItem();
-
- JMenu outputMenu = new JMenu();
-
- JMenuItem sequenceFeature = new JMenuItem();
-
- JMenuItem textColour = new JMenuItem();
-
- JMenu jMenu1 = new JMenu();
-
- JMenu structureMenu = new JMenu();
-
- JMenu viewStructureMenu = new JMenu();
-
- // JMenu colStructureMenu = new JMenu();
- JMenuItem editSequence = new JMenuItem();
-
- // JMenuItem annotationMenuItem = new JMenuItem();
-
- JMenu groupLinksMenu;
-
- /**
- * Creates a new PopupMenu object.
- *
- * @param ap
- * DOCUMENT ME!
- * @param seq
- * DOCUMENT ME!
- */
- public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
- {
- this(ap, seq, links, null);
- }
-
- /**
- *
- * @param ap
- * @param seq
- * @param links
- * @param groupLinks
- */
- public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links,
- Vector groupLinks)
- {
- // /////////////////////////////////////////////////////////
- // If this is activated from the sequence panel, the user may want to
- // edit or annotate a particular residue. Therefore display the residue menu
- //
- // If from the IDPanel, we must display the sequence menu
- // ////////////////////////////////////////////////////////
- this.ap = ap;
- sequence = seq;
-
- ButtonGroup colours = new ButtonGroup();
- colours.add(noColourmenuItem);
- colours.add(clustalColour);
- colours.add(zappoColour);
- colours.add(taylorColour);
- colours.add(hydrophobicityColour);
- colours.add(helixColour);
- colours.add(strandColour);
- colours.add(turnColour);
- colours.add(buriedColour);
- colours.add(abovePIDColour);
- colours.add(userDefinedColour);
- colours.add(PIDColour);
- colours.add(BLOSUM62Colour);
-
- for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
- {
- JMenuItem item = new JMenuItem(
- jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
-
- item.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- outputText_actionPerformed(e);
- }
- });
-
- outputMenu.add(item);
- }
-
- try
- {
- jbInit();
- } catch (Exception e)
- {
- e.printStackTrace();
- }
-
- if (seq != null)
- {
- sequenceMenu.setText(sequence.getName());
-
- JMenuItem menuItem;
- if (seq.getDatasetSequence().getPDBId() != null
- && seq.getDatasetSequence().getPDBId().size() > 0)
- {
- 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 java.awt.event.ActionListener()
- {
- 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);
- // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
- }
- });
- 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);
- */
- }
- }
- else
- {
- structureMenu.remove(viewStructureMenu);
- // structureMenu.remove(colStructureMenu);
- }
-
- menuItem = new JMenuItem("Hide Sequences");
- menuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- hideSequences(false);
- }
- });
- add(menuItem);
-
- if (ap.av.getSelectionGroup() != null
- && ap.av.getSelectionGroup().getSize() > 1)
- {
- menuItem = new JMenuItem("Represent Group with " + seq.getName());
- menuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- hideSequences(true);
- }
- });
- sequenceMenu.add(menuItem);
- }
-
- if (ap.av.hasHiddenRows)
- {
- final int index = ap.av.alignment.findIndex(seq);
-
- if (ap.av.adjustForHiddenSeqs(index)
- - ap.av.adjustForHiddenSeqs(index - 1) > 1)
- {
- menuItem = new JMenuItem("Reveal Sequences");
- menuItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- ap.av.showSequence(index);
- if (ap.overviewPanel != null)
- {
- ap.overviewPanel.updateOverviewImage();
- }
- }
- });
- add(menuItem);
- }
-
- menuItem = new JMenuItem("Reveal All");
- menuItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- ap.av.showAllHiddenSeqs();
- if (ap.overviewPanel != null)
- {
- ap.overviewPanel.updateOverviewImage();
- }
- }
- });
-
- add(menuItem);
- }
-
- }
-
- SequenceGroup sg = ap.av.getSelectionGroup();
-
- if (sg != null)
- {
- groupName.setText(sg.getName());
-
- if (sg.cs instanceof ZappoColourScheme)
- {
- zappoColour.setSelected(true);
- }
- else if (sg.cs instanceof TaylorColourScheme)
- {
- taylorColour.setSelected(true);
- }
- else if (sg.cs instanceof PIDColourScheme)
- {
- PIDColour.setSelected(true);
- }
- else if (sg.cs instanceof Blosum62ColourScheme)
- {
- BLOSUM62Colour.setSelected(true);
- }
- else if (sg.cs instanceof UserColourScheme)
- {
- userDefinedColour.setSelected(true);
- }
- else if (sg.cs instanceof HydrophobicColourScheme)
- {
- hydrophobicityColour.setSelected(true);
- }
- else if (sg.cs instanceof HelixColourScheme)
- {
- helixColour.setSelected(true);
- }
- else if (sg.cs instanceof StrandColourScheme)
- {
- strandColour.setSelected(true);
- }
- else if (sg.cs instanceof TurnColourScheme)
- {
- turnColour.setSelected(true);
- }
- else if (sg.cs instanceof BuriedColourScheme)
- {
- buriedColour.setSelected(true);
- }
- else if (sg.cs instanceof ClustalxColourScheme)
- {
- clustalColour.setSelected(true);
- }
- else
- {
- noColourmenuItem.setSelected(true);
- }
-
- if (sg.cs != null && sg.cs.conservationApplied())
- {
- conservationMenuItem.setSelected(true);
- }
- 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)
- {
- buildGroupURLMenu(sg, groupLinks);
- }
- }
- else
- {
- groupMenu.setVisible(false);
- editMenu.setVisible(false);
- }
-
- if (!ap.av.alignment.getGroups().contains(sg))
- {
- unGroupMenuItem.setVisible(false);
- }
-
- if (seq == null)
- {
- sequenceMenu.setVisible(false);
- structureMenu.setVisible(false);
- }
-
- if (links != null && links.size() > 0)
- {
-
- JMenu linkMenu = new JMenu("Link");
- Vector linkset = new Vector();
- for (int i = 0; i < links.size(); i++)
- {
- String link = links.elementAt(i).toString();
- UrlLink urlLink = null;
- try
- {
- urlLink = new UrlLink(link);
- } catch (Exception foo)
- {
- jalview.bin.Cache.log.error("Exception for URLLink '" + link
- + "'", foo);
- continue;
- }
- ;
- if (!urlLink.isValid())
- {
- jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
- continue;
- }
- final String label = urlLink.getLabel();
- if (urlLink.isDynamic())
- {
-
- // collect matching db-refs
- DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
- .getDBRef(), new String[]
- { urlLink.getTarget() });
- // collect id string too
- String id = seq.getName();
- String descr = seq.getDescription();
- if (descr != null && descr.length() < 1)
- {
- descr = null;
- }
-
- if (dbr != null)
- {
- for (int r = 0; r < dbr.length; r++)
- {
- if (id != null && dbr[r].getAccessionId().equals(id))
- {
- // suppress duplicate link creation for the bare sequence ID
- // string with this link
- id = null;
- }
- // create Bare ID link for this RUL
- String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
- true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
- {
- linkset.addElement(urls[u] + "|" + urls[u + 1]);
- addshowLink(linkMenu, label + "|" + urls[u],
- urls[u + 1]);
- }
- }
- }
- }
- }
- if (id != null)
- {
- // create Bare ID link for this RUL
- String[] urls = urlLink.makeUrls(id, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
- {
- linkset.addElement(urls[u] + "|" + urls[u + 1]);
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- }
- }
- // Create urls from description but only for URL links which are regex
- // links
- if (descr != null && urlLink.getRegexReplace() != null)
- {
- // create link for this URL from description where regex matches
- String[] urls = urlLink.makeUrls(descr, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
- {
- linkset.addElement(urls[u] + "|" + urls[u + 1]);
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- }
- }
- }
- else
- {
- if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
- {
- linkset.addElement(label + "|" + urlLink.getUrl_prefix());
- // Add a non-dynamic link
- addshowLink(linkMenu, label, urlLink.getUrl_prefix());
- }
- }
- }
- if (sequence != null)
- {
- sequenceMenu.add(linkMenu);
- }
- else
- {
- add(linkMenu);
- }
- }
- }
-
- private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
- {
-
- // 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();
- String[][] idandseqs = GroupUrlLink.formStrings(seqs);
- Hashtable commonDbrefs = new Hashtable();
- for (int sq = 0; sq < seqs.length; sq++)
- {
-
- int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
- .findPosition(sg.getEndRes());
- // just collect ids from dataset sequence
- // TODO: check if IDs collected from selecton group intersects with the
- // current selection, too
- SequenceI sqi = seqs[sq];
- while (sqi.getDatasetSequence() != null)
- {
- sqi = sqi.getDatasetSequence();
- }
- DBRefEntry[] dbr = sqi.getDBRef();
- if (dbr != null && dbr.length > 0)
- {
- for (int d = 0; d < dbr.length; d++)
- {
- String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
- Object[] sarray = (Object[]) commonDbrefs.get(src);
- if (sarray == null)
- {
- sarray = new Object[2];
- sarray[0] = new int[]
- { 0 };
- sarray[1] = new String[seqs.length];
-
- commonDbrefs.put(src, sarray);
- }
-
- if (((String[]) sarray[1])[sq] == null)
- {
- if (!dbr[d].hasMap()
- || (dbr[d].getMap().locateMappedRange(start, end) != null))
- {
- ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
- ((int[]) sarray[0])[0]++;
- }
- }
- }
- }
- }
- // now create group links for all distinct ID/sequence sets.
- boolean addMenu = false; // indicates if there are any group links to give
- // to user
- for (int i = 0; i < groupLinks.size(); i++)
- {
- String link = groupLinks.elementAt(i).toString();
- GroupUrlLink urlLink = null;
- try
- {
- urlLink = new GroupUrlLink(link);
- } catch (Exception foo)
- {
- jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
- + "'", foo);
- continue;
- }
- ;
- if (!urlLink.isValid())
- {
- jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
- continue;
- }
- final String label = urlLink.getLabel();
- boolean usingNames = false;
- // Now see which parts of the group apply for this URL
- String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
- Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
- String[] seqstr, ids; // input to makeUrl
- if (idset != null)
- {
- int numinput = ((int[]) idset[0])[0];
- String[] allids = ((String[]) idset[1]);
- seqstr = new String[numinput];
- ids = new String[numinput];
- for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
- {
- if (allids[sq] != null)
- {
- ids[idcount] = allids[sq];
- seqstr[idcount++] = idandseqs[1][sq];
- }
- }
- }
- else
- {
- // just use the id/seq set
- seqstr = idandseqs[1];
- ids = idandseqs[0];
- usingNames = true;
- }
- // and try and make the groupURL!
-
- Object[] urlset = null;
- try
- {
- urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
- + System.currentTimeMillis(), false);
- } catch (UrlStringTooLongException e)
- {
- }
- if (urlset != null)
- {
- int type = urlLink.getGroupURLType() & 3;
- // System.out.println(urlLink.getGroupURLType()
- // +" "+((String[])urlset[3])[0]);
- // first two bits ofurlLink type bitfield are sequenceids and sequences
- // TODO: FUTURE: ensure the groupURL menu structure can be generalised
- addshowLink(linkMenus[type], label
- + (((type & 1) == 1) ? ("("
- + (usingNames ? "Names" : ltarget) + ")") : ""),
- urlLink, urlset);
- addMenu = true;
- }
- }
- if (addMenu)
- {
- groupLinksMenu = new JMenu("Group Links");
- for (int m = 0; m < linkMenus.length; m++)
- {
- if (linkMenus[m] != null
- && linkMenus[m].getMenuComponentCount() > 0)
- {
- groupLinksMenu.add(linkMenus[m]);
- }
- }
-
- groupMenu.add(groupLinksMenu);
- }
- }
-
- /**
- * add a show URL menu item to the given linkMenu
- *
- * @param linkMenu
- * @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.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- new Thread(new Runnable()
- {
-
- public void run()
- {
- showLink(url);
- }
-
- }).start();
- }
- });
-
- linkMenu.add(item);
- }
-
- /**
- * 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("open URL (" + urlgenerator.getUrl_prefix()
- + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // 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!
- */
- private void jbInit() throws Exception
- {
- groupMenu.setText("Group");
- groupMenu.setText("Selection");
- groupName.setText("Name");
- groupName.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- groupName_actionPerformed();
- }
- });
- sequenceMenu.setText("Sequence");
- sequenceName.setText("Edit Name/Description");
- sequenceName.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- sequenceName_actionPerformed();
- }
- });
- PIDColour.setFocusPainted(false);
- unGroupMenuItem.setText("Remove Group");
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- unGroupMenuItem_actionPerformed();
- }
- });
-
- outline.setText("Border colour");
- outline.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- outline_actionPerformed();
- }
- });
- nucleotideMenuItem.setText("Nucleotide");
- nucleotideMenuItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- nucleotideMenuItem_actionPerformed();
- }
- });
- colourMenu.setText("Group Colour");
- showBoxes.setText("Boxes");
- showBoxes.setState(true);
- showBoxes.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- showBoxes_actionPerformed();
- }
- });
- showText.setText("Text");
- showText.setState(true);
- showText.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- showText_actionPerformed();
- }
- });
- showColourText.setText("Colour Text");
- showColourText.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- showColourText_actionPerformed();
- }
- });
- displayNonconserved.setText("Show Nonconserved");
- displayNonconserved.setState(true);
- displayNonconserved.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- showNonconserved_actionPerformed();
- }
- });
- editMenu.setText("Edit");
- cut.setText("Cut");
- cut.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- cut_actionPerformed();
- }
- });
- upperCase.setText("To Upper Case");
- upperCase.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- changeCase(e);
- }
- });
- copy.setText("Copy");
- copy.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- copy_actionPerformed();
- }
- });
- lowerCase.setText("To Lower Case");
- lowerCase.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- changeCase(e);
- }
- });
- toggle.setText("Toggle Case");
- toggle.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- changeCase(e);
- }
- });
- pdbMenu.setText("Associate Structure with Sequence");
- pdbFromFile.setText("From File");
- pdbFromFile.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- pdbFromFile_actionPerformed();
- }
- });
- enterPDB.setText("Enter PDB Id");
- enterPDB.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- enterPDB_actionPerformed();
- }
- });
- discoverPDB.setText("Discover PDB ids");
- discoverPDB.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- discoverPDB_actionPerformed();
- }
- });
- outputMenu.setText("Output to Textbox...");
- sequenceFeature.setText("Create Sequence Feature");
- sequenceFeature.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- sequenceFeature_actionPerformed();
- }
- });
- textColour.setText("Text Colour");
- textColour.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- textColour_actionPerformed();
- }
- });
- jMenu1.setText("Group");
- structureMenu.setText("Structure");
- viewStructureMenu.setText("View Structure");
- // colStructureMenu.setText("Colour By Structure");
- editSequence.setText("Edit Sequence...");
- editSequence.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- editSequence_actionPerformed(actionEvent);
- }
- });
- /*
- * annotationMenuItem.setText("By Annotation");
- * annotationMenuItem.addActionListener(new ActionListener() { public void
- * actionPerformed(ActionEvent actionEvent) {
- * annotationMenuItem_actionPerformed(actionEvent); } });
- */
-
- add(groupMenu);
-
- add(sequenceMenu);
- this.add(structureMenu);
- groupMenu.add(editMenu);
- groupMenu.add(outputMenu);
- groupMenu.add(sequenceFeature);
- groupMenu.add(jMenu1);
- sequenceMenu.add(sequenceName);
- colourMenu.add(textColour);
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- colourMenu.add(BLOSUM62Colour);
- colourMenu.add(PIDColour);
- colourMenu.add(zappoColour);
- colourMenu.add(taylorColour);
- colourMenu.add(hydrophobicityColour);
- colourMenu.add(helixColour);
- colourMenu.add(strandColour);
- colourMenu.add(turnColour);
- colourMenu.add(buriedColour);
- colourMenu.add(nucleotideMenuItem);
- colourMenu.add(userDefinedColour);
-
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
- {
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
- .getUserColourSchemes().keys();
-
- while (userColours.hasMoreElements())
- {
- JMenuItem item = new JMenuItem(userColours.nextElement().toString());
- item.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- colourMenu.add(item);
- }
- }
-
- colourMenu.addSeparator();
- colourMenu.add(abovePIDColour);
- colourMenu.add(conservationMenuItem);
- // colourMenu.add(annotationMenuItem);
- editMenu.add(copy);
- editMenu.add(cut);
- editMenu.add(editSequence);
- editMenu.add(upperCase);
- editMenu.add(lowerCase);
- editMenu.add(toggle);
- pdbMenu.add(pdbFromFile);
- pdbMenu.add(enterPDB);
- pdbMenu.add(discoverPDB);
- jMenu1.add(groupName);
- jMenu1.add(unGroupMenuItem);
- jMenu1.add(colourMenu);
- jMenu1.add(showBoxes);
- jMenu1.add(showText);
- jMenu1.add(showColourText);
- jMenu1.add(outline);
- jMenu1.add(displayNonconserved);
- structureMenu.add(pdbMenu);
- structureMenu.add(viewStructureMenu);
- // structureMenu.add(colStructureMenu);
- noColourmenuItem.setText("None");
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed();
- }
- });
-
- clustalColour.setText("Clustalx colours");
- clustalColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- clustalColour_actionPerformed();
- }
- });
- zappoColour.setText("Zappo");
- zappoColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- zappoColour_actionPerformed();
- }
- });
- taylorColour.setText("Taylor");
- taylorColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- taylorColour_actionPerformed();
- }
- });
- hydrophobicityColour.setText("Hydrophobicity");
- hydrophobicityColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed();
- }
- });
- helixColour.setText("Helix propensity");
- helixColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- helixColour_actionPerformed();
- }
- });
- strandColour.setText("Strand propensity");
- strandColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- strandColour_actionPerformed();
- }
- });
- turnColour.setText("Turn propensity");
- turnColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- turnColour_actionPerformed();
- }
- });
- buriedColour.setText("Buried Index");
- buriedColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- buriedColour_actionPerformed();
- }
- });
- abovePIDColour.setText("Above % Identity");
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- abovePIDColour_actionPerformed();
- }
- });
- userDefinedColour.setText("User Defined...");
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- userDefinedColour_actionPerformed(e);
- }
- });
- PIDColour.setText("Percentage Identity");
- PIDColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- PIDColour_actionPerformed();
- }
- });
- BLOSUM62Colour.setText("BLOSUM62");
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- BLOSUM62Colour_actionPerformed();
- }
- });
- conservationMenuItem.setText("Conservation");
- conservationMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed();
- }
- });
- }
-
- protected void showNonconserved_actionPerformed()
- {
- getGroup().setShowNonconserved(displayNonconserved.isSelected());
- refresh();
- }
-
- /**
- * call to refresh view after settings change
- */
- void refresh()
- {
- ap.updateAnnotation();
- ap.paintAlignment(true);
-
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void clustalColour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg
- .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
- .getWidth());
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void zappoColour_actionPerformed()
- {
- getGroup().cs = new ZappoColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void taylorColour_actionPerformed()
- {
- getGroup().cs = new TaylorColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void hydrophobicityColour_actionPerformed()
- {
- getGroup().cs = new HydrophobicColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void helixColour_actionPerformed()
- {
- getGroup().cs = new HelixColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void strandColour_actionPerformed()
- {
- getGroup().cs = new StrandColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void turnColour_actionPerformed()
- {
- getGroup().cs = new TurnColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void buriedColour_actionPerformed()
- {
- getGroup().cs = new BuriedColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void nucleotideMenuItem_actionPerformed()
- {
- getGroup().cs = new NucleotideColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void abovePIDColour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- if (sg.cs == null)
- {
- return;
- }
-
- if (abovePIDColour.isSelected())
- {
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
- .getEndRes() + 1));
-
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
- .getName());
-
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
-
- SliderPanel.showPIDSlider();
- }
- else
- // remove PIDColouring
- {
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
- }
-
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void userDefinedColour_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
-
- if (e.getActionCommand().equals("User Defined..."))
- {
- new UserDefinedColours(ap, sg);
- }
- else
- {
- UserColourScheme udc = (UserColourScheme) UserDefinedColours
- .getUserColourSchemes().get(e.getActionCommand());
-
- sg.cs = udc;
- }
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * 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));
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void BLOSUM62Colour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
-
- sg.cs = new Blosum62ColourScheme();
-
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
- .getEndRes() + 1));
-
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void noColourmenuItem_actionPerformed()
- {
- getGroup().cs = null;
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void conservationMenuItem_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- if (sg.cs == null)
- {
- return;
- }
-
- if (conservationMenuItem.isSelected())
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg
- .getSequences(ap.av.hiddenRepSequences), sg
- .getStartRes(), sg.getEndRes() + 1);
-
- c.calculate();
- c.verdict(false, ap.av.ConsPercGaps);
-
- sg.cs.setConservation(c);
-
- SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
- SliderPanel.showConservationSlider();
- }
- else
- // remove ConservationColouring
- {
- sg.cs.setConservation(null);
- }
-
- refresh();
- }
-
- public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
- {
- SequenceGroup sg = getGroup();
- if (sg == null)
- {
- return;
- }
-
- AnnotationColourGradient acg = new AnnotationColourGradient(sequence
- .getAnnotation()[0], null,
- AnnotationColourGradient.NO_THRESHOLD);
-
- acg.predefinedColours = true;
- sg.cs = acg;
-
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * 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", ap.alignFrame);
-
- if (!dialog.accept)
- {
- return;
- }
-
- sg.setName(dialog.getName());
- sg.setDescription(dialog.getDescription());
- refresh();
- }
-
- /**
- * Get selection group - adding it to the alignment if necessary.
- *
- * @return sequence group to operate on
- */
- SequenceGroup getGroup()
- {
- SequenceGroup sg = ap.av.getSelectionGroup();
- // this method won't add a new group if it already exists
- if (sg != null)
- {
- ap.av.alignment.addGroup(sg);
- }
-
- return sg;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- void sequenceName_actionPerformed()
- {
- EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
- .getDescription(), " Sequence Name ",
- "Sequence Description ", "Edit Sequence Name/Description", ap.alignFrame);
-
- if (!dialog.accept)
- {
- return;
- }
-
- if (dialog.getName() != null)
- {
- if (dialog.getName().indexOf(" ") > -1)
- {
- JOptionPane.showMessageDialog(ap,
- "Spaces have been converted to \"_\"",
- "No spaces allowed in Sequence Name",
- JOptionPane.WARNING_MESSAGE);
- }
-
- sequence.setName(dialog.getName().replace(' ', '_'));
- ap.paintAlignment(false);
- }
-
- sequence.setDescription(dialog.getDescription());
-
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- void unGroupMenuItem_actionPerformed()
- {
- SequenceGroup sg = ap.av.getSelectionGroup();
- ap.av.alignment.deleteGroup(sg);
- ap.av.setSelectionGroup(null);
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void outline_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- Color col = JColorChooser.showDialog(this, "Select Outline Colour",
- Color.BLUE);
-
- if (col != null)
- {
- sg.setOutlineColour(col);
- }
-
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void showBoxes_actionPerformed()
- {
- getGroup().setDisplayBoxes(showBoxes.isSelected());
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void showText_actionPerformed()
- {
- getGroup().setDisplayText(showText.isSelected());
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void showColourText_actionPerformed()
- {
- getGroup().setColourText(showColourText.isSelected());
- refresh();
- }
-
- public void showLink(String url)
- {
- try
- {
- jalview.util.BrowserLauncher.openURL(url);
- } catch (Exception ex)
- {
- 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);
-
- ex.printStackTrace();
- }
- }
-
- void hideSequences(boolean representGroup)
- {
- SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg == null || sg.getSize() < 1)
- {
- ap.av.hideSequence(new SequenceI[]
- { sequence });
- return;
- }
-
- ap.av.setSelectionGroup(null);
-
- if (representGroup)
- {
- ap.av.hideRepSequences(sequence, sg);
-
- return;
- }
-
- int gsize = sg.getSize();
- SequenceI[] hseqs;
-
- hseqs = new SequenceI[gsize];
-
- int index = 0;
- for (int i = 0; i < gsize; i++)
- {
- hseqs[index++] = sg.getSequenceAt(i);
- }
-
- ap.av.hideSequence(hseqs);
- // refresh(); TODO: ? needed ?
- ap.av.sendSelection();
- }
-
- public void copy_actionPerformed()
- {
- ap.alignFrame.copy_actionPerformed(null);
- }
-
- public void cut_actionPerformed()
- {
- ap.alignFrame.cut_actionPerformed(null);
- }
-
- void changeCase(ActionEvent e)
- {
- Object source = e.getSource();
- SequenceGroup sg = ap.av.getSelectionGroup();
-
- if (sg != null)
- {
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
- sg.getEndRes() + 1);
-
- String description;
- int caseChange;
-
- if (source == toggle)
- {
- description = "Toggle Case";
- caseChange = ChangeCaseCommand.TOGGLE_CASE;
- }
- else if (source == upperCase)
- {
- description = "To Upper Case";
- caseChange = ChangeCaseCommand.TO_UPPER;
- }
- else
- {
- description = "To Lower Case";
- caseChange = ChangeCaseCommand.TO_LOWER;
- }
-
- ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
- .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
- caseChange);
-
- ap.alignFrame.addHistoryItem(caseCommand);
-
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
-
- }
- }
-
- public void outputText_actionPerformed(ActionEvent e)
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setForInput(null);
- Desktop.addInternalFrame(cap, "Alignment output - "
- + 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
- 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();
- if (nala!=null) {
- 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));
- oal = null;
- }
-
- public void pdbFromFile_actionPerformed()
- {
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Select a PDB file");
- chooser.setToolTipText("Load a PDB file");
-
- 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);
- }
-
- }
-
- public void enterPDB_actionPerformed()
- {
- String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
- "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
-
- if (id != null && id.length() > 0)
- {
- PDBEntry entry = new PDBEntry();
- entry.setId(id.toUpperCase());
- sequence.getDatasetSequence().addPDBId(entry);
- }
- }
-
- public void discoverPDB_actionPerformed()
- {
-
- final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
- { sequence }
- : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
- Thread discpdb = new Thread(new Runnable()
- {
- public void run()
- {
-
- new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
- .fetchDBRefs(false);
- }
-
- });
- discpdb.start();
- }
-
- public void sequenceFeature_actionPerformed()
- {
- SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg == null)
- {
- return;
- }
-
- 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)
- {
- seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
- 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))
- {
- ap.alignFrame.setShowSeqFeatures(true);
- ap.highlightSearchResults(null);
- }
- }
-
- public void textColour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- if (sg != null)
- {
- new TextColourChooser().chooseColour(ap, sg);
- }
- }
-
- public void colourByStructure(String pdbid)
- {
- Annotation[] anots = jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().colourSequenceFromStructure(
- sequence, pdbid);
-
- AlignmentAnnotation an = new AlignmentAnnotation("Structure",
- "Coloured by " + pdbid, anots);
-
- ap.av.alignment.addAnnotation(an);
- an.createSequenceMapping(sequence, 0, true);
- // an.adjustForAlignment();
- ap.av.alignment.setAnnotationIndex(an, 0);
-
- ap.adjustAnnotationHeight();
-
- sequence.addAlignmentAnnotation(an);
-
- }
-
- public void editSequence_actionPerformed(ActionEvent actionEvent)
- {
- SequenceGroup sg = ap.av.getSelectionGroup();
-
- if (sg != null)
- {
- 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", ap.alignFrame);
-
- if (dialog.accept)
- {
- 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.alignFrame.addHistoryItem(editCommand);
-
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
- }
- }
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package jalview.gui;\r
+\r
+import java.util.*;\r
+\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import javax.swing.*;\r
+\r
+import jalview.analysis.*;\r
+import jalview.commands.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.schemes.*;\r
+import jalview.util.GroupUrlLink;\r
+import jalview.util.GroupUrlLink.UrlStringTooLongException;\r
+import jalview.util.MessageManager;\r
+import jalview.util.UrlLink;\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @author $author$\r
+ * @version $Revision: 1.118 $\r
+ */\r
+public class PopupMenu extends JPopupMenu\r
+{\r
+ JMenu groupMenu = new JMenu();\r
+\r
+ JMenuItem groupName = new JMenuItem();\r
+\r
+ protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
+\r
+ protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
+\r
+ protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
+\r
+ protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
+\r
+ protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
+\r
+ protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
+\r
+ protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
+\r
+ protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
+\r
+ protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
+\r
+ protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
+\r
+ protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
+\r
+ protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
+\r
+ protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();\r
+\r
+ // protected JRadioButtonMenuItem covariationColour = new\r
+ // JRadioButtonMenuItem();\r
+\r
+ JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
+\r
+ protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
+\r
+ AlignmentPanel ap;\r
+\r
+ JMenu sequenceMenu = new JMenu();\r
+\r
+ JMenuItem sequenceName = new JMenuItem();\r
+\r
+ JMenuItem sequenceDetails = new JMenuItem();\r
+\r
+ JMenuItem sequenceSelDetails = new JMenuItem();\r
+\r
+ SequenceI sequence;\r
+ JMenuItem createGroupMenuItem = new JMenuItem();\r
+ JMenuItem unGroupMenuItem = new JMenuItem();\r
+\r
+ JMenuItem outline = new JMenuItem();\r
+\r
+ JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
+\r
+ JMenu colourMenu = new JMenu();\r
+\r
+ JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
+\r
+ JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
+\r
+ JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
+\r
+ JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();\r
+\r
+ JMenu editMenu = new JMenu();\r
+\r
+ JMenuItem cut = new JMenuItem();\r
+\r
+ JMenuItem copy = new JMenuItem();\r
+\r
+ JMenuItem upperCase = new JMenuItem();\r
+\r
+ JMenuItem lowerCase = new JMenuItem();\r
+\r
+ JMenuItem toggle = new JMenuItem();\r
+\r
+ JMenu pdbMenu = new JMenu();\r
+\r
+ JMenuItem pdbFromFile = new JMenuItem();\r
+\r
+ JMenuItem enterPDB = new JMenuItem();\r
+\r
+ JMenuItem discoverPDB = new JMenuItem();\r
+\r
+ JMenu outputMenu = new JMenu();\r
+\r
+ JMenuItem sequenceFeature = new JMenuItem();\r
+\r
+ JMenuItem textColour = new JMenuItem();\r
+\r
+ JMenu jMenu1 = new JMenu();\r
+\r
+ JMenu structureMenu = new JMenu();\r
+\r
+ JMenu viewStructureMenu = new JMenu();\r
+\r
+ // JMenu colStructureMenu = new JMenu();\r
+ JMenuItem editSequence = new JMenuItem();\r
+\r
+ // JMenuItem annotationMenuItem = new JMenuItem();\r
+\r
+ JMenu groupLinksMenu;\r
+\r
+ /**\r
+ * Creates a new PopupMenu object.\r
+ * \r
+ * @param ap\r
+ * DOCUMENT ME!\r
+ * @param seq\r
+ * DOCUMENT ME!\r
+ */\r
+ public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)\r
+ {\r
+ this(ap, seq, links, null);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param ap\r
+ * @param seq\r
+ * @param links\r
+ * @param groupLinks\r
+ */\r
+ public PopupMenu(final AlignmentPanel ap, final SequenceI seq,\r
+ Vector links, Vector groupLinks)\r
+ {\r
+ // /////////////////////////////////////////////////////////\r
+ // If this is activated from the sequence panel, the user may want to\r
+ // edit or annotate a particular residue. Therefore display the residue menu\r
+ //\r
+ // If from the IDPanel, we must display the sequence menu\r
+ // ////////////////////////////////////////////////////////\r
+ this.ap = ap;\r
+ sequence = seq;\r
+\r
+ ButtonGroup colours = new ButtonGroup();\r
+ colours.add(noColourmenuItem);\r
+ colours.add(clustalColour);\r
+ colours.add(zappoColour);\r
+ colours.add(taylorColour);\r
+ colours.add(hydrophobicityColour);\r
+ colours.add(helixColour);\r
+ colours.add(strandColour);\r
+ colours.add(turnColour);\r
+ colours.add(buriedColour);\r
+ colours.add(abovePIDColour);\r
+ colours.add(userDefinedColour);\r
+ colours.add(PIDColour);\r
+ colours.add(BLOSUM62Colour);\r
+ colours.add(purinePyrimidineColour);\r
+ // colours.add(covariationColour);\r
+\r
+ for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
+ {\r
+ JMenuItem item = new JMenuItem(\r
+ jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);\r
+\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ outputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ outputMenu.add(item);\r
+ }\r
+\r
+ try\r
+ {\r
+ jbInit();\r
+ } catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
+ JMenuItem menuItem;\r
+ if (seq != null)\r
+ {\r
+ sequenceMenu.setText(sequence.getName());\r
+\r
+ if (seq.getDatasetSequence().getPDBId() != null\r
+ && seq.getDatasetSequence().getPDBId().size() > 0)\r
+ {\r
+ java.util.Enumeration e = seq.getDatasetSequence().getPDBId()\r
+ .elements();\r
+\r
+ while (e.hasMoreElements())\r
+ {\r
+ final PDBEntry pdb = (PDBEntry) e.nextElement();\r
+\r
+ menuItem = new JMenuItem();\r
+ menuItem.setText(pdb.getId());\r
+ menuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ // TODO re JAL-860: optionally open dialog or provide a menu entry\r
+ // allowing user to open just one structure per sequence\r
+ new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]\r
+ { pdb })[0], null, ap);\r
+ // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);\r
+ }\r
+\r
+ });\r
+ viewStructureMenu.add(menuItem);\r
+\r
+ /*\r
+ * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());\r
+ * menuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ * public void actionPerformed(ActionEvent e) {\r
+ * colourByStructure(pdb.getId()); } });\r
+ * colStructureMenu.add(menuItem);\r
+ */\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (ap.av.getAlignment().isNucleotide() == false)\r
+ {\r
+ structureMenu.remove(viewStructureMenu);\r
+ }\r
+ // structureMenu.remove(colStructureMenu);\r
+ }\r
+\r
+ if (ap.av.getAlignment().isNucleotide() == true)\r
+ {\r
+ AlignmentAnnotation[] aa = ap.av.getAlignment()\r
+ .getAlignmentAnnotation();\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (aa[i].getRNAStruc() != null)\r
+ {\r
+ final String rnastruc = aa[i].getRNAStruc();\r
+ final String structureLine = aa[i].label;\r
+ menuItem = new JMenuItem();\r
+ menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));\r
+ menuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ new AppVarna(structureLine, seq, seq.getSequenceAsString(),\r
+ rnastruc, seq.getName(), ap);\r
+ }\r
+ });\r
+ viewStructureMenu.add(menuItem);\r
+ }\r
+ }\r
+\r
+ // SequenceFeatures[] test = seq.getSequenceFeatures();\r
+\r
+ if (seq.getAnnotation() != null)\r
+ {\r
+ AlignmentAnnotation seqAnno[] = seq.getAnnotation();\r
+ for (int i = 0; i < seqAnno.length; i++)\r
+ {\r
+ if (seqAnno[i].getRNAStruc() != null)\r
+ {\r
+ final String rnastruc = seqAnno[i].getRNAStruc();\r
+\r
+ // TODO: make rnastrucF a bit more nice\r
+ menuItem = new JMenuItem();\r
+ menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()}));\r
+ menuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ // TODO: VARNA does'nt print gaps in the sequence\r
+ new AppVarna(seq.getName() + " structure", seq, seq\r
+ .getSequenceAsString(), rnastruc, seq.getName(),\r
+ ap);\r
+ }\r
+ });\r
+ viewStructureMenu.add(menuItem);\r
+ }\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences"));\r
+ menuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ hideSequences(false);\r
+ }\r
+ });\r
+ add(menuItem);\r
+\r
+ if (ap.av.getSelectionGroup() != null\r
+ && ap.av.getSelectionGroup().getSize() > 1)\r
+ {\r
+ menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));\r
+ menuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ hideSequences(true);\r
+ }\r
+ });\r
+ sequenceMenu.add(menuItem);\r
+ }\r
+\r
+ if (ap.av.hasHiddenRows())\r
+ {\r
+ final int index = ap.av.getAlignment().findIndex(seq);\r
+\r
+ if (ap.av.adjustForHiddenSeqs(index)\r
+ - ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
+ {\r
+ menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences"));\r
+ menuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ ap.av.showSequence(index);\r
+ if (ap.overviewPanel != null)\r
+ {\r
+ ap.overviewPanel.updateOverviewImage();\r
+ }\r
+ }\r
+ });\r
+ add(menuItem);\r
+ }\r
+ }\r
+ }\r
+ // for the case when no sequences are even visible\r
+ if (ap.av.hasHiddenRows())\r
+ {\r
+ {\r
+ menuItem = new JMenuItem(MessageManager.getString("action.reveal_all"));\r
+ menuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ ap.av.showAllHiddenSeqs();\r
+ if (ap.overviewPanel != null)\r
+ {\r
+ ap.overviewPanel.updateOverviewImage();\r
+ }\r
+ }\r
+ });\r
+\r
+ add(menuItem);\r
+ }\r
+\r
+ }\r
+\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;\r
+\r
+ if (sg != null && sg.getSize() > 0)\r
+ { \r
+ groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));\r
+ groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group"));\r
+\r
+ if (sg.cs instanceof ZappoColourScheme)\r
+ {\r
+ zappoColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof TaylorColourScheme)\r
+ {\r
+ taylorColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof PIDColourScheme)\r
+ {\r
+ PIDColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof Blosum62ColourScheme)\r
+ {\r
+ BLOSUM62Colour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof UserColourScheme)\r
+ {\r
+ userDefinedColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof HydrophobicColourScheme)\r
+ {\r
+ hydrophobicityColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof HelixColourScheme)\r
+ {\r
+ helixColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof StrandColourScheme)\r
+ {\r
+ strandColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof TurnColourScheme)\r
+ {\r
+ turnColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof BuriedColourScheme)\r
+ {\r
+ buriedColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof ClustalxColourScheme)\r
+ {\r
+ clustalColour.setSelected(true);\r
+ }\r
+ else if (sg.cs instanceof PurinePyrimidineColourScheme)\r
+ {\r
+ purinePyrimidineColour.setSelected(true);\r
+ }\r
+ /*\r
+ * else if (sg.cs instanceof CovariationColourScheme) {\r
+ * covariationColour.setSelected(true); }\r
+ */\r
+ else\r
+ {\r
+ noColourmenuItem.setSelected(true);\r
+ }\r
+\r
+ if (sg.cs != null && sg.cs.conservationApplied())\r
+ {\r
+ conservationMenuItem.setSelected(true);\r
+ }\r
+ displayNonconserved.setSelected(sg.getShowNonconserved());\r
+ showText.setSelected(sg.getDisplayText());\r
+ showColourText.setSelected(sg.getColourText());\r
+ showBoxes.setSelected(sg.getDisplayBoxes());\r
+ // add any groupURLs to the groupURL submenu and make it visible\r
+ if (groupLinks != null && groupLinks.size() > 0)\r
+ {\r
+ buildGroupURLMenu(sg, groupLinks);\r
+ }\r
+ // Add a 'show all structures' for the current selection\r
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();\r
+ SequenceI sqass = null;\r
+ for (SequenceI sq : ap.av.getSequenceSelection())\r
+ {\r
+ Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()\r
+ .getPDBId();\r
+ if (pes != null)\r
+ {\r
+ for (PDBEntry pe : pes)\r
+ {\r
+ pdbe.put(pe.getId(), pe);\r
+ if (sqass == null)\r
+ {\r
+ sqass = sq;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if (pdbe.size() > 0)\r
+ {\r
+ final PDBEntry[] pe = pdbe.values().toArray(\r
+ new PDBEntry[pdbe.size()]);\r
+ final JMenuItem gpdbview;\r
+ if (pdbe.size() == 1)\r
+ {\r
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));\r
+ }\r
+ else\r
+ {\r
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));\r
+ }\r
+ gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));\r
+ gpdbview.addActionListener(new ActionListener()\r
+ {\r
+\r
+ @Override\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ new AppJmol(ap, pe, ap.av.collateForPDB(pe));\r
+ }\r
+ });\r
+ }\r
+ }\r
+ else\r
+ {\r
+ groupMenu.setVisible(false);\r
+ editMenu.setVisible(false);\r
+ }\r
+\r
+ if (!isDefinedGroup)\r
+ {\r
+ createGroupMenuItem.setVisible(true);\r
+ unGroupMenuItem.setVisible(false);\r
+ jMenu1.setText(MessageManager.getString("action.edit_new_group"));\r
+ } else {\r
+ createGroupMenuItem.setVisible(false);\r
+ unGroupMenuItem.setVisible(true);\r
+ jMenu1.setText(MessageManager.getString("action.edit_group"));\r
+ }\r
+\r
+ if (seq == null)\r
+ {\r
+ sequenceMenu.setVisible(false);\r
+ structureMenu.setVisible(false);\r
+ }\r
+\r
+ if (links != null && links.size() > 0)\r
+ {\r
+\r
+ JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));\r
+ Vector linkset = new Vector();\r
+ for (int i = 0; i < links.size(); i++)\r
+ {\r
+ String link = links.elementAt(i).toString();\r
+ UrlLink urlLink = null;\r
+ try\r
+ {\r
+ urlLink = new UrlLink(link);\r
+ } catch (Exception foo)\r
+ {\r
+ jalview.bin.Cache.log.error("Exception for URLLink '" + link\r
+ + "'", foo);\r
+ continue;\r
+ }\r
+ ;\r
+ if (!urlLink.isValid())\r
+ {\r
+ jalview.bin.Cache.log.error(urlLink.getInvalidMessage());\r
+ continue;\r
+ }\r
+ final String label = urlLink.getLabel();\r
+ if (seq != null && urlLink.isDynamic())\r
+ {\r
+\r
+ // collect matching db-refs\r
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(\r
+ seq.getDBRef(), new String[]\r
+ { urlLink.getTarget() });\r
+ // collect id string too\r
+ String id = seq.getName();\r
+ String descr = seq.getDescription();\r
+ if (descr != null && descr.length() < 1)\r
+ {\r
+ descr = null;\r
+ }\r
+\r
+ if (dbr != null)\r
+ {\r
+ for (int r = 0; r < dbr.length; r++)\r
+ {\r
+ if (id != null && dbr[r].getAccessionId().equals(id))\r
+ {\r
+ // suppress duplicate link creation for the bare sequence ID\r
+ // string with this link\r
+ id = null;\r
+ }\r
+ // create Bare ID link for this RUL\r
+ String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),\r
+ true);\r
+ if (urls != null)\r
+ {\r
+ for (int u = 0; u < urls.length; u += 2)\r
+ {\r
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))\r
+ {\r
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);\r
+ addshowLink(linkMenu, label + "|" + urls[u],\r
+ urls[u + 1]);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if (id != null)\r
+ {\r
+ // create Bare ID link for this RUL\r
+ String[] urls = urlLink.makeUrls(id, true);\r
+ if (urls != null)\r
+ {\r
+ for (int u = 0; u < urls.length; u += 2)\r
+ {\r
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))\r
+ {\r
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);\r
+ addshowLink(linkMenu, label, urls[u + 1]);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ // Create urls from description but only for URL links which are regex\r
+ // links\r
+ if (descr != null && urlLink.getRegexReplace() != null)\r
+ {\r
+ // create link for this URL from description where regex matches\r
+ String[] urls = urlLink.makeUrls(descr, true);\r
+ if (urls != null)\r
+ {\r
+ for (int u = 0; u < urls.length; u += 2)\r
+ {\r
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))\r
+ {\r
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);\r
+ addshowLink(linkMenu, label, urls[u + 1]);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))\r
+ {\r
+ linkset.addElement(label + "|" + urlLink.getUrl_prefix());\r
+ // Add a non-dynamic link\r
+ addshowLink(linkMenu, label, urlLink.getUrl_prefix());\r
+ }\r
+ }\r
+ }\r
+ if (sequence != null)\r
+ {\r
+ sequenceMenu.add(linkMenu);\r
+ }\r
+ else\r
+ {\r
+ add(linkMenu);\r
+ }\r
+ }\r
+ }\r
+\r
+ private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)\r
+ {\r
+\r
+ // TODO: usability: thread off the generation of group url content so root\r
+ // menu appears asap\r
+ // sequence only URLs\r
+ // ID/regex match URLs\r
+ groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
+ JMenu[] linkMenus = new JMenu[]\r
+ { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),\r
+ new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be\r
+ // created.\r
+ SequenceI[] seqs = ap.av.getSelectionAsNewSequence();\r
+ String[][] idandseqs = GroupUrlLink.formStrings(seqs);\r
+ Hashtable commonDbrefs = new Hashtable();\r
+ for (int sq = 0; sq < seqs.length; sq++)\r
+ {\r
+\r
+ int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]\r
+ .findPosition(sg.getEndRes());\r
+ // just collect ids from dataset sequence\r
+ // TODO: check if IDs collected from selecton group intersects with the\r
+ // current selection, too\r
+ SequenceI sqi = seqs[sq];\r
+ while (sqi.getDatasetSequence() != null)\r
+ {\r
+ sqi = sqi.getDatasetSequence();\r
+ }\r
+ DBRefEntry[] dbr = sqi.getDBRef();\r
+ if (dbr != null && dbr.length > 0)\r
+ {\r
+ for (int d = 0; d < dbr.length; d++)\r
+ {\r
+ String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();\r
+ Object[] sarray = (Object[]) commonDbrefs.get(src);\r
+ if (sarray == null)\r
+ {\r
+ sarray = new Object[2];\r
+ sarray[0] = new int[]\r
+ { 0 };\r
+ sarray[1] = new String[seqs.length];\r
+\r
+ commonDbrefs.put(src, sarray);\r
+ }\r
+\r
+ if (((String[]) sarray[1])[sq] == null)\r
+ {\r
+ if (!dbr[d].hasMap()\r
+ || (dbr[d].getMap().locateMappedRange(start, end) != null))\r
+ {\r
+ ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();\r
+ ((int[]) sarray[0])[0]++;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ // now create group links for all distinct ID/sequence sets.\r
+ boolean addMenu = false; // indicates if there are any group links to give\r
+ // to user\r
+ for (int i = 0; i < groupLinks.size(); i++)\r
+ {\r
+ String link = groupLinks.elementAt(i).toString();\r
+ GroupUrlLink urlLink = null;\r
+ try\r
+ {\r
+ urlLink = new GroupUrlLink(link);\r
+ } catch (Exception foo)\r
+ {\r
+ jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link\r
+ + "'", foo);\r
+ continue;\r
+ }\r
+ ;\r
+ if (!urlLink.isValid())\r
+ {\r
+ jalview.bin.Cache.log.error(urlLink.getInvalidMessage());\r
+ continue;\r
+ }\r
+ final String label = urlLink.getLabel();\r
+ boolean usingNames = false;\r
+ // Now see which parts of the group apply for this URL\r
+ String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());\r
+ Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());\r
+ String[] seqstr, ids; // input to makeUrl\r
+ if (idset != null)\r
+ {\r
+ int numinput = ((int[]) idset[0])[0];\r
+ String[] allids = ((String[]) idset[1]);\r
+ seqstr = new String[numinput];\r
+ ids = new String[numinput];\r
+ for (int sq = 0, idcount = 0; sq < seqs.length; sq++)\r
+ {\r
+ if (allids[sq] != null)\r
+ {\r
+ ids[idcount] = allids[sq];\r
+ seqstr[idcount++] = idandseqs[1][sq];\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // just use the id/seq set\r
+ seqstr = idandseqs[1];\r
+ ids = idandseqs[0];\r
+ usingNames = true;\r
+ }\r
+ // and try and make the groupURL!\r
+\r
+ Object[] urlset = null;\r
+ try\r
+ {\r
+ urlset = urlLink.makeUrlStubs(ids, seqstr,\r
+ "FromJalview" + System.currentTimeMillis(), false);\r
+ } catch (UrlStringTooLongException e)\r
+ {\r
+ }\r
+ if (urlset != null)\r
+ {\r
+ int type = urlLink.getGroupURLType() & 3;\r
+ // System.out.println(urlLink.getGroupURLType()\r
+ // +" "+((String[])urlset[3])[0]);\r
+ // first two bits ofurlLink type bitfield are sequenceids and sequences\r
+ // TODO: FUTURE: ensure the groupURL menu structure can be generalised\r
+ addshowLink(linkMenus[type], label\r
+ + (((type & 1) == 1) ? ("("\r
+ + (usingNames ? "Names" : ltarget) + ")") : ""),\r
+ urlLink, urlset);\r
+ addMenu = true;\r
+ }\r
+ }\r
+ if (addMenu)\r
+ {\r
+ groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
+ for (int m = 0; m < linkMenus.length; m++)\r
+ {\r
+ if (linkMenus[m] != null\r
+ && linkMenus[m].getMenuComponentCount() > 0)\r
+ {\r
+ groupLinksMenu.add(linkMenus[m]);\r
+ }\r
+ }\r
+\r
+ groupMenu.add(groupLinksMenu);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * add a show URL menu item to the given linkMenu\r
+ * \r
+ * @param linkMenu\r
+ * @param label\r
+ * - menu label string\r
+ * @param url\r
+ * - url to open\r
+ */\r
+ private void addshowLink(JMenu linkMenu, String label, final String url)\r
+ {\r
+ JMenuItem item = new JMenuItem(label);\r
+ item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ new Thread(new Runnable()\r
+ {\r
+\r
+ public void run()\r
+ {\r
+ showLink(url);\r
+ }\r
+\r
+ }).start();\r
+ }\r
+ });\r
+\r
+ linkMenu.add(item);\r
+ }\r
+\r
+ /**\r
+ * add a late bound groupURL item to the given linkMenu\r
+ * \r
+ * @param linkMenu\r
+ * @param label\r
+ * - menu label string\r
+ * @param urlgenerator\r
+ * GroupURLLink used to generate URL\r
+ * @param urlstub\r
+ * Object array returned from the makeUrlStubs function.\r
+ */\r
+ private void addshowLink(JMenu linkMenu, String label,\r
+ final GroupUrlLink urlgenerator, final Object[] urlstub)\r
+ {\r
+ JMenuItem item = new JMenuItem(label);\r
+ item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));\r
+ // TODO: put in info about what is being sent.\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ new Thread(new Runnable()\r
+ {\r
+\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ showLink(urlgenerator.constructFrom(urlstub));\r
+ } catch (UrlStringTooLongException e)\r
+ {\r
+ }\r
+ }\r
+\r
+ }).start();\r
+ }\r
+ });\r
+\r
+ linkMenu.add(item);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @throws Exception\r
+ * DOCUMENT ME!\r
+ */\r
+ private void jbInit() throws Exception\r
+ {\r
+ groupMenu.setText(MessageManager.getString("label.group"));\r
+ groupMenu.setText(MessageManager.getString("label.selection"));\r
+ groupName.setText(MessageManager.getString("label.name"));\r
+ groupName.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ groupName_actionPerformed();\r
+ }\r
+ });\r
+ sequenceMenu.setText(MessageManager.getString("label.sequence"));\r
+ sequenceName.setText(MessageManager.getString("label.edit_name_description"));\r
+ sequenceName.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ sequenceName_actionPerformed();\r
+ }\r
+ });\r
+ sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
+ sequenceDetails.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ sequenceDetails_actionPerformed();\r
+ }\r
+ });\r
+ sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
+ sequenceSelDetails\r
+ .addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ sequenceSelectionDetails_actionPerformed();\r
+ }\r
+ });\r
+ PIDColour.setFocusPainted(false);\r
+ unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));\r
+ unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ unGroupMenuItem_actionPerformed();\r
+ }\r
+ });\r
+ createGroupMenuItem.setText(MessageManager.getString("action.create_group"));\r
+ createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ createGroupMenuItem_actionPerformed();\r
+ }\r
+ });\r
+\r
+ outline.setText(MessageManager.getString("action.border_colour"));\r
+ outline.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ outline_actionPerformed();\r
+ }\r
+ });\r
+ nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));\r
+ nucleotideMenuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ nucleotideMenuItem_actionPerformed();\r
+ }\r
+ });\r
+ colourMenu.setText(MessageManager.getString("label.group_colour"));\r
+ showBoxes.setText(MessageManager.getString("action.boxes"));\r
+ showBoxes.setState(true);\r
+ showBoxes.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showBoxes_actionPerformed();\r
+ }\r
+ });\r
+ showText.setText(MessageManager.getString("action.text"));\r
+ showText.setState(true);\r
+ showText.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showText_actionPerformed();\r
+ }\r
+ });\r
+ showColourText.setText(MessageManager.getString("label.colour_text"));\r
+ showColourText.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showColourText_actionPerformed();\r
+ }\r
+ });\r
+ displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));\r
+ displayNonconserved.setState(true);\r
+ displayNonconserved.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showNonconserved_actionPerformed();\r
+ }\r
+ });\r
+ editMenu.setText(MessageManager.getString("action.edit"));\r
+ cut.setText(MessageManager.getString("action.cut"));\r
+ cut.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ cut_actionPerformed();\r
+ }\r
+ });\r
+ upperCase.setText(MessageManager.getString("label.to_upper_case"));\r
+ upperCase.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ changeCase(e);\r
+ }\r
+ });\r
+ copy.setText(MessageManager.getString("action.copy"));\r
+ copy.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ });\r
+ lowerCase.setText(MessageManager.getString("label.to_lower_case"));\r
+ lowerCase.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ changeCase(e);\r
+ }\r
+ });\r
+ toggle.setText(MessageManager.getString("label.toggle_case"));\r
+ toggle.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ changeCase(e);\r
+ }\r
+ });\r
+ pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));\r
+ pdbFromFile.setText(MessageManager.getString("label.from_file"));\r
+ pdbFromFile.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ pdbFromFile_actionPerformed();\r
+ }\r
+ });\r
+ enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));\r
+ enterPDB.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ enterPDB_actionPerformed();\r
+ }\r
+ });\r
+ discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));\r
+ discoverPDB.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ discoverPDB_actionPerformed();\r
+ }\r
+ });\r
+ outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");\r
+ sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));\r
+ sequenceFeature.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ sequenceFeature_actionPerformed();\r
+ }\r
+ });\r
+ textColour.setText(MessageManager.getString("label.text_colour"));\r
+ textColour.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ textColour_actionPerformed();\r
+ }\r
+ });\r
+ jMenu1.setText(MessageManager.getString("label.group"));\r
+ structureMenu.setText(MessageManager.getString("label.structure"));\r
+ viewStructureMenu.setText(MessageManager.getString("label.view_structure"));\r
+ // colStructureMenu.setText("Colour By Structure");\r
+ editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");\r
+ editSequence.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ editSequence_actionPerformed(actionEvent);\r
+ }\r
+ });\r
+\r
+ /*\r
+ * annotationMenuItem.setText("By Annotation");\r
+ * annotationMenuItem.addActionListener(new ActionListener() { public void\r
+ * actionPerformed(ActionEvent actionEvent) {\r
+ * annotationMenuItem_actionPerformed(actionEvent); } });\r
+ */\r
+ groupMenu.add(sequenceSelDetails);\r
+ add(groupMenu);\r
+ add(sequenceMenu);\r
+ this.add(structureMenu);\r
+ groupMenu.add(editMenu);\r
+ groupMenu.add(outputMenu);\r
+ groupMenu.add(sequenceFeature);\r
+ groupMenu.add(createGroupMenuItem);\r
+ groupMenu.add(unGroupMenuItem);\r
+ groupMenu.add(jMenu1);\r
+ sequenceMenu.add(sequenceName);\r
+ sequenceMenu.add(sequenceDetails);\r
+ colourMenu.add(textColour);\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideMenuItem);\r
+ if (ap.getAlignment().isNucleotide())\r
+ {\r
+ colourMenu.add(purinePyrimidineColour);\r
+ }\r
+ // colourMenu.add(covariationColour);\r
+ colourMenu.add(userDefinedColour);\r
+\r
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
+ {\r
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours\r
+ .getUserColourSchemes().keys();\r
+\r
+ while (userColours.hasMoreElements())\r
+ {\r
+ JMenuItem item = new JMenuItem(userColours.nextElement().toString());\r
+ item.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ userDefinedColour_actionPerformed(evt);\r
+ }\r
+ });\r
+ colourMenu.add(item);\r
+ }\r
+ }\r
+\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(abovePIDColour);\r
+ colourMenu.add(conservationMenuItem);\r
+ // colourMenu.add(annotationMenuItem);\r
+ editMenu.add(copy);\r
+ editMenu.add(cut);\r
+ editMenu.add(editSequence);\r
+ editMenu.add(upperCase);\r
+ editMenu.add(lowerCase);\r
+ editMenu.add(toggle);\r
+ pdbMenu.add(pdbFromFile);\r
+ pdbMenu.add(enterPDB);\r
+ pdbMenu.add(discoverPDB);\r
+ jMenu1.add(groupName);\r
+ jMenu1.add(colourMenu);\r
+ jMenu1.add(showBoxes);\r
+ jMenu1.add(showText);\r
+ jMenu1.add(showColourText);\r
+ jMenu1.add(outline);\r
+ jMenu1.add(displayNonconserved);\r
+ structureMenu.add(pdbMenu);\r
+ structureMenu.add(viewStructureMenu);\r
+ // structureMenu.add(colStructureMenu);\r
+ noColourmenuItem.setText(MessageManager.getString("label.none"));\r
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ noColourmenuItem_actionPerformed();\r
+ }\r
+ });\r
+\r
+ clustalColour.setText(MessageManager.getString("label.clustalx_colours"));\r
+ clustalColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ clustalColour_actionPerformed();\r
+ }\r
+ });\r
+ zappoColour.setText(MessageManager.getString("label.zappo"));\r
+ zappoColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ zappoColour_actionPerformed();\r
+ }\r
+ });\r
+ taylorColour.setText(MessageManager.getString("label.taylor"));\r
+ taylorColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ taylorColour_actionPerformed();\r
+ }\r
+ });\r
+ hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));\r
+ hydrophobicityColour\r
+ .addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ hydrophobicityColour_actionPerformed();\r
+ }\r
+ });\r
+ helixColour.setText(MessageManager.getString("label.helix_propensity"));\r
+ helixColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ helixColour_actionPerformed();\r
+ }\r
+ });\r
+ strandColour.setText(MessageManager.getString("label.strand_propensity"));\r
+ strandColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ strandColour_actionPerformed();\r
+ }\r
+ });\r
+ turnColour.setText(MessageManager.getString("label.turn_propensity"));\r
+ turnColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ turnColour_actionPerformed();\r
+ }\r
+ });\r
+ buriedColour.setText(MessageManager.getString("label.buried_index"));\r
+ buriedColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ buriedColour_actionPerformed();\r
+ }\r
+ });\r
+ abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));\r
+ abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ abovePIDColour_actionPerformed();\r
+ }\r
+ });\r
+ userDefinedColour.setText(MessageManager.getString("action.user_defined"));\r
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ userDefinedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ PIDColour.setText(MessageManager.getString("label.percentage_identity"));\r
+ PIDColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ PIDColour_actionPerformed();\r
+ }\r
+ });\r
+ BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));\r
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ BLOSUM62Colour_actionPerformed();\r
+ }\r
+ });\r
+ purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));\r
+ purinePyrimidineColour\r
+ .addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ purinePyrimidineColour_actionPerformed();\r
+ }\r
+ });\r
+ /*\r
+ * covariationColour.addActionListener(new java.awt.event.ActionListener() {\r
+ * public void actionPerformed(ActionEvent e) {\r
+ * covariationColour_actionPerformed(); } });\r
+ */\r
+\r
+ conservationMenuItem.setText(MessageManager.getString("label.conservation"));\r
+ conservationMenuItem\r
+ .addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ conservationMenuItem_actionPerformed();\r
+ }\r
+ });\r
+ }\r
+\r
+ protected void sequenceSelectionDetails_actionPerformed()\r
+ {\r
+ createSequenceDetailsReport(ap.av.getSequenceSelection());\r
+ }\r
+\r
+ protected void sequenceDetails_actionPerformed()\r
+ {\r
+ createSequenceDetailsReport(new SequenceI[]\r
+ { sequence });\r
+ }\r
+\r
+ public void createSequenceDetailsReport(SequenceI[] sequences)\r
+ {\r
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();\r
+ StringBuffer contents = new StringBuffer();\r
+ for (SequenceI seq : sequences)\r
+ { \r
+ contents.append("<p><h2>" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})\r
+ + "</h2></p><p>");\r
+ new SequenceAnnotationReport(null)\r
+ .createSequenceAnnotationReport(\r
+ contents,\r
+ seq,\r
+ true,\r
+ true,\r
+ false,\r
+ (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax\r
+ : null);\r
+ contents.append("</p>");\r
+ }\r
+ cap.setText("<html>" + contents.toString() + "</html>");\r
+\r
+ 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")}))\r
+ ,500, 400);\r
+\r
+ }\r
+\r
+ protected void showNonconserved_actionPerformed()\r
+ {\r
+ getGroup().setShowNonconserved(displayNonconserved.isSelected());\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * call to refresh view after settings change\r
+ */\r
+ void refresh()\r
+ {\r
+ ap.updateAnnotation();\r
+ ap.paintAlignment(true);\r
+\r
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void clustalColour_actionPerformed()\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void zappoColour_actionPerformed()\r
+ {\r
+ getGroup().cs = new ZappoColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void taylorColour_actionPerformed()\r
+ {\r
+ getGroup().cs = new TaylorColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void hydrophobicityColour_actionPerformed()\r
+ {\r
+ getGroup().cs = new HydrophobicColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void helixColour_actionPerformed()\r
+ {\r
+ getGroup().cs = new HelixColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void strandColour_actionPerformed()\r
+ {\r
+ getGroup().cs = new StrandColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void turnColour_actionPerformed()\r
+ {\r
+ getGroup().cs = new TurnColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void buriedColour_actionPerformed()\r
+ {\r
+ getGroup().cs = new BuriedColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ public void nucleotideMenuItem_actionPerformed()\r
+ {\r
+ getGroup().cs = new NucleotideColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ protected void purinePyrimidineColour_actionPerformed()\r
+ {\r
+ getGroup().cs = new PurinePyrimidineColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ /*\r
+ * protected void covariationColour_actionPerformed() { getGroup().cs = new\r
+ * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }\r
+ */\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void abovePIDColour_actionPerformed()\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ if (sg.cs == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (abovePIDColour.isSelected())\r
+ {\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(ap.av.getHiddenRepSequences()),\r
+ sg.getStartRes(), sg.getEndRes() + 1));\r
+\r
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()\r
+ .getName());\r
+\r
+ sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
+\r
+ SliderPanel.showPIDSlider();\r
+ }\r
+ else\r
+ // remove PIDColouring\r
+ {\r
+ sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
+ }\r
+\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void userDefinedColour_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+\r
+ if (e.getSource().equals(userDefinedColour))\r
+ {\r
+ new UserDefinedColours(ap, sg);\r
+ }\r
+ else\r
+ {\r
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours\r
+ .getUserColourSchemes().get(e.getActionCommand());\r
+\r
+ sg.cs = udc;\r
+ }\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void PIDColour_actionPerformed()\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ sg.cs = new PIDColourScheme();\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(ap.av.getHiddenRepSequences()),\r
+ sg.getStartRes(), sg.getEndRes() + 1));\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void BLOSUM62Colour_actionPerformed()\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+\r
+ sg.cs = new Blosum62ColourScheme();\r
+\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(ap.av.getHiddenRepSequences()),\r
+ sg.getStartRes(), sg.getEndRes() + 1));\r
+\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void noColourmenuItem_actionPerformed()\r
+ {\r
+ getGroup().cs = null;\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void conservationMenuItem_actionPerformed()\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ if (sg.cs == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (conservationMenuItem.isSelected())\r
+ {\r
+ Conservation c = new Conservation(MessageManager.getString("label.group"),\r
+ ResidueProperties.propHash, 3, sg.getSequences(ap.av\r
+ .getHiddenRepSequences()), sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+\r
+ c.calculate();\r
+ c.verdict(false, ap.av.getConsPercGaps());\r
+\r
+ sg.cs.setConservation(c);\r
+\r
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
+ SliderPanel.showConservationSlider();\r
+ }\r
+ else\r
+ // remove ConservationColouring\r
+ {\r
+ sg.cs.setConservation(null);\r
+ }\r
+\r
+ refresh();\r
+ }\r
+\r
+ public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ if (sg == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ AnnotationColourGradient acg = new AnnotationColourGradient(\r
+ sequence.getAnnotation()[0], null,\r
+ AnnotationColourGradient.NO_THRESHOLD);\r
+\r
+ acg.setPredefinedColours(true);\r
+ sg.cs = acg;\r
+\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void groupName_actionPerformed()\r
+ {\r
+\r
+ SequenceGroup sg = getGroup();\r
+ EditNameDialog dialog = new EditNameDialog(sg.getName(),\r
+ sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ",\r
+ MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),\r
+ ap.alignFrame);\r
+\r
+ if (!dialog.accept)\r
+ {\r
+ return;\r
+ }\r
+\r
+ sg.setName(dialog.getName());\r
+ sg.setDescription(dialog.getDescription());\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * Get selection group - adding it to the alignment if necessary.\r
+ * \r
+ * @return sequence group to operate on\r
+ */\r
+ SequenceGroup getGroup()\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ // this method won't add a new group if it already exists\r
+ if (sg != null)\r
+ {\r
+ ap.av.getAlignment().addGroup(sg);\r
+ }\r
+\r
+ return sg;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ void sequenceName_actionPerformed()\r
+ {\r
+ EditNameDialog dialog = new EditNameDialog(sequence.getName(),\r
+ sequence.getDescription(), " " + MessageManager.getString("label.sequence_name") + " ",\r
+ MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),\r
+ ap.alignFrame);\r
+\r
+ if (!dialog.accept)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (dialog.getName() != null)\r
+ {\r
+ if (dialog.getName().indexOf(" ") > -1)\r
+ {\r
+ JOptionPane.showMessageDialog(ap,\r
+ MessageManager.getString("label.spaces_converted_to_backslashes"),\r
+ MessageManager.getString("label.no_spaces_allowed_sequence_name"),\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+\r
+ sequence.setName(dialog.getName().replace(' ', '_'));\r
+ ap.paintAlignment(false);\r
+ }\r
+\r
+ sequence.setDescription(dialog.getDescription());\r
+\r
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
+ .getSequences());\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ void unGroupMenuItem_actionPerformed()\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ ap.av.getAlignment().deleteGroup(sg);\r
+ ap.av.setSelectionGroup(null);\r
+ refresh();\r
+ }\r
+ void createGroupMenuItem_actionPerformed()\r
+ {\r
+ getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void outline_actionPerformed()\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),\r
+ Color.BLUE);\r
+\r
+ if (col != null)\r
+ {\r
+ sg.setOutlineColour(col);\r
+ }\r
+\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ public void showBoxes_actionPerformed()\r
+ {\r
+ getGroup().setDisplayBoxes(showBoxes.isSelected());\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ public void showText_actionPerformed()\r
+ {\r
+ getGroup().setDisplayText(showText.isSelected());\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ public void showColourText_actionPerformed()\r
+ {\r
+ getGroup().setColourText(showColourText.isSelected());\r
+ refresh();\r
+ }\r
+\r
+ public void showLink(String url)\r
+ {\r
+ try\r
+ {\r
+ jalview.util.BrowserLauncher.openURL(url);\r
+ } catch (Exception ex)\r
+ {\r
+ JOptionPane\r
+ .showInternalMessageDialog(\r
+ Desktop.desktop,\r
+ MessageManager.getString("label.web_browser_not_found_unix"),\r
+ MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);\r
+\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ void hideSequences(boolean representGroup)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg == null || sg.getSize() < 1)\r
+ {\r
+ ap.av.hideSequence(new SequenceI[]\r
+ { sequence });\r
+ return;\r
+ }\r
+\r
+ ap.av.setSelectionGroup(null);\r
+\r
+ if (representGroup)\r
+ {\r
+ ap.av.hideRepSequences(sequence, sg);\r
+\r
+ return;\r
+ }\r
+\r
+ int gsize = sg.getSize();\r
+ SequenceI[] hseqs;\r
+\r
+ hseqs = new SequenceI[gsize];\r
+\r
+ int index = 0;\r
+ for (int i = 0; i < gsize; i++)\r
+ {\r
+ hseqs[index++] = sg.getSequenceAt(i);\r
+ }\r
+\r
+ ap.av.hideSequence(hseqs);\r
+ // refresh(); TODO: ? needed ?\r
+ ap.av.sendSelection();\r
+ }\r
+\r
+ public void copy_actionPerformed()\r
+ {\r
+ ap.alignFrame.copy_actionPerformed(null);\r
+ }\r
+\r
+ public void cut_actionPerformed()\r
+ {\r
+ ap.alignFrame.cut_actionPerformed(null);\r
+ }\r
+\r
+ void changeCase(ActionEvent e)\r
+ {\r
+ Object source = e.getSource();\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+\r
+ if (sg != null)\r
+ {\r
+ int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+\r
+ String description;\r
+ int caseChange;\r
+\r
+ if (source == toggle)\r
+ {\r
+ description = MessageManager.getString("label.toggle_case");\r
+ caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
+ }\r
+ else if (source == upperCase)\r
+ {\r
+ description = MessageManager.getString("label.to_upper_case");\r
+ caseChange = ChangeCaseCommand.TO_UPPER;\r
+ }\r
+ else\r
+ {\r
+ description = MessageManager.getString("label.to_lower_case");\r
+ caseChange = ChangeCaseCommand.TO_LOWER;\r
+ }\r
+\r
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,\r
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),\r
+ startEnd, caseChange);\r
+\r
+ ap.alignFrame.addHistoryItem(caseCommand);\r
+\r
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
+ .getSequences());\r
+\r
+ }\r
+ }\r
+\r
+ public void outputText_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ cap.setForInput(null);\r
+ Desktop.addInternalFrame(cap,\r
+ MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);\r
+\r
+ String[] omitHidden = null;\r
+\r
+ System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens\r
+ // or we simply trust the user wants\r
+ // wysiwig behaviour\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());\r
+ omitHidden = ap.av.getViewAsString(true);\r
+ Alignment oal = new Alignment(ap.av.getSequenceSelection());\r
+ AlignmentAnnotation[] nala = ap.av.getAlignment()\r
+ .getAlignmentAnnotation();\r
+ if (nala != null)\r
+ {\r
+ for (int i = 0; i < nala.length; i++)\r
+ {\r
+ AlignmentAnnotation na = nala[i];\r
+ oal.addAnnotation(na);\r
+ }\r
+ }\r
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),\r
+ oal, omitHidden, csel, sg));\r
+ oal = null;\r
+ }\r
+\r
+ public void pdbFromFile_actionPerformed()\r
+ {\r
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));\r
+ chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));\r
+\r
+ int value = chooser.showOpenDialog(null);\r
+\r
+ if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+ new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,\r
+ jalview.io.AppletFormatAdapter.FILE, sequence, true);\r
+ }\r
+\r
+ }\r
+\r
+ public void enterPDB_actionPerformed()\r
+ {\r
+ String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+ MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if (id != null && id.length() > 0)\r
+ {\r
+ PDBEntry entry = new PDBEntry();\r
+ entry.setId(id.toUpperCase());\r
+ sequence.getDatasetSequence().addPDBId(entry);\r
+ }\r
+ }\r
+\r
+ public void discoverPDB_actionPerformed()\r
+ {\r
+\r
+ final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]\r
+ { sequence }\r
+ : ap.av.getSequenceSelection());\r
+ Thread discpdb = new Thread(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+\r
+ new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)\r
+ .fetchDBRefs(false);\r
+ }\r
+\r
+ });\r
+ discpdb.start();\r
+ }\r
+\r
+ public void sequenceFeature_actionPerformed()\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ int rsize = 0, gSize = sg.getSize();\r
+ SequenceI[] rseqs, seqs = new SequenceI[gSize];\r
+ SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];\r
+\r
+ for (int i = 0; i < gSize; i++)\r
+ {\r
+ int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
+ int end = sg.findEndRes(sg.getSequenceAt(i));\r
+ if (start <= end)\r
+ {\r
+ seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();\r
+ features[rsize] = new SequenceFeature(null, null, null, start, end,\r
+ "Jalview");\r
+ rsize++;\r
+ }\r
+ }\r
+ rseqs = new SequenceI[rsize];\r
+ tfeatures = new SequenceFeature[rsize];\r
+ System.arraycopy(seqs, 0, rseqs, 0, rsize);\r
+ System.arraycopy(features, 0, tfeatures, 0, rsize);\r
+ features = tfeatures;\r
+ seqs = rseqs;\r
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,\r
+ features, true, ap))\r
+ {\r
+ ap.alignFrame.setShowSeqFeatures(true);\r
+ ap.highlightSearchResults(null);\r
+ }\r
+ }\r
+\r
+ public void textColour_actionPerformed()\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ if (sg != null)\r
+ {\r
+ new TextColourChooser().chooseColour(ap, sg);\r
+ }\r
+ }\r
+\r
+ public void colourByStructure(String pdbid)\r
+ {\r
+ Annotation[] anots = ap.av.getStructureSelectionManager()\r
+ .colourSequenceFromStructure(sequence, pdbid);\r
+\r
+ AlignmentAnnotation an = new AlignmentAnnotation("Structure",\r
+ "Coloured by " + pdbid, anots);\r
+\r
+ ap.av.getAlignment().addAnnotation(an);\r
+ an.createSequenceMapping(sequence, 0, true);\r
+ // an.adjustForAlignment();\r
+ ap.av.getAlignment().setAnnotationIndex(an, 0);\r
+\r
+ ap.adjustAnnotationHeight();\r
+\r
+ sequence.addAlignmentAnnotation(an);\r
+\r
+ }\r
+\r
+ public void editSequence_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+\r
+ if (sg != null)\r
+ {\r
+ if (sequence == null)\r
+ sequence = (Sequence) sg.getSequenceAt(0);\r
+\r
+ EditNameDialog dialog = new EditNameDialog(\r
+ sequence.getSequenceAsString(sg.getStartRes(),\r
+ sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,\r
+ MessageManager.getString("label.edit_sequence"), ap.alignFrame);\r
+\r
+ if (dialog.accept)\r
+ {\r
+ EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),\r
+ EditCommand.REPLACE, dialog.getName().replace(' ',\r
+ ap.av.getGapCharacter()),\r
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),\r
+ sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());\r
+\r
+ ap.alignFrame.addHistoryItem(editCommand);\r
+\r
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
+ .getSequences());\r
+ }\r
+ }\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalview.git / blobdiff