2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 import jalview.bin.Cache;
21 import jalview.datamodel.DBRefEntry;
22 import jalview.datamodel.SequenceGroup;
23 import jalview.datamodel.SequenceI;
24 import jalview.gui.AlignFrame;
25 import jalview.gui.Desktop;
26 import jalview.gui.JvSwingUtils;
27 import jalview.util.GroupUrlLink;
28 import jalview.util.GroupUrlLink.UrlStringTooLongException;
30 import java.awt.Component;
31 import java.awt.Cursor;
32 import java.awt.event.ActionEvent;
33 import java.awt.event.ActionListener;
34 import java.awt.event.ItemEvent;
35 import java.awt.event.ItemListener;
36 import java.io.BufferedReader;
37 import java.io.InputStreamReader;
38 import java.io.UnsupportedEncodingException;
40 import java.net.URLEncoder;
41 import java.util.Hashtable;
43 import java.util.Vector;
45 import javax.swing.JMenu;
46 import javax.swing.JMenuItem;
47 import javax.swing.JOptionPane;
48 import javax.swing.event.MenuEvent;
49 import javax.swing.event.MenuListener;
50 import javax.xml.parsers.SAXParser;
51 import javax.xml.parsers.SAXParserFactory;
53 import org.xml.sax.Attributes;
54 import org.xml.sax.SAXException;
55 import org.xml.sax.helpers.DefaultHandler;
58 * Lightweight runnable to discover dynamic 'one way' group URL services
63 public class EnfinEnvision2OneWay extends DefaultHandler implements
64 Runnable, WSMenuEntryProviderI
66 private static EnfinEnvision2OneWay groupURLLinksGatherer = null;
68 public static EnfinEnvision2OneWay getInstance()
70 if (groupURLLinksGatherer == null)
72 groupURLLinksGatherer = new EnfinEnvision2OneWay();
74 return groupURLLinksGatherer;
77 private void waitForCompletion()
79 if (groupURLLinksGatherer.isRunning())
81 // wait around and show a visual delay indicator
82 Cursor oldCursor = Desktop.instance.getCursor();
83 Desktop.instance.setCursor(new Cursor(Cursor.WAIT_CURSOR));
84 while (groupURLLinksGatherer.isRunning())
89 } catch (InterruptedException e)
94 Desktop.instance.setCursor(oldCursor);
98 public Vector getEnvisionServiceGroupURLS()
101 return groupURLLinks;
107 private static String BACKGROUND = "BACKGROUNDPARAM";
110 * contains null strings or one of the above constants - indicate if this URL
113 private Vector additionalPar = new Vector();
116 * the enfin service URL
118 private String enfinService = null;
120 private String description = null;
122 private String wfname;
127 * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String,
128 * java.lang.String, java.lang.String)
130 public void endElement(String uri, String localName, String qName)
134 // System.err.println("End element: : '"+uri+" "+localName+" "+qName);
135 if (qName.equalsIgnoreCase("workflow") && description != null
136 && description.length() > 0)
138 // groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
139 // groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
140 System.err.println("Adding entry for " + wfname + " " + description);
141 if (wfname.toLowerCase().indexOf("funcnet") == -1)
143 groupURLdescr.addElement(description);
144 groupURLdescr.addElement(description);
145 String urlstub=wfname;
146 if (wfname.indexOf(" ")>-1)
148 // make the name safe!
150 urlstub = URLEncoder.encode(wfname,"utf-8");
151 } catch (UnsupportedEncodingException e) {
152 // TODO Auto-generated catch block
159 + "http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="
161 + "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,"); // #"+description+"#");
165 + "http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="
167 + "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); // #"+description+"#");
175 * @see org.xml.sax.helpers.DefaultHandler#characters(char[], int, int)
177 public void characters(char[] ch, int start, int length)
180 if (description != null)
182 for (int i = start; i < start + length; i++)
184 description += ch[i];
192 * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String,
193 * java.lang.String, java.lang.String, org.xml.sax.Attributes)
195 public void startElement(String uri, String localName, String qName,
196 Attributes attributes) throws SAXException
198 if (qName.equalsIgnoreCase("workflow"))
201 wfname = attributes.getValue("name");
203 if (qName.equalsIgnoreCase("description"))
208 // System.err.println("Start element: : '"+uri+" "+localName+" "+qName+" attributes"+attributes);
209 // super.startElement(uri,localName,qname,attributes);
212 private boolean started = false;
214 private boolean running = false;
216 private Vector groupURLLinks = null;
218 private Vector groupURLdescr = null;
220 private static String[] allowedDb = new String[]
221 { "UNIPROT", "EMBL", "PDB" };
223 public EnfinEnvision2OneWay()
225 groupURLLinks = new Vector();
226 groupURLdescr = new Vector();
228 enfinService = Cache.getDefault("ENVISION2_WORKFLOWSERVICE",
229 "http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml");
230 new Thread(this).start();
239 SAXParserFactory spf = SAXParserFactory.newInstance();
240 SAXParser sp = spf.newSAXParser();
241 sp.parse(new URL(enfinService).openStream(), this);
242 } catch (Exception e)
244 Cache.log.warn("Exception when discovering One Way services: ", e);
247 Cache.log.warn("Error when discovering One Way services: ", e);
250 Cache.log.debug("Finished running.");
254 * have we finished running yet ?
256 * @return false if we have been run.
258 public boolean isRunning()
261 // TODO Auto-generated method stub
262 return !started || running;
265 public static void main(String[] args)
268 EnfinEnvision2OneWay ow = new EnfinEnvision2OneWay();
269 while (ow.isRunning())
274 } catch (Exception e)
280 for (int i = 0; i < ow.groupURLLinks.size(); i++)
282 System.err.println("Description" + ow.groupURLdescr.elementAt(i)
283 + "Service URL: " + ow.groupURLLinks.elementAt(i));
287 // / Copied from jalview.gui.PopupMenu
289 * add a late bound URL service item to the given menu
293 * - menu label string
294 * @param urlgenerator
295 * GroupURLLink used to generate URL
297 * Object array returned from the makeUrlStubs function.
299 private void addshowLink(JMenu linkMenu, String label, String descr,
300 String dbname, final GroupUrlLink urlgenerator,
301 final Object[] urlstub)
303 Component[] jmi = linkMenu.getMenuComponents();
304 for (int i = 0; i < jmi.length; i++)
306 if (jmi[i] instanceof JMenuItem
307 && ((JMenuItem) jmi[i]).getText().equalsIgnoreCase(label))
309 // don't add this - its a repeat of an existing URL.
313 boolean seqsorids = (urlgenerator.getGroupURLType() & urlgenerator.SEQUENCEIDS) == 0;
314 int i = urlgenerator.getNumberInvolved(urlstub);
315 JMenuItem item = new JMenuItem(label);
317 if (dbname == null || dbname.trim().length() == 0)
321 item.setToolTipText("<html>"
322 + JvSwingUtils.wrapTooltip("Submit " + i + " " + dbname + " "
323 + (seqsorids ? "sequence" : "sequence id")
326 + " to<br/>" + descr) + "</html>");
327 item.addActionListener(new java.awt.event.ActionListener()
329 public void actionPerformed(ActionEvent e)
331 new Thread(new Runnable()
338 showLink(urlgenerator.constructFrom(urlstub));
339 } catch (UrlStringTooLongException ex)
341 Cache.log.warn("Not showing link: URL is too long!", ex);
353 * open the given link in a new browser window
357 public void showLink(String url)
361 jalview.util.BrowserLauncher.openURL(url);
362 } catch (Exception ex)
365 .showInternalMessageDialog(
367 "Unixers: Couldn't find default web browser."
368 + "\nAdd the full path to your browser in Preferences.",
369 "Web browser not found", JOptionPane.WARNING_MESSAGE);
371 ex.printStackTrace();
376 * called by a web service menu instance when it is opened.
378 * @param enfinServiceMenu
381 private void buildGroupLinkMenu(JMenu enfinServiceMenu,
382 AlignFrame alignFrame)
384 if (running || !started)
388 SequenceI[] seqs = alignFrame.getViewport().getSelectionAsNewSequence();
389 SequenceGroup sg = alignFrame.getViewport().getSelectionGroup();
392 // consider visible regions here/
394 enfinServiceMenu.removeAll();
395 JMenu entries = buildGroupURLMenu(seqs, sg);
398 for (int i = 0, iSize = entries.getMenuComponentCount(); i < iSize; i++)
400 // transfer - menu component is removed from entries automatically
401 enfinServiceMenu.add(entries.getMenuComponent(0));
403 // entries.removeAll();
404 enfinServiceMenu.setEnabled(true);
408 enfinServiceMenu.setEnabled(false);
413 * construct a dynamic enfin services menu given a sequence selection
420 private JMenu buildGroupURLMenu(SequenceI[] seqs, SequenceGroup sg)
422 if (groupURLdescr == null || groupURLLinks == null)
424 // TODO: usability: thread off the generation of group url content so root
426 // sequence only URLs
427 // ID/regex match URLs
428 JMenu groupLinksMenu = new JMenu("Group Link");
429 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
430 Hashtable commonDbrefs = new Hashtable();
431 for (int sq = 0; sq < seqs.length; sq++)
437 start = seqs[sq].findPosition(sg.getStartRes());
438 end = seqs[sq].findPosition(sg.getEndRes());
442 // get total width of alignment.
443 start = seqs[sq].getStart();
444 end = seqs[sq].findPosition(seqs[sq].getLength());
446 // we skip sequences which do not have any non-gaps in the region of
452 // just collect ids from dataset sequence
453 // TODO: check if IDs collected from selecton group intersects with the
454 // current selection, too
455 SequenceI sqi = seqs[sq];
456 while (sqi.getDatasetSequence() != null)
458 sqi = sqi.getDatasetSequence();
460 DBRefEntry[] dbr = sqi.getDBRef();
461 if (dbr != null && dbr.length > 0)
463 for (int d = 0; d < dbr.length; d++)
465 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
466 Object[] sarray = (Object[]) commonDbrefs.get(src);
469 sarray = new Object[2];
470 sarray[0] = new int[]
472 sarray[1] = new String[seqs.length];
474 commonDbrefs.put(src, sarray);
477 if (((String[]) sarray[1])[sq] == null)
480 || (dbr[d].getMap().locateMappedRange(start, end) != null))
482 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
483 ((int[]) sarray[0])[0]++;
489 // now create group links for all distinct ID/sequence sets.
490 Hashtable<String, JMenu[]> gurlMenus = new Hashtable<String, JMenu[]>();
492 * last number of sequences where URL generation failed
494 int[] nsqtype = new int[]
495 { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
496 for (int i = 0; i < groupURLLinks.size(); i++)
498 String link = (String) groupURLLinks.elementAt(i);
499 String descr = (String) groupURLdescr.elementAt(i);
501 // boolean specialCase =
502 // additionalPar.elementAt(i).toString().equals(BACKGROUND);
503 GroupUrlLink urlLink = null;
506 urlLink = new GroupUrlLink(link);
507 } catch (Exception foo)
509 jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
514 if (!urlLink.isValid())
516 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
519 final String label = urlLink.getLabel();
520 // create/recover the sub menus that might be populated for this link.
521 JMenu[] wflinkMenus = gurlMenus.get(label);
522 if (wflinkMenus == null)
524 // three types of url that might be
526 wflinkMenus = new JMenu[]
527 { null, new JMenu("IDS"), new JMenu("Sequences"),
528 new JMenu("IDS and Sequences") };
529 gurlMenus.put(label, wflinkMenus);
532 boolean usingNames = false;
533 // Now see which parts of the group apply for this URL
535 String[] seqstr, ids; // input to makeUrl
536 for (int t = 0; t < allowedDb.length; t++)
538 ltarget = allowedDb[t]; // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
539 Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
542 int numinput = ((int[]) idset[0])[0];
543 String[] allids = ((String[]) idset[1]);
544 seqstr = new String[numinput];
545 ids = new String[numinput];
546 if (nsqtype[urlLink.getGroupURLType()] > 0
547 && numinput >= nsqtype[urlLink.getGroupURLType()])
551 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
553 if (allids[sq] != null)
555 ids[idcount] = allids[sq];
556 seqstr[idcount++] = idandseqs[1][sq];
561 createAndAddLinks(wflinkMenus, false, urlLink, ltarget, null,
563 } catch (UrlStringTooLongException ex)
565 nsqtype[urlLink.getGroupURLType()] = numinput;
569 // also do names only.
570 seqstr = idandseqs[1];
572 if (nsqtype[urlLink.getGroupURLType()] > 0
573 && idandseqs[0].length >= nsqtype[urlLink.getGroupURLType()])
580 createAndAddLinks(wflinkMenus, true, urlLink, "Any", null, descr,
582 } catch (UrlStringTooLongException ex)
584 nsqtype[urlLink.getGroupURLType()] = idandseqs[0].length;
587 boolean anyadded = false; // indicates if there are any group links to give
589 for (Map.Entry<String, JMenu[]> menues : gurlMenus.entrySet())
591 JMenu grouplinkset = new JMenu(menues.getKey());
592 JMenu[] wflinkMenus = menues.getValue();
593 for (int m = 0; m < wflinkMenus.length; m++)
595 if (wflinkMenus[m] != null
596 && wflinkMenus[m].getMenuComponentCount() > 0)
599 grouplinkset.add(wflinkMenus[m]);
602 groupLinksMenu.add(grouplinkset);
606 return groupLinksMenu;
611 private boolean createAndAddLinks(JMenu[] linkMenus, boolean usingNames,
612 GroupUrlLink urlLink, String label, String ltarget, String descr,
613 String[] ids, String[] seqstr) throws UrlStringTooLongException
615 Object[] urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
616 + System.currentTimeMillis(), false);
620 int type = urlLink.getGroupURLType() & 3;
621 // System.out.println(urlLink.getGroupURLType()
622 // +" "+((String[])urlset[3])[0]);
623 // first two bits ofurlLink type bitfield are sequenceids and sequences
624 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
629 + (ltarget == null ? (((type & 1) == 1 ? "ID"
630 : "Sequence") + (urlLink
631 .getNumberInvolved(urlset) > 1 ? "s" : ""))
632 : (usingNames ? (((type & 1) == 1) ? "(Names)"
634 : ("(" + ltarget + ")"))), descr,
635 usingNames ? null : label, urlLink, urlset);
641 // / end of stuff copied from popupmenu
642 public void attachWSMenuEntry(final JMenu wsmenu,
643 final AlignFrame alignFrame)
645 final JMenu enfinServiceMenu = new JMenu("Envision 2");
646 wsmenu.add(enfinServiceMenu);
647 enfinServiceMenu.setEnabled(false);
648 wsmenu.addMenuListener(new MenuListener()
650 // this listener remembers when the menu was first selected, and
651 // doesn't rebuild the session list until it has been cleared and
653 boolean refresh = true;
655 public void menuCanceled(MenuEvent e)
660 public void menuDeselected(MenuEvent e)
665 public void menuSelected(MenuEvent e)
667 if (refresh && !isRunning())
669 new Thread(new Runnable()
675 buildGroupLinkMenu(enfinServiceMenu, alignFrame);
676 } catch (OutOfMemoryError ex)
679 .error("Out of memory when calculating the Envision2 links.",
681 enfinServiceMenu.setEnabled(false);