/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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.
- *
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
import jalview.util.GroupUrlLink;
+import jalview.util.MessageManager;
+import jalview.util.GroupUrlLink.UrlStringTooLongException;
import java.awt.Component;
import java.awt.Cursor;
import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.io.BufferedReader;
-import java.io.InputStreamReader;
+import java.io.UnsupportedEncodingException;
import java.net.URL;
+import java.net.URLEncoder;
import java.util.Hashtable;
+import java.util.Map;
import java.util.Vector;
+import java.util.regex.Pattern;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.DefaultHandler;
+import com.lowagie.text.html.HtmlEncoder;
+
/**
* Lightweight runnable to discover dynamic 'one way' group URL services
*
+ * as of Jalview 2.8.1 this class is mothballed and will be dropped in v3.
+ *
* @author JimP
+ * @deprecated
*
*/
public class EnfinEnvision2OneWay extends DefaultHandler implements
System.err.println("Adding entry for " + wfname + " " + description);
if (wfname.toLowerCase().indexOf("funcnet") == -1)
{
+ description = Pattern.compile("\\s+", Pattern.MULTILINE)
+ .matcher(description).replaceAll(" ");
groupURLdescr.addElement(description);
groupURLdescr.addElement(description);
+ String urlstub = wfname;
+ if (wfname.indexOf(" ") > -1)
+ {
+ // make the name safe!
+ try
+ {
+ urlstub = URLEncoder.encode(wfname, "utf-8");
+ } catch (UnsupportedEncodingException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
groupURLLinks
.addElement(wfname
+ "|"
+ "http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="
- + wfname
+ + urlstub
+ "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,"); // #"+description+"#");
groupURLLinks
.addElement(wfname
+ "|"
+ "http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="
- + wfname
+ + urlstub
+ "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); // #"+description+"#");
}
}
* Object array returned from the makeUrlStubs function.
*/
private void addshowLink(JMenu linkMenu, String label, String descr,
- final GroupUrlLink urlgenerator, final Object[] urlstub)
+ String dbname, final GroupUrlLink urlgenerator,
+ final Object[] urlstub)
{
Component[] jmi = linkMenu.getMenuComponents();
for (int i = 0; i < jmi.length; i++)
return;
}
}
+ try
+ {
+ descr = HtmlEncoder.encode(descr);
+ } catch (Exception e)
+ {
+ }
+ ;
+
+ boolean seqsorids = (urlgenerator.getGroupURLType() & urlgenerator.SEQUENCEIDS) == 0;
+ int i = urlgenerator.getNumberInvolved(urlstub);
JMenuItem item = new JMenuItem(label);
- item.setToolTipText("Submit ("
- + urlgenerator.getNumberInvolved(urlstub)
- + " seqs) to workflow: " + descr);
+ //
+ if (dbname == null || dbname.trim().length() == 0)
+ {
+ dbname = "";
+ }
+ item.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.submit_sequence", new String[]{Integer.valueOf(i).toString(), dbname, (seqsorids ? "sequence" : "sequence id"), (i > 1 ? "s" : "")})));
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
public void run()
{
- showLink(urlgenerator.constructFrom(urlstub));
+ try
+ {
+ showLink(urlgenerator.constructFrom(urlstub));
+ } catch (UrlStringTooLongException ex)
+ {
+ Cache.log.warn("Not showing link: URL is too long!", ex);
+ }
}
}).start();
JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- "Unixers: Couldn't find default web browser."
- + "\nAdd the full path to your browser in Preferences.",
- "Web browser not found", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
private void buildGroupLinkMenu(JMenu enfinServiceMenu,
AlignFrame alignFrame)
{
+ if (running || !started)
+ {
+ return;
+ }
SequenceI[] seqs = alignFrame.getViewport().getSelectionAsNewSequence();
SequenceGroup sg = alignFrame.getViewport().getSelectionGroup();
if (sg == null)
*/
private JMenu buildGroupURLMenu(SequenceI[] seqs, SequenceGroup sg)
{
-
+ if (groupURLdescr == null || groupURLLinks == null)
+ return null;
// TODO: usability: thread off the generation of group url content so root
// menu appears asap
// sequence only URLs
// ID/regex match URLs
- JMenu 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.
+ JMenu groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
Hashtable commonDbrefs = new Hashtable();
for (int sq = 0; sq < seqs.length; sq++)
}
}
// now create group links for all distinct ID/sequence sets.
- boolean addMenu = false; // indicates if there are any group links to give
- // to user
+ Hashtable<String, JMenu[]> gurlMenus = new Hashtable<String, JMenu[]>();
+ /**
+ * last number of sequences where URL generation failed
+ */
+ int[] nsqtype = new int[]
+ { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
for (int i = 0; i < groupURLLinks.size(); i++)
{
- String link = groupURLLinks.elementAt(i).toString();
- String descr = groupURLdescr.elementAt(i).toString();
+ String link = (String) groupURLLinks.elementAt(i);
+ String descr = (String) groupURLdescr.elementAt(i);
+
// boolean specialCase =
// additionalPar.elementAt(i).toString().equals(BACKGROUND);
GroupUrlLink urlLink = null;
continue;
}
final String label = urlLink.getLabel();
+ // create/recover the sub menus that might be populated for this link.
+ JMenu[] wflinkMenus = gurlMenus.get(label);
+ if (wflinkMenus == null)
+ {
+ // three types of url that might be
+ // created.
+ wflinkMenus = new JMenu[]
+ { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),
+ new JMenu(MessageManager.getString("action.ids_sequences")) };
+ gurlMenus.put(label, wflinkMenus);
+ }
+
boolean usingNames = false;
// Now see which parts of the group apply for this URL
String ltarget;
String[] allids = ((String[]) idset[1]);
seqstr = new String[numinput];
ids = new String[numinput];
+ if (nsqtype[urlLink.getGroupURLType()] > 0
+ && numinput >= nsqtype[urlLink.getGroupURLType()])
+ {
+ continue;
+ }
for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
{
if (allids[sq] != null)
seqstr[idcount++] = idandseqs[1][sq];
}
}
- addMenu = addMenu
- | createAndAddLinks(linkMenus, false, urlLink, label,
- ltarget, descr, ids, seqstr);
+ try
+ {
+ createAndAddLinks(wflinkMenus, false, urlLink, ltarget, null,
+ descr, ids, seqstr);
+ } catch (UrlStringTooLongException ex)
+ {
+ nsqtype[urlLink.getGroupURLType()] = numinput;
+ }
}
}
// also do names only.
seqstr = idandseqs[1];
ids = idandseqs[0];
- addMenu = addMenu
- | createAndAddLinks(linkMenus, true, urlLink, label, "Names",
- descr, ids, seqstr);
+ if (nsqtype[urlLink.getGroupURLType()] > 0
+ && idandseqs[0].length >= nsqtype[urlLink.getGroupURLType()])
+ {
+ continue;
+ }
+
+ try
+ {
+ createAndAddLinks(wflinkMenus, true, urlLink, "Any", null, descr,
+ ids, seqstr);
+ } catch (UrlStringTooLongException ex)
+ {
+ nsqtype[urlLink.getGroupURLType()] = idandseqs[0].length;
+ }
}
- if (addMenu)
+ boolean anyadded = false; // indicates if there are any group links to give
+ // to user
+ for (Map.Entry<String, JMenu[]> menues : gurlMenus.entrySet())
{
- groupLinksMenu = new JMenu("Group Links");
- for (int m = 0; m < linkMenus.length; m++)
+ JMenu grouplinkset = new JMenu(menues.getKey());
+ JMenu[] wflinkMenus = menues.getValue();
+ for (int m = 0; m < wflinkMenus.length; m++)
{
- if (linkMenus[m] != null
- && linkMenus[m].getMenuComponentCount() > 0)
+ if (wflinkMenus[m] != null
+ && wflinkMenus[m].getMenuComponentCount() > 0)
{
- groupLinksMenu.add(linkMenus[m]);
+ anyadded = true;
+ grouplinkset.add(wflinkMenus[m]);
}
}
-
+ groupLinksMenu.add(grouplinkset);
+ }
+ if (anyadded)
+ {
return groupLinksMenu;
}
return null;
private boolean createAndAddLinks(JMenu[] linkMenus, boolean usingNames,
GroupUrlLink urlLink, String label, String ltarget, String descr,
- String[] ids, String[] seqstr)
+ String[] ids, String[] seqstr) throws UrlStringTooLongException
{
Object[] urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
+ System.currentTimeMillis(), false);
+
if (urlset != null)
{
int type = urlLink.getGroupURLType() & 3;
// +" "+((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
- + " "
- + (usingNames ? (((type & 1) == 1) ? "(Names)" : "") : ("("
- + ltarget + ")")), descr, urlLink, urlset);
+ addshowLink(
+ linkMenus[type],
+ label
+ + " "
+ + (ltarget == null ? (((type & 1) == 1 ? "ID"
+ : "Sequence") + (urlLink
+ .getNumberInvolved(urlset) > 1 ? "s" : ""))
+ : (usingNames ? (((type & 1) == 1) ? "(Names)"
+ : "")
+ : ("(" + ltarget + ")"))), descr,
+ usingNames ? null : label, urlLink, urlset);
return true;
}
return false;
public void menuSelected(MenuEvent e)
{
- if (refresh)
+ if (refresh && !isRunning())
{
- try
- {
- buildGroupLinkMenu(enfinServiceMenu, alignFrame);
- } catch (OutOfMemoryError ex)
+ new Thread(new Runnable()
{
- Cache.log.error(
- "Out of memory when calculating the Envision2 links.",
- ex);
- enfinServiceMenu.setEnabled(false);
- }
+ public void run()
+ {
+ try
+ {
+ buildGroupLinkMenu(enfinServiceMenu, alignFrame);
+ } catch (OutOfMemoryError ex)
+ {
+ Cache.log
+ .error("Out of memory when calculating the Envision2 links.",
+ ex);
+ enfinServiceMenu.setEnabled(false);
+ }
+ }
+ }).start();
refresh = false;
}
}
git://source.jalview.org / jalview.git / blobdiff