/*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
+import java.io.BufferedOutputStream;
import java.io.BufferedReader;
import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.io.UnsupportedEncodingException;
import java.net.URL;
+import java.net.URLEncoder;
+import java.nio.charset.Charset;
+import java.nio.charset.CharsetEncoder;
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 javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
+import org.apache.axis.utils.StringUtils;
+import org.apache.http.client.utils.URLEncodedUtils;
+import org.apache.http.entity.StringEntity;
import org.xml.sax.Attributes;
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
*
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,
- String dbname, 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);
- //
- if (dbname==null || dbname.trim().length()==0)
+ //
+ if (dbname == null || dbname.trim().length() == 0)
{
dbname = "";
}
item.setToolTipText("<html>"
- + JvSwingUtils.wrapTooltip("Submit " + i + " " +
- dbname +" "
- + (seqsorids ? "sequence" : "sequence id") + (i > 1 ? "s" : "")
-
- + " to<br/>" + descr) + "</html>");
+ + JvSwingUtils.wrapTooltip("Submit " + i + " " + dbname + " "
+ + (seqsorids ? "sequence" : "sequence id")
+ + (i > 1 ? "s" : "")
+
+ + " to<br/>" + descr) + "</html>");
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
public void run()
{
- try {
+ try
+ {
showLink(urlgenerator.constructFrom(urlstub));
} catch (UrlStringTooLongException ex)
{
*/
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
/**
* last number of sequences where URL generation failed
*/
- int[] nsqtype = new int[] { 0,0,0,0,0,0,0,0,0,0};
+ 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);
String[] allids = ((String[]) idset[1]);
seqstr = new String[numinput];
ids = new String[numinput];
- if (nsqtype[urlLink.getGroupURLType()]>0 && numinput>=nsqtype[urlLink.getGroupURLType()])
+ if (nsqtype[urlLink.getGroupURLType()] > 0
+ && numinput >= nsqtype[urlLink.getGroupURLType()])
{
continue;
}
seqstr[idcount++] = idandseqs[1][sq];
}
}
- try {createAndAddLinks(wflinkMenus, false, urlLink, ltarget, null,
- 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];
- if (nsqtype[urlLink.getGroupURLType()]>0 && idandseqs[0].length>=nsqtype[urlLink.getGroupURLType()])
+ 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)
+
+ try
+ {
+ createAndAddLinks(wflinkMenus, true, urlLink, "Any", null, descr,
+ ids, seqstr);
+ } catch (UrlStringTooLongException ex)
{
nsqtype[urlLink.getGroupURLType()] = idandseqs[0].length;
}
GroupUrlLink urlLink, String label, String ltarget, String descr,
String[] ids, String[] seqstr) throws UrlStringTooLongException
{
- Object[] urlset= urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
+ Object[] urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
+ System.currentTimeMillis(), false);
if (urlset != null)
}
return false;
}
+
// / end of stuff copied from popupmenu
public void attachWSMenuEntry(final JMenu wsmenu,
final AlignFrame alignFrame)
public void menuSelected(MenuEvent e)
{
- if (refresh)
+ if (refresh && !isRunning())
{
- new Thread(new Runnable() {
- public void run() {
- try
+ new Thread(new Runnable()
{
- buildGroupLinkMenu(enfinServiceMenu, alignFrame);
- } catch (OutOfMemoryError ex)
- {
- Cache.log.error(
- "Out of memory when calculating the Envision2 links.",
- ex);
- enfinServiceMenu.setEnabled(false);
- }
- }}).start();
+ 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