/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * 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, 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+"#");
}
}
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);