update author list in license for (JAL-826)

[jalview.git] / src / jalview / ws / EnfinEnvision2OneWay.java

diff --git a/src/jalview/ws/EnfinEnvision2OneWay.java b/src/jalview/ws/EnfinEnvision2OneWay.java
index 6a9371b..503245b 100644 (file)
--- a/src/jalview/ws/EnfinEnvision2OneWay.java
+++ b/src/jalview/ws/EnfinEnvision2OneWay.java
@@ -1,6 +1,6 @@
 /*
- * 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, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -33,12 +33,21 @@ import java.awt.event.ActionEvent;
 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;
@@ -48,10 +57,15 @@ import javax.swing.event.MenuListener;
 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
  * 
@@ -138,19 +152,31 @@ 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+"#");
       }
     }
@@ -297,6 +323,10 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
         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);