JAL-1432 updated copyright notices

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

diff --git a/src/jalview/ws/EnfinEnvision2OneWay.java b/src/jalview/ws/EnfinEnvision2OneWay.java
index 6a9371b..12d81ed 100644 (file)
--- a/src/jalview/ws/EnfinEnvision2OneWay.java
+++ b/src/jalview/ws/EnfinEnvision2OneWay.java
@@ -1,19 +1,20 @@
 /*
- * 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 2.8.0b1)
+ * 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.
- * 
+ *  
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws;
 
@@ -30,15 +31,13 @@ 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;
@@ -52,6 +51,8 @@ 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 +139,34 @@ 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 +313,14 @@ 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);