X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FEnfinEnvision2OneWay.java;h=239a62687082f286aa5362ea1083dc589a0e9df9;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=6a9371bd84c0af99bbfd6c4f5e4e703a2feca671;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/ws/EnfinEnvision2OneWay.java b/src/jalview/ws/EnfinEnvision2OneWay.java
index 6a9371b..239a626 100644
--- a/src/jalview/ws/EnfinEnvision2OneWay.java
+++ b/src/jalview/ws/EnfinEnvision2OneWay.java
@@ -1,19 +1,22 @@
 /*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
 
@@ -25,20 +28,19 @@ 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;
@@ -52,10 +54,15 @@ 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
  * 
+ * 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
@@ -138,19 +145,34 @@ 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 +319,14 @@ 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);
@@ -305,12 +335,7 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
     {
       dbname = "";
     }
-    item.setToolTipText("<html>"
-            + JvSwingUtils.wrapTooltip("Submit " + i + " " + dbname + " "
-                    + (seqsorids ? "sequence" : "sequence id")
-                    + (i > 1 ? "s" : "")
-
-                    + " to<br/>" + descr) + "</html>");
+    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)
@@ -351,9 +376,8 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
       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();
     }
@@ -412,7 +436,7 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
     // menu appears asap
     // sequence only URLs
     // ID/regex match URLs
-    JMenu groupLinksMenu = new JMenu("Group Link");
+    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++)
@@ -511,8 +535,8 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements
         // three types of url that might be
         // created.
         wflinkMenus = new JMenu[]
-        { null, new JMenu("IDS"), new JMenu("Sequences"),
-            new JMenu("IDS and Sequences") };
+        { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),
+            new JMenu(MessageManager.getString("action.ids_sequences")) };
         gurlMenus.put(label, wflinkMenus);
       }