X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FGroupUrlLink.java;h=e4c4ad05bda134e535426307d02059f2832dc425;hb=b74cdec4b07000bee431a7cca86a948f44d3ffbe;hp=1654aef1650f5c1e9bc4fcf97cfb8fa7d958323d;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git

diff --git a/src/jalview/util/GroupUrlLink.java b/src/jalview/util/GroupUrlLink.java
index 1654aef..e4c4ad0 100644
--- a/src/jalview/util/GroupUrlLink.java
+++ b/src/jalview/util/GroupUrlLink.java
@@ -1,31 +1,41 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.util;
 
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
 import java.util.Hashtable;
-import java.util.Vector;
 
+import com.stevesoft.pat.Regex;
+
+/**
+ * This class is not implemented because Preferences never puts anything in
+ * groupURLLinks.
+ * 
+ * @author hansonr
+ *
+ */
 public class GroupUrlLink
 {
+  @SuppressWarnings("serial")
   public class UrlStringTooLongException extends Exception
   {
     public UrlStringTooLongException(int lng)
@@ -35,6 +45,7 @@ public class GroupUrlLink
 
     public int urlLength;
 
+    @Override
     public String toString()
     {
       return "Generated url is estimated to be too long (" + urlLength
@@ -64,11 +75,6 @@ public class GroupUrlLink
   private String invalidMessage = null;
 
   /**
-   * tokens that can be replaced in the URL.
-   */
-  private static String[] tokens;
-
-  /**
    * position of each token (which can appear once only) in the url
    */
   private int[] segs;
@@ -77,33 +83,34 @@ public class GroupUrlLink
    * contains tokens in the order they appear in the URL template.
    */
   private String[] mtch;
-  static
-  {
-    if (tokens == null)
-    {
-      tokens = new String[]
-      { "SEQUENCEIDS", "SEQUENCES", "DATASETID" };
-    }
-  }
-
-  /**
-   * test for GroupURLType bitfield (with default tokens)
-   */
-  public static final int SEQUENCEIDS = 1;
-
-  /**
-   * test for GroupURLType bitfield (with default tokens)
-   */
-  public static final int SEQUENCES = 2;
 
   /**
-   * test for GroupURLType bitfield (with default tokens)
+   * tokens that can be replaced in the URL.
    */
-  public static final int DATASETID = 4;
-
+  private static final String[] tokens = new String[] { "SEQUENCEIDS",
+      "SEQUENCES", "DATASETID" };
+
+  // /**
+  // * test for GroupURLType bitfield (with default tokens)
+  // */
+  // private static final int SEQUENCEIDS = 1;
+  //
+  // /**
+  // * test for GroupURLType bitfield (with default tokens)
+  // */
+  // private static final int SEQUENCES = 2;
+  //
+  // /**
+  // * test for GroupURLType bitfield (with default tokens)
+  // */
+  // private static final int DATASETID = 4;
+  //
   // private int idseg = -1, seqseg = -1;
 
   /**
+   * 
+   * called by PopupMenu.buildGroupURLMenu()
+   * 
    * parse the given linkString of the form '<label>|<url>|separator
    * char[|optional sequence separator char]' into parts. url may contain a
    * string $SEQUENCEIDS<=optional regex=>$ where <=optional regex=> must be of
@@ -198,9 +205,8 @@ public class GroupUrlLink
     for (int pass = 0; pass < mtch.length; pass++)
     {
       int mlength = 3 + mtch[pass].length();
-      if (link.indexOf("$" + mtch[pass] + "=/") == ptok[pass]
-              && (p = link.indexOf("/=$", ptok[pass] + mlength)) > ptok[pass]
-                      + mlength)
+      if (link.indexOf("$" + mtch[pass] + "=/") == ptok[pass] && (p = link
+              .indexOf("/=$", ptok[pass] + mlength)) > ptok[pass] + mlength)
       {
         // Extract Regex and suffix
         if (ptok[pass + 1] < p + 3)
@@ -215,8 +221,7 @@ public class GroupUrlLink
         regexReplace[pass] = link.substring(ptok[pass] + mlength, p);
         try
         {
-          com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
-                  + regexReplace[pass] + "/");
+          Regex rg = Platform.newRegexPerl("/" + regexReplace[pass] + "/");
           if (rg == null)
           {
             invalidMessage = "Invalid Regular Expression : '"
@@ -284,6 +289,9 @@ public class GroupUrlLink
   }
 
   /**
+   * 
+   * called by PopupMenu.addShowLink()
+   * 
    * @return the url_prefix
    */
   public String getUrl_prefix()
@@ -292,6 +300,8 @@ public class GroupUrlLink
   }
 
   /**
+   * called by PopupMenu.buildGroupURLMenu()
+   * 
    * @return the target
    */
   public String getTarget()
@@ -300,6 +310,9 @@ public class GroupUrlLink
   }
 
   /**
+   * 
+   * called by PopupMenu.buildGroupURLMenu()
+   * 
    * @return the label
    */
   public String getLabel()
@@ -308,32 +321,9 @@ public class GroupUrlLink
   }
 
   /**
-   * @return the sequence ID regexReplace
-   */
-  public String getIDRegexReplace()
-  {
-    return _replaceFor(tokens[0]);
-  }
-
-  private String _replaceFor(String token)
-  {
-    for (int i = 0; i < mtch.length; i++)
-      if (segs[i] > -1 && mtch[i].equals(token))
-      {
-        return regexReplace[i];
-      }
-    return null;
-  }
-
-  /**
-   * @return the sequence ID regexReplace
-   */
-  public String getSeqRegexReplace()
-  {
-    return _replaceFor(tokens[1]);
-  }
-
-  /**
+   * 
+   * called by PopupMenu.buildGroupURLMenu()
+   * 
    * @return the invalidMessage
    */
   public String getInvalidMessage()
@@ -342,6 +332,8 @@ public class GroupUrlLink
   }
 
   /**
+   * called by PopupMenu.buildGroupURLMenu()
+   * 
    * Check if URL string was parsed properly.
    * 
    * @return boolean - if false then <code>getInvalidMessage</code> returns an
@@ -353,27 +345,34 @@ public class GroupUrlLink
   }
 
   /**
-   * return one or more URL strings by applying regex to the given idstring
    * 
-   * @param idstrings
-   *          array of id strings to pass to service
-   * @param seqstrings
-   *          array of seq strings to pass to service
+   * called by PopupMenu.buildGroupURLMenu()
+   * 
+   * This method is never called, because PopupMenu.buildGroupMenu() is never
+   * called. It relates to the popup menu for the idPanel.
+   * 
+   * @param ids
+   * @param seqstr
+   * @param string
    * @param onlyIfMatches
-   *          - when true url strings are only made if regex is defined and
-   *          matches for all qualified tokens in groupURL - TODO: consider if
-   *          onlyIfMatches is really a useful parameter!
-   * @return null or Object[] { int[] { number of seqs substituted},boolean[] {
-   *         which seqs were substituted }, StringBuffer[] { substituted lists
-   *         for each token }, String[] { url } }
+   * @return URL stub objects ready to pass to constructFrom in the form of
+   *         Object[] { int[], boolean[], Hashtable&lt;String, String[]&gt;,
+   *         boolean[] }
    * @throws UrlStringTooLongException
    */
-  public Object[] makeUrls(String[] idstrings, String[] seqstrings,
-          String dsstring, boolean onlyIfMatches)
-          throws UrlStringTooLongException
+  public Object[] makeUrlStubs(String[] ids, String[] seqstr, String string,
+          boolean onlyIfMatches) throws UrlStringTooLongException
   {
-    Hashtable rstrings = replacementArgs(idstrings, seqstrings, dsstring);
-    return makeUrls(rstrings, onlyIfMatches);
+    Hashtable<String, String[]> rstrings = replacementArgs(ids, seqstr,
+            string);
+    boolean createFullURL = false;
+    Object[] stubs = makeUrlsIf(createFullURL, rstrings, onlyIfMatches);
+    // stubs is just { int[] boolean[] }
+    return stubs == null ? null
+            : new Object[]
+            { stubs[0], stubs[1], rstrings,
+                new boolean[]
+                { onlyIfMatches } }; // int[] boolean[] Hashtable boolean[]
   }
 
   /**
@@ -384,66 +383,49 @@ public class GroupUrlLink
    * @param dsstring
    * @return
    */
-  private Hashtable replacementArgs(String[] idstrings,
+  private Hashtable<String, String[]> replacementArgs(String[] idstrings,
           String[] seqstrings, String dsstring)
   {
-    Hashtable rstrings = new Hashtable();
+    Hashtable<String, String[]> rstrings = new Hashtable<>();
     rstrings.put(tokens[0], idstrings);
     rstrings.put(tokens[1], seqstrings);
-    rstrings.put(tokens[2], new String[]
-    { dsstring });
+    rstrings.put(tokens[2], new String[] { dsstring });
     if (idstrings.length != seqstrings.length)
     {
-      throw new Error(
-              "idstrings and seqstrings contain one string each per sequence.");
+      throw new Error(MessageManager.getString(
+              "error.idstring_seqstrings_only_one_per_sequence"));
     }
     return rstrings;
   }
 
-  public Object[] makeUrls(Hashtable repstrings, boolean onlyIfMatches)
-          throws UrlStringTooLongException
-  {
-    return makeUrlsIf(true, repstrings, onlyIfMatches);
-  }
-
   /**
+   * Called from PopupMenu.addShowLink action listener
    * 
-   * @param ids
-   * @param seqstr
-   * @param string
-   * @param b
-   * @return URL stub objects ready to pass to constructFrom
-   * @throws UrlStringTooLongException
-   */
-  public Object[] makeUrlStubs(String[] ids, String[] seqstr,
-          String string, boolean b) throws UrlStringTooLongException
-  {
-    Hashtable rstrings = replacementArgs(ids, seqstr, string);
-    Object[] stubs = makeUrlsIf(false, rstrings, b);
-    if (stubs != null)
-    {
-      return new Object[]
-      { stubs[0], stubs[1], rstrings, new boolean[]
-      { b } };
-    }
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /**
    * generate the URL for the given URL stub object array returned from
    * makeUrlStubs
    * 
    * @param stubs
-   * @return URL string.
+   *          Object[] { int[] { number of matches seqs }, boolean[] { which
+   *          matched }, (if createFullUrl also has StringBuffer[] { segment
+   *          generated from inputs that is used in URL }, String[] { url })}
+   * @return URL string
    * @throws UrlStringTooLongException
    */
+  @SuppressWarnings("unchecked")
   public String constructFrom(Object[] stubs)
           throws UrlStringTooLongException
   {
-    Object[] results = makeUrlsIf(true, (Hashtable) stubs[2],
-            ((boolean[]) stubs[3])[0]);
-    return ((String[]) results[3])[0];
+    // Object[] {
+    // int[] { number of matches seqs },
+    // boolean[] { which matched }
+    // }
+
+    boolean createFullURL = true;
+    Hashtable<String, String[]> repstrings = (Hashtable<String, String[]>) stubs[2];
+    boolean onlyIfMatches = ((boolean[]) stubs[3])[0];
+    String url = ((String[]) makeUrlsIf(createFullURL, repstrings,
+            onlyIfMatches)[3])[0];
+    return url;
   }
 
   /**
@@ -459,9 +441,9 @@ public class GroupUrlLink
    *         }, String[] { url })}
    * @throws UrlStringTooLongException
    */
-  protected Object[] makeUrlsIf(boolean createFullUrl,
-          Hashtable repstrings, boolean onlyIfMatches)
-          throws UrlStringTooLongException
+  private Object[] makeUrlsIf(boolean createFullUrl,
+          Hashtable<String, String[]> repstrings,
+          boolean onlyIfMatches) throws UrlStringTooLongException
   {
     int pass = 0;
 
@@ -470,7 +452,7 @@ public class GroupUrlLink
     int mins = 0, maxs = 0; // allowed two values, 1 or n-sequences.
     for (int i = 0; i < mtch.length; i++)
     {
-      idseq[i] = (String[]) repstrings.get(mtch[i]);
+      idseq[i] = repstrings.get(mtch[i]);
       if (idseq[i].length >= 1)
       {
         if (mins == 0 && idseq[i].length == 1)
@@ -485,31 +467,31 @@ public class GroupUrlLink
         {
           if (maxs != idseq[i].length)
           {
-            throw new Error(
-                    "Cannot have mixed length replacement vectors. Replacement vector for "
-                            + (mtch[i]) + " is " + idseq[i].length
-                            + " strings long, and have already seen a "
-                            + maxs + " length vector.");
+            throw new Error(MessageManager.formatMessage(
+                    "error.cannot_have_mixed_length_replacement_vectors",
+                    new String[]
+                    { (mtch[i]),
+                        Integer.valueOf(idseq[i].length).toString(),
+                        Integer.valueOf(maxs).toString() }));
           }
         }
       }
       else
       {
-        throw new Error(
-                "Cannot have zero length vector of replacement strings - either 1 value or n values.");
+        throw new Error(MessageManager.getString(
+                "error.cannot_have_zero_length_vector_replacement_strings"));
       }
     }
     // iterate through input, collating segments to be inserted into url
     StringBuffer matched[] = new StringBuffer[idseq.length];
     // and precompile regexes
-    com.stevesoft.pat.Regex[] rgxs = new com.stevesoft.pat.Regex[matched.length];
+    Regex[] rgxs = new Regex[matched.length];
     for (pass = 0; pass < matched.length; pass++)
     {
       matched[pass] = new StringBuffer();
       if (regexReplace[pass] != null)
       {
-        rgxs[pass] = com.stevesoft.pat.Regex.perlCode("/"
-                + regexReplace[pass] + "/");
+        rgxs[pass] = Platform.newRegexPerl("/" + regexReplace[pass] + "/");
       }
       else
       {
@@ -692,9 +674,8 @@ public class GroupUrlLink
     {
       // just return the essential info about what the URL would be generated
       // from
-      return new Object[]
-      { new int[]
-      { seqsmatched }, thismatched };
+      return new Object[] { new int[] { seqsmatched }, thismatched // boolean[]
+      };
     }
     // otherwise, create the URL completely.
 
@@ -709,14 +690,17 @@ public class GroupUrlLink
       }
     }
 
-    return new Object[]
-    { new int[]
-    { seqsmatched }, thismatched, matched, new String[]
-    { submiturl.toString() } };
+    // full return
+    return new Object[] { new int[] { seqsmatched }, thismatched, // boolean[]
+        matched, // StringBuffer[]
+        new String[]
+        { submiturl.toString() } };
   }
 
   /**
    * 
+   * Called by PopupMenu.addShowLinks()
+   * 
    * @param urlstub
    * @return number of distinct sequence (id or seuqence) replacements predicted
    *         for this stub
@@ -728,6 +712,8 @@ public class GroupUrlLink
   }
 
   /**
+   * called by PopupMenu.buildGroupURLMenu()
+   * 
    * get token types present in this url as a bitfield indicating presence of
    * each token from tokens (LSB->MSB).
    * 
@@ -749,6 +735,216 @@ public class GroupUrlLink
     return r;
   }
 
+  /**
+   * called by PopupMenu.buildGroupURLMenu()
+   * 
+   * covenience method to generate the id and sequence string vector from a set
+   * of seuqences using each sequence's getName() and getSequenceAsString()
+   * method
+   * 
+   * @param seqs
+   * @return String[][] {{sequence ids},{sequence strings}}
+   */
+  public static String[][] formStrings(SequenceI[] seqs)
+  {
+    String[][] idset = new String[2][seqs.length];
+    for (int i = 0; i < seqs.length; i++)
+    {
+      idset[0][i] = seqs[i].getName();
+      idset[1][i] = seqs[i].getSequenceAsString();
+    }
+    return idset;
+  }
+
+  // commented out test code
+  //
+  // /**
+  // *
+  // * @param argv
+  // * @j2sIgnore
+  // */
+  // public static void main(String argv[])
+  // {
+  // // note - JAL-1383 - these services are all dead
+  // String[] links = new String[] {
+  // "EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=linkInDatasetFromJalview&input=$SEQUENCEIDS$&inputType=0|,",
+  // "EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=linkInDatasetFromJalview&input=$SEQUENCES$&inputType=1|,",
+  // "EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,",
+  // "EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=$DATASETID$&input=$SEQUENCES$&inputType=1|,",
+  // "EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=$SEQUENCEIDS$&datasetName=linkInDatasetFromJalview&input=$SEQUENCEIDS$&inputType=0|,",
+  // "EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=$SEQUENCEIDS$&datasetName=$DATASETID$&input=$SEQUENCES$&inputType=1|,",
+  // "EnVision2
+  // Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([a-zA-Z]+)/=$&inputType=1|,",
+  // "EnVision2
+  // Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/[A-Za-z]+/=$&inputType=1|,"
+  // /*
+  // *
+  // http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?input=P38389,P38398
+  // * &inputType=0&workflow=Enfin%20Default%20Workflow&datasetName=
+  // * linkInDatasetFromPRIDE
+  // */
+  // };
+  //
+  // SequenceI[] seqs = new SequenceI[] {
+  // new Sequence("StupidLabel:gi|9234|pdb|102L|A",
+  // "asdiasdpasdpadpwpadasdpaspdw"), };
+  // String[][] seqsandids = formStrings(seqs);
+  // for (int i = 0; i < links.length; i++)
+  // {
+  // GroupUrlLink ul = new GroupUrlLink(links[i]);
+  // if (ul.isValid())
+  // {
+  // System.out.println("\n\n\n");
+  // System.out.println(
+  // "Link " + i + " " + links[i] + " : " + ul.toString());
+  // System.out.println(" pref : " + ul.getUrl_prefix());
+  // System.out.println(" IdReplace : " + ul.getIDRegexReplace());
+  // System.out.println(" SeqReplace : " + ul.getSeqRegexReplace());
+  // System.out.println(" Suffixes : " + ul.getUrl_suffix());
+  //
+  // System.out.println(
+  // "<insert input id and sequence strings here> Without onlyIfMatches:");
+  // Object[] urls;
+  // try
+  // {
+  // urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset",
+  // false);
+  // testUrls(ul, seqsandids, urls);
+  // } catch (UrlStringTooLongException ex)
+  // {
+  // System.out.println("too long exception " + ex);
+  // }
+  // System.out.println(
+  // "<insert input id and sequence strings here> With onlyIfMatches set:");
+  // try
+  // {
+  // urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset",
+  // true);
+  // testUrls(ul, seqsandids, urls);
+  // } catch (UrlStringTooLongException ex)
+  // {
+  // System.out.println("too long exception " + ex);
+  // }
+  // }
+  // else
+  // {
+  // System.err.println("Invalid URLLink : " + links[i] + " : "
+  // + ul.getInvalidMessage());
+  // }
+  // }
+  // }
+  // /**
+  // * @return the sequence ID regexReplace
+  // */
+  // private String getIDRegexReplace()
+  // {
+  // String token = tokens[0];
+  // for (int i = 0; i < mtch.length; i++)
+  // {
+  // if (segs[i] > -1 && mtch[i].equals(token))
+  // {
+  // return regexReplace[i];
+  // }
+  // }
+  // return null;
+  // }
+  //
+  // /**
+  // * @return the sequence ID regexReplace
+  // */
+  // private String getSeqRegexReplace()
+  // {
+  // return _replaceFor(tokens[1]);
+  // }
+  //
+  // /**
+  // * report stats about the generated url string given an input set
+  // *
+  // * @param ul
+  // * @param idstring
+  // * @param url
+  // */
+  // private static void testUrls(GroupUrlLink ul, String[][] idstring,
+  // Object[] url)
+  // {
+  //
+  // if (url == null)
+  // {
+  // System.out.println("Created NO urls.");
+  // }
+  // else
+  // {
+  // System.out.println("Created a url from " + ((int[]) url[0])[0]
+  // + "out of " + idstring[0].length + " sequences.");
+  // System.out.println("Sequences that did not match:");
+  // for (int sq = 0; sq < idstring[0].length; sq++)
+  // {
+  // if (!((boolean[]) url[1])[sq])
+  // {
+  // System.out.println("Seq " + sq + ": " + idstring[0][sq] + "\t: "
+  // + idstring[1][sq]);
+  // }
+  // }
+  // System.out.println("Sequences that DID match:");
+  // for (int sq = 0; sq < idstring[0].length; sq++)
+  // {
+  // if (((boolean[]) url[1])[sq])
+  // {
+  // System.out.println("Seq " + sq + ": " + idstring[0][sq] + "\t: "
+  // + idstring[1][sq]);
+  // }
+  // }
+  // System.out.println("The generated URL:");
+  // System.out.println(((String[]) url[3])[0]);
+  // }
+  // }
+  //
+  // public void setLabel(String newlabel)
+  // {
+  // this.label = newlabel;
+  // }
+  // /**
+  // * return one or more URL strings by applying regex to the given idstring
+  // *
+  // * @param idstrings
+  // * array of id strings to pass to service
+  // * @param seqstrings
+  // * array of seq strings to pass to service
+  // * @param onlyIfMatches
+  // * - when true url strings are only made if regex is defined and
+  // * matches for all qualified tokens in groupURL - TODO: consider if
+  // * onlyIfMatches is really a useful parameter!
+  // * @return null or Object[] { int[] { number of seqs substituted},boolean[]
+  // {
+  // * which seqs were substituted }, StringBuffer[] { substituted lists
+  // * for each token }, String[] { url } }
+  // * @throws UrlStringTooLongException
+  // */
+  // private Object[] makeUrls(String[] idstrings, String[] seqstrings,
+  // String dsstring, boolean onlyIfMatches)
+  // throws UrlStringTooLongException
+  // {
+  // Hashtable<String, String[]> rstrings = replacementArgs(idstrings,
+  // seqstrings, dsstring);
+  // return makeUrls(rstrings, onlyIfMatches);
+  // }
+  //
+  // /**
+  // *
+  // * @param repstrings
+  // * @param onlyIfMatches
+  // * @return Object[] {int[], boolean[], StringBuffer[], String[] }
+  // * @throws UrlStringTooLongException
+  // */
+  // private Object[] makeUrls(Hashtable<String, String[]> repstrings,
+  // boolean onlyIfMatches)
+  // throws UrlStringTooLongException
+  // {
+  // return makeUrlsIf(true, repstrings, onlyIfMatches);
+  // }
+  //
+
+  @Override
   public String toString()
   {
     StringBuffer result = new StringBuffer();
@@ -775,139 +971,4 @@ public class GroupUrlLink
     return result.toString();
   }
 
-  /**
-   * report stats about the generated url string given an input set
-   * 
-   * @param ul
-   * @param idstring
-   * @param url
-   */
-  private static void testUrls(GroupUrlLink ul, String[][] idstring,
-          Object[] url)
-  {
-
-    if (url == null)
-    {
-      System.out.println("Created NO urls.");
-    }
-    else
-    {
-      System.out.println("Created a url from " + ((int[]) url[0])[0]
-              + "out of " + idstring[0].length + " sequences.");
-      System.out.println("Sequences that did not match:");
-      for (int sq = 0; sq < idstring[0].length; sq++)
-      {
-        if (!((boolean[]) url[1])[sq])
-        {
-          System.out.println("Seq " + sq + ": " + idstring[0][sq] + "\t: "
-                  + idstring[1][sq]);
-        }
-      }
-      System.out.println("Sequences that DID match:");
-      for (int sq = 0; sq < idstring[0].length; sq++)
-      {
-        if (((boolean[]) url[1])[sq])
-        {
-          System.out.println("Seq " + sq + ": " + idstring[0][sq] + "\t: "
-                  + idstring[1][sq]);
-        }
-      }
-      System.out.println("The generated URL:");
-      System.out.println(((String[]) url[3])[0]);
-    }
-  }
-
-  public static void main(String argv[])
-  {
-    // note - JAL-1383 - these services are all dead
-    String[] links = new String[]
-    {
-        "EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=linkInDatasetFromJalview&input=$SEQUENCEIDS$&inputType=0|,",
-        "EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=linkInDatasetFromJalview&input=$SEQUENCES$&inputType=1|,",
-        "EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,",
-        "EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=$DATASETID$&input=$SEQUENCES$&inputType=1|,",
-        "EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=$SEQUENCEIDS$&datasetName=linkInDatasetFromJalview&input=$SEQUENCEIDS$&inputType=0|,",
-        "EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=$SEQUENCEIDS$&datasetName=$DATASETID$&input=$SEQUENCES$&inputType=1|,",
-        "EnVision2 Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([a-zA-Z]+)/=$&inputType=1|,",
-        "EnVision2 Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/[A-Za-z]+/=$&inputType=1|,"
-    /*
-     * http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?input=P38389,P38398
-     * &inputType=0&workflow=Enfin%20Default%20Workflow&datasetName=
-     * linkInDatasetFromPRIDE
-     */
-    };
-
-    SequenceI[] seqs = new SequenceI[]
-    { new Sequence("StupidLabel:gi|9234|pdb|102L|A",
-            "asdiasdpasdpadpwpadasdpaspdw"), };
-    String[][] seqsandids = formStrings(seqs);
-    for (int i = 0; i < links.length; i++)
-    {
-      GroupUrlLink ul = new GroupUrlLink(links[i]);
-      if (ul.isValid())
-      {
-        System.out.println("\n\n\n");
-        System.out.println("Link " + i + " " + links[i] + " : "
-                + ul.toString());
-        System.out.println(" pref : " + ul.getUrl_prefix());
-        System.out.println(" IdReplace : " + ul.getIDRegexReplace());
-        System.out.println(" SeqReplace : " + ul.getSeqRegexReplace());
-        System.out.println(" Suffixes : " + ul.getUrl_suffix());
-
-        System.out
-                .println("<insert input id and sequence strings here> Without onlyIfMatches:");
-        Object[] urls;
-        try
-        {
-          urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset",
-                  false);
-          testUrls(ul, seqsandids, urls);
-        } catch (UrlStringTooLongException ex)
-        {
-          System.out.println("too long exception " + ex);
-        }
-        System.out
-                .println("<insert input id and sequence strings here> With onlyIfMatches set:");
-        try
-        {
-          urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset",
-                  true);
-          testUrls(ul, seqsandids, urls);
-        } catch (UrlStringTooLongException ex)
-        {
-          System.out.println("too long exception " + ex);
-        }
-      }
-      else
-      {
-        System.err.println("Invalid URLLink : " + links[i] + " : "
-                + ul.getInvalidMessage());
-      }
-    }
-  }
-
-  /**
-   * covenience method to generate the id and sequence string vector from a set
-   * of seuqences using each sequence's getName() and getSequenceAsString()
-   * method
-   * 
-   * @param seqs
-   * @return String[][] {{sequence ids},{sequence strings}}
-   */
-  public static String[][] formStrings(SequenceI[] seqs)
-  {
-    String[][] idset = new String[2][seqs.length];
-    for (int i = 0; i < seqs.length; i++)
-    {
-      idset[0][i] = seqs[i].getName();
-      idset[1][i] = seqs[i].getSequenceAsString();
-    }
-    return idset;
-  }
-
-  public void setLabel(String newlabel)
-  {
-    this.label = newlabel;
-  }
-
 }