From d26702695acf46851ff61384cdc9589203ca6531 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 26 Mar 2010 14:31:59 +0000
Subject: [PATCH] sync for cvs wierdness

---
 src/jalview/util/GroupUrlLink.java | 1543 +++++++++++++++++++-----------------
 1 file changed, 814 insertions(+), 729 deletions(-)

diff --git a/src/jalview/util/GroupUrlLink.java b/src/jalview/util/GroupUrlLink.java
index f319eb1..55e3bd9 100644
--- a/src/jalview/util/GroupUrlLink.java
+++ b/src/jalview/util/GroupUrlLink.java
@@ -1,729 +1,814 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- * 
- * This program 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 2
- * of the License, or (at your option) any later version.
- * 
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.util;
-
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-
-import java.util.Hashtable;
-import java.util.Vector;
-
-public class GroupUrlLink
-{
-  /**
-   * Helper class based on the UrlLink class which enables URLs to be
-   * constructed from sequences or IDs associated with a group of sequences. URL
-   * definitions consist of a pipe separated string containing a <label>|<url
-   * construct>|<separator character>[|<sequence separator character>]. The url
-   * construct includes regex qualified tokens which are replaced with seuqence
-   * IDs ($SEQUENCE_IDS$) and/or seuqence regions ($SEQUENCES$) that are
-   * extracted from the group. See <code>UrlLink</code> for more information
-   * about the approach, and the original implementation.
-   * 
-   */
-  private String url_prefix, target, label;
-
-  /**
-   * these are all filled in order of the occurence of each token in the url
-   * string template
-   */
-  private String url_suffix[], separators[], regexReplace[];
-
-  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;
-
-  /**
-   * contains tokens in the order they appear in the URL template.
-   */
-  private String[] mtch;
-  static
-  {
-    if (tokens == null)
-    {
-      tokens = new String[]
-      { "SEQUENCEIDS", "SEQUENCES", "DATASETID" };
-    }
-  }
-
-  // private int idseg = -1, seqseg = -1;
-
-  /**
-   * 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
-   * the form =/<perl style regex>/=$ or $SEQUENCES<=optional regex=>$ or
-   * $SEQUENCES<=optional regex=>$.
-   * 
-   * @param link
-   */
-  public GroupUrlLink(String link)
-  {
-    int sep = link.indexOf("|");
-    segs = new int[tokens.length];
-    int ntoks = 0;
-    for (int i = 0; i < segs.length; i++)
-    {
-      if ((segs[i] = link.indexOf("$" + tokens[i])) > -1)
-      {
-        ntoks++;
-      }
-    }
-    // expect at least one token
-    if (ntoks == 0)
-    {
-      invalidMessage = "Group URL string must contain at least one of ";
-      for (int i = 0; i < segs.length; i++)
-      {
-        invalidMessage += " '$" + tokens[i] + "[=/regex=/]$'";
-      }
-      return;
-    }
-
-    int[] ptok = new int[ntoks + 1];
-    String[] tmtch = new String[ntoks + 1];
-    mtch = new String[ntoks];
-    for (int i = 0, t = 0; i < segs.length; i++)
-    {
-      if (segs[i] > -1)
-      {
-        ptok[t] = segs[i];
-        tmtch[t++] = tokens[i];
-      }
-    }
-    ptok[ntoks] = link.length();
-    tmtch[ntoks] = "$$$$$$$$$";
-    jalview.util.QuickSort.sort(ptok, tmtch);
-    for (int i = 0; i < ntoks; i++)
-    {
-      mtch[i] = tmtch[i]; // TODO: check order is ascending
-    }
-    /*
-     * replaces the specific code below {}; if (psqids > -1 && pseqs > -1) { if
-     * (psqids > pseqs) { idseg = 1; seqseg = 0;
-     * 
-     * ptok = new int[] { pseqs, psqids, link.length() }; mtch = new String[] {
-     * "$SEQUENCES", "$SEQUENCEIDS" }; } else { idseg = 0; seqseg = 1; ptok =
-     * new int[] { psqids, pseqs, link.length() }; mtch = new String[] {
-     * "$SEQUENCEIDS", "$SEQUENCES" }; } } else { if (psqids != -1) { idseg = 0;
-     * ptok = new int[] { psqids, link.length() }; mtch = new String[] {
-     * "$SEQUENCEIDS" }; } else { seqseg = 0; ptok = new int[] { pseqs,
-     * link.length() }; mtch = new String[] { "$SEQUENCES" }; } }
-     */
-
-    int p = sep;
-    // first get the label and target part before the first |
-    do
-    {
-      sep = p;
-      p = link.indexOf("|", sep + 1);
-    } while (p > sep && p < ptok[0]);
-    // Assuming that the URL itself does not contain any '|' symbols
-    // sep now contains last pipe symbol position prior to any regex symbols
-    label = link.substring(0, sep);
-    if (label.indexOf("|") > -1)
-    {
-      // | terminated database name / www target at start of Label
-      target = label.substring(0, label.indexOf("|"));
-    }
-    else if (label.indexOf(" ") > 2)
-    {
-      // space separated Label - matches database name
-      target = label.substring(0, label.indexOf(" "));
-    }
-    else
-    {
-      target = label;
-    }
-    // Now Parse URL : Whole URL string first
-    url_prefix = link.substring(sep + 1, ptok[0]);
-    url_suffix = new String[mtch.length];
-    regexReplace = new String[mtch.length];
-    // and loop through tokens
-    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)
-      {
-        // Extract Regex and suffix
-        if (ptok[pass + 1] < p + 3)
-        {
-          // tokens are not allowed inside other tokens - e.g. inserting a
-          // $sequences$ into the regex match for the sequenceid
-          invalidMessage = "Token regexes cannot contain other regexes (did you terminate the $"
-                  + mtch[pass] + " regex with a '/=$' ?";
-          return;
-        }
-        url_suffix[pass] = link.substring(p + 3, ptok[pass + 1]);
-        regexReplace[pass] = link.substring(ptok[pass] + mlength, p);
-        try
-        {
-          com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
-                  + regexReplace[pass] + "/");
-          if (rg == null)
-          {
-            invalidMessage = "Invalid Regular Expression : '"
-                    + regexReplace[pass] + "'\n";
-          }
-        } catch (Exception e)
-        {
-          invalidMessage = "Invalid Regular Expression : '"
-                  + regexReplace[pass] + "'\n";
-        }
-      }
-      else
-      {
-        regexReplace[pass] = null;
-        // verify format is really correct.
-        if ((p = link.indexOf("$" + mtch[pass] + "$")) == ptok[pass])
-        {
-          url_suffix[pass] = link.substring(p + mtch[pass].length() + 2,
-                  ptok[pass + 1]);
-        }
-        else
-        {
-          invalidMessage = "Warning: invalid regex structure (after '"
-                  + mtch[0] + "') for URL link : " + link;
-        }
-      }
-    }
-    int pass = 0;
-    separators = new String[url_suffix.length];
-    String suffices = url_suffix[url_suffix.length - 1], lastsep = ",";
-    // have a look in the last suffix for any more separators.
-    while ((p = suffices.indexOf('|')) > -1)
-    {
-      separators[pass] = suffices.substring(p + 1);
-      if (pass == 0)
-      {
-        // trim the original suffix string
-        url_suffix[url_suffix.length - 1] = suffices.substring(0, p);
-      }
-      else
-      {
-        lastsep = (separators[pass - 1] = separators[pass - 1].substring(0,
-                p));
-      }
-      suffices = separators[pass];
-      pass++;
-    }
-    if (pass > 0)
-    {
-      lastsep = separators[pass - 1];
-    }
-    // last separator is always used for all the remaining separators
-    while (pass < separators.length)
-    {
-      separators[pass++] = lastsep;
-    }
-  }
-
-  /**
-   * @return the url_suffix
-   */
-  public String getUrl_suffix()
-  {
-    return url_suffix[url_suffix.length - 1];
-  }
-
-  /**
-   * @return the url_prefix
-   */
-  public String getUrl_prefix()
-  {
-    return url_prefix;
-  }
-
-  /**
-   * @return the target
-   */
-  public String getTarget()
-  {
-    return target;
-  }
-
-  /**
-   * @return the label
-   */
-  public String getLabel()
-  {
-    return label;
-  }
-
-  /**
-   * @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]);
-  }
-
-  /**
-   * @return the invalidMessage
-   */
-  public String getInvalidMessage()
-  {
-    return invalidMessage;
-  }
-
-  /**
-   * Check if URL string was parsed properly.
-   * 
-   * @return boolean - if false then <code>getInvalidMessage</code> returns an
-   *         error message
-   */
-  public boolean isValid()
-  {
-    return invalidMessage == null;
-  }
-
-  /**
-   * 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 } }
-   */
-  public Object[] makeUrls(String[] idstrings, String[] seqstrings,
-          String dsstring, boolean onlyIfMatches)
-  {
-    Hashtable rstrings = new Hashtable();
-    rstrings.put(tokens[0], idstrings);
-    rstrings.put(tokens[1], seqstrings);
-    rstrings.put(tokens[2], new String[]
-    { dsstring });
-    if (idstrings.length != seqstrings.length)
-    {
-      throw new Error(
-              "idstrings and seqstrings contain one string each per sequence.");
-    }
-    return makeUrls(rstrings, onlyIfMatches);
-  }
-
-  public Object[] makeUrls(Hashtable repstrings, boolean onlyIfMatches)
-  {
-    // prepare string arrays in correct order to be assembled into URL input
-    String[][] idseq = new String[mtch.length][]; // indexed by pass
-    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]);
-      if (idseq[i].length >= 1)
-      {
-        if (mins == 0 && idseq[i].length == 1)
-        {
-          mins = 1;
-        }
-        if (maxs < 2)
-        {
-          maxs = idseq[i].length;
-        }
-        else
-        {
-          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.");
-          }
-        }
-      }
-      else
-      {
-        throw new Error(
-                "Cannot have zero length vector of replacement strings - either 1 value or n values.");
-      }
-    }
-    int pass = 0;
-    // 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];
-    for (pass = 0; pass < matched.length; pass++)
-    {
-      matched[pass] = new StringBuffer();
-      if (regexReplace[pass] != null)
-      {
-        rgxs[pass] = com.stevesoft.pat.Regex.perlCode("/" + regexReplace[pass]
-                + "/");
-      }
-      else
-      {
-        rgxs[pass] = null;
-      }
-    }
-    // record which of the input sequences were actually used to generate the
-    // url
-    boolean[] thismatched = new boolean[maxs];
-    int seqsmatched = 0;
-    for (int sq = 0; sq < maxs; sq++)
-    {
-      // initialise flag for match
-      thismatched[sq] = false;
-      String[] thematches = new String[rgxs.length];
-      for (pass = 0; pass < rgxs.length; pass++)
-      {
-        thematches[pass] = ""; // initialise - in case there are no more
-        // matches.
-        // if a regex is provided, then it must match for all sequences in all
-        // tokens for it to be considered.
-        if (idseq[pass].length <= sq)
-        {
-          // no more replacement strings to try for this token
-          continue;
-        }
-        if (rgxs[pass] != null)
-        {
-          com.stevesoft.pat.Regex rg = rgxs[pass];
-          int rematchat = 0;
-          // concatenate all matches of re in the given string!
-          while (rg.searchFrom(idseq[pass][sq], rematchat))
-          {
-            rematchat = rg.matchedTo();
-            thismatched[sq] |= true;
-            // do we take the cartesian products of the substituents ?
-            int ns = rg.numSubs();
-            if (ns == 0)
-            {
-              thematches[pass] += rg.stringMatched();// take whole regex
-            }
-            /*
-             * else if (ns==1) { // take only subgroup match return new String[]
-             * { rg.stringMatched(1), url_prefix+rg.stringMatched(1)+url_suffix
-             * }; }
-             */
-            // deal with multiple submatch case - for moment we do the simplest
-            // - concatenate the matched regions, instead of creating a complete
-            // list for each alternate match over all sequences.
-            // TODO: specify a 'replace pattern' - next refinement
-            else
-            {
-              // debug
-              for (int s = 0; s <= rg.numSubs(); s++)
-              {
-                System.err.println("Sub " + s + " : " + rg.matchedFrom(s)
-                        + " : " + rg.matchedTo(s) + " : '"
-                        + rg.stringMatched(s) + "'");
-              }
-              // try to collate subgroup matches
-              StringBuffer subs = new StringBuffer();
-              // have to loop through submatches, collating them at top level
-              // match
-              int s = 0; // 1;
-              while (s <= ns)
-              {
-                if (s + 1 <= ns && rg.matchedTo(s) > -1
-                        && rg.matchedTo(s + 1) > -1
-                        && rg.matchedTo(s + 1) < rg.matchedTo(s))
-                {
-                  // s is top level submatch. search for submatches enclosed by
-                  // this one
-                  int r = s + 1;
-                  String rmtch = "";
-                  while (r <= ns && rg.matchedTo(r) <= rg.matchedTo(s))
-                  {
-                    if (rg.matchedFrom(r) > -1)
-                    {
-                      rmtch += rg.stringMatched(r);
-                    }
-                    r++;
-                  }
-                  if (rmtch.length() > 0)
-                  {
-                    subs.append(rmtch); // simply concatenate
-                  }
-                  s = r;
-                }
-                else
-                {
-                  if (rg.matchedFrom(s) > -1)
-                  {
-                    subs.append(rg.stringMatched(s)); // concatenate
-                  }
-                  s++;
-                }
-              }
-              thematches[pass] += subs.toString();
-            }
-          }
-        }
-        else
-        {
-          // are we only supposed to take regex matches ?
-          if (!onlyIfMatches)
-          {
-            thismatched[sq] |= true;
-            thematches[pass] = idseq[pass][sq]; // take whole string -
-            // regardless - probably not a
-            // good idea!
-            /*
-             * TODO: do some boilerplate trimming of the fields to make them
-             * sensible e.g. trim off any 'prefix' in the id string (see UrlLink
-             * for the below) - pre 2.4 Jalview behaviour if
-             * (idstring.indexOf("|") > -1) { idstring =
-             * idstring.substring(idstring.lastIndexOf("|") + 1); }
-             */
-
-          }
-        }
-      }
-
-      // check if we are going to add this sequence's results ? all token
-      // replacements must be valid for this to happen!
-      // (including single value replacements - eg. dataset name)
-      if (thismatched[sq])
-      {
-        for (pass = 0; pass < matched.length; pass++)
-        {
-          if (idseq[pass].length > 1 && matched[pass].length() > 0)
-          {
-            matched[pass].append(separators[pass]);
-          }
-          matched[pass].append(thematches[pass]);
-        }
-        seqsmatched++;
-      }
-    }
-    // finally, if any sequences matched, then form the URL and return
-    if (matched[0].length() == 0)
-    {
-      // no matches - no url generated
-      return null;
-    }
-    StringBuffer submiturl = new StringBuffer();
-    submiturl.append(url_prefix);
-    for (pass = 0; pass < matched.length; pass++)
-    {
-      submiturl.append(matched[pass]);
-      if (url_suffix[pass] != null)
-      {
-        submiturl.append(url_suffix[pass]);
-      }
-    }
-
-    return new Object[]
-    { new int[]
-    { seqsmatched }, thismatched, matched, new String[]
-    { submiturl.toString() } };
-  }
-
-  /**
-   * get token types present in this url as a bitfield indicating presence of each token from tokens (LSB->MSB).
-   * @return groupURL class as integer
-   */
-  public int getGroupURLType()
-  {
-    int r = 0;
-    for (int pass = 0; pass < tokens.length; pass++)
-    {
-      for (int i = 0; i < mtch.length; i++)
-      {
-        if (mtch[i].equals(tokens[pass]))
-        {
-          r += 1 << pass;
-        }
-      }
-    }
-    return r;
-  }
-
-  public String toString()
-  {
-    StringBuffer result = new StringBuffer();
-    result.append(label + "|" + url_prefix);
-    int r;
-    for (r = 0; r < url_suffix.length; r++)
-    {
-      result.append("$");
-      result.append(mtch[r]);
-      if (regexReplace[r] != null)
-      {
-        result.append("=/");
-        result.append(regexReplace[r]);
-        result.append("/=");
-      }
-      result.append("$");
-      result.append(url_suffix[r]);
-    }
-    for (r = 0; r < separators.length; r++)
-    {
-      result.append("|");
-      result.append(separators[r]);
-    }
-    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[])
-  {
-    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 = ul.makeUrls(seqsandids[0], seqsandids[1],
-                "mydataset", false);
-        testUrls(ul, seqsandids, urls);
-        System.out
-                .println("<insert input id and sequence strings here> With onlyIfMatches set:");
-        urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset", true);
-        testUrls(ul, seqsandids, urls);
-      }
-      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;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.util;
+
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.util.Hashtable;
+import java.util.Vector;
+
+public class GroupUrlLink
+{
+  /**
+   * Helper class based on the UrlLink class which enables URLs to be
+   * constructed from sequences or IDs associated with a group of sequences. URL
+   * definitions consist of a pipe separated string containing a <label>|<url
+   * construct>|<separator character>[|<sequence separator character>]. The url
+   * construct includes regex qualified tokens which are replaced with seuqence
+   * IDs ($SEQUENCE_IDS$) and/or seuqence regions ($SEQUENCES$) that are
+   * extracted from the group. See <code>UrlLink</code> for more information
+   * about the approach, and the original implementation.
+   * Documentation to come. Note - groupUrls can be very big!
+   */
+  private String url_prefix, target, label;
+
+  /**
+   * these are all filled in order of the occurence of each token in the url
+   * string template
+   */
+  private String url_suffix[], separators[], regexReplace[];
+
+  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;
+
+  /**
+   * contains tokens in the order they appear in the URL template.
+   */
+  private String[] mtch;
+  static
+  {
+    if (tokens == null)
+    {
+      tokens = new String[]
+      { "SEQUENCEIDS", "SEQUENCES", "DATASETID" };
+    }
+  }
+
+  // private int idseg = -1, seqseg = -1;
+
+  /**
+   * 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
+   * the form =/<perl style regex>/=$ or $SEQUENCES<=optional regex=>$ or
+   * $SEQUENCES<=optional regex=>$.
+   * 
+   * @param link
+   */
+  public GroupUrlLink(String link)
+  {
+    int sep = link.indexOf("|");
+    segs = new int[tokens.length];
+    int ntoks = 0;
+    for (int i = 0; i < segs.length; i++)
+    {
+      if ((segs[i] = link.indexOf("$" + tokens[i])) > -1)
+      {
+        ntoks++;
+      }
+    }
+    // expect at least one token
+    if (ntoks == 0)
+    {
+      invalidMessage = "Group URL string must contain at least one of ";
+      for (int i = 0; i < segs.length; i++)
+      {
+        invalidMessage += " '$" + tokens[i] + "[=/regex=/]$'";
+      }
+      return;
+    }
+
+    int[] ptok = new int[ntoks + 1];
+    String[] tmtch = new String[ntoks + 1];
+    mtch = new String[ntoks];
+    for (int i = 0, t = 0; i < segs.length; i++)
+    {
+      if (segs[i] > -1)
+      {
+        ptok[t] = segs[i];
+        tmtch[t++] = tokens[i];
+      }
+    }
+    ptok[ntoks] = link.length();
+    tmtch[ntoks] = "$$$$$$$$$";
+    jalview.util.QuickSort.sort(ptok, tmtch);
+    for (int i = 0; i < ntoks; i++)
+    {
+      mtch[i] = tmtch[i]; // TODO: check order is ascending
+    }
+    /*
+     * replaces the specific code below {}; if (psqids > -1 && pseqs > -1) { if
+     * (psqids > pseqs) { idseg = 1; seqseg = 0;
+     * 
+     * ptok = new int[] { pseqs, psqids, link.length() }; mtch = new String[] {
+     * "$SEQUENCES", "$SEQUENCEIDS" }; } else { idseg = 0; seqseg = 1; ptok =
+     * new int[] { psqids, pseqs, link.length() }; mtch = new String[] {
+     * "$SEQUENCEIDS", "$SEQUENCES" }; } } else { if (psqids != -1) { idseg = 0;
+     * ptok = new int[] { psqids, link.length() }; mtch = new String[] {
+     * "$SEQUENCEIDS" }; } else { seqseg = 0; ptok = new int[] { pseqs,
+     * link.length() }; mtch = new String[] { "$SEQUENCES" }; } }
+     */
+
+    int p = sep;
+    // first get the label and target part before the first |
+    do
+    {
+      sep = p;
+      p = link.indexOf("|", sep + 1);
+    } while (p > sep && p < ptok[0]);
+    // Assuming that the URL itself does not contain any '|' symbols
+    // sep now contains last pipe symbol position prior to any regex symbols
+    label = link.substring(0, sep);
+    if (label.indexOf("|") > -1)
+    {
+      // | terminated database name / www target at start of Label
+      target = label.substring(0, label.indexOf("|"));
+    }
+    else if (label.indexOf(" ") > 2)
+    {
+      // space separated Label - matches database name
+      target = label.substring(0, label.indexOf(" "));
+    }
+    else
+    {
+      target = label;
+    }
+    // Now Parse URL : Whole URL string first
+    url_prefix = link.substring(sep + 1, ptok[0]);
+    url_suffix = new String[mtch.length];
+    regexReplace = new String[mtch.length];
+    // and loop through tokens
+    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)
+      {
+        // Extract Regex and suffix
+        if (ptok[pass + 1] < p + 3)
+        {
+          // tokens are not allowed inside other tokens - e.g. inserting a
+          // $sequences$ into the regex match for the sequenceid
+          invalidMessage = "Token regexes cannot contain other regexes (did you terminate the $"
+                  + mtch[pass] + " regex with a '/=$' ?";
+          return;
+        }
+        url_suffix[pass] = link.substring(p + 3, ptok[pass + 1]);
+        regexReplace[pass] = link.substring(ptok[pass] + mlength, p);
+        try
+        {
+          com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
+                  + regexReplace[pass] + "/");
+          if (rg == null)
+          {
+            invalidMessage = "Invalid Regular Expression : '"
+                    + regexReplace[pass] + "'\n";
+          }
+        } catch (Exception e)
+        {
+          invalidMessage = "Invalid Regular Expression : '"
+                  + regexReplace[pass] + "'\n";
+        }
+      }
+      else
+      {
+        regexReplace[pass] = null;
+        // verify format is really correct.
+        if ((p = link.indexOf("$" + mtch[pass] + "$")) == ptok[pass])
+        {
+          url_suffix[pass] = link.substring(p + mtch[pass].length() + 2,
+                  ptok[pass + 1]);
+        }
+        else
+        {
+          invalidMessage = "Warning: invalid regex structure (after '"
+                  + mtch[0] + "') for URL link : " + link;
+        }
+      }
+    }
+    int pass = 0;
+    separators = new String[url_suffix.length];
+    String suffices = url_suffix[url_suffix.length - 1], lastsep = ",";
+    // have a look in the last suffix for any more separators.
+    while ((p = suffices.indexOf('|')) > -1)
+    {
+      separators[pass] = suffices.substring(p + 1);
+      if (pass == 0)
+      {
+        // trim the original suffix string
+        url_suffix[url_suffix.length - 1] = suffices.substring(0, p);
+      }
+      else
+      {
+        lastsep = (separators[pass - 1] = separators[pass - 1].substring(0,
+                p));
+      }
+      suffices = separators[pass];
+      pass++;
+    }
+    if (pass > 0)
+    {
+      lastsep = separators[pass - 1];
+    }
+    // last separator is always used for all the remaining separators
+    while (pass < separators.length)
+    {
+      separators[pass++] = lastsep;
+    }
+  }
+
+  /**
+   * @return the url_suffix
+   */
+  public String getUrl_suffix()
+  {
+    return url_suffix[url_suffix.length - 1];
+  }
+
+  /**
+   * @return the url_prefix
+   */
+  public String getUrl_prefix()
+  {
+    return url_prefix;
+  }
+
+  /**
+   * @return the target
+   */
+  public String getTarget()
+  {
+    return target;
+  }
+
+  /**
+   * @return the label
+   */
+  public String getLabel()
+  {
+    return label;
+  }
+
+  /**
+   * @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]);
+  }
+
+  /**
+   * @return the invalidMessage
+   */
+  public String getInvalidMessage()
+  {
+    return invalidMessage;
+  }
+
+  /**
+   * Check if URL string was parsed properly.
+   * 
+   * @return boolean - if false then <code>getInvalidMessage</code> returns an
+   *         error message
+   */
+  public boolean isValid()
+  {
+    return invalidMessage == null;
+  }
+
+  /**
+   * 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 } }
+   */
+  public Object[] makeUrls(String[] idstrings, String[] seqstrings,
+          String dsstring, boolean onlyIfMatches)
+  {
+    Hashtable rstrings = replacementArgs(idstrings, seqstrings, dsstring);
+    return makeUrls(rstrings, onlyIfMatches);
+  }
+
+  /**
+   * gathers input into a hashtable
+   * @param idstrings
+   * @param seqstrings
+   * @param dsstring
+   * @return
+   */
+  private Hashtable replacementArgs(String[] idstrings,
+          String[] seqstrings, String dsstring)
+  {
+    Hashtable rstrings = new Hashtable();
+    rstrings.put(tokens[0], idstrings);
+    rstrings.put(tokens[1], seqstrings);
+    rstrings.put(tokens[2], new String[]
+    { dsstring });
+    if (idstrings.length != seqstrings.length)
+    {
+      throw new Error(
+              "idstrings and seqstrings contain one string each per sequence.");
+    }
+    return rstrings;
+  }
+
+  public Object[] makeUrls(Hashtable repstrings, boolean onlyIfMatches)
+  {
+    return makeUrlsIf(true,repstrings,onlyIfMatches);
+  }
+  /**
+   * 
+   * @param ids
+   * @param seqstr
+   * @param string
+   * @param b
+   * @return URL stub objects ready to pass to constructFrom  
+   */
+  public Object[] makeUrlStubs(String[] ids, String[] seqstr,
+          String string, boolean b)
+  {
+    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.
+   */
+  public String constructFrom(Object[] stubs)
+  {
+    Object[] results = makeUrlsIf(true, (Hashtable) stubs[2], ((boolean[])stubs[3])[0]);    
+    return ((String[]) results[3])[0];
+  }
+  /**
+   * conditionally generate urls or stubs for a given input.
+   * @param createFullUrl set to false if you only want to test if URLs would be generated.
+   * @param repstrings
+   * @param onlyIfMatches
+   * @return null if no url is generated. 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 })}
+   */
+  protected Object[] makeUrlsIf(boolean createFullUrl, Hashtable repstrings, boolean onlyIfMatches)
+  {
+    // prepare string arrays in correct order to be assembled into URL input
+    String[][] idseq = new String[mtch.length][]; // indexed by pass
+    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]);
+      if (idseq[i].length >= 1)
+      {
+        if (mins == 0 && idseq[i].length == 1)
+        {
+          mins = 1;
+        }
+        if (maxs < 2)
+        {
+          maxs = idseq[i].length;
+        }
+        else
+        {
+          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.");
+          }
+        }
+      }
+      else
+      {
+        throw new Error(
+                "Cannot have zero length vector of replacement strings - either 1 value or n values.");
+      }
+    }
+    int pass = 0;
+    // 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];
+    for (pass = 0; pass < matched.length; pass++)
+    {
+      matched[pass] = new StringBuffer();
+      if (regexReplace[pass] != null)
+      {
+        rgxs[pass] = com.stevesoft.pat.Regex.perlCode("/" + regexReplace[pass]
+                + "/");
+      }
+      else
+      {
+        rgxs[pass] = null;
+      }
+    }
+    // record which of the input sequences were actually used to generate the
+    // url
+    boolean[] thismatched = new boolean[maxs];
+    int seqsmatched = 0;
+    for (int sq = 0; sq < maxs; sq++)
+    {
+      // initialise flag for match
+      thismatched[sq] = false;
+      String[] thematches = new String[rgxs.length];
+      for (pass = 0; pass < rgxs.length; pass++)
+      {
+        thematches[pass] = ""; // initialise - in case there are no more
+        // matches.
+        // if a regex is provided, then it must match for all sequences in all
+        // tokens for it to be considered.
+        if (idseq[pass].length <= sq)
+        {
+          // no more replacement strings to try for this token
+          continue;
+        }
+        if (rgxs[pass] != null)
+        {
+          com.stevesoft.pat.Regex rg = rgxs[pass];
+          int rematchat = 0;
+          // concatenate all matches of re in the given string!
+          while (rg.searchFrom(idseq[pass][sq], rematchat))
+          {
+            rematchat = rg.matchedTo();
+            thismatched[sq] |= true;
+            if (!createFullUrl)
+            {
+              continue; // don't bother making the URL replacement text.
+            }
+            // do we take the cartesian products of the substituents ?
+            int ns = rg.numSubs();
+            if (ns == 0)
+            {
+              thematches[pass] += rg.stringMatched();// take whole regex
+            }
+            /*
+             * else if (ns==1) { // take only subgroup match return new String[]
+             * { rg.stringMatched(1), url_prefix+rg.stringMatched(1)+url_suffix
+             * }; }
+             */
+            // deal with multiple submatch case - for moment we do the simplest
+            // - concatenate the matched regions, instead of creating a complete
+            // list for each alternate match over all sequences.
+            // TODO: specify a 'replace pattern' - next refinement
+            else
+            {
+              // debug
+              for (int s = 0; s <= rg.numSubs(); s++)
+              {
+                System.err.println("Sub " + s + " : " + rg.matchedFrom(s)
+                        + " : " + rg.matchedTo(s) + " : '"
+                        + rg.stringMatched(s) + "'");
+              }
+              // try to collate subgroup matches
+              StringBuffer subs = new StringBuffer();
+              // have to loop through submatches, collating them at top level
+              // match
+              int s = 0; // 1;
+              while (s <= ns)
+              {
+                if (s + 1 <= ns && rg.matchedTo(s) > -1
+                        && rg.matchedTo(s + 1) > -1
+                        && rg.matchedTo(s + 1) < rg.matchedTo(s))
+                {
+                  // s is top level submatch. search for submatches enclosed by
+                  // this one
+                  int r = s + 1;
+                  String rmtch = "";
+                  while (r <= ns && rg.matchedTo(r) <= rg.matchedTo(s))
+                  {
+                    if (rg.matchedFrom(r) > -1)
+                    {
+                      rmtch += rg.stringMatched(r);
+                    }
+                    r++;
+                  }
+                  if (rmtch.length() > 0)
+                  {
+                    subs.append(rmtch); // simply concatenate
+                  }
+                  s = r;
+                }
+                else
+                {
+                  if (rg.matchedFrom(s) > -1)
+                  {
+                    subs.append(rg.stringMatched(s)); // concatenate
+                  }
+                  s++;
+                }
+              }
+              thematches[pass] += subs.toString();
+            }
+          }
+        }
+        else
+        {
+          // are we only supposed to take regex matches ?
+          if (!onlyIfMatches)
+          {
+            thismatched[sq] |= true;
+            if (createFullUrl)
+            {
+            thematches[pass] = idseq[pass][sq]; // take whole string -
+            // regardless - probably not a
+            // good idea!
+            /*
+             * TODO: do some boilerplate trimming of the fields to make them
+             * sensible e.g. trim off any 'prefix' in the id string (see UrlLink
+             * for the below) - pre 2.4 Jalview behaviour if
+             * (idstring.indexOf("|") > -1) { idstring =
+             * idstring.substring(idstring.lastIndexOf("|") + 1); }
+             */
+            }
+            
+          }
+        }
+      }
+
+      // check if we are going to add this sequence's results ? all token
+      // replacements must be valid for this to happen!
+      // (including single value replacements - eg. dataset name)
+      if (thismatched[sq])
+      {
+        if (createFullUrl) {
+          for (pass = 0; pass < matched.length; pass++)
+          {
+          if (idseq[pass].length > 1 && matched[pass].length() > 0)
+          {
+            matched[pass].append(separators[pass]);
+          }
+            matched[pass].append(thematches[pass]);
+          }
+        }
+        seqsmatched++;
+      }
+    }
+    // finally, if any sequences matched, then form the URL and return
+    if (seqsmatched==0 || (createFullUrl && matched[0].length() == 0))
+    {
+      // no matches - no url generated
+      return null;
+    }
+    if (!createFullUrl)
+    {
+      // just return the essential info about what the URL would be generated from
+      return new Object[]
+                        { new int[]
+                        { seqsmatched }, thismatched};
+    }
+    // otherwise, create the URL completely.
+    StringBuffer submiturl = new StringBuffer();
+    submiturl.append(url_prefix);
+    for (pass = 0; pass < matched.length; pass++)
+    {
+      submiturl.append(matched[pass]);
+      if (url_suffix[pass] != null)
+      {
+        submiturl.append(url_suffix[pass]);
+      }
+    }
+
+    return new Object[]
+    { new int[]
+    { seqsmatched }, thismatched, matched, new String[]
+    { submiturl.toString() } };
+  }
+
+  /**
+   * 
+   * @param urlstub
+   * @return number of distinct sequence (id or seuqence) replacements predicted for this stub
+   */
+  public int getNumberInvolved(Object[] urlstub)
+  {
+    return ((int[])urlstub[0])[0]; // returns seqsmatched from makeUrlsIf(false,...)
+  }
+
+  /**
+   * get token types present in this url as a bitfield indicating presence of each token from tokens (LSB->MSB).
+   * @return groupURL class as integer
+   */
+  public int getGroupURLType()
+  {
+    int r = 0;
+    for (int pass = 0; pass < tokens.length; pass++)
+    {
+      for (int i = 0; i < mtch.length; i++)
+      {
+        if (mtch[i].equals(tokens[pass]))
+        {
+          r += 1 << pass;
+        }
+      }
+    }
+    return r;
+  }
+
+  public String toString()
+  {
+    StringBuffer result = new StringBuffer();
+    result.append(label + "|" + url_prefix);
+    int r;
+    for (r = 0; r < url_suffix.length; r++)
+    {
+      result.append("$");
+      result.append(mtch[r]);
+      if (regexReplace[r] != null)
+      {
+        result.append("=/");
+        result.append(regexReplace[r]);
+        result.append("/=");
+      }
+      result.append("$");
+      result.append(url_suffix[r]);
+    }
+    for (r = 0; r < separators.length; r++)
+    {
+      result.append("|");
+      result.append(separators[r]);
+    }
+    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[])
+  {
+    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 = ul.makeUrls(seqsandids[0], seqsandids[1],
+                "mydataset", false);
+        testUrls(ul, seqsandids, urls);
+        System.out
+                .println("<insert input id and sequence strings here> With onlyIfMatches set:");
+        urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset", true);
+        testUrls(ul, seqsandids, urls);
+      }
+      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;
+  }
+
+
+}
-- 
1.7.10.2