X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FUrlLink.java;h=007b5024eb529e5c28454631eaf588467135d7fc;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=a82ef59dde92689293d14cee018c9b6baf32dbff;hpb=56fd15ca5a6e0dd96930474d1fb02b3c5fb0f00f;p=jalview.git

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index a82ef59..007b502 100644
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -1,20 +1,19 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
- * This 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 file is part of Jalview.
  * 
- * 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.
+ * 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.
  * 
- * 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
+ * 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/>.
  */
 package jalview.util;
 
@@ -28,7 +27,8 @@ public class UrlLink
    * Jalview 2.4 extension allows regular expressions to be used to parse ID
    * strings and replace the result in the URL. Regex's operate on the whole ID
    * string given to the matchURL method, if no regex is supplied, then only
-   * text following the first pipe symbol will be susbstituted.
+   * text following the first pipe symbol will be susbstituted. Usage
+   * documentation todo.
    */
   private String url_suffix, url_prefix, target, label, regexReplace;
 
@@ -172,7 +172,9 @@ public class UrlLink
 
   /**
    * Check if URL string was parsed properly.
-   * @return boolean - if false then <code>getInvalidMessage</code> returns an error message
+   * 
+   * @return boolean - if false then <code>getInvalidMessage</code> returns an
+   *         error message
    */
   public boolean isValid()
   {
@@ -183,9 +185,9 @@ public class UrlLink
    * return one or more URL strings by applying regex to the given idstring
    * 
    * @param idstring
-   * @param onlyIfMatches -
-   *                when true url strings are only made if regex is defined and
-   *                matches
+   * @param onlyIfMatches
+   *          - when true url strings are only made if regex is defined and
+   *          matches
    * @return String[] { part of idstring substituted, full substituted url , ..
    *         next part, next url..}
    */
@@ -207,8 +209,9 @@ public class UrlLink
             { rg.stringMatched(),
                 url_prefix + rg.stringMatched() + url_suffix };
           } /*
-             * else if (ns==1) { // take only subgroup match return new String[] {
-             * rg.stringMatched(1), url_prefix+rg.stringMatched(1)+url_suffix }; }
+             * else if (ns==1) { // take only subgroup match return new String[]
+             * { rg.stringMatched(1), url_prefix+rg.stringMatched(1)+url_suffix
+             * }; }
              */
           else
           {
@@ -328,13 +331,16 @@ public class UrlLink
     /*
      * "AlinkT|Target|http://foo.foo.soo/",
      * "myUrl1|http://$SEQUENCE_ID=/[0-9]+/=$.someserver.org/foo",
-     * "myUrl2|http://$SEQUENCE_ID=/(([0-9]+).+([A-Za-z]+))/=$.someserver.org/foo",
-     * "myUrl3|http://$SEQUENCE_ID=/([0-9]+).+([A-Za-z]+)/=$.someserver.org/foo",
-     * "myUrl4|target|http://$SEQUENCE_ID$.someserver.org/foo|too",
-     * "PF1|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(?:PFAM:)?(.+)/=$",
-     * "PF2|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(PFAM:)?(.+)/=$",
-     * "PF3|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/PFAM:(.+)/=$",
-     * "NOTFER|http://notfer.org/$SEQUENCE_ID=/(?<!\\s)(.+)/=$",
+     * "myUrl2|http://$SEQUENCE_ID=/(([0-9]+).+([A-Za-z]+))/=$.someserver.org/foo"
+     * ,
+     * "myUrl3|http://$SEQUENCE_ID=/([0-9]+).+([A-Za-z]+)/=$.someserver.org/foo"
+     * , "myUrl4|target|http://$SEQUENCE_ID$.someserver.org/foo|too",
+     * "PF1|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(?:PFAM:)?(.+)/=$"
+     * ,
+     * "PF2|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(PFAM:)?(.+)/=$"
+     * ,
+     * "PF3|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/PFAM:(.+)/=$"
+     * , "NOTFER|http://notfer.org/$SEQUENCE_ID=/(?<!\\s)(.+)/=$",
      */
     "NESTED|http://nested/$SEQUENCE_ID=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=$/nested" };
     String[] idstrings = new String[]