update author list in license for (JAL-826)

[jalview.git] / src / jalview / util / UrlLink.java

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 00e33b2..007b502 100644 (file)
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -1,20 +1,19 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
  * \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
+ * This file is part of Jalview.\r
  * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
  * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE.  See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
  */\r
 package jalview.util;\r
 \r
@@ -28,8 +27,8 @@ public class UrlLink
    * Jalview 2.4 extension allows regular expressions to be used to parse ID\r
    * strings and replace the result in the URL. Regex's operate on the whole ID\r
    * string given to the matchURL method, if no regex is supplied, then only\r
-   * text following the first pipe symbol will be susbstituted.\r
-   * Usage documentation todo.\r
+   * text following the first pipe symbol will be susbstituted. Usage\r
+   * documentation todo.\r
    */\r
   private String url_suffix, url_prefix, target, label, regexReplace;\r
 \r
@@ -173,7 +172,9 @@ public class UrlLink
 \r
   /**\r
    * Check if URL string was parsed properly.\r
-   * @return boolean - if false then <code>getInvalidMessage</code> returns an error message\r
+   * \r
+   * @return boolean - if false then <code>getInvalidMessage</code> returns an\r
+   *         error message\r
    */\r
   public boolean isValid()\r
   {\r
@@ -184,9 +185,9 @@ public class UrlLink
    * return one or more URL strings by applying regex to the given idstring\r
    * \r
    * @param idstring\r
-   * @param onlyIfMatches -\r
-   *                when true url strings are only made if regex is defined and\r
-   *                matches\r
+   * @param onlyIfMatches\r
+   *          - when true url strings are only made if regex is defined and\r
+   *          matches\r
    * @return String[] { part of idstring substituted, full substituted url , ..\r
    *         next part, next url..}\r
    */\r
@@ -208,8 +209,9 @@ public class UrlLink
             { rg.stringMatched(),\r
                 url_prefix + rg.stringMatched() + url_suffix };\r
           } /*\r
-             * else if (ns==1) { // take only subgroup match return new String[] {\r
-             * rg.stringMatched(1), url_prefix+rg.stringMatched(1)+url_suffix }; }\r
+             * else if (ns==1) { // take only subgroup match return new String[]\r
+             * { rg.stringMatched(1), url_prefix+rg.stringMatched(1)+url_suffix\r
+             * }; }\r
              */\r
           else\r
           {\r
@@ -329,13 +331,16 @@ public class UrlLink
     /*\r
      * "AlinkT|Target|http://foo.foo.soo/",\r
      * "myUrl1|http://$SEQUENCE_ID=/[0-9]+/=$.someserver.org/foo",\r
-     * "myUrl2|http://$SEQUENCE_ID=/(([0-9]+).+([A-Za-z]+))/=$.someserver.org/foo",\r
-     * "myUrl3|http://$SEQUENCE_ID=/([0-9]+).+([A-Za-z]+)/=$.someserver.org/foo",\r
-     * "myUrl4|target|http://$SEQUENCE_ID$.someserver.org/foo|too",\r
-     * "PF1|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(?:PFAM:)?(.+)/=$",\r
-     * "PF2|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(PFAM:)?(.+)/=$",\r
-     * "PF3|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/PFAM:(.+)/=$",\r
-     * "NOTFER|http://notfer.org/$SEQUENCE_ID=/(?<!\\s)(.+)/=$",\r
+     * "myUrl2|http://$SEQUENCE_ID=/(([0-9]+).+([A-Za-z]+))/=$.someserver.org/foo"\r
+     * ,\r
+     * "myUrl3|http://$SEQUENCE_ID=/([0-9]+).+([A-Za-z]+)/=$.someserver.org/foo"\r
+     * , "myUrl4|target|http://$SEQUENCE_ID$.someserver.org/foo|too",\r
+     * "PF1|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(?:PFAM:)?(.+)/=$"\r
+     * ,\r
+     * "PF2|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/(PFAM:)?(.+)/=$"\r
+     * ,\r
+     * "PF3|http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID=/PFAM:(.+)/=$"\r
+     * , "NOTFER|http://notfer.org/$SEQUENCE_ID=/(?<!\\s)(.+)/=$",\r
      */\r
     "NESTED|http://nested/$SEQUENCE_ID=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=$/nested" };\r
     String[] idstrings = new String[]\r