Jalview 2.6 source licence

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

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 21dee38..52a8140 100644 (file)
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -1,3 +1,20 @@
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \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
+ * 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
 import java.util.Vector;\r
@@ -10,7 +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
+   * 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
@@ -99,7 +117,7 @@ public class UrlLink
       label = link.substring(0, sep = link.lastIndexOf("|"));\r
       url_prefix = link.substring(sep + 1);\r
       regexReplace = null; // implies we trim any prefix if necessary //\r
-                            // regexReplace=".*\\|?(.*)";\r
+      // regexReplace=".*\\|?(.*)";\r
       url_suffix = null;\r
     }\r
   }\r
@@ -153,8 +171,10 @@ public class UrlLink
   }\r
 \r
   /**\r
+   * Check if URL string was parsed properly.\r
    * \r
-   * @return true if URL string could not be parsed properly.\r
+   * @return boolean - if false then <code>getInvalidMessage</code> returns an\r
+   *         error message\r
    */\r
   public boolean isValid()\r
   {\r
@@ -165,9 +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
@@ -189,8 +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
@@ -310,13 +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
@@ -326,7 +350,7 @@ public class UrlLink
      * //"123123312", "123123 ABCDE foo", "PFAM:PF23943",\r
      */\r
     "Label:gi|9234|pdb|102L|A" };\r
-\r
+    // TODO: test the setLabel method.\r
     for (int i = 0; i < links.length; i++)\r
     {\r
       UrlLink ul = new UrlLink(links[i]);\r
@@ -366,4 +390,9 @@ public class UrlLink
     // TODO Auto-generated method stub\r
     return dynamic;\r
   }\r
+\r
+  public void setLabel(String newlabel)\r
+  {\r
+    this.label = newlabel;\r
+  }\r
 }\r