JAL-2282 URLLink unit tests updated

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

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index e14ff63..218da6c 100644 (file)
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -83,7 +83,7 @@ public class UrlLink
       target = link.substring(0, sep);
       sep = link.lastIndexOf("|");
       label = link.substring(0, sep);
-      url_prefix = link.substring(sep + 1);
+      url_prefix = link.substring(sep + 1).trim();
       regexReplace = null; // implies we trim any prefix if necessary //
       // regexReplace=".*\\|?(.*)";
       url_suffix = null;
@@ -331,7 +331,7 @@ public class UrlLink
    */
   protected void parseUrl(String link, String varName, int sqidPos, int sep)
   {
-    url_prefix = link.substring(sep + 1, sqidPos);
+    url_prefix = link.substring(sep + 1, sqidPos).trim();
 
     // delimiter at start of regex: e.g. $SEQUENCE_ID=/
     String startDelimiter = "$" + varName + "=/";
@@ -384,10 +384,12 @@ public class UrlLink
   }
 
   /**
+   * Create a set of URL links for a sequence
    * 
-   * @param urlLink
    * @param seq
+   *          The sequence to create links for
    * @param linkset
+   *          Map of links: key = id | link, value = [target, label, id, link]
    */
   public void createLinksFromSeq(final SequenceI seq,
           Map<String, List<String>> linkset)
@@ -406,8 +408,9 @@ public class UrlLink
    * Create a static URL link
    * 
    * @param linkset
+   *          Map of links: key = id | link, value = [target, label, id, link]
    */
-  public void createStaticLink(Map<String, List<String>> linkset)
+  protected void createStaticLink(Map<String, List<String>> linkset)
   {
     if (!linkset.containsKey(label + "|" + getUrl_prefix()))
     {
@@ -418,12 +421,14 @@ public class UrlLink
   }
 
   /**
-   * Create a dynamic URL link
+   * Create dynamic URL links
    * 
    * @param seq
+   *          The sequence to create links for
    * @param linkset
+   *          Map of links: key = id | link, value = [target, label, id, link]
    */
-  public void createDynamicLinks(final SequenceI seq,
+  protected void createDynamicLinks(final SequenceI seq,
           Map<String, List<String>> linkset)
   {
     // collect id string too
@@ -446,14 +451,14 @@ public class UrlLink
         for (int r = 0; r < dbr.length; r++)
         {
           // create Bare ID link for this URL
-          createBareURLLink(dbr[r].getAccessionId(), linkset, true);
+          createBareURLLink(dbr[r].getAccessionId(), true, linkset);
         }
       }
     }
     else if (!usesSeqId() && id != null) // link is name
     {
       // create Bare ID link for this URL
-      createBareURLLink(id, linkset, false);
+      createBareURLLink(id, false, linkset);
     }
 
     // Create urls from description but only for URL links which are regex
@@ -461,15 +466,16 @@ public class UrlLink
     if (descr != null && getRegexReplace() != null)
     {
       // create link for this URL from description where regex matches
-      createBareURLLink(descr, linkset, false);
+      createBareURLLink(descr, false, linkset);
     }
   }
 
   /*
    * Create a bare URL Link
+   * Returns map where key = id | link, and value = [target, label, id, link]
    */
-  protected void createBareURLLink(String id,
-          Map<String, List<String>> linkset, Boolean combineLabel)
+  protected void createBareURLLink(String id, Boolean combineLabel,
+          Map<String, List<String>> linkset)
   {
     String[] urls = makeUrls(id, true);
     if (urls != null)
@@ -481,6 +487,7 @@ public class UrlLink
           String thisLabel = label;
           if (combineLabel)
           {
+            // incorporate label with idstring
             thisLabel = label + "|" + urls[u];
           }