Jalview-JS/JAL-3253-applet also comments relating to JAL-3268

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

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index dda9e0e..8a60b56 100644 (file)
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -35,6 +35,8 @@ import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
+import com.stevesoft.pat.Regex;
+
 /**
  * A helper class to parse URL Link strings taken from applet parameters or
  * jalview properties file using the com.stevesoft.pat.Regex implementation.
@@ -46,11 +48,17 @@ import java.util.Vector;
  */
 public class UrlLink
 {
+  private static final String SEQUENCEID_PLACEHOLDER = DELIM + SEQUENCE_ID
+          + DELIM;
+
+  private static final String ACCESSION_PLACEHOLDER = DELIM + DB_ACCESSION
+          + DELIM;
+
   /**
    * A comparator that puts SEQUENCE_ID template links before DB_ACCESSION
-   * links, and otherwise orders by link name (not case sensitive). It expects
-   * to compare strings formatted as "Name|URLTemplate" where the template may
-   * include $SEQUENCE_ID$ or $DB_ACCESSION$ or neither.
+   * links, and otherwise orders by link name + url (not case sensitive). It
+   * expects to compare strings formatted as "Name|URLTemplate" where the
+   * template may include $SEQUENCE_ID$ or $DB_ACCESSION$ or neither.
    */
   public static final Comparator<String> LINK_COMPARATOR = new Comparator<String>()
   {
@@ -61,29 +69,17 @@ public class UrlLink
       {
         return 0; // for failsafe only
       }
-      String[] tokens1 = link1.split("\\|");
-      String[] tokens2 = link2.split("\\|");
-      if (tokens1.length < 2 || tokens2.length < 2)
-      {
-        // for failsafe only
-        return String.CASE_INSENSITIVE_ORDER.compare(link1, link2);
-      }
-      String name1 = tokens1[0];
-      String name2 = tokens2[0];
-      String pattern1 = tokens1[1];
-      String pattern2 = tokens2[1];
-      if (pattern1.contains(UrlConstants.SEQUENCE_ID)
-              && pattern2.contains(UrlConstants.DB_ACCESSION))
+      if (link1.contains(SEQUENCEID_PLACEHOLDER)
+              && link2.contains(ACCESSION_PLACEHOLDER))
       {
         return -1;
       }
-      if (pattern2.contains(UrlConstants.SEQUENCE_ID)
-              && pattern1.contains(UrlConstants.DB_ACCESSION))
+      if (link2.contains(SEQUENCEID_PLACEHOLDER)
+              && link1.contains(ACCESSION_PLACEHOLDER))
       {
         return 1;
       }
-      return String.CASE_INSENSITIVE_ORDER.compare(name1, name2);
-
+      return String.CASE_INSENSITIVE_ORDER.compare(link1, link2);
     }
   };
 
@@ -308,8 +304,7 @@ public class UrlLink
     {
       if (regexReplace != null)
       {
-        com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
-                .perlCode("/" + regexReplace + "/");
+        Regex rg = Platform.newRegexPerl("/" + regexReplace + "/");
         if (rg.search(idstring))
         {
           int ns = rg.numSubs();
@@ -513,21 +508,8 @@ public class UrlLink
     {
       // Extract Regex and suffix
       urlSuffix = link.substring(p + endDelimiter.length());
-      regexReplace = link.substring(sqidPos + startLength, p);
-      try
-      {
-        com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
-                .perlCode("/" + regexReplace + "/");
-        if (rg == null)
-        {
-          invalidMessage = "Invalid Regular Expression : '" + regexReplace
-                  + "'\n";
-        }
-      } catch (Exception e)
-      {
-        invalidMessage = "Invalid Regular Expression : '" + regexReplace
-                + "'\n";
-      }
+      testRegexPerl(
+              regexReplace = link.substring(sqidPos + startLength, p));
     }
     else
     {
@@ -556,6 +538,21 @@ public class UrlLink
     return p;
   }
 
+  private void testRegexPerl(String r)
+  {
+    Regex rg = null;
+    try
+    {
+      rg = Platform.newRegexPerl("/" + r + "/");
+    } catch (Exception e)
+    {
+    }
+    if (rg == null)
+    {
+      invalidMessage = "Invalid Regular Expression : '" + r + "'\n";
+    }
+  }
+
   /**
    * Create a set of URL links for a sequence
    * 
@@ -618,17 +615,17 @@ public class UrlLink
     if (usesDBAccession()) // link is ID
     {
       // collect matching db-refs
-      DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
+      List<DBRefEntry> dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
               new String[]
               { target });
 
       // if there are any dbrefs which match up with the link
       if (dbr != null)
       {
-        for (int r = 0; r < dbr.length; r++)
+        for (int r = 0, nd = dbr.size(); r < nd; r++)
         {
           // create Bare ID link for this URL
-          createBareURLLink(dbr[r].getAccessionId(), true, linkset);
+          createBareURLLink(dbr.get(r).getAccessionId(), true, linkset);
         }
       }
     }