X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FUrlLink.java;h=8a60b563d3272affa6cb17bd0f6248f0953b2138;hb=a62e172dc725a573a85ca49552020cc75cfdc1f1;hp=41c306231814c7535ac5ed35503b235f341f1d8a;hpb=26b115b0a77d521da92a06572d9b7819c2d0d49a;p=jalview.git

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 41c3062..8a60b56 100644
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -29,21 +29,59 @@ import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
 
 import java.util.Arrays;
+import java.util.Collections;
+import java.util.Comparator;
 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.
+ * 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 substituted. Usage documentation
+ * todo.
+ */
 public class UrlLink
 {
+  private static final String SEQUENCEID_PLACEHOLDER = DELIM + SEQUENCE_ID
+          + DELIM;
+
+  private static final String ACCESSION_PLACEHOLDER = DELIM + DB_ACCESSION
+          + DELIM;
+
   /**
-   * helper class to parse URL Link strings taken from applet parameters or
-   * jalview properties file using the com.stevesoft.pat.Regex implementation.
-   * 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 substituted. Usage
-   * documentation todo.
+   * A comparator that puts SEQUENCE_ID template links before DB_ACCESSION
+   * 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>()
+  {
+    @Override
+    public int compare(String link1, String link2)
+    {
+      if (link1 == null || link2 == null)
+      {
+        return 0; // for failsafe only
+      }
+      if (link1.contains(SEQUENCEID_PLACEHOLDER)
+              && link2.contains(ACCESSION_PLACEHOLDER))
+      {
+        return -1;
+      }
+      if (link2.contains(SEQUENCEID_PLACEHOLDER)
+              && link1.contains(ACCESSION_PLACEHOLDER))
+      {
+        return 1;
+      }
+      return String.CASE_INSENSITIVE_ORDER.compare(link1, link2);
+    }
+  };
 
   private static final String EQUALS = "=";
 
@@ -266,8 +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();
@@ -291,7 +328,7 @@ public class UrlLink
                       + rg.stringMatched(s) + "'");
             }
             // try to collate subgroup matches
-            Vector<String> subs = new Vector<String>();
+            Vector<String> subs = new Vector<>();
             // have to loop through submatches, collating them at top level
             // match
             int s = 0; // 1;
@@ -471,21 +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
     {
@@ -514,6 +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
    * 
@@ -632,4 +671,20 @@ public class UrlLink
       }
     }
   }
+
+  /**
+   * Sorts links (formatted as LinkName|LinkPattern) suitable for display in a
+   * menu
+   * <ul>
+   * <li>SEQUENCE_ID links precede DB_ACCESSION links (i.e. canonical lookup
+   * before cross-references)</li>
+   * <li>otherwise by Link name (case insensitive)</li>
+   * </ul>
+   * 
+   * @param nlinks
+   */
+  public static void sort(List<String> nlinks)
+  {
+    Collections.sort(nlinks, LINK_COMPARATOR);
+  }
 }