X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FUrlLink.java;h=0141a6ac2b35eae4446a973982cca6fd25f17625;hb=d89bd711a41eb3c1cd66d01c0067e1ddb5261ef9;hp=0529c73790acf1a05841714563d0b1755b59a44f;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 0529c73..0141a6a 100644
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -29,21 +29,57 @@ 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;
 
+/**
+ * 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 = "=";
 
@@ -176,8 +212,12 @@ public class UrlLink
     String var = (usesDBaccession ? DB_ACCESSION : SEQUENCE_ID);
 
     return urlPrefix
-            + (dynamic ? (DELIM + var + ((regexReplace != null) ? EQUALS
-                    + regexReplace + EQUALS + DELIM : DELIM)) : "")
+            + (dynamic
+                    ? (DELIM + var
+                            + ((regexReplace != null)
+                                    ? EQUALS + regexReplace + EQUALS + DELIM
+                                    : DELIM))
+                    : "")
             + ((urlSuffix == null) ? "" : urlSuffix);
   }
 
@@ -262,8 +302,8 @@ public class UrlLink
     {
       if (regexReplace != null)
       {
-        com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
-                + regexReplace + "/");
+        com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
+                .perlCode("/" + regexReplace + "/");
         if (rg.search(idstring))
         {
           int ns = rg.numSubs();
@@ -287,7 +327,7 @@ 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;
@@ -321,8 +361,8 @@ public class UrlLink
                 if (rg.matchedFrom(s) > -1)
                 {
                   subs.addElement(rg.stringMatched(s));
-                  subs.addElement(urlPrefix + rg.stringMatched(s)
-                          + urlSuffix);
+                  subs.addElement(
+                          urlPrefix + rg.stringMatched(s) + urlSuffix);
                 }
                 s++;
               }
@@ -470,8 +510,8 @@ public class UrlLink
       regexReplace = link.substring(sqidPos + startLength, p);
       try
       {
-        com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
-                + regexReplace + "/");
+        com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
+                .perlCode("/" + regexReplace + "/");
         if (rg == null)
         {
           invalidMessage = "Invalid Regular Expression : '" + regexReplace
@@ -572,16 +612,17 @@ public class UrlLink
     if (usesDBAccession()) // link is ID
     {
       // collect matching db-refs
-      DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
-              new String[] { target });
+      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);
         }
       }
     }
@@ -627,4 +668,20 @@ 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);
+  }
 }