Working links menu

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 7ab6022..e2d397f 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -636,20 +636,22 @@ public class PopupMenu extends JPopupMenu
         continue;
       }
       final String label = urlLink.getLabel();
-      if (seq != null && urlLink.isDynamic())
+
+      // collect id string too
+      String id = seq.getName();
+      String descr = seq.getDescription();
+      if (descr != null && descr.length() < 1)
       {
+        descr = null;
+      }
 
+      if (seq != null && urlLink.usesSeqId()) // link is ID
+      {
         // collect matching db-refs
         DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
                 new String[] { urlLink.getTarget() });
-        // collect id string too
-        String id = seq.getName();
-        String descr = seq.getDescription();
-        if (descr != null && descr.length() < 1)
-        {
-          descr = null;
-        }
 
+        // if there are any dbrefs which match up with the link
         if (dbr != null)
         {
           for (int r = 0; r < dbr.length; r++)
@@ -661,53 +663,33 @@ public class PopupMenu extends JPopupMenu
               id = null;
             }
             // create Bare ID link for this URL
-            String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
-            if (urls != null)
-            {
-              for (int u = 0; u < urls.length; u += 2)
-              {
-                if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
-                {
-                  linkset.add(urls[u] + "|" + urls[u + 1]);
-                  addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
-                }
-              }
-            }
+            createBareURLLink(urlLink, dbr[r].getAccessionId(), linkset,
+                    linkMenu, label, true);
           }
         }
+
+        // Create urls from description but only for URL links which are regex
+        // links
+        if (descr != null && urlLink.getRegexReplace() != null)
+        {
+          // create link for this URL from description where regex matches
+          createBareURLLink(urlLink, descr, linkset, linkMenu, label, false);
+        }
+
+      }
+      else if (seq != null && !urlLink.usesSeqId()) // link is name
+      {
         if (id != null)
         {
           // create Bare ID link for this URL
-          String[] urls = urlLink.makeUrls(id, true);
-          if (urls != null)
-          {
-            for (int u = 0; u < urls.length; u += 2)
-            {
-              if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
-              {
-                linkset.add(urls[u] + "|" + urls[u + 1]);
-                addshowLink(linkMenu, label, urls[u + 1]);
-              }
-            }
-          }
+          createBareURLLink(urlLink, id, linkset, linkMenu, label, false);
         }
         // Create urls from description but only for URL links which are regex
         // links
         if (descr != null && urlLink.getRegexReplace() != null)
         {
           // create link for this URL from description where regex matches
-          String[] urls = urlLink.makeUrls(descr, true);
-          if (urls != null)
-          {
-            for (int u = 0; u < urls.length; u += 2)
-            {
-              if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
-              {
-                linkset.add(urls[u] + "|" + urls[u + 1]);
-                addshowLink(linkMenu, label, urls[u + 1]);
-              }
-            }
-          }
+          createBareURLLink(urlLink, descr, linkset, linkMenu, label, false);
         }
       }
       else
@@ -719,6 +701,7 @@ public class PopupMenu extends JPopupMenu
           addshowLink(linkMenu, label, urlLink.getUrl_prefix());
         }
       }
+
     }
     if (sequence != null)
     {
@@ -730,6 +713,34 @@ public class PopupMenu extends JPopupMenu
     }
   }
 
+  /*
+   * Create a bare URL Link
+   */
+  private void createBareURLLink(UrlLink urlLink, String id,
+          List<String> linkset, JMenu linkMenu, String label,
+          Boolean addSepToLabel)
+  {
+    String[] urls = urlLink.makeUrls(id, true);
+    if (urls != null)
+    {
+      for (int u = 0; u < urls.length; u += 2)
+      {
+        if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
+        {
+          linkset.add(urls[u] + "|" + urls[u + 1]);
+          if (addSepToLabel)
+          {
+            addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
+          }
+          else
+          {
+            addshowLink(linkMenu, label, urls[u + 1]);
+          }
+        }
+      }
+    }
+  }
+
   /**
    * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
    * "All" is added first, followed by a separator. Then add any annotation

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index b43989a..b36a73d 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import static jalview.util.UrlConstants.EMBLEBI_STRING;
+import static jalview.util.UrlConstants.OLD_EMBLEBI_STRING;
 import static jalview.util.UrlConstants.SEQUENCE_ID;
 import static jalview.util.UrlConstants.SRS_STRING;
 
@@ -143,6 +144,12 @@ public class Preferences extends GPreferences
       {
         sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos);
       }
+      // upgrade old EMBL-EBI link
+      int emblPos = sequenceURLLinks.indexOf(OLD_EMBLEBI_STRING);
+      if (emblPos > -1)
+      {
+        sequenceURLLinks.setElementAt(EMBLEBI_STRING, emblPos);
+      }
     }
 
     /**

diff --git a/src/jalview/util/UrlConstants.java b/src/jalview/util/UrlConstants.java
index fc6dfdd..ce6d980 100644 (file)
--- a/src/jalview/util/UrlConstants.java
+++ b/src/jalview/util/UrlConstants.java
@@ -25,25 +25,31 @@ package jalview.util;
  */
 public class UrlConstants
 {
+
   /*
-   * Default sequence URL link string for EMBL-EBI search
+   * Sequence ID string
    */
-  public static final String EMBLEBI_STRING = "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$";
+  public static final String SEQUENCE_ID = "SEQUENCE_ID";
 
   /*
-   * Default sequence URL link string for SRS 
+   * Sequence Name string
    */
-  public static final String SRS_STRING = "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry";
+  public static final String SEQUENCE_NAME = "SEQUENCE_NAME";
 
   /*
-   * Sequence ID string
+   * Default sequence URL link string for EMBL-EBI search
    */
-  public static final String SEQUENCE_ID = "SEQUENCE_ID";
+  public static final String EMBLEBI_STRING = "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_NAME$";
 
   /*
-   * Sequence Name string
+   * Default sequence URL link string for EMBL-EBI search
    */
-  public static final String SEQUENCE_NAME = "SEQUENCE_NAME";
+  public static final String OLD_EMBLEBI_STRING = "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$";
+
+  /*
+   * Default sequence URL link string for SRS 
+   */
+  public static final String SRS_STRING = "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry";
 
   /*
    * not instantiable

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index e196c8c..a8c0b32 100644 (file)
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -21,6 +21,7 @@
 package jalview.util;
 
 import static jalview.util.UrlConstants.SEQUENCE_ID;
+import static jalview.util.UrlConstants.SEQUENCE_NAME;
 
 import java.util.Vector;
 
@@ -39,6 +40,8 @@ public class UrlLink
 
   private boolean dynamic = false;
 
+  private boolean uses_seq_id = false;
+
   private String invalidMessage = null;
 
   /**
@@ -50,34 +53,18 @@ public class UrlLink
    */
   public UrlLink(String link)
   {
-    int sep = link.indexOf("|"), psqid = link.indexOf("$" + SEQUENCE_ID);
+    int sep = link.indexOf("|");
+    int psqid = link.indexOf("$" + SEQUENCE_ID);
+    int nsqid = link.indexOf("$" + SEQUENCE_NAME);
     if (psqid > -1)
     {
       dynamic = true;
-      int p = sep;
-      do
-      {
-        sep = p;
-        p = link.indexOf("|", sep + 1);
-      } while (p > sep && p < psqid);
-      // Assuming that the URL itself does not contain any '|' symbols
-      // sep now contains last pipe symbol position prior to any regex symbols
-      label = link.substring(0, sep);
-      if (label.indexOf("|") > -1)
-      {
-        // | terminated database name / www target at start of Label
-        target = label.substring(0, label.indexOf("|"));
-      }
-      else if (label.indexOf(" ") > 2)
-      {
-        // space separated Label - matches database name
-        target = label.substring(0, label.indexOf(" "));
-      }
-      else
-      {
-        target = label;
-      }
+      uses_seq_id = true;
+
+      sep = parseTargetAndLabel(sep, psqid, link);
+
       // Parse URL : Whole URL string first
+      int p;
       url_prefix = link.substring(sep + 1, psqid);
       if (link.indexOf("$" + SEQUENCE_ID + "=/") == psqid
               && (p = link.indexOf("/=$", psqid + 14)) > psqid + 14)
@@ -116,6 +103,50 @@ public class UrlLink
         }
       }
     }
+    else if (nsqid > -1)
+    {
+      dynamic = true;
+      sep = parseTargetAndLabel(sep, nsqid, link);
+
+      int p;
+      url_prefix = link.substring(sep + 1, nsqid);
+      if (link.indexOf("$" + SEQUENCE_NAME + "=/") == nsqid
+              && (p = link.indexOf("/=$", nsqid + 16)) > nsqid + 16)
+      {
+        // Extract Regex and suffix
+        url_suffix = link.substring(p + 3);
+        regexReplace = link.substring(nsqid + 16, p);
+        try
+        {
+          com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
+                  + regexReplace + "/");
+          if (rg == null)
+          {
+            invalidMessage = "Invalid Regular Expression : '"
+                    + regexReplace + "'\n";
+          }
+        } catch (Exception e)
+        {
+          invalidMessage = "Invalid Regular Expression : '" + regexReplace
+                  + "'\n";
+        }
+      }
+      else
+      {
+        regexReplace = null;
+        // verify format is really correct.
+        if (link.indexOf("$" + SEQUENCE_NAME + "$") == nsqid)
+        {
+          url_suffix = link.substring(nsqid + 15);
+          regexReplace = null;
+        }
+        else
+        {
+          invalidMessage = "Warning: invalid regex structure for URL link : "
+                  + link;
+        }
+      }
+    }
     else
     {
       target = link.substring(0, sep);
@@ -309,6 +340,34 @@ public class UrlLink
 
   }
 
+  private int parseTargetAndLabel(int sep, int psqid, String link)
+  {
+    int p = sep;
+    do
+    {
+      sep = p;
+      p = link.indexOf("|", sep + 1);
+    } while (p > sep && p < psqid);
+    // Assuming that the URL itself does not contain any '|' symbols
+    // sep now contains last pipe symbol position prior to any regex symbols
+    label = link.substring(0, sep);
+    if (label.indexOf("|") > -1)
+    {
+      // | terminated database name / www target at start of Label
+      target = label.substring(0, label.indexOf("|"));
+    }
+    else if (label.indexOf(" ") > 2)
+    {
+      // space separated Label - matches database name
+      target = label.substring(0, label.indexOf(" "));
+    }
+    else
+    {
+      target = label;
+    }
+    return sep;
+  }
+
   private static void testUrls(UrlLink ul, String idstring, String[] urls)
   {
 
@@ -393,6 +452,11 @@ public class UrlLink
     return dynamic;
   }
 
+  public boolean usesSeqId()
+  {
+    return uses_seq_id;
+  }
+
   public void setLabel(String newlabel)
   {
     this.label = newlabel;