regular expression based URL link generation

[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index ff1c3c8..7c1ea3f 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -28,6 +28,7 @@ import jalview.analysis.*;
 import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.util.UrlLink;
 import jalview.io.AppletFormatAdapter;
 
 public class APopupMenu
@@ -134,10 +135,59 @@ public class APopupMenu
       for (int i = 0; i < links.size(); i++)
       {
         link = links.elementAt(i).toString();
-        final String target = link.substring(0, link.indexOf("|"));
-        
-        final String url;
+        UrlLink urlLink = new UrlLink(link);
+        if (!urlLink.isValid())
+        {
+          System.err.println(urlLink.getInvalidMessage());
+          continue;
+        }
+        final String target = urlLink.getTarget(); // link.substring(0, link.indexOf("|"));
+        final String label = urlLink.getLabel();
+        if (urlLink.isDynamic())
+        {
 
+          // collect matching db-refs
+          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{target});
+          // collect id string too
+          String id = seq.getName();
+          if (dbr!=null)
+          {
+            for (int r=0;r<dbr.length; r++)
+            {
+              if (id!=null && dbr[r].getAccessionId().equals(id))
+              {
+                // suppress duplicate link creation for the bare sequence ID string with this link
+                id = null;
+              }
+              // create Bare ID link for this RUL
+              String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
+              if (urls!=null)
+              {
+                for (int u=0; u<urls.length; u+=2)
+                {
+                  addshowLink(linkMenu, label+"|"+urls[u],urls[u+1]);
+                }
+              }
+            }
+          }
+          if (id!=null)
+          {
+            // create Bare ID link for this RUL
+            String[] urls = urlLink.makeUrls(id, true);
+            if (urls!=null)
+            {
+              for (int u=0; u<urls.length; u+=2)
+              {
+                addshowLink(linkMenu, label,urls[u+1]);
+              }
+            }
+            // addshowLink(linkMenu, target,  url_pref + id + url_suff);
+          }
+        } else {
+          addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
+        }
+        /*final String url;
+        
         if (link.indexOf("$SEQUENCE_ID$") > -1)
         {
           // Substitute SEQUENCE_ID string and any matching database reference accessions
@@ -174,7 +224,7 @@ public class APopupMenu
           }
         } else {
           addshowLink(linkMenu, target, link.substring(link.lastIndexOf("|")+1));
-        }
+        } */
       }
     
       if (seq != null)