JAL-2282 Refactor applet too

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index c30fdad..6f83cec 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -24,12 +24,12 @@ import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
+import jalview.bin.Cache;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -59,6 +59,7 @@ import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -253,122 +254,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     if (links != null && links.size() > 0)
     {
-      Menu linkMenu = new Menu(MessageManager.getString("action.link"));
-      for (int i = 0; i < links.size(); i++)
-      {
-        String link = links.elementAt(i);
-        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 (seq != null && urlLink.isDynamic())
-        {
-
-          // collect matching db-refs
-          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
-                  seq.getDBRefs(), new String[] { target });
-          // collect id string too
-          String id = seq.getName();
-          String descr = seq.getDescription();
-          if (descr != null && descr.length() < 1)
-          {
-            descr = null;
-          }
-          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);
-          }
-          // Now construct URLs from description but only try to do it for regex
-          // URL links
-          if (descr != null && urlLink.getRegexReplace() != null)
-          {
-            // create link for this URL from description only if regex matches
-            String[] urls = urlLink.makeUrls(descr, true);
-            if (urls != null)
-            {
-              for (int u = 0; u < urls.length; u += 2)
-              {
-                addshowLink(linkMenu, label, urls[u + 1]);
-              }
-            }
-          }
-        }
-        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 String url_pref
-         * = link.substring(link.indexOf("|") + 1,
-         * link.indexOf("$SEQUENCE_ID$"));
-         * 
-         * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
-         * // collect matching db-refs DBRefEntry[] dbr =
-         * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
-         * String[]{target}); // collect id string too String id =
-         * seq.getName(); if (id.indexOf("|") > -1) { id =
-         * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
-         * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
-         * suppress duplicate link creation for the bare sequence ID string with
-         * this link id = null; } addshowLink(linkMenu,
-         * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
-         * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
-         * create Bare ID link for this RUL addshowLink(linkMenu, target,
-         * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
-         * link.substring(link.lastIndexOf("|")+1)); }
-         */
-      }
-      if (linkMenu.getItemCount() > 0)
-      {
-        if (seq != null)
-        {
-          seqMenu.add(linkMenu);
-        }
-        else
-        {
-          add(linkMenu);
-        }
-      }
+      addFeatureLinks(seq, links);
     }
+
     // TODO: add group link menu entry here
     if (seq != null)
     {
@@ -414,6 +302,62 @@ public class APopupMenu extends java.awt.PopupMenu implements
   }
 
   /**
+   * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
+   * 
+   * @param seq
+   * @param links
+   */
+  void addFeatureLinks(final SequenceI seq, List<String> links)
+  {
+    Menu linkMenu = new Menu(MessageManager.getString("action.link"));
+    Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+
+    for (String link : links)
+    {
+      UrlLink urlLink = null;
+      try
+      {
+        urlLink = new UrlLink(link);
+      } catch (Exception foo)
+      {
+        Cache.log.error("Exception for URLLink '" + link + "'", foo);
+        continue;
+      }
+
+      if (!urlLink.isValid())
+      {
+        Cache.log.error(urlLink.getInvalidMessage());
+        continue;
+      }
+
+      urlLink.createLinksFromSeq(seq, linkset);
+    }
+
+    addshowLinks(linkMenu, linkset.values());
+
+    if (linkMenu.getItemCount() > 0)
+    {
+      if (seq != null)
+      {
+        seqMenu.add(linkMenu);
+      }
+      else
+      {
+        add(linkMenu);
+      }
+    }
+  }
+
+  private void addshowLinks(Menu linkMenu, Collection<List<String>> linkset)
+  {
+    for (List<String> linkstrset : linkset)
+    {
+      // split linkstr into label and url
+      addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
+    }
+  }
+
+  /**
    * Build menus for annotation types that may be shown or hidden, and for
    * 'reference annotations' that may be added to the alignment.
    */