JAL-2282 Refactored URL link creation into UrlLink

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 939c087..aa3cad4 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -54,7 +54,6 @@ import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
-import jalview.util.DBRefUtils;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
@@ -63,8 +62,8 @@ import jalview.util.UrlLink;
 import java.awt.Color;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.Hashtable;
 import java.util.LinkedHashMap;
@@ -617,7 +616,8 @@ public class PopupMenu extends JPopupMenu
   void addFeatureLinks(final SequenceI seq, List<String> links)
   {
     JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
-    List<String> linkset = new ArrayList<String>();
+    Map<String, String[]> linkset = new LinkedHashMap<String, String[]>();
+
     for (String link : links)
     {
       UrlLink urlLink = null;
@@ -629,97 +629,18 @@ public class PopupMenu extends JPopupMenu
         Cache.log.error("Exception for URLLink '" + link + "'", foo);
         continue;
       }
-      ;
+
       if (!urlLink.isValid())
       {
         Cache.log.error(urlLink.getInvalidMessage());
         continue;
       }
-      final String label = urlLink.getLabel();
-      if (seq != null && urlLink.isDynamic())
-      {
 
-        // 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 (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 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]);
-                }
-              }
-            }
-          }
-        }
-        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]);
-              }
-            }
-          }
-        }
-        // 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]);
-              }
-            }
-          }
-        }
-      }
-      else
-      {
-        if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
-        {
-          linkset.add(label + "|" + urlLink.getUrl_prefix());
-          // Add a non-dynamic link
-          addshowLink(linkMenu, label, urlLink.getUrl_prefix());
-        }
-      }
+      urlLink.createLinksFromSeq(seq, linkset);
     }
+
+    addshowLinks(linkMenu, linkset.values());
+
     if (sequence != null)
     {
       sequenceMenu.add(linkMenu);
@@ -730,6 +651,8 @@ public class PopupMenu extends JPopupMenu
     }
   }
 
+
+
   /**
    * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
    * "All" is added first, followed by a separator. Then add any annotation
@@ -928,8 +851,7 @@ public class PopupMenu extends JPopupMenu
         urlLink = new GroupUrlLink(link);
       } catch (Exception foo)
       {
-        Cache.log.error("Exception for GroupURLLink '" + link
-                + "'", foo);
+        Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
         continue;
       }
       ;
@@ -1005,6 +927,15 @@ public class PopupMenu extends JPopupMenu
     }
   }
 
+  private void addshowLinks(JMenu linkMenu, Collection<String[]> linkset)
+  {
+    for (String[] linkstrset : linkset)
+    {
+      // split linkstr into label and url
+      addshowLink(linkMenu, linkstrset[1], linkstrset[3]);
+    }
+  }
+
   /**
    * add a show URL menu item to the given linkMenu
    *