From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 1 Nov 2016 12:00:55 +0000 (+0000)
Subject: JAL-2282 Refactored URL link creation into UrlLink
X-Git-Tag: Release_2_10_1^2~18^2~2^2~10
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bb90751010ab798f54dabddb8cfb6f51e847072c;p=jalview.git

JAL-2282 Refactored URL link creation into UrlLink
---

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index e2d397f..aa3cad4 100644
--- 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;
@@ -629,80 +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();
-
-      // 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() });
-
-        // if there are any dbrefs which match up with the link
-        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
-            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);
-        }
+      urlLink.createLinksFromSeq(seq, linkset);
+    }
 
-      }
-      else if (seq != null && !urlLink.usesSeqId()) // link is name
-      {
-        if (id != null)
-        {
-          // create Bare ID link for this URL
-          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
-          createBareURLLink(urlLink, descr, linkset, linkMenu, label, false);
-        }
-      }
-      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());
-        }
-      }
+    addshowLinks(linkMenu, linkset.values());
 
-    }
     if (sequence != null)
     {
       sequenceMenu.add(linkMenu);
@@ -713,33 +651,7 @@ 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.
@@ -1015,6 +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
    * 
diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 872f432..0968d36 100644
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -23,6 +23,10 @@ package jalview.util;
 import static jalview.util.UrlConstants.SEQUENCE_ID;
 import static jalview.util.UrlConstants.SEQUENCE_NAME;
 
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
+
+import java.util.Map;
 import java.util.Vector;
 
 public class UrlLink
@@ -377,6 +381,114 @@ public class UrlLink
     }
   }
 
+  /**
+   * 
+   * @param urlLink
+   * @param seq
+   * @param linkset
+   */
+  public void createLinksFromSeq(final SequenceI seq,
+          Map<String, String[]> linkset)
+  {
+    if (seq != null && dynamic)
+    {
+      createDynamicLinks(seq, linkset);
+    }
+    else
+    {
+      createStaticLink(linkset);
+    }
+  }
+
+  /**
+   * Create a static URL link
+   * 
+   * @param linkset
+   */
+  public void createStaticLink(Map<String, String[]> linkset)
+  {
+    if (!linkset.containsKey(label + "|" + getUrl_prefix()))
+    {
+      // Add a non-dynamic link
+      linkset.put(label + "|" + getUrl_prefix(), new String[] { "", label,
+          "", getUrl_prefix() });
+    }
+  }
+
+  /**
+   * Create a dynamic URL link
+   * 
+   * @param seq
+   * @param linkset
+   */
+  public void createDynamicLinks(final SequenceI seq,
+          Map<String, String[]> linkset)
+  {
+    // collect id string too
+    String id = seq.getName();
+    String descr = seq.getDescription();
+    if (descr != null && descr.length() < 1)
+    {
+      descr = null;
+    }
+
+    if (usesSeqId()) // link is ID
+    {
+      // collect matching db-refs
+      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++)
+        {
+          // create Bare ID link for this URL
+          createBareURLLink(dbr[r].getAccessionId(), linkset, true);
+        }
+      }
+    }
+    else if (!usesSeqId() && id != null) // link is name
+    {
+      // create Bare ID link for this URL
+      createBareURLLink(id, linkset, false);
+    }
+
+    // Create urls from description but only for URL links which are regex
+    // links
+    if (descr != null && getRegexReplace() != null)
+    {
+      // create link for this URL from description where regex matches
+      createBareURLLink(descr, linkset, false);
+    }
+  }
+
+  /*
+   * Create a bare URL Link
+   */
+  protected void createBareURLLink(String id,
+          Map<String, String[]> linkset, Boolean combineLabel)
+  {
+    String[] urls = makeUrls(id, true);
+    if (urls != null)
+    {
+      for (int u = 0; u < urls.length; u += 2)
+      {
+        if (!linkset.containsKey(urls[u] + "|" + urls[u + 1]))
+        {
+          String thisLabel = label;
+          if (combineLabel)
+          {
+            thisLabel = label + "|" + urls[u];
+          }
+
+          linkset.put(urls[u] + "|" + urls[u + 1], new String[] { target,
+              thisLabel, urls[u], urls[u + 1] });
+        }
+      }
+    }
+  }
+
   private static void testUrls(UrlLink ul, String idstring, String[] urls)
   {
 
@@ -457,7 +569,6 @@ public class UrlLink
 
   public boolean isDynamic()
   {
-    // TODO Auto-generated method stub
     return dynamic;
   }