Merge branch 'develop' into features/JAL-1723_sequenceReport

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 7ab6022..3b79fdc 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
@@ -1734,7 +1745,7 @@ public class PopupMenu extends JPopupMenu
   public void createSequenceDetailsReport(SequenceI[] sequences)
   {
     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
-    StringBuffer contents = new StringBuffer();
+    StringBuilder contents = new StringBuilder(128);
     for (SequenceI seq : sequences)
     {
       contents.append("<p><h2>"
@@ -1749,7 +1760,6 @@ public class PopupMenu extends JPopupMenu
                       seq,
                       true,
                       true,
-                      false,
                       (ap.getSeqPanel().seqCanvas.fr != null) ? ap
                               .getSeqPanel().seqCanvas.fr.getMinMax()
                               : null);