Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

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

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index ed96b55..e47c50a 100755 (executable)
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -24,7 +24,9 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.util.UrlLink;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.applet.AppletUrlProviderFactory;
 import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.BorderLayout;
@@ -33,8 +35,8 @@ import java.awt.event.InputEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.util.HashMap;
 import java.util.List;
-import java.util.Vector;
 
 public class IdPanel extends Panel implements MouseListener,
         MouseMotionListener
@@ -52,7 +54,7 @@ public class IdPanel extends Panel implements MouseListener,
 
   boolean mouseDragging = false;
 
-  java.util.Vector links = new java.util.Vector();
+  UrlProviderI urlProvider = null;
 
   public IdPanel(AlignViewport av, AlignmentPanel parent)
   {
@@ -66,6 +68,9 @@ public class IdPanel extends Panel implements MouseListener,
 
     String label, url;
     // TODO: add in group link parameter
+
+    // make a list of label,url pairs
+    HashMap<String, String> urlList = new HashMap<String, String>();
     if (av.applet != null)
     {
       for (int i = 1; i < 10; i++)
@@ -73,29 +78,22 @@ public class IdPanel extends Panel implements MouseListener,
         label = av.applet.getParameter("linkLabel_" + i);
         url = av.applet.getParameter("linkURL_" + i);
 
-        if (label != null && url != null)
+        // only add non-null parameters
+        if (label != null)
         {
-          links.addElement(label + "|" + url);
+          urlList.put(label, url);
         }
-
       }
-    }
-    {
-      // upgrade old SRS link
-      int srsPos = links
-              .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
-      if (srsPos > -1)
+
+      if (!urlList.isEmpty())
       {
-        links.setElementAt(
-                "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
-                srsPos);
+        // set default as first entry in list
+        String defaultUrl = av.applet.getParameter("linkLabel_1");
+        UrlProviderFactoryI factory = new AppletUrlProviderFactory(
+                defaultUrl, urlList);
+        urlProvider = factory.createUrlProvider();
       }
     }
-    if (links.size() < 1)
-    {
-      links = new java.util.Vector();
-      links.addElement("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
-    }
   }
 
   Tooltip tooltip;
@@ -217,7 +215,7 @@ public class IdPanel extends Panel implements MouseListener,
       return;
     }
 
-    // DEFAULT LINK IS FIRST IN THE LINK LIST
+    // get the sequence details
     int seq = alignPanel.seqPanel.findSeq(e);
     SequenceI sq = av.getAlignment().getSequenceAt(seq);
     if (sq == null)
@@ -226,46 +224,11 @@ public class IdPanel extends Panel implements MouseListener,
     }
     String id = sq.getName();
 
-    String target = null;
-    String url = null;
-    int i = 0;
-    while (url == null && i < links.size())
-    {
-      // DEFAULT LINK IS FIRST IN THE LINK LIST
-      // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
-      url = links.elementAt(i++).toString();
-      jalview.util.UrlLink urlLink = null;
-      try
-      {
-        urlLink = new UrlLink(url);
-        target = urlLink.getTarget();
-      } catch (Exception foo)
-      {
-        System.err.println("Exception for URLLink '" + url + "'");
-        foo.printStackTrace();
-        url = null;
-        continue;
-      }
-      ;
-      if (!urlLink.isValid())
-      {
-        System.err.println(urlLink.getInvalidMessage());
-        url = null;
-        continue;
-      }
-
-      String urls[] = urlLink.makeUrls(id, true);
-      if (urls == null || urls[0] == null || urls[0].length() < 1)
-      {
-        url = null;
-        continue;
-      }
-      // just take first URL made from regex
-      url = urls[1];
-    }
+    // get the default url with the sequence details filled in
+    String url = urlProvider.getPrimaryUrl(id);
+    String target = urlProvider.getPrimaryTarget(id);
     try
     {
-
       alignPanel.alignFrame.showURL(url, target);
     } catch (Exception ex)
     {
@@ -290,13 +253,13 @@ public class IdPanel extends Panel implements MouseListener,
       return;
     }
 
-    if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)
+    if (mouseDragging && e.getY() < 0 && av.getRanges().getStartSeq() > 0)
     {
       scrollThread = new ScrollThread(true);
     }
 
     if (mouseDragging && e.getY() >= getSize().height
-            && av.getAlignment().getHeight() > av.getEndSeq())
+            && av.getAlignment().getHeight() > av.getRanges().getEndSeq())
     {
       scrollThread = new ScrollThread(false);
     }
@@ -324,11 +287,8 @@ public class IdPanel extends Panel implements MouseListener,
 
       // build a new links menu based on the current links + any non-positional
       // features
-      Vector nlinks = new Vector();
-      for (int l = 0, lSize = links.size(); l < lSize; l++)
-      {
-        nlinks.addElement(links.elementAt(l));
-      }
+      List<String> nlinks = urlProvider.getLinksForMenu();
+
       SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
       for (int sl = 0; sf != null && sl < sf.length; sl++)
       {
@@ -338,7 +298,7 @@ public class IdPanel extends Panel implements MouseListener,
           {
             for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
             {
-              nlinks.addElement(sf[sl].links.elementAt(l));
+              nlinks.add(sf[sl].links.elementAt(l));
             }
           }
         }
@@ -438,9 +398,10 @@ public class IdPanel extends Panel implements MouseListener,
     int index = av.getAlignment().findIndex(list.get(0));
 
     // do we need to scroll the panel?
-    if (av.getStartSeq() > index || av.getEndSeq() < index)
+    if (av.getRanges().getStartSeq() > index
+            || av.getRanges().getEndSeq() < index)
     {
-      alignPanel.setScrollValues(av.getStartRes(), index);
+      alignPanel.setScrollValues(av.getRanges().getStartRes(), index);
     }
   }
 
@@ -471,10 +432,10 @@ public class IdPanel extends Panel implements MouseListener,
         if (alignPanel.scrollUp(up))
         {
           // scroll was ok, so add new sequence to selection
-          int seq = av.getStartSeq();
+          int seq = av.getRanges().getStartSeq();
           if (!up)
           {
-            seq = av.getEndSeq();
+            seq = av.getRanges().getEndSeq();
           }
 
           if (seq < lastid)