JAL-2629 hmmsearch now adds the E-value as an annotation

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

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index f9f1676..8ac02be 100755 (executable)
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -24,9 +24,9 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.urls.AppletUrlProviderFactory;
-import jalview.urls.UrlProviderFactoryI;
-import jalview.urls.UrlProviderI;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.applet.AppletUrlProviderFactory;
 import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.BorderLayout;
@@ -35,12 +35,12 @@ import java.awt.event.InputEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Vector;
 
-public class IdPanel extends Panel implements MouseListener,
-        MouseMotionListener
+public class IdPanel extends Panel
+        implements MouseListener, MouseMotionListener
 {
 
   protected IdCanvas idCanvas;
@@ -79,7 +79,11 @@ public class IdPanel extends Panel implements MouseListener,
         label = av.applet.getParameter("linkLabel_" + i);
         url = av.applet.getParameter("linkURL_" + i);
 
-        urlList.put(label, url);
+        // only add non-null parameters
+        if (label != null)
+        {
+          urlList.put(label, url);
+        }
       }
 
       if (!urlList.isEmpty())
@@ -173,13 +177,14 @@ public class IdPanel extends Panel implements MouseListener,
     }
     if (tooltip == null)
     {
-      tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
-              + tooltiptext.toString(), idCanvas);
+      tooltip = new Tooltip(
+              sequence.getDisplayId(true) + "\n" + tooltiptext.toString(),
+              idCanvas);
     }
     else
     {
-      tooltip.setTip(sequence.getDisplayId(true) + "\n"
-              + tooltiptext.toString());
+      tooltip.setTip(
+              sequence.getDisplayId(true) + "\n" + tooltiptext.toString());
     }
     tooltiptext = null;
   }
@@ -222,8 +227,12 @@ public class IdPanel extends Panel implements MouseListener,
     String id = sq.getName();
 
     // get the default url with the sequence details filled in
-    String url = urlProvider.getDefaultUrl(id);
-    String target = urlProvider.getDefaultTarget(id);
+    if (urlProvider == null)
+    {
+      return;
+    }
+    String url = urlProvider.getPrimaryUrl(id);
+    String target = urlProvider.getPrimaryTarget(id);
     try
     {
       alignPanel.alignFrame.showURL(url, target);
@@ -250,13 +259,13 @@ 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);
     }
@@ -278,14 +287,22 @@ public class IdPanel extends Panel implements MouseListener,
 
     int seq = alignPanel.seqPanel.findSeq(e);
 
-    if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ((e.getModifiers()
+            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
       Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
 
       // build a new links menu based on the current links + any non-positional
       // features
-      Vector<String> nlinks = urlProvider.getLinksForMenu();
-
+      List<String> nlinks;
+      if (urlProvider != null)
+      {
+        nlinks = urlProvider.getLinksForMenu();
+      }
+      else
+      {
+        nlinks = new ArrayList<String>();
+      }
       SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
       for (int sl = 0; sf != null && sl < sf.length; sl++)
       {
@@ -295,7 +312,7 @@ 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));
             }
           }
         }
@@ -308,8 +325,8 @@ public class IdPanel extends Panel implements MouseListener,
     }
 
     if ((av.getSelectionGroup() == null)
-            || ((!jalview.util.Platform.isControlDown(e) && !e
-                    .isShiftDown()) && av.getSelectionGroup() != null))
+            || ((!jalview.util.Platform.isControlDown(e)
+                    && !e.isShiftDown()) && av.getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
@@ -358,8 +375,8 @@ public class IdPanel extends Panel implements MouseListener,
     }
     for (int i = start; i <= end; i++)
     {
-      av.getSelectionGroup().addSequence(
-              av.getAlignment().getSequenceAt(i), i == end);
+      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+              i == end);
     }
 
   }
@@ -395,9 +412,10 @@ 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);
+      av.getRanges().setStartSeq(index);
     }
   }
 
@@ -425,13 +443,13 @@ public class IdPanel extends Panel implements MouseListener,
       running = true;
       while (running)
       {
-        if (alignPanel.scrollUp(up))
+        if (av.getRanges().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)