X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=80f03a144139ef3e88b5255eb0ab1c6d7d6f79e2;hb=c28dc7d17e5f61210c70217996f9153458f07de0;hp=feca8461cbd492a19e725a0e88eaee311fe506d1;hpb=a889a61789f15e79ecde7043cddfdea18ad00166;p=jalview.git

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index feca846..80f03a1 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -20,12 +20,12 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.urls.UrlProvider;
-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;
@@ -36,7 +36,6 @@ 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
@@ -78,14 +77,20 @@ 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())
       {
         // set default as first entry in list
         String defaultUrl = av.applet.getParameter("linkLabel_1");
-        urlProvider = new UrlProvider(defaultUrl, urlList);
+        UrlProviderFactoryI factory = new AppletUrlProviderFactory(
+                defaultUrl, urlList);
+        urlProvider = factory.createUrlProvider();
       }
     }
   }
@@ -99,64 +104,57 @@ public class IdPanel extends Panel implements MouseListener,
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
-    // look for non-pos features
     StringBuffer tooltiptext = new StringBuffer();
-    if (sequence != null)
+    if (sequence == null)
+    {
+      return;
+    }
+    if (sequence.getDescription() != null)
     {
-      if (sequence.getDescription() != null)
+      tooltiptext.append(sequence.getDescription());
+      tooltiptext.append("\n");
+    }
+
+    for (SequenceFeature sf : sequence.getFeatures()
+            .getNonPositionalFeatures())
+    {
+      boolean nl = false;
+      if (sf.getFeatureGroup() != null)
       {
-        tooltiptext.append(sequence.getDescription());
-        tooltiptext.append("\n");
+        tooltiptext.append(sf.getFeatureGroup());
+        nl = true;
       }
-
-      SequenceFeature sf[] = sequence.getSequenceFeatures();
-      for (int sl = 0; sf != null && sl < sf.length; sl++)
+      if (sf.getType() != null)
       {
-        if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
-        {
-          boolean nl = false;
-          if (sf[sl].getFeatureGroup() != null)
-          {
-            tooltiptext.append(sf[sl].getFeatureGroup());
-            nl = true;
-          }
-          ;
-          if (sf[sl].getType() != null)
-          {
-            tooltiptext.append(" ");
-            tooltiptext.append(sf[sl].getType());
-            nl = true;
-          }
-          ;
-          if (sf[sl].getDescription() != null)
-          {
-            tooltiptext.append(" ");
-            tooltiptext.append(sf[sl].getDescription());
-            nl = true;
-          }
-          ;
-          if (!Float.isNaN(sf[sl].getScore()) && sf[sl].getScore() != 0f)
-          {
-            tooltiptext.append(" Score = ");
-            tooltiptext.append(sf[sl].getScore());
-            nl = true;
-          }
-          ;
-          if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0)
-          {
-            tooltiptext.append(" (");
-            tooltiptext.append(sf[sl].getStatus());
-            tooltiptext.append(")");
-            nl = true;
-          }
-          ;
-          if (nl)
-          {
-            tooltiptext.append("\n");
-          }
-        }
+        tooltiptext.append(" ");
+        tooltiptext.append(sf.getType());
+        nl = true;
+      }
+      if (sf.getDescription() != null)
+      {
+        tooltiptext.append(" ");
+        tooltiptext.append(sf.getDescription());
+        nl = true;
+      }
+      if (!Float.isNaN(sf.getScore()) && sf.getScore() != 0f)
+      {
+        tooltiptext.append(" Score = ");
+        tooltiptext.append(sf.getScore());
+        nl = true;
+      }
+      if (sf.getStatus() != null && sf.getStatus().length() > 0)
+      {
+        tooltiptext.append(" (");
+        tooltiptext.append(sf.getStatus());
+        tooltiptext.append(")");
+        nl = true;
+      }
+      if (nl)
+      {
+        tooltiptext.append("\n");
       }
     }
+
     if (tooltiptext.length() == 0)
     {
       // nothing to display - so clear tooltip if one is visible
@@ -219,8 +217,8 @@ 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);
+    String url = urlProvider.getPrimaryUrl(id);
+    String target = urlProvider.getPrimaryTarget(id);
     try
     {
       alignPanel.alignFrame.showURL(url, target);
@@ -247,13 +245,13 @@ 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);
     }
@@ -277,23 +275,21 @@ public class IdPanel extends Panel implements MouseListener,
 
     if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
-      Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
+      SequenceI sq = av.getAlignment().getSequenceAt(seq);
 
-      // build a new links menu based on the current links + any non-positional
-      // features
-      Vector<String> nlinks = urlProvider.getLinksForMenu();
+      /*
+       *  build a new links menu based on the current links
+       *  and any non-positional features
+       */
+      List<String> nlinks = urlProvider.getLinksForMenu();
 
-      SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
-      for (int sl = 0; sf != null && sl < sf.length; sl++)
+      for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
       {
-        if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+        if (sf.links != null)
         {
-          if (sf[sl].links != null && sf[sl].links.size() > 0)
+          for (String link : sf.links)
           {
-            for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
-            {
-              nlinks.addElement(sf[sl].links.elementAt(l));
-            }
+            nlinks.add(link);
           }
         }
       }
@@ -392,9 +388,10 @@ 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);
     }
   }
 
@@ -425,10 +422,10 @@ 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)