JAL-2492 use SequenceFeatures.getNonPositionalFeatures()

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

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index e47c50a..80f03a1 100755 (executable)
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -20,7 +20,6 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -105,64 +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)
     {
-      if (sequence.getDescription() != null)
+      return;
+    }
+    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
@@ -283,23 +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
+      /*
+       *  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.add(sf[sl].links.elementAt(l));
-            }
+            nlinks.add(link);
           }
         }
       }