From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 16 Nov 2016 10:50:37 +0000 (+0000)
Subject: JAL-2295 don't exclude RESNUM from transfer to Chimera
X-Git-Tag: Release_2_11_0~62^2~47
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6901823e2a786413c64e8225c4b530e0d9c829d0;p=jalview.git

JAL-2295 don't exclude RESNUM from transfer to Chimera
---

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index 533b441..07c0015 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -38,8 +38,6 @@ import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 
-import MCview.PDBChain;
-
 /**
  * Routines for generating Chimera commands for Jalview/Chimera binding
  * 
@@ -407,8 +405,7 @@ public class ChimeraCommands
        */
       boolean isFromViewer = JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
               .equals(sf.getFeatureGroup());
-      if (isFromViewer || !visibleFeatures.contains(type)
-              || suppressFeature(type))
+      if (isFromViewer || !visibleFeatures.contains(type))
       {
         continue;
       }
@@ -443,18 +440,6 @@ public class ChimeraCommands
   }
 
   /**
-   * Answers true if the feature type is one we don't wish to propagate to
-   * Chimera - for now, RESNUM
-   * 
-   * @param type
-   * @return
-   */
-  static boolean suppressFeature(String type)
-  {
-    return PDBChain.RESNUM_FEATURE.equals(type);
-  }
-
-  /**
    * Traverse the map of features/values/models/chains/positions to construct a
    * list of 'setattr' commands (one per distinct feature type and value).
    * <p>
diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
index 1b7d9d0..a31a065 100644
--- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
+++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
@@ -246,6 +246,8 @@ public class JalviewChimeraView
             62, -2.1f, null));
     sq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 65,
             65, 3.6f, null));
+    sq.addSequenceFeature(new SequenceFeature("RESNUM", "ALA:   2  4zhoA",
+            53, 53, Float.NaN, null));
 
     /*
      * set all features visible except for chain
@@ -257,6 +259,7 @@ public class JalviewChimeraView
     fr.setVisible("metal ion-binding site");
     fr.setVisible("helix");
     fr.setVisible("kd");
+    fr.setVisible("RESNUM");
 
     /*
      * 'perform' menu action to copy visible features to
@@ -285,6 +288,7 @@ public class JalviewChimeraView
     assertTrue(reply.contains("resattr jv_metal_ion_binding_site"));
     assertTrue(reply.contains("resattr jv_helix"));
     assertTrue(reply.contains("resattr jv_kd"));
+    assertTrue(reply.contains("resattr jv_RESNUM"));
     // feature is not on a mapped region - no attribute created
     assertFalse(reply.contains("resattr jv_transit_peptide"));
     // feature is not visible - no attribute created