JAL-2805 more name changes for clarity

diff --git a/src/jalview/ext/archaeopteryx/JalviewToAptxAssociation.java b/src/jalview/ext/archaeopteryx/AptxAssociation.java
similarity index 95%
rename from src/jalview/ext/archaeopteryx/JalviewToAptxAssociation.java
rename to src/jalview/ext/archaeopteryx/AptxAssociation.java
index 2daa7ce..0dfccdf 100644 (file)
--- a/src/jalview/ext/archaeopteryx/JalviewToAptxAssociation.java
+++ b/src/jalview/ext/archaeopteryx/AptxAssociation.java
@@ -9,14 +9,14 @@ import java.util.List;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
 
-public class JalviewToAptxAssociation
+public class AptxAssociation
         implements ExternalLoadedTreeAssociationI<Phylogeny>
 {
   SequenceI[] alignSequences;
 
   Phylogeny tree;
 
-  public JalviewToAptxAssociation(SequenceI[] alignmentSequences,
+  public AptxAssociation(SequenceI[] alignmentSequences,
           Phylogeny aptxTree)
   {
     alignSequences = alignmentSequences;

diff --git a/src/jalview/ext/archaeopteryx/JalviewAptxBinding.java b/src/jalview/ext/archaeopteryx/AptxBinding.java
similarity index 98%
rename from src/jalview/ext/archaeopteryx/JalviewAptxBinding.java
rename to src/jalview/ext/archaeopteryx/AptxBinding.java
index 5a49470..00462aa 100644 (file)
--- a/src/jalview/ext/archaeopteryx/JalviewAptxBinding.java
+++ b/src/jalview/ext/archaeopteryx/AptxBinding.java
@@ -28,7 +28,7 @@ import org.forester.phylogeny.PhylogenyNode;
  * @author kjvanderheide
  *
  */
-public final class JalviewAptxBinding
+public final class AptxBinding
         implements ExternalTreeViewerBindingI<PhylogenyNode>
 {
   private org.forester.archaeopteryx.TreePanel treeView;
@@ -56,7 +56,7 @@ public final class JalviewAptxBinding
    *          map with tree nodes and matching sequences used to calculate the
    *          tree as key, value pair respectively.
    */
-  public JalviewAptxBinding(final MainFrame archaeopteryx,
+  public AptxBinding(final MainFrame archaeopteryx,
           final AlignmentViewport jalviewAlignmentViewport,
           final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
           final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
index f8f1682..364260e 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
@@ -87,7 +87,7 @@ public final class ArchaeopteryxInit
           final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
           final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
   {
-    return new JalviewAptxBinding(aptxApp, jalviewAlignViewport,
+    return new AptxBinding(aptxApp, jalviewAlignViewport,
             alignMappedToNodes, nodesMappedToAlign);
   }