From ba5f79b1e7e332d7603b8cdf144d5cf37ddaa3fb Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Mon, 13 Nov 2017 20:03:31 +0000
Subject: [PATCH 1/1] JAL-2805 more name changes for clarity

---
 .../{JalviewToAptxAssociation.java => AptxAssociation.java}        |    4 ++--
 .../archaeopteryx/{JalviewAptxBinding.java => AptxBinding.java}    |    4 ++--
 src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java               |    2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)
 rename src/jalview/ext/archaeopteryx/{JalviewToAptxAssociation.java => AptxAssociation.java} (95%)
 rename src/jalview/ext/archaeopteryx/{JalviewAptxBinding.java => AptxBinding.java} (98%)

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
--- 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
--- 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
--- 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);
   }
 
-- 
1.7.10.2