From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Mon, 13 Nov 2017 20:07:06 +0000 (+0000)
Subject: JAL-2805 some more name changes
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9c2e22bf15e9679ff71cc1e6d0d490c26b4df5ad;p=jalview.git

JAL-2805 some more name changes
---

diff --git a/src/jalview/ext/archaeopteryx/AptxAssociation.java b/src/jalview/ext/archaeopteryx/AptxNodeAssociation.java
similarity index 96%
rename from src/jalview/ext/archaeopteryx/AptxAssociation.java
rename to src/jalview/ext/archaeopteryx/AptxNodeAssociation.java
index 0dfccdf..ec7ca27 100644
--- a/src/jalview/ext/archaeopteryx/AptxAssociation.java
+++ b/src/jalview/ext/archaeopteryx/AptxNodeAssociation.java
@@ -9,14 +9,14 @@ import java.util.List;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
 
-public class AptxAssociation
+public class AptxNodeAssociation
         implements ExternalLoadedTreeAssociationI<Phylogeny>
 {
   SequenceI[] alignSequences;
 
   Phylogeny tree;
 
-  public AptxAssociation(SequenceI[] alignmentSequences,
+  public AptxNodeAssociation(SequenceI[] alignmentSequences,
           Phylogeny aptxTree)
   {
     alignSequences = alignmentSequences;
diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
index 02ecdf0..af270c2 100644
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
@@ -2,7 +2,7 @@ package jalview.ext.archaeopteryx;
 
 import jalview.analysis.TreeBuilder;
 import jalview.datamodel.SequenceI;
-import jalview.ext.forester.ForesterConversions;
+import jalview.ext.forester.ForesterDataConversions;
 import jalview.ext.forester.ForesterMatrix;
 import jalview.util.MessageManager;
 
@@ -80,7 +80,7 @@ public class ArchaeopteryxTreeBuilder
 
     for (SequenceI sequence : sequences)
     {
-      Sequence seq = ForesterConversions
+      Sequence seq = ForesterDataConversions
               .createForesterSequence(sequence, true);
       PhylogenyNode sequenceNode = new PhylogenyNode(sequence.getName());
       NodeData nodeData = sequenceNode.getNodeData();
diff --git a/src/jalview/ext/forester/ForesterConversions.java b/src/jalview/ext/forester/ForesterDataConversions.java
similarity index 98%
rename from src/jalview/ext/forester/ForesterConversions.java
rename to src/jalview/ext/forester/ForesterDataConversions.java
index 5a66974..6168820 100644
--- a/src/jalview/ext/forester/ForesterConversions.java
+++ b/src/jalview/ext/forester/ForesterDataConversions.java
@@ -6,7 +6,7 @@ import jalview.math.MatrixI;
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 
-public final class ForesterConversions
+public final class ForesterDataConversions
 {
   public static org.forester.phylogeny.data.Sequence createForesterSequence(
           final SequenceI jalviewSequence, final boolean sequenceIsAligned)
diff --git a/src/jalview/ext/forester/ForesterMatrix.java b/src/jalview/ext/forester/ForesterMatrix.java
index 7d3d295..6c60622 100644
--- a/src/jalview/ext/forester/ForesterMatrix.java
+++ b/src/jalview/ext/forester/ForesterMatrix.java
@@ -166,7 +166,7 @@ public class ForesterMatrix implements DistanceMatrix
           final MatrixI jalviewInputMatrix,
           final SequenceI[] matrixSequences)
   {
-    return ForesterConversions.createForesterDistanceMatrix(
+    return ForesterDataConversions.createForesterDistanceMatrix(
             jalviewInputMatrix, matrixSequences);
 
   }
@@ -175,7 +175,7 @@ public class ForesterMatrix implements DistanceMatrix
           final MatrixI jalviewInputMatrix,
           final String[] matrixIdentifiers)
   {
-    return ForesterConversions.createForesterDistanceMatrix(
+    return ForesterDataConversions.createForesterDistanceMatrix(
             jalviewInputMatrix, matrixIdentifiers);
 
   }