From a43e0e073ab9be98b836905f1b843f0389af29be Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Fri, 12 Jan 2018 15:18:27 +0000
Subject: [PATCH] JAL-2805 removed unused Aptx instance creation code

---
 src/jalview/ext/archaeopteryx/AptxInit.java |   24 ------------------------
 1 file changed, 24 deletions(-)

diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java
index b209796..9b89cea 100644
--- a/src/jalview/ext/archaeopteryx/AptxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -8,7 +8,6 @@ import jalview.ext.treeviewer.TreeI;
 import jalview.ext.treeviewer.TreeViewerUtils;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
-import jalview.io.NewickFile;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -73,19 +72,6 @@ public final class AptxInit
   private final static NHXParser.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION = APTX_CONFIG
           .getTaxonomyExtraction();
 
-  // public static TreeFrameI createInstanceFromCalculation(
-  // final TreeBuilder calculatedTree)
-  // {
-  // TreeBuilderI aptxTreeBuilder = new AptxTreeBuilder(
-  // calculatedTree);
-  //
-  // TreeI aptxTree = aptxTreeBuilder.buildTree();
-  //
-  // TreeFrameI aptxApp = createAptxFrame(aptxTree,
-  // calculatedTree.getAvport(), null);
-  //
-  // return aptxApp;
-  // }
 
   public static TreeFrameI createInstanceFromNhx(String treeTitle,
           String nhxString, AlignmentViewport viewport)
@@ -96,8 +82,6 @@ public final class AptxInit
       Desktop.instance.startLoading(treeTitle);
     }
 
-
-
     Phylogeny aptxPhylogeny = Phylogeny
             .createInstanceFromNhxString(nhxString);
     aptxPhylogeny.setName(treeTitle);
@@ -105,7 +89,6 @@ public final class AptxInit
     TreeFrameI aptxFrame = createAptxFrame(aptxPhylogeny, viewport,
             treeTitle);
 
-
     if (Desktop.instance != null)
     {
       Desktop.instance.stopLoading();
@@ -202,13 +185,6 @@ public final class AptxInit
 
     }
 
-  public static TreeFrameI[] createInstancesFromFile(NewickFile newickFile,
-          AlignmentViewport viewport)
-  {
-    return null;
-  }
-
-
   public static TreeFrameI[] createInstancesFromUrl(URL treeUrl,
           AlignmentViewport viewport)
           throws FileNotFoundException, IOException, RuntimeException
-- 
1.7.10.2