JAL-1953 first pass of adding javadoc, some methods renamed

[jalview.git] / src / jalview / ext / archaeopteryx / AptxInit.java

diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java
index 9b89cea..cbdd237 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -451,7 +451,7 @@ public final class AptxInit
             // APTX_CONFIG);
             aptxApp.getTreeControls().displayEntireTree();
 
-            aptxApp.checkMultipleTrees();
+            aptxApp.enableMultipleTrees();
             aptxFrames[i++] = aptxApp;
           }
         }
@@ -501,7 +501,7 @@ public final class AptxInit
     LoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
             jalviewAlignport.getAlignment().getSequencesArray(),
             jalviewTree);
-    bindAptxNodes.associateLeavesToSequences();
+    bindAptxNodes.associateNodesToSequences();
 
     TreeViewerUtils.associateNodesWithJalviewSequences(aptxApp, jalviewAlignport,
             bindAptxNodes.getAlignmentWithNodes(),
@@ -524,14 +524,13 @@ public final class AptxInit
     LoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
             jalviewAlignport.getAlignment().getSequencesArray(),
             jalviewTree);
-    bindAptxNodes.associateLeavesToSequences();
+    bindAptxNodes.associateNodesToSequences();
 
     TreeViewerUtils.associateNodesWithJalviewSequences(aptxApp, jalviewAlignport,
             bindAptxNodes.getAlignmentWithNodes(),
             bindAptxNodes.getNodesWithAlignment());
     TreeViewerUtils.addTreeViewFrameToJalview(aptxApp);
 
-    // adaptAptxGui(aptxApp); //moved to AptxFrame
     return aptxApp;
   }