From db12baeea5789f5d7c6152f85e432255b460c08b Mon Sep 17 00:00:00 2001 From: kjvdheide Date: Mon, 9 Oct 2017 22:39:54 +0100 Subject: [PATCH] Start of creating tree nodes for Aptx --- src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java | 7 +++++++ src/jalview/gui/CalculationChooser.java | 3 +++ 2 files changed, 10 insertions(+) diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java index 18ac083..07b5bb4 100644 --- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java +++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java @@ -1,8 +1,15 @@ package jalview.ext.archaeopteryx; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; + import org.forester.phylogeny.Phylogeny; +import org.forester.phylogeny.PhylogenyNode; public class ArchaeopteryxTreeBuilder extends Phylogeny { + List nodes = Collections + .synchronizedList(new ArrayList()); } diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java index 811957b..de4fd37 100644 --- a/src/jalview/gui/CalculationChooser.java +++ b/src/jalview/gui/CalculationChooser.java @@ -28,6 +28,7 @@ import jalview.analysis.scoremodels.SimilarityParams; import jalview.api.analysis.ScoreModelI; import jalview.api.analysis.SimilarityParamsI; import jalview.datamodel.SequenceGroup; +import jalview.ext.archaeopteryx.ArchaeopteryxTreeBuilder; import jalview.util.MessageManager; import java.awt.BorderLayout; @@ -480,6 +481,8 @@ public class CalculationChooser extends JPanel TreeModel tree = new TreeModel(calculatedTree); openTreePanel(tree, treeAlgo, params); + ArchaeopteryxTreeBuilder aptxTree = new ArchaeopteryxTreeBuilder(); + } -- 1.7.10.2