From 62fe03a53b984269705b575ce1eb82dd314d63e7 Mon Sep 17 00:00:00 2001 From: kjvdheide Date: Fri, 13 Oct 2017 15:32:56 +0100 Subject: [PATCH] simplified aptx frame creation code --- .../ext/archaeopteryx/ArchaeopteryxFrame.java | 38 ++++++++++---------- 1 file changed, 20 insertions(+), 18 deletions(-) diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxFrame.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxFrame.java index 3c9e175..64750ad 100644 --- a/src/jalview/ext/archaeopteryx/ArchaeopteryxFrame.java +++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxFrame.java @@ -11,43 +11,45 @@ import org.forester.phylogeny.Phylogeny; public class ArchaeopteryxFrame { - - public static ArchaeopteryxFrame createInstance(Phylogeny aptxTree) - { - return new ArchaeopteryxFrame(aptxTree); - - } - - public static ArchaeopteryxFrame createInstance( - TreeBuilder calculatedTree) + public static ArchaeopteryxFrame createInstance(Phylogeny[] aptxTrees) { - return new ArchaeopteryxFrame(calculatedTree); + return new ArchaeopteryxFrame(aptxTrees); } - private ArchaeopteryxFrame(Phylogeny aptxTree) + public static ArchaeopteryxFrame createInstance(Phylogeny aptxTree) { - MainFrame aptxApp = Archaeopteryx.createApplication(aptxTree); - start(aptxApp); + Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in + // several trees simultaneously + return new ArchaeopteryxFrame(aptxTrees); } - private ArchaeopteryxFrame(TreeBuilder calculatedTree) + public static ArchaeopteryxFrame createInstance( + TreeBuilder calculatedTree) { ArchaeopteryxTreeBuilder aptxTreeBuilder = new ArchaeopteryxTreeBuilder(); Phylogeny aptxTree = aptxTreeBuilder.buildAptxTree(calculatedTree); - Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in // several trees simultaneously + return new ArchaeopteryxFrame(aptxTrees); + + } + + + private ArchaeopteryxFrame(Phylogeny[] aptxTrees) + { MainFrame aptxApp = Archaeopteryx.createApplication(aptxTrees, "_aptx_jalview_configuration_file", null); - start(aptxApp); - } + bindFrameToJalview(aptxApp); + } - public void start(MainFrame aptxApp) + // public so that, should an Aptx main frame ever get created outside this + // class, it can be bound to jalview anyway + public void bindFrameToJalview(MainFrame aptxApp) { int width = 400; int height = 550; -- 1.7.10.2