From 53b99b41ed7f26f2724f3ed87d524eb83c5208f4 Mon Sep 17 00:00:00 2001 From: kjvdheide Date: Fri, 6 Oct 2017 16:33:17 +0100 Subject: [PATCH] Start of creating the objects Archaeopteryx needs --- .../ext/archaeopteryx/AlignConvertForArchaeopteryx.java | 6 ++++++ src/jalview/ext/archaeopteryx/AlignmentToTreeViewerI.java | 8 ++++++++ src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java | 6 ++++++ src/jalview/gui/CalculationChooser.java | 6 ++---- 4 files changed, 22 insertions(+), 4 deletions(-) create mode 100644 src/jalview/ext/archaeopteryx/AlignConvertForArchaeopteryx.java create mode 100644 src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java diff --git a/src/jalview/ext/archaeopteryx/AlignConvertForArchaeopteryx.java b/src/jalview/ext/archaeopteryx/AlignConvertForArchaeopteryx.java new file mode 100644 index 0000000..22aec97 --- /dev/null +++ b/src/jalview/ext/archaeopteryx/AlignConvertForArchaeopteryx.java @@ -0,0 +1,6 @@ +package jalview.ext.archaeopteryx; + +public class AlignConvertForArchaeopteryx +{ + +} diff --git a/src/jalview/ext/archaeopteryx/AlignmentToTreeViewerI.java b/src/jalview/ext/archaeopteryx/AlignmentToTreeViewerI.java index 3b3747c..0dddbf1 100644 --- a/src/jalview/ext/archaeopteryx/AlignmentToTreeViewerI.java +++ b/src/jalview/ext/archaeopteryx/AlignmentToTreeViewerI.java @@ -20,8 +20,16 @@ */ package jalview.ext.archaeopteryx; +import java.util.Collection; interface AlignmentToTreeViewerI { + public void rootNode(Object node); + + public Object makeTreeNode(String nodeName); + + public Object addNodeChild(Object childNode, Object parentNode); + + public Collection getNodes(); } diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java new file mode 100644 index 0000000..e8c5109 --- /dev/null +++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java @@ -0,0 +1,6 @@ +package jalview.ext.archaeopteryx; + +public class ArchaeopteryxTreeBuilder +{ + +} diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java index 58a28c0..bd6c5ee 100644 --- a/src/jalview/gui/CalculationChooser.java +++ b/src/jalview/gui/CalculationChooser.java @@ -21,7 +21,6 @@ package jalview.gui; import jalview.analysis.TreeBuilder; -import jalview.analysis.TreeCalculator; import jalview.analysis.scoremodels.ScoreModels; import jalview.analysis.scoremodels.SimilarityParams; import jalview.api.analysis.ScoreModelI; @@ -472,9 +471,8 @@ public class CalculationChooser extends JPanel { String treeAlgo = determineTreeAlgo(); - TreeCalculator calculateTree = new TreeCalculator(treeAlgo, - substitutionMatrix, - params); + // TreeCalculator calculateTree = new TreeCalculator(treeAlgo, + // substitutionMatrix, params); openTreePanel(treeAlgo, substitutionMatrix, params); } -- 1.7.10.2