From 324c8f8f1d1090664f6f49e86825c8543a55f08b Mon Sep 17 00:00:00 2001 From: kjvdheide Date: Tue, 9 Jan 2018 11:18:07 +0000 Subject: [PATCH] JAL-2805 added nexus specific parser settings --- src/jalview/ext/archaeopteryx/AptxInit.java | 5 ----- src/jalview/ext/forester/io/ForesterParser.java | 5 +++++ 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java index 0337829..f8347bd 100644 --- a/src/jalview/ext/archaeopteryx/AptxInit.java +++ b/src/jalview/ext/archaeopteryx/AptxInit.java @@ -74,11 +74,6 @@ public final class AptxInit private final static NHXParser.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION = APTX_CONFIG .getTaxonomyExtraction(); - - - - - public static TreeFrameI createInstanceFromCalculation( final TreeBuilder calculatedTree) { diff --git a/src/jalview/ext/forester/io/ForesterParser.java b/src/jalview/ext/forester/io/ForesterParser.java index a6d7831..4cd84b1 100644 --- a/src/jalview/ext/forester/io/ForesterParser.java +++ b/src/jalview/ext/forester/io/ForesterParser.java @@ -1,5 +1,6 @@ package jalview.ext.forester.io; +import jalview.ext.archaeopteryx.AptxInit; import jalview.ext.archaeopteryx.Tree; import jalview.ext.treeviewer.TreeI; import jalview.ext.treeviewer.TreeParserI; @@ -30,6 +31,10 @@ public class ForesterParser public static ForesterParser createNexusParser(File file) throws PhylogenyParserException, IOException { + NexusPhylogeniesParser nxParser = new NexusPhylogeniesParser(); + nxParser.setReplaceUnderscores( + AptxInit.APTX_CONFIG.isReplaceUnderscoresInNhParsing()); + nxParser.setIgnoreQuotes(false); return new ForesterParser(new NexusPhylogeniesParser(), file); } -- 1.7.10.2