From 6d58a23a91302f7730d514a84b7501befc5aa3f1 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 25 Feb 2014 01:27:21 +0000 Subject: [PATCH] kind of pointless addition --- .../java/src/org/forester/archaeopteryx/MainFrameApplication.java | 2 +- forester/java/src/org/forester/io/parsers/nhx/NHXParser.java | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index a4cf12a..4b860a1 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -941,7 +941,7 @@ public final class MainFrameApplication extends MainFrame { .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) ); _options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) ); _options_jmenu - .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Value Format Errors" ) ); + .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) ); // _options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) ); _options_jmenu diff --git a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java index f87160f..72c95d3 100644 --- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java +++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java @@ -678,7 +678,8 @@ public final class NHXParser implements PhylogenyParser, IteratingPhylogenyParse node_to_annotate.getNodeData().getSequence().setName( s.substring( 3 ) ); } else if ( s.indexOf( '=' ) < 0 ) { - if ( node_to_annotate.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) { + if ( node_to_annotate.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT + && !allow_errors_in_distance_to_parent ) { throw new NHXFormatException( "error in NHX formatted data: more than one distance to parent:" + "\"" + s + "\"" ); } -- 1.7.10.2