From e8c7440196e8fe798bd5dc2b83cc1e194c77f0d0 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 20 Dec 2012 00:53:40 +0000 Subject: [PATCH] "rio" work --- forester/java/src/org/forester/application/rio.java | 10 ++++++---- .../src/org/forester/archaeopteryx/MainFrameApplication.java | 1 + forester/java/src/org/forester/util/ForesterConstants.java | 4 ++-- 3 files changed, 9 insertions(+), 6 deletions(-) diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java index d1a317a..e47e31a 100644 --- a/forester/java/src/org/forester/application/rio.java +++ b/forester/java/src/org/forester/application/rio.java @@ -328,11 +328,13 @@ public class rio { System.out.println( " disallowed, as are most options)" ); System.out.println(); System.out.println( " Formats" ); - System.out.println( " The species tree is expected to be in phyloXML format." ); System.out - .println( " The gene trees ideally are in phyloXML as well, but can also be in New Hamphshire (Newick)" ); - System.out.println( " or Nexus format as long as species information can be extracted from the gene names" ); - System.out.println( " (e.g. \"HUMAN\" from \"BCL2_HUMAN\")." ); + .println( " The gene trees, as well as the species tree, ideally are in phyloXML (www.phyloxml.org) format," ); + System.out + .println( " but can also be in New Hamphshire (Newick) or Nexus format as long as species information can be" ); + System.out + .println( " extracted from the gene names (e.g. \"HUMAN\" from \"BCL2_HUMAN\") and matched to a single species" ); + System.out.println( " in the species tree." ); System.out.println(); System.out.println( " Examples" ); System.out.println( " \"rio gene_trees.nh species.xml outtable.tsv log.txt\"" ); diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 7b3f411..d566c75 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -2350,6 +2350,7 @@ public final class MainFrameApplication extends MainFrame { private void setSpecialOptionsForNexParser( final NexusPhylogeniesParser nex ) { nex.setReplaceUnderscores( getOptions().isReplaceUnderscoresInNhParsing() ); + nex.setTaxonomyExtraction( getOptions().getTaxonomyExtraction() ); } private void setSpecialOptionsForNhxParser( final NHXParser nhx ) { diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java index bff716b..a096bf5 100644 --- a/forester/java/src/org/forester/util/ForesterConstants.java +++ b/forester/java/src/org/forester/util/ForesterConstants.java @@ -27,8 +27,8 @@ package org.forester.util; public final class ForesterConstants { - public final static String FORESTER_VERSION = "1.011"; - public final static String FORESTER_DATE = "121214"; + public final static String FORESTER_VERSION = "1.012"; + public final static String FORESTER_DATE = "121219"; public final static String PHYLO_XML_VERSION = "1.10"; public final static String PHYLO_XML_LOCATION = "http://www.phyloxml.org"; public final static String PHYLO_XML_XSD = "phyloxml.xsd"; -- 1.7.10.2