From 0f6e7d07eb1a625dd7ff3df0da406cafd4850fea Mon Sep 17 00:00:00 2001 From: cmzmasek Date: Wed, 15 Nov 2017 14:55:09 -0800 Subject: [PATCH] in progress --- .../src/org/forester/application/cladinator.java | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/forester/java/src/org/forester/application/cladinator.java b/forester/java/src/org/forester/application/cladinator.java index e00dd20..9d84bc3 100644 --- a/forester/java/src/org/forester/application/cladinator.java +++ b/forester/java/src/org/forester/application/cladinator.java @@ -52,8 +52,8 @@ import org.forester.util.UserException; public final class cladinator { final static private String PRG_NAME = "cladinator"; - final static private String PRG_VERSION = "1.06"; - final static private String PRG_DATE = "171115"; + final static private String PRG_VERSION = "1.07"; + final static private String PRG_DATE = "1711xx"; final static private String PRG_DESC = "clades within clades of annotated labels -- analysis of pplacer-type outputs"; final static private String E_MAIL = "phyloxml@gmail.com"; final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"; @@ -70,7 +70,7 @@ public final class cladinator { final static private String SPECIAL_PROCESSING_OPTION = "S"; final static private String VERBOSE_OPTION = "v"; final static private String REMOVE_ANNOT_SEP_OPTION = "rs"; - final static private double SPECIFICS_CUTOFF_DEFAULT = 0.8; + final static private double SPECIFICS_CUTOFF_DEFAULT = 0.7; final static private String SEP_DEFAULT = "."; final static private Pattern QUERY_PATTERN_DEFAULT = AnalysisMulti.DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE; final static private String EXTRA_PROCESSING1_SEP_DEFAULT = "|"; @@ -570,8 +570,8 @@ public final class cladinator { System.out.println( " -" + SPECIFICS_CUTOFF_OPTION + "= : the minimal confidence value for \"specific-hits\" to be reported (default: " + SPECIFICS_CUTOFF_DEFAULT + ")" ); - System.out.println( " -" + SEP_OPTION + "= : the annotation-separator to be used (default: " - + SEP_DEFAULT + ")" ); + System.out.println( " -" + SEP_OPTION + "= : the annotation-separator to be used (default: \"" + + SEP_DEFAULT + "\")" ); System.out.println( " -" + MAPPING_FILE_OPTION + "= : to map node names to appropriate annotations (tab-separated, two columns) (default: no mapping)" ); System.out.println( " -" + EXTRA_PROCESSING_OPTION1 @@ -584,12 +584,14 @@ public final class cladinator { System.out.println( " -" + SPECIAL_PROCESSING_OPTION + "= : special processing with pattern (e.g. \"(\\d+)([a-z]+)_.+\" for changing \"6q_EF42\" to \"6.q\")" ); System.out.println( " -" + REMOVE_ANNOT_SEP_OPTION - + " : to remove the annotation-separator in the output" ); + + " : to remove the annotation-separator in the output (e.g. the \"" + SEP_DEFAULT + + "\")" ); System.out.println( " -" + VERBOSE_OPTION + " : verbose" ); - System.out.println( " -" + QUIET_OPTION + " : quiet (for when used in a pipeline)" ); + System.out.println( " -" + QUIET_OPTION + + " : quiet (no output to console, for when used in a pipeline)" ); System.out.println( " --" + QUERY_PATTERN_OPTION - + "= : the regular expression pattern for the query (default: \"" + QUERY_PATTERN_DEFAULT - + "\" for pplacer output)" ); + + "= : expert option: the regular expression pattern for the query (default: \"" + + QUERY_PATTERN_DEFAULT + "\" for pplacer output)" ); System.out.println(); System.out.println( "Examples:" ); System.out.println(); -- 1.7.10.2