From: cmzmasek@gmail.com Date: Thu, 28 Jun 2012 03:52:29 +0000 (+0000) Subject: cleanup X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d30f8d155dee1fbfa17946cf80a203cc886ffdd6;p=jalview.git cleanup --- diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java index 4c17f0e..e63c23a 100644 --- a/forester/java/src/org/forester/application/gsdi.java +++ b/forester/java/src/org/forester/application/gsdi.java @@ -62,23 +62,22 @@ public final class gsdi { private enum BASE_ALGORITHM { GSDI, SDI } - final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true; - final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION = "g"; - final static private String SDI_OPTION = "b"; - final static private String MOST_PARSIMONIOUS_OPTION = "m"; - final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q"; - final static private String HELP_OPTION_1 = "help"; - final static private String HELP_OPTION_2 = "h"; - final static private String DEFAULT_OUTFILE_SUFFIX = "_gsdi_out.xml"; - final static private String SUFFIX_FOR_LIST_OF_STIPPED_GENE_TREE_NODES = "_stripped_gene_tree_nodes.txt"; - final static private String SUFFIX_FOR_SPECIES_TREE_USED = "_species_tree_used.xml"; - final static private String LOGFILE_SUFFIX = "_gsdi_log.txt"; - final static private String PRG_NAME = "gsdi"; - final static private String PRG_VERSION = "0.901"; - final static private String PRG_DATE = "120608"; - final static private String PRG_DESC = "general speciation duplication inference"; - final static private String E_MAIL = "phylosoft@gmail.com"; - final static private String WWW = "www.phylosoft.org/forester"; + final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true; + final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION = "g"; + final static private String SDISE_OPTION = "b"; + final static private String MOST_PARSIMONIOUS_OPTION = "m"; + final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q"; + final static private String HELP_OPTION_1 = "help"; + final static private String HELP_OPTION_2 = "h"; + final static private String DEFAULT_OUTFILE_SUFFIX = "_gsdi_out.xml"; + final static private String SUFFIX_FOR_SPECIES_TREE_USED = "_species_tree_used.xml"; + final static private String LOGFILE_SUFFIX = "_gsdi_log.txt"; + final static private String PRG_NAME = "gsdi"; + final static private String PRG_VERSION = "1.000"; + final static private String PRG_DATE = "120608"; + final static private String PRG_DESC = "general speciation duplication inference"; + final static private String E_MAIL = "phylosoft@gmail.com"; + final static private String WWW = "www.phylosoft.org/forester"; public static void main( final String args[] ) { try { @@ -109,7 +108,7 @@ public final class gsdi { System.exit( -1 ); } final List allowed_options = new ArrayList(); - allowed_options.add( gsdi.SDI_OPTION ); + allowed_options.add( gsdi.SDISE_OPTION ); allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE ); allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION ); allowed_options.add( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ); @@ -129,7 +128,7 @@ public final class gsdi { boolean most_parsimonous_duplication_model = false; boolean species_tree_in_phyloxml = true; boolean allow_stripping_of_gene_tree = false; - if ( cla.isOptionSet( gsdi.SDI_OPTION ) ) { + if ( cla.isOptionSet( gsdi.SDISE_OPTION ) ) { base_algorithm = BASE_ALGORITHM.SDI; } if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) { @@ -459,31 +458,28 @@ public final class gsdi { private static void print_help() { System.out.println( "Usage: " + gsdi.PRG_NAME - + " [-options] [outfile]" ); + + " [-options] [outfile]" ); System.out.println(); System.out.println( "Options:" ); - // System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION + ": to allow stripping of gene tree nodes without a matching species in the species tree (writes list of stripped nodes to " + ); - System.out.println( " -" + gsdi.SDI_OPTION + ": to use SDI algorithm instead of GSDI algorithm" );//TODO gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION not allowed + System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION + + ": to allow stripping of gene tree nodes without a matching species" ); System.out.println( " -" + gsdi.MOST_PARSIMONIOUS_OPTION + ": use most parimonious duplication model for GSDI: " ); System.out.println( " assign nodes as speciations which would otherwise be assiged" ); - System.out.println( " as unknown because of polytomies in the species tree" ); + System.out.println( " as potential duplications dueof polytomies in the species tree" ); System.out.println( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + ": to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" ); - System.out.println(); - System.out.println( "Species tree:" ); - System.out - .println( " In phyloXML format (unless option -" - + gsdi.GUESS_FORMAT_OF_SPECIES_TREE - + " is used, in which case the species matching between gene tree and species tree must be via scientific name), with taxonomy data in appropriate fields" ); + System.out.println( " -" + gsdi.SDISE_OPTION + + ": to use SDIse algorithm instead of GSDI algorithm (for binary species trees)" ); System.out.println(); System.out.println( "Gene tree:" ); - System.out.println( " In phyloXM format, with taxonomy and sequence data in appropriate fields" ); + System.out.println( " in phyloXM format, with taxonomy and sequence data in appropriate fields" ); + System.out.println(); + System.out.println( "Species tree:" ); + System.out.println( " in phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + " is used)" ); System.out.println(); - System.out.println( "Example:" ); - // System.out.println( "gsdi - // System.out.println(); - System.out.println( "Note -- GSDI algorithm is under development" ); + System.out.println( "Example: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION + + " gene_tree.xml tree_of_life.xml out.xml" ); System.out.println(); } } diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java index d61f9d1..0e48d32 100644 --- a/forester/java/src/org/forester/sdi/GSDI.java +++ b/forester/java/src/org/forester/sdi/GSDI.java @@ -224,7 +224,6 @@ public final class GSDI extends SDI { final Map species_to_node_map = new HashMap(); final List species_tree_ext_nodes = new ArrayList(); _tax_comp_base = determineTaxonomyComparisonBase( _gene_tree ); - // System.out.println( "comp base is: " + tax_comp_base ); // Stringyfied taxonomy is the key, node is the value. for( final PhylogenyNodeIterator iter = _species_tree.iteratorExternalForward(); iter.hasNext(); ) { final PhylogenyNode s = iter.next(); @@ -272,7 +271,6 @@ public final class GSDI extends SDI { else { g.setLink( s ); _mapped_species_tree_nodes.add( s ); - // System.out.println( "setting link of " + g + " to " + s ); } } }