From 85bd50f60e349023cb62ad33caeef922fa680aa1 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 26 Apr 2013 22:48:27 +0000 Subject: [PATCH] inprogress --- .../src/org/forester/application/decorator.java | 30 ++++++++++++++++++-- 1 file changed, 28 insertions(+), 2 deletions(-) diff --git a/forester/java/src/org/forester/application/decorator.java b/forester/java/src/org/forester/application/decorator.java index acf8c50..d4bc1e4 100644 --- a/forester/java/src/org/forester/application/decorator.java +++ b/forester/java/src/org/forester/application/decorator.java @@ -35,6 +35,8 @@ import org.forester.io.parsers.PhylogenyParser; import org.forester.io.parsers.util.ParserUtils; import org.forester.io.writers.PhylogenyWriter; import org.forester.phylogeny.Phylogeny; +import org.forester.phylogeny.PhylogenyMethods; +import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY; import org.forester.phylogeny.data.Identifier; import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; @@ -59,6 +61,8 @@ public final class decorator { final static private String TREE_NAME_OPTION = "pn"; final static private String TREE_ID_OPTION = "pi"; final static private String TREE_DESC_OPTION = "pd"; + final static private String MIDPOINT_ROOT_OPTION = "mp"; + final static private String ORDER_TREE_OPTION = "or"; final static private String EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION = "sn"; final static private String EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION = "tc"; final static private String PROCESS_NAME_INTELLIGENTLY_OPTION = "x"; @@ -71,8 +75,8 @@ public final class decorator { final static private String MAPPING_FILE_SEPARATOR_OPTION = "s"; final static private char MAPPING_FILE_SEPARATOR_DEFAULT = '\t'; final static private String PRG_NAME = "decorator"; - final static private String PRG_VERSION = "1.13"; - final static private String PRG_DATE = "2013.01.19"; + final static private String PRG_VERSION = "1.14"; + final static private String PRG_DATE = "130426"; public static void main( final String args[] ) { ForesterUtil.printProgramInformation( decorator.PRG_NAME, decorator.PRG_VERSION, decorator.PRG_DATE ); @@ -112,6 +116,8 @@ public final class decorator { allowed_options.add( decorator.TREE_ID_OPTION ); allowed_options.add( decorator.TREE_DESC_OPTION ); allowed_options.add( decorator.TRIM_AFTER_TILDE_OPTION ); + allowed_options.add( decorator.ORDER_TREE_OPTION ); + allowed_options.add( decorator.MIDPOINT_ROOT_OPTION ); final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); if ( dissallowed_options.length() > 0 ) { ForesterUtil.fatalError( decorator.PRG_NAME, "unknown option(s): " + dissallowed_options ); @@ -144,6 +150,8 @@ public final class decorator { boolean extract_bracketed_scientific_name = false; boolean extract_bracketed_tax_code = false; boolean trim_after_tilde = false; + boolean order_tree = false; + boolean midpoint_root = false; String tree_name = ""; String tree_id = ""; String tree_desc = ""; @@ -209,6 +217,12 @@ public final class decorator { numbers_of_chars_allowed_to_remove_if_not_found_in_map = cla .getOptionValueAsInt( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION ); } + if ( cla.isOptionSet( decorator.MIDPOINT_ROOT_OPTION ) ) { + midpoint_root = true; + } + if ( cla.isOptionSet( decorator.ORDER_TREE_OPTION ) ) { + order_tree = true; + } if ( cla.isOptionSet( decorator.FIELD_OPTION ) ) { field_str = cla.getOptionValue( decorator.FIELD_OPTION ); if ( field_str.equals( NODE_NAME_FIELD ) ) { @@ -346,6 +360,16 @@ public final class decorator { catch ( final Exception e ) { ForesterUtil.fatalError( decorator.PRG_NAME, e.getLocalizedMessage() ); } + if ( midpoint_root || order_tree ) { + for( final Phylogeny phy : phylogenies ) { + if ( midpoint_root ) { + PhylogenyMethods.midpointRoot( phy ); + } + if ( order_tree ) { + PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.TAXONOMY ); + } + } + } try { final PhylogenyWriter w = new PhylogenyWriter(); w.toPhyloXML( phylogenies, 0, phylogenies_outfile, ForesterUtil.getLineSeparator() ); @@ -400,6 +424,8 @@ public final class decorator { System.out.println( " -c : cut name after first space (only for -f=n)" ); System.out.println( " -" + decorator.TRIM_AFTER_TILDE_OPTION + " : trim node name to be replaced after tilde" ); + System.out.println( " -" + decorator.MIDPOINT_ROOT_OPTION + " : to midpoint-root the tree" ); + System.out.println( " -" + decorator.ORDER_TREE_OPTION + " : to order tree branches" ); System.out.println(); System.exit( -1 ); } -- 1.7.10.2