// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
public class phyloxml_converter {
- final static private String HELP_OPTION_1 = "help";
- final static private String HELP_OPTION_2 = "h";
- final static private String FIELD_OPTION = "f";
- final static private String FIELD_CLADE_NAME = "nn";
- final static private String FIELD_TAXONOMY_CODE = "tc";
- final static private String FIELD_TAXONOMY_SCI_NAME = "sn";
- final static private String FIELD_TAXONOMY_COMM_NAME = "cn";
- final static private String FIELD_SEQUENCE_GENE_NAME = "gn";
- final static private String FIELD_SEQUENCE_SYMBOL = "sy";
- final static private String FIELD_DUMMY = "dummy";
- final static private String INTERNAL_NAMES_ARE_BOOT_SUPPPORT = "i";
- final static private String MIDPOINT_REROOT = "m";
- final static private String EXTRACT_TAXONOMY = "xt";
- final static private String EXTRACT_TAXONOMY_PF = "xp";
- final static private String ORDER_SUBTREES = "o";
- final static private String NO_TREE_LEVEL_INDENDATION = "ni";
- final static private String REPLACE_UNDER_SCORES = "ru";
- final static private String PRG_NAME = "phyloxml_converter";
- final static private String PRG_VERSION = "1.21";
- final static private String PRG_DATE = "2010.10.02";
- final static private String E_MAIL = "czmasek@burnham.org";
- final static private String WWW = "www.phylosoft.org/forester/";
- final static private boolean SPECIAL = false;
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String FIELD_OPTION = "f";
+ final static private String FIELD_CLADE_NAME = "nn";
+ final static private String FIELD_TAXONOMY_CODE = "tc";
+ final static private String FIELD_TAXONOMY_SCI_NAME = "sn";
+ final static private String FIELD_TAXONOMY_COMM_NAME = "cn";
+ final static private String FIELD_SEQUENCE_GENE_NAME = "gn";
+ final static private String FIELD_SEQUENCE_SYMBOL = "sy";
+ final static private String FIELD_UNIPROT_TAXONOMY_ID_SPLIT_1 = "i1";
+ final static private String FIELD_UNIPROT_TAXONOMY_ID_SPLIT_2 = "i2";
+ final static private String FIELD_DUMMY = "dummy";
+ final static private String INTERNAL_NAMES_ARE_BOOT_SUPPPORT = "i";
+ final static private String MIDPOINT_REROOT = "m";
+ final static private String EXTRACT_TAXONOMY = "xt";
+ final static private String EXTRACT_TAXONOMY_PF = "xp";
+ final static private String ORDER_SUBTREES = "o";
+ final static private String NO_TREE_LEVEL_INDENDATION = "ni";
+ final static private String REPLACE_UNDER_SCORES = "ru";
+ final static private String PRG_NAME = "phyloxml_converter";
+ final static private String PRG_VERSION = "1.30";
+ final static private String PRG_DATE = "2011.03.01";
+ final static private String E_MAIL = "phylosoft@gmail.com";
+ final static private String WWW = "www.phylosoft.org/forester/";
+ final static private boolean SPECIAL = false;
public static void main( final String args[] ) {
ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
else if ( field_option_value.equals( FIELD_SEQUENCE_SYMBOL ) ) {
field = PhylogenyNodeField.SEQUENCE_SYMBOL;
}
+ else if ( field_option_value.equals( FIELD_UNIPROT_TAXONOMY_ID_SPLIT_1 ) ) {
+ field = PhylogenyNodeField.TAXONOMY_ID_UNIPROT_1;
+ }
+ else if ( field_option_value.equals( FIELD_UNIPROT_TAXONOMY_ID_SPLIT_2 ) ) {
+ field = PhylogenyNodeField.TAXONOMY_ID_UNIPROT_2;
+ }
else if ( field_option_value.equals( FIELD_DUMMY ) ) {
}
else {
System.out.println( " " + FIELD_TAXONOMY_COMM_NAME + ": transfer name to taxonomy common name" );
System.out.println( " " + FIELD_SEQUENCE_GENE_NAME + ": transfer name to sequence name" );
System.out.println( " " + FIELD_SEQUENCE_SYMBOL + ": transfer name to sequence symbol" );
+ System.out
+ .println( " "
+ + FIELD_UNIPROT_TAXONOMY_ID_SPLIT_1
+ + ": transfer/split name to taxonomy uniprot identifier\n (split at underscore if \"id_name\" pattern, e.g. \"817_SusD\")" );
+ System.out
+ .println( " "
+ + FIELD_UNIPROT_TAXONOMY_ID_SPLIT_2
+ + ": transfer/split name to taxonomy uniprot identifier\n (split at underscore if \"name_id\" pattern, e.g. \"SusD_817\")" );
System.out.println();
System.out.println( " options: " );
System.out.println( " -" + INTERNAL_NAMES_ARE_BOOT_SUPPPORT