X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fphyloxml_converter.java;h=d2c0a5cd283aed3cc5cf33dfcf83158332a250c0;hb=4e202b796a689419621ddc2c3934797c39af9026;hp=9822e1fc40a6e11964037d126c9a55410fc46abb;hpb=493e40b0c936b65da342134da37e8b856b9b80af;p=jalview.git diff --git a/forester/java/src/org/forester/application/phyloxml_converter.java b/forester/java/src/org/forester/application/phyloxml_converter.java index 9822e1f..d2c0a5c 100644 --- a/forester/java/src/org/forester/application/phyloxml_converter.java +++ b/forester/java/src/org/forester/application/phyloxml_converter.java @@ -6,7 +6,7 @@ // 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 @@ -16,7 +16,7 @@ // 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 @@ -47,29 +47,31 @@ import org.forester.util.ForesterUtil.PhylogenyNodeField; 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 ); @@ -142,6 +144,12 @@ public class phyloxml_converter { 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 { @@ -353,6 +361,14 @@ public class phyloxml_converter { 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