From: cmzmasek@gmail.com Date: Fri, 16 May 2014 21:25:11 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=327fc7c7a9a46cbe8983b0ca2a54cc6f45cd1695;p=jalview.git inprogress --- diff --git a/forester/java/src/org/forester/application/phyloxml_converter.java b/forester/java/src/org/forester/application/phyloxml_converter.java index 164bfee..d258bfc 100644 --- a/forester/java/src/org/forester/application/phyloxml_converter.java +++ b/forester/java/src/org/forester/application/phyloxml_converter.java @@ -70,10 +70,10 @@ public class phyloxml_converter { final static private String REPLACE_UNDER_SCORES = "ru"; final static private String IGNORE_QUOTES = "iqs"; final static private String PRG_NAME = "phyloxml_converter"; - final static private String PRG_VERSION = "1.301"; - final static private String PRG_DATE = "2012.08.31"; - final static private String E_MAIL = "phylosoft@gmail.com"; - final static private String WWW = "www.phylosoft.org/forester/"; + final static private String PRG_VERSION = "1.302"; + final static private String PRG_DATE = "140516"; + final static private String E_MAIL = "phyloxml@gmail.com"; + final static private String WWW = "sites.google.com/site/cmzmasek/home/software/forester"; final static private boolean SPECIAL = false; public static void main( final String args[] ) throws PhyloXmlDataFormatException { @@ -367,20 +367,19 @@ public class phyloxml_converter { System.out.println(); System.out.println( " field options: " ); System.out.println(); - System.out.println( " " + FIELD_CLADE_NAME + ": transfer name to node/clade name" ); - System.out.println( " " + FIELD_TAXONOMY_CODE + ": transfer name to taxonomy code" ); - System.out.println( " " + FIELD_TAXONOMY_SCI_NAME + ": transfer name to taxonomy scientific name" ); - 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( " " + FIELD_CLADE_NAME + ": transfer name to node/clade name" ); + System.out.println( " " + FIELD_TAXONOMY_CODE + ": transfer name to taxonomy code" ); + System.out.println( " " + FIELD_TAXONOMY_SCI_NAME + ": transfer name to taxonomy scientific name" ); + 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_DUMMY + ": to convert NHX formatted trees to phyloXML" ); + System.out.println( " " + FIELD_UNIPROT_TAXONOMY_ID_SPLIT_1 + + ": transfer/split name to taxonomy uniprot identifier" ); + System.out.println( " (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" ); + System.out.println( " (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