inprogress

[jalview.git] / forester / java / src / org / forester / application / decorator.java

diff --git a/forester/java/src/org/forester/application/decorator.java b/forester/java/src/org/forester/application/decorator.java
index 8084ee2..d4bc1e4 100644 (file)
--- a/forester/java/src/org/forester/application/decorator.java
+++ b/forester/java/src/org/forester/application/decorator.java
@@ -21,7 +21,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.application;
 
@@ -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";
@@ -69,10 +73,10 @@ public final class decorator {
     final static private String KEY_COLUMN                              = "k";
     final static private String VALUE_COLUMN                            = "v";
     final static private String MAPPING_FILE_SEPARATOR_OPTION           = "s";
-    final static private String MAPPING_FILE_SEPARATOR_DEFAULT          = ": ";
+    final static private char   MAPPING_FILE_SEPARATOR_DEFAULT          = '\t';
     final static private String PRG_NAME                                = "decorator";
-    final static private String PRG_VERSION                             = "1.12";
-    final static private String PRG_DATE                                = "2012.12.21";
+    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 );
@@ -126,12 +132,12 @@ public final class decorator {
             }
         }
         final boolean picky = cla.isOptionSet( decorator.PICKY_OPTION );
-        String separator = decorator.MAPPING_FILE_SEPARATOR_DEFAULT;
+        char separator = decorator.MAPPING_FILE_SEPARATOR_DEFAULT;
         if ( cla.isOptionSet( decorator.MAPPING_FILE_SEPARATOR_OPTION ) ) {
             if ( advanced_table ) {
                 argumentsError();
             }
-            separator = cla.getOptionValue( decorator.MAPPING_FILE_SEPARATOR_OPTION );
+            separator = cla.getOptionValueAsChar( decorator.MAPPING_FILE_SEPARATOR_OPTION );
         }
         int key_column = 0;
         int value_column = 1;
@@ -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 ) ) {
@@ -277,7 +291,7 @@ public final class decorator {
         if ( !advanced_table ) {
             BasicTable<String> mapping_table = null;
             try {
-                mapping_table = BasicTableParser.parse( mapping_infile, separator, false, true );
+                mapping_table = BasicTableParser.parse( mapping_infile, separator, true, false );
             }
             catch ( final Exception e ) {
                 ForesterUtil.fatalError( decorator.PRG_NAME,
@@ -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 );
     }