"rio" work

diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java
index b9a1573..18fa912 100644 (file)
--- a/forester/java/src/org/forester/application/rio.java
+++ b/forester/java/src/org/forester/application/rio.java
@@ -30,121 +30,130 @@ package org.forester.application;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.sdi.RIO;
+import org.forester.util.CommandLineArguments;
 import org.forester.util.ForesterUtil;
 
 public class rio {
 
-    final static private String  PRG_NAME    = "RIO";
-    final static private String  PRG_VERSION = "2.03 ALPHA";
-    final static private String  PRG_DATE    = "2010.01.15";
-    final static private String  E_MAIL      = "czmasek@burnham.org";
-    final static private String  WWW         = "www.phylosoft.org/forester/";
-    final static private boolean TIME        = true;
-    final static private boolean VERBOSE     = true;
-
-    private final static void errorInCommandLine() {
-        System.out.println( "\nrio: Error in command line.\n" );
-        printHelp();
-        System.exit( -1 );
-    }
+    final static private String PRG_NAME              = "rio";
+    final static private String PRG_VERSION           = "3.00 beta 1";
+    final static private String PRG_DATE              = "2010.01.15";
+    final static private String E_MAIL                = "czmasek@burnham.org";
+    final static private String WWW                   = "www.phylosoft.org/forester/";
+    final static private String HELP_OPTION_1         = "help";
+    final static private String HELP_OPTION_2         = "h";
+    final static private String QUERY_OPTION          = "q";
+    final static private String SORT_OPTION           = "s";
+    final static private String OUTPUT_ULTRA_P_OPTION = "u";
+    final static private String CUTOFF_ULTRA_P_OPTION = "cu";
+    final static private String CUTOFF_ORTHO_OPTION   = "co";
+    final static private String TABLE_OUTPUT_OPTION   = "t";
 
     public static void main( final String[] args ) {
-        ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
-        File species_tree_file = null;
-        File multiple_trees_file = null;
-        File outfile = null;
-        String seq_name = "";
-        String arg = "";
-        boolean output_ultraparalogs = false;
-        double t_orthologs = 0.0;
-        double t_orthologs_dc = 0.0;
-        double threshold_ultra_paralogs = 0.0;
-        int sort = 13;
-        Phylogeny species_tree = null;
-        RIO rio_instance = null;
-        PrintWriter out = null;
-        long time = 0;
-        if ( args.length < 2 ) {
+        ForesterUtil.printProgramInformation( PRG_NAME,
+                                              "resampled inference of orthologs",
+                                              PRG_VERSION,
+                                              PRG_DATE,
+                                              E_MAIL,
+                                              WWW,
+                                              ForesterUtil.getForesterLibraryInformation() );
+        CommandLineArguments cla = null;
+        try {
+            cla = new CommandLineArguments( args );
+        }
+        catch ( final Exception e ) {
+            ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+        }
+        if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
             printHelp();
             System.exit( 0 );
         }
-        else if ( ( args.length < 3 ) || ( args.length > 18 ) ) {
-            errorInCommandLine();
-        }
-        for( final String arg2 : args ) {
-            if ( arg2.trim().charAt( 0 ) != 'p' ) {
-                if ( arg2.trim().length() < 3 ) {
-                    errorInCommandLine();
-                }
-                else {
-                    arg = arg2.trim().substring( 2 );
-                }
+        if ( ( args.length < 3 ) || ( args.length > 10 ) ) {
+            System.out.println();
+            System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" );
+            System.out.println();
+            printHelp();
+            System.exit( -1 );
+        }
+        final List<String> allowed_options = new ArrayList<String>();
+        allowed_options.add( QUERY_OPTION );
+        allowed_options.add( SORT_OPTION );
+        allowed_options.add( CUTOFF_ULTRA_P_OPTION );
+        allowed_options.add( CUTOFF_ORTHO_OPTION );
+        allowed_options.add( TABLE_OUTPUT_OPTION );
+        allowed_options.add( OUTPUT_ULTRA_P_OPTION );
+        final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+        if ( dissallowed_options.length() > 0 ) {
+            ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
+        }
+        final File multiple_trees_file = cla.getFile( 0 );
+        final File species_tree_file = cla.getFile( 1 );
+        final File outfile = cla.getFile( 2 );
+        ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, multiple_trees_file );
+        ForesterUtil.fatalErrorIfFileNotReadable( PRG_NAME, species_tree_file );
+        if ( outfile.exists() ) {
+            ForesterUtil.fatalError( PRG_NAME, "[" + outfile + "] already exists" );
+        }
+        String seq_name = null;
+        if ( cla.isOptionSet( QUERY_OPTION ) ) {
+            seq_name = cla.getOptionValue( QUERY_OPTION );
+        }
+        File table_outfile = null;
+        if ( cla.isOptionSet( TABLE_OUTPUT_OPTION ) ) {
+            table_outfile = new File( cla.getOptionValue( TABLE_OUTPUT_OPTION ) );
+            if ( table_outfile.exists() ) {
+                ForesterUtil.fatalError( PRG_NAME, "[" + outfile + "] already exists" );
             }
-            try {
-                switch ( arg2.trim().charAt( 0 ) ) {
-                    case 'M':
-                        multiple_trees_file = new File( arg );
-                        break;
-                    case 'N':
-                        seq_name = arg;
-                        break;
-                    case 'S':
-                        species_tree_file = new File( arg );
-                        break;
-                    case 'O':
-                        outfile = new File( arg );
-                        break;
-                    case 'p':
-                        output_ultraparalogs = true;
-                        break;
-                    case 'P':
-                        sort = Integer.parseInt( arg );
-                        if ( ( sort < 0 ) || ( sort > 17 ) ) {
-                            errorInCommandLine();
-                        }
-                        break;
-                    case 'L':
-                        t_orthologs = Double.parseDouble( arg );
-                        break;
-                    case 'v':
-                        threshold_ultra_paralogs = Double.parseDouble( arg );
-                        break;
-                    default:
-                        errorInCommandLine();
-                }
+        }
+        boolean output_ultraparalogs = false;
+        if ( cla.isOptionSet( OUTPUT_ULTRA_P_OPTION ) ) {
+            output_ultraparalogs = true;
+        }
+        double t_orthologs = 0.0;
+        double threshold_ultra_paralogs = 0.0;
+        int sort = 2;
+        try {
+            if ( cla.isOptionSet( CUTOFF_ORTHO_OPTION ) ) {
+                t_orthologs = cla.getOptionValueAsDouble( CUTOFF_ORTHO_OPTION );
             }
-            catch ( final Exception e ) {
-                errorInCommandLine();
+            if ( cla.isOptionSet( CUTOFF_ULTRA_P_OPTION ) ) {
+                threshold_ultra_paralogs = cla.getOptionValueAsDouble( CUTOFF_ULTRA_P_OPTION );
             }
-        }
-        if ( ( seq_name == "" ) || ( species_tree_file == null ) || ( multiple_trees_file == null )
-                || ( outfile == null ) ) {
-            errorInCommandLine();
-        }
-        if ( ( sort < 0 ) || ( sort > 2 ) ) {
-            errorInCommandLine();
-        }
-        if ( VERBOSE ) {
-            System.out.println( "\nMultiple trees file:                          " + multiple_trees_file );
-            System.out.println( "Seq name:                                     " + seq_name );
-            System.out.println( "Species tree file:                            " + species_tree_file );
-            System.out.println( "Outfile:                                      " + outfile );
-            System.out.println( "Sort:                                         " + sort );
-            System.out.println( "Threshold orthologs:                          " + t_orthologs );
-            System.out.println( "Threshold orthologs for distance calc.:       " + t_orthologs_dc );
-            if ( output_ultraparalogs ) {
-                System.out.println( "Threshold ultra paralogs:                     " + threshold_ultra_paralogs );
+            if ( cla.isOptionSet( SORT_OPTION ) ) {
+                sort = cla.getOptionValueAsInt( SORT_OPTION );
             }
         }
-        if ( TIME && VERBOSE ) {
-            time = System.currentTimeMillis();
+        catch ( final Exception e ) {
+            ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getLocalizedMessage() );
+        }
+        if ( sort < 0 ) {
+            sort = 0;
         }
+        else if ( sort > 2 ) {
+            sort = 2;
+        }
+        long time = 0;
+        System.out.println( "\n" );
+        System.out.println( "Gene trees:                              " + multiple_trees_file );
+        System.out.println( "Species tree:                            " + species_tree_file );
+        System.out.println( "Query:                                     " + seq_name );
+        System.out.println( "Outfile:                                      " + outfile );
+        System.out.println( "Outfile:                                      " + table_outfile );
+        System.out.println( "Sort:                                         " + sort );
+        System.out.println( "Threshold orthologs:                          " + t_orthologs );
+        if ( output_ultraparalogs ) {
+            System.out.println( "Threshold ultra paralogs:                     " + threshold_ultra_paralogs );
+        }
+        time = System.currentTimeMillis();
+        Phylogeny species_tree = null;
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
             species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
@@ -161,8 +170,9 @@ public class rio {
             ForesterUtil.printErrorMessage( PRG_NAME, "Species tree is not completely binary" );
             System.exit( -1 );
         }
-        rio_instance = new RIO();
+        final RIO rio_instance = new RIO();
         final StringBuffer output = new StringBuffer();
+        PrintWriter out = null;
         try {
             rio_instance.inferOrthologs( multiple_trees_file, species_tree.copy(), seq_name );
             output.append( rio_instance.inferredOrthologsToString( seq_name, sort, t_orthologs ) );
@@ -183,26 +193,38 @@ public class rio {
         out.println( output );
         out.close();
         ForesterUtil.programMessage( PRG_NAME, "wrote results to \"" + outfile + "\"" );
-        if ( TIME && VERBOSE ) {
-            time = System.currentTimeMillis() - time;
-            ForesterUtil.programMessage( PRG_NAME, "time: " + time + "ms" );
-        }
+        time = System.currentTimeMillis() - time;
+        ForesterUtil.programMessage( PRG_NAME, "time: " + time + "ms" );
         ForesterUtil.programMessage( PRG_NAME, "OK." );
         System.exit( 0 );
     }
 
     private final static void printHelp() {
-        System.out.println( "M= (String) Multiple gene tree file (mandatory)" );
-        System.out.println( "N= (String) Query sequence name (mandatory)" );
-        System.out.println( "S= (String) Species tree file (mandatory)" );
-        System.out.println( "O= (String) Output file name -- overwritten without warning! (mandatory)" );
-        System.out.println( "P= (int)    Sort priority" );
-        System.out.println( "L= (double) Threshold orthologs for output" );
-        System.out.println( " Sort priority (\"P=\"):" );
+        System.out.println( "Usage:" );
+        System.out.println();
+        System.out.println( PRG_NAME + " [options] <gene trees file> <species tree file> [outfile]" );
+        System.out.println();
+        System.out.println( "options:" );
+        System.out.println();
+        //        System.out.println( " -" + STRICT_OPTION
+        //                + "    : strict [default: non-strict]: all nodes between 'target' and 'evaluators' must match" );
+        //        System.out.println( " -" + NORMALIZE_OPTION
+        //                + "=<d>: normalize to this value (e.g. 100 for most bootstrap analyses) [default: no normalization]" );
+        //        System.out.println( " -" + FIRST_OPTION + "=<i>: first evaluator topology to use (0-based) [default: 0]" );
+        //        System.out.println( " -" + LAST_OPTION
+        //                + "=<i>: last evaluator topology to use (0-based) [default: use all until final topology]" );
+        //        System.out.println();
+        //        System.out.println( "M= (String) Multiple gene tree file (mandatory)" );
+        //        System.out.println( "N= (String) Query sequence name (mandatory)" );
+        //        System.out.println( "S= (String) Species tree file (mandatory)" );
+        //        System.out.println( "O= (String) Output file name -- overwritten without warning! (mandatory)" );
+        //        System.out.println( "P= (int)    Sort priority" );
+        //        System.out.println( "L= (double) Threshold orthologs for output" );
+        //        System.out.println( " Sort priority (\"P=\"):" );
         System.out.println( RIO.getOrderHelp().toString() );
         System.out.println();
         System.out
-                .println( " Example: \"rio M=gene_trees.xml N=bcl2_NEMVE S=species_tree.xml D=distances P=13 p O=out\"" );
+                .println( " Example: \"rio -q=D_NEMVE -s=1 -t=out -u Bcl-2_e1_20_mafft_05_40_fme.mlt species.xml out\"" );
         System.out.println();
     }
 }

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index c881906..3c33301 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -583,16 +583,14 @@ public class PhylogenyMethods {
         return PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT;
     }
 
-    // Helper for getUltraParalogousNodes( PhylogenyNode ).
-    public static boolean areAllChildrenDuplications( final PhylogenyNode n ) {
+    public final static boolean isAllDecendentsAreDuplications( final PhylogenyNode n ) {
         if ( n.isExternal() ) {
-            return false;
+            return true;
         }
         else {
             if ( n.isDuplication() ) {
-                //FIXME test me!
                 for( final PhylogenyNode desc : n.getDescendants() ) {
-                    if ( !areAllChildrenDuplications( desc ) ) {
+                    if ( !isAllDecendentsAreDuplications( desc ) ) {
                         return false;
                     }
                 }
@@ -1148,9 +1146,9 @@ public class PhylogenyMethods {
         // FIXME test me
         PhylogenyNode node = n;
         if ( !node.isExternal() ) {
-            return null;
+            throw new IllegalArgumentException( "attempt to get ultra-paralogous nodes of internal node" );
         }
-        while ( !node.isRoot() && node.getParent().isDuplication() && areAllChildrenDuplications( node.getParent() ) ) {
+        while ( !node.isRoot() && node.getParent().isDuplication() && isAllDecendentsAreDuplications( node.getParent() ) ) {
             node = node.getParent();
         }
         final List<PhylogenyNode> nodes = node.getAllExternalDescendants();

diff --git a/forester/java/src/org/forester/sdi/RIO.java b/forester/java/src/org/forester/sdi/RIO.java
index 62b2c21..3c2c298 100644 (file)
--- a/forester/java/src/org/forester/sdi/RIO.java
+++ b/forester/java/src/org/forester/sdi/RIO.java
@@ -53,9 +53,8 @@ import org.forester.util.ForesterUtil;
  */
 public final class RIO {
 
-    private final static boolean                      ROOT_BY_MINIMIZING_MAPPING_COST = false;
-    private final static boolean                      ROOT_BY_MINIMIZING_SUM_OF_DUPS  = true;
-    private final static boolean                      ROOT_BY_MINIMIZING_TREE_HEIGHT  = true;
+    private final static boolean                      ROOT_BY_MINIMIZING_SUM_OF_DUPS = true;
+    private final static boolean                      ROOT_BY_MINIMIZING_TREE_HEIGHT = true;
     private HashMap<String, HashMap<String, Integer>> _o_hash_maps;
     private HashMap<String, HashMap<String, Integer>> _so_hash_maps;
     private HashMap<String, HashMap<String, Integer>> _up_hash_maps;
@@ -289,7 +288,7 @@ public final class RIO {
         List<PhylogenyNode> ultra_paralogs = null;
         assigned_tree = sdiunrooted.infer( gene_tree,
                                            species_tree,
-                                           RIO.ROOT_BY_MINIMIZING_MAPPING_COST,
+                                           false,
                                            RIO.ROOT_BY_MINIMIZING_SUM_OF_DUPS,
                                            RIO.ROOT_BY_MINIMIZING_TREE_HEIGHT,
                                            true,

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index 08c3b9e..9d9570d 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -335,6 +335,16 @@ public final class ForesterUtil {
         System.exit( -1 );
     }
 
+    public static void fatalErrorIfFileNotReadable( final String prg_name, final File file ) {
+        final String error = isReadableFile( file );
+        if ( !isEmpty( error ) ) {
+            System.err.println();
+            System.err.println( "[" + prg_name + "] > " + error );
+            System.err.println();
+            System.exit( -1 );
+        }
+    }
+
     public static String[] file2array( final File file ) throws IOException {
         final List<String> list = file2list( file );
         final String[] ary = new String[ list.size() ];