new tool

diff --git a/forester/java/src/org/forester/application/annotator.java b/forester/java/src/org/forester/application/annotator.java
new file mode 100644 (file)
index 0000000..8ecc9a4
--- /dev/null
+++ b/forester/java/src/org/forester/application/annotator.java
@@ -0,0 +1,132 @@
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// 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
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// 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
+//
+// Contact: phylosoft @ gmail . com
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
+
+package org.forester.application;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.forester.analysis.AncestralTaxonomyInference;
+import org.forester.analysis.AncestralTaxonomyInferenceException;
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+import org.forester.ws.seqdb.SequenceDbWsTools;
+
+public final class annotator {
+
+    final static private String PRG_NAME    = "annotator";
+    final static private String PRG_VERSION = "1.00";
+    final static private String PRG_DATE    = "131122";
+
+    public static void main( final String args[] ) {
+        ForesterUtil.printProgramInformation( annotator.PRG_NAME, annotator.PRG_VERSION, annotator.PRG_DATE );
+        System.out.println();
+        if ( ( args.length != 2 ) ) {
+            annotator.argumentsError();
+        }
+        CommandLineArguments cla = null;
+        try {
+            cla = new CommandLineArguments( args );
+        }
+        catch ( final Exception e ) {
+            ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+        }
+        final File indir = cla.getFile( 0 );
+        final File outdir = cla.getFile( 1 );
+        if ( !indir.isDirectory() ) {
+            ForesterUtil.fatalError( PRG_NAME, indir + " is not a directory" );
+        }
+        if ( !outdir.isDirectory() ) {
+            ForesterUtil.fatalError( PRG_NAME, outdir + " is not a directory" );
+        }
+        final File[] list_of_files = indir.listFiles();
+        final List<File> infiles = new ArrayList<File>();
+        for( final File file : list_of_files ) {
+            if ( file.isFile() && file.canRead() && file.toString().toLowerCase().endsWith( ".xml" ) ) {
+                infiles.add( file );
+            }
+        }
+        int c = 0;
+        for( final File infile : infiles ) {
+            System.out.println( ++c + "/" + infiles.size() + ": " + infile );
+            Phylogeny phy = null;
+            try {
+                final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+                final Phylogeny[] phylogenies = factory.create( infile,
+                                                                PhyloXmlParser.createPhyloXmlParserXsdValidating() );
+                phy = phylogenies[ 0 ];
+            }
+            catch ( final Exception e ) {
+                ForesterUtil.fatalError( PRG_NAME, "failed to read phylgenies from [" + infile + "] [" + e.getMessage()
+                        + "]" );
+            }
+            try {
+                obtainSeqInformation( phy );
+            }
+            catch ( final IOException e ) {
+                ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+            }
+            try {
+                inferTaxonomyFromDescendents( phy );
+            }
+            catch ( final IOException e ) {
+                ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+            }
+            catch ( final AncestralTaxonomyInferenceException e ) {
+                ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+            }
+            final File outfile = new File( outdir.getAbsolutePath().toString() + "/" + infile.getName() );
+            try {
+                final PhylogenyWriter w = new PhylogenyWriter();
+                w.toPhyloXML( phy, 0, outfile );
+            }
+            catch ( final IOException e ) {
+                ForesterUtil.fatalError( PRG_NAME, "failed to write output [" + e.getMessage() + "]" );
+            }
+        }
+    }
+
+    private static void obtainSeqInformation( final Phylogeny phy ) throws IOException {
+        SequenceDbWsTools.obtainSeqInformation( phy, true, true, SequenceDbWsTools.DEFAULT_LINES_TO_RETURN );
+    }
+
+    private static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
+            AncestralTaxonomyInferenceException {
+        AncestralTaxonomyInference.inferTaxonomyFromDescendents( phy );
+    }
+
+    private static void argumentsError() {
+        System.out.println( annotator.PRG_NAME + " <indir> <outdir>" );
+        System.out.println();
+        System.exit( -1 );
+    }
+}

diff --git a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
index d7cafd1..ed6387e 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
+++ b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
@@ -56,7 +56,6 @@ public final class SequenceDbWsTools {
 
     public final static String   BASE_UNIPROT_URL        = "http://www.uniprot.org/";
     public final static int      DEFAULT_LINES_TO_RETURN = 4000;
-    //public final static String   EMBL_DBS_EMBL           = "embl";
     public final static String   EMBL_DBS_REFSEQ_N       = "refseqn";
     public final static String   EMBL_DBS_REFSEQ_P       = "refseqp";
     public final static String   EMBL_GENBANK            = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=GENBANK&style=raw&id=";
@@ -64,6 +63,7 @@ public final class SequenceDbWsTools {
     public final static String   EMBL_EMBL               = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=EMBL&style=raw&id=";
     private final static boolean DEBUG                   = true;
     private final static String  URL_ENC                 = "UTF-8";
+    private final static int     SLEEP                   = 200;
 
     public static List<UniProtTaxonomy> getTaxonomiesFromCommonNameStrict( final String cn,
                                                                            final int max_taxonomies_return )
@@ -250,7 +250,7 @@ public final class SequenceDbWsTools {
         in.close();
         try {
             // To prevent accessing online dbs in too quick succession. 
-            Thread.sleep( 20 );
+            Thread.sleep( SLEEP );
         }
         catch ( final InterruptedException e ) {
             e.printStackTrace();
@@ -417,7 +417,7 @@ public final class SequenceDbWsTools {
             }
         }
         try {
-            Thread.sleep( 10 );// Sleep for 10 ms
+            Thread.sleep( SLEEP );
         }
         catch ( final InterruptedException ie ) {
         }