inprogress

diff --git a/forester/java/src/org/forester/application/check_fasta.java b/forester/java/src/org/forester/application/check_fasta.java
new file mode 100644 (file)
index 0000000..2bac934
--- /dev/null
+++ b/forester/java/src/org/forester/application/check_fasta.java
@@ -0,0 +1,128 @@
+// $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.FileInputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.forester.io.parsers.FastaParser;
+import org.forester.io.writers.SequenceWriter;
+import org.forester.io.writers.SequenceWriter.SEQ_FORMAT;
+import org.forester.sequence.BasicSequence;
+import org.forester.sequence.Sequence;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public final class check_fasta {
+
+    final static private String PRG_NAME    = "check_fasta";
+    final static private String PRG_VERSION = "1.00";
+    final static private String PRG_DATE    = "131202";
+
+    public static void main( final String args[] ) {
+        ForesterUtil.printProgramInformation( check_fasta.PRG_NAME, check_fasta.PRG_VERSION, check_fasta.PRG_DATE );
+        System.out.println();
+        if ( ( args.length != 2 ) ) {
+            check_fasta.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( ".fasta" ) || file.toString().toLowerCase()
+                            .endsWith( ".fas" ) ) ) {
+                infiles.add( file );
+            }
+        }
+        Collections.sort( infiles );
+        int c = 0;
+        for( final File infile : infiles ) {
+            System.out.println( ++c + "/" + infiles.size() + ": " + infile );
+            execute( outdir, infile );
+        }
+    }
+
+    private static void execute( final File outdir, final File infile ) {
+        final File outfile = new File( outdir.getAbsolutePath().toString() + "/" + infile.getName() );
+        if ( outfile.exists() ) {
+            System.out.println( outfile + " already exists" );
+        }
+        else {
+            try {
+                final List<Sequence> seqs = FastaParser.parse( new FileInputStream( infile ) );
+                final Map<String, Short> names = new HashMap<String, Short>();
+                for( final Sequence seq : seqs ) {
+                    procSeq( infile.toString(), names, seq );
+                }
+                SequenceWriter.writeSeqs( seqs, outfile, SEQ_FORMAT.FASTA, 60 );
+            }
+            catch ( final IOException e ) {
+                ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+            }
+        }
+    }
+
+    private static void procSeq( final String infile, final Map<String, Short> names, final Sequence seq ) {
+        final String name = seq.getIdentifier();
+        if ( !names.containsKey( name ) ) {
+            names.put( name, ( short ) 1 );
+        }
+        else {
+            final short i = names.get( name );
+            ( ( BasicSequence ) seq ).setIdentifier( name + "_" + i );
+            names.put( name, ( short ) ( i + 1 ) );
+            System.out.println( "  " + infile + i + ": " + seq.getIdentifier() );
+        }
+    }
+
+    private static void argumentsError() {
+        System.out.println( PRG_NAME + " <indir> <outdir>" );
+        System.out.println();
+        System.exit( -1 );
+    }
+}

diff --git a/forester/java/src/org/forester/io/writers/SequenceWriter.java b/forester/java/src/org/forester/io/writers/SequenceWriter.java
index 8e6ef95..ddcb378 100644 (file)
--- a/forester/java/src/org/forester/io/writers/SequenceWriter.java
+++ b/forester/java/src/org/forester/io/writers/SequenceWriter.java
@@ -1,6 +1,7 @@
 
 package org.forester.io.writers;
 
+import java.io.File;
 import java.io.IOException;
 import java.io.Writer;
 import java.util.List;
@@ -66,6 +67,13 @@ public class SequenceWriter {
         }
     }
 
+    public static void writeSeqs( final List<Sequence> seqs, final File file, final SEQ_FORMAT format, final int width )
+            throws IOException {
+        final Writer w = ForesterUtil.createBufferedWriter( file );
+        SequenceWriter.writeSeqs( seqs, w, format, width );
+        w.close();
+    }
+
     public static void writeSeqs( final List<Sequence> seqs,
                                   final Writer writer,
                                   final SEQ_FORMAT format,

diff --git a/forester/java/src/org/forester/sequence/BasicSequence.java b/forester/java/src/org/forester/sequence/BasicSequence.java
index 4a4662a..f850205 100644 (file)
--- a/forester/java/src/org/forester/sequence/BasicSequence.java
+++ b/forester/java/src/org/forester/sequence/BasicSequence.java
@@ -31,7 +31,7 @@ import org.forester.util.ForesterUtil;
 public class BasicSequence implements Sequence {
 
     private final char[] _mol_sequence;
-    private final String _identifier;
+    private String       _identifier;
     private final TYPE   _type;
 
     private BasicSequence( final String identifier, final String mol_sequence, final TYPE type ) {
@@ -59,6 +59,10 @@ public class BasicSequence implements Sequence {
         _type = type;
     }
 
+    public void setIdentifier( final String id ) {
+        _identifier = id;
+    }
+
     @Override
     public String getIdentifier() {
         return _identifier;