moved

diff --git a/forester/java/src/org/forester/application/aa.java b/forester/java/src/org/forester/application/aa.java
deleted file mode 100644 (file)
index b835e52..0000000
--- a/forester/java/src/org/forester/application/aa.java
+++ /dev/null
@@ -1,86 +0,0 @@
-//
-
-package org.forester.application;
-
-import java.io.FileInputStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.forester.io.parsers.FastaParser;
-import org.forester.msa.Msa;
-import org.forester.sequence.BasicSequence;
-import org.forester.sequence.Sequence;
-import org.forester.util.ForesterUtil;
-
-public class aa {
-
-    public static void main( final String args[] ) {
-        try {
-            System.out.println( "STARTING..." );
-            final List<Sequence> orig = FastaParser
-                    .parse( new FileInputStream( "C:\\Users\\zma\\Desktop\\RRMa_domains_ext_20.fasta" ) );
-            final Msa msa = FastaParser.parseMsa( new FileInputStream( "C:\\Users\\zma\\Desktop\\test3_sorted.fasta" ) );
-            final Set<Sequence> all_found_seqs = new HashSet<Sequence>();
-            for( int i = 0; i < msa.getNumberOfSequences(); ++i ) {
-                final String id = msa.getIdentifier( i );
-                final String id_ = id.substring( 0, id.indexOf( "_" ) );
-                final String range = id.substring( id.indexOf( "[" ) + 1, id.indexOf( "]" ) );
-                //System.out.println( i + ": " + id + "=>" + id_ + " " + range );
-                if ( ForesterUtil.isEmpty( id_ ) ) {
-                    System.out.println( "ERROR: id is empty for: " + id );
-                    System.exit( -1 );
-                }
-                if ( ForesterUtil.isEmpty( range ) ) {
-                    System.out.println( "ERROR: range is empty for: " + id );
-                    System.exit( -1 );
-                }
-                int found = 0;
-                final List<Sequence> found_seqs = new ArrayList<Sequence>();
-                for( final Sequence orig_seq : orig ) {
-                    final String orig_seq_id = orig_seq.getIdentifier();
-                    if ( ( orig_seq_id.indexOf( id_ ) >= 0 ) && ( orig_seq_id.indexOf( "[" + range + "]" ) >= 0 ) ) {
-                        found++;
-                        found_seqs.add( orig_seq );
-                    }
-                }
-                if ( found > 0 ) {
-                    for( final Sequence found_seq : found_seqs ) {
-                        if ( found_seq.getLength() >= 85 ) {
-                            all_found_seqs.add( BasicSequence.createAaSequence( id, found_seq
-                                    .getMolecularSequenceAsString() ) );
-                        }
-                    }
-                    if ( found > 1 ) {
-                        System.out.println( i + ": " + id + "=>" + id_ + " " + range );
-                        System.out.println( "  found: " + found );
-                        for( final Sequence found_seq : found_seqs ) {
-                            System.out.println( found_seq.toString() );
-                        }
-                    }
-                }
-                else {
-                    System.out.println( "ERROR: not found: " + id );
-                    System.exit( -1 );
-                }
-            }
-            final String fasta_ary[] = new String[ all_found_seqs.size() ];
-            int i = 0;
-            for( final Sequence sequence : all_found_seqs ) {
-                fasta_ary[ i ] = ">" + sequence.getIdentifier() + "\n" + sequence.getMolecularSequenceAsString();
-                System.out.println( sequence );
-                i++;
-            }
-            Arrays.sort( fasta_ary );
-            for( final String element : fasta_ary ) {
-                System.out.println( element );
-            }
-            System.out.println( "DONE." );
-        }
-        catch ( final Exception e ) {
-            e.printStackTrace();
-        }
-    }
-}

diff --git a/forester/java/src/org/forester/application/aaa.java b/forester/java/src/org/forester/application/aaa.java
deleted file mode 100644 (file)
index ac643c4..0000000
--- a/forester/java/src/org/forester/application/aaa.java
+++ /dev/null
@@ -1,151 +0,0 @@
-
-package org.forester.application;
-
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.forester.io.parsers.FastaParser;
-import org.forester.sequence.Sequence;
-import org.forester.util.EasyWriter;
-import org.forester.util.ForesterUtil;
-
-public class aaa {
-
-    public final static Pattern GN_PATTERN    = Pattern.compile( "GN=(\\S+)\\s" );     //use w+ instead of S+ for more stringent setting.
-    public final static Pattern RANGE_PATTERN = Pattern.compile( "\\[(\\d+-\\d+)\\]" ); //use w+ instead of S+ for more stringent setting.
-    public final static int     MIN_LENGTH    = 85;
-
-    public static void main( final String args[] ) {
-        try {
-            final EasyWriter out = ( EasyWriter ) ForesterUtil.createEasyWriter( "aaa_out" );
-            System.out.println( "STARTING..." );
-            final List<Sequence> too_short = new ArrayList<Sequence>();
-            final List<Sequence> orig = FastaParser
-                    .parse( new FileInputStream( "C:\\Users\\zma\\Desktop\\RRMa_domains_ext_20_2.fasta" ) );
-            final int initial_number = orig.size();
-            final List<String> new_seqs = new ArrayList<String>();
-            for( final Sequence seq : orig ) {
-                if ( seq.getLength() < MIN_LENGTH ) {
-                    too_short.add( seq );
-                    continue;
-                }
-                final Matcher matcher = GN_PATTERN.matcher( seq.getIdentifier() );
-                String gn = "";
-                if ( matcher.find() ) {
-                    gn = matcher.group( 1 );
-                }
-                else {
-                    System.out.println( "ERROR: no gene for: " + seq.getIdentifier() );
-                    System.exit( -1 );
-                }
-                new_seqs.add( ">" + gn + "|" + seq.getIdentifier() + "\n" + seq.getMolecularSequenceAsString() );
-            }
-            final Set<String> gn_ra_set = new HashSet<String>();
-            final Set<String> mol_seq_set = new HashSet<String>();
-            Collections.sort( new_seqs );
-            int unique_counter = 0;
-            final List<String> duplicate_gn_ra = new ArrayList<String>();
-            final List<String> duplicate_mol_seq = new ArrayList<String>();
-            final List<String> new_seqs_unique = new ArrayList<String>();
-            for( final String seq : new_seqs ) {
-                final Matcher matcher_ra = RANGE_PATTERN.matcher( seq );
-                final Matcher matcher_gn = GN_PATTERN.matcher( seq );
-                String range = "";
-                if ( matcher_ra.find() ) {
-                    range = matcher_ra.group( 1 );
-                }
-                else {
-                    System.out.println( "ERROR: no range for: " + seq );
-                    System.exit( -1 );
-                }
-                matcher_gn.find();
-                final String gn = matcher_gn.group( 1 );
-                final String gn_ra = gn + "_" + range;
-                if ( !gn_ra_set.contains( gn_ra ) ) {
-                    gn_ra_set.add( gn_ra );
-                    final String mol_seq = seq.split( "\n" )[ 1 ];
-                    if ( !mol_seq_set.contains( mol_seq ) ) {
-                        mol_seq_set.add( mol_seq );
-                        new_seqs_unique.add( seq );
-                        unique_counter++;
-                    }
-                    else {
-                        duplicate_mol_seq.add( seq );
-                    }
-                }
-                else {
-                    duplicate_gn_ra.add( seq );
-                }
-            }
-            String prev_gn = "___";
-            boolean is_first = true;
-            List<String> seqs_from_same_protein = new ArrayList<String>();
-            for( final String seq : new_seqs_unique ) {
-                final Matcher matcher_gn = GN_PATTERN.matcher( seq );
-                matcher_gn.find();
-                final String gn = matcher_gn.group( 1 );
-                if ( !prev_gn.equals( gn ) && !is_first ) {
-                    doit( seqs_from_same_protein, out );
-                    seqs_from_same_protein = new ArrayList<String>();
-                }
-                prev_gn = gn;
-                is_first = false;
-                seqs_from_same_protein.add( seq );
-            }
-            doit( seqs_from_same_protein, out );
-            out.println( "" );
-            out.println( "" );
-            out.println( "Removed because same GN and region:" );
-            for( final String s : duplicate_gn_ra ) {
-                out.println( s );
-            }
-            out.println( "" );
-            out.println( "" );
-            out.println( "Removed because identical mol sequence:" );
-            for( final String s : duplicate_mol_seq ) {
-                out.println( s );
-            }
-            out.println( "" );
-            out.println( "" );
-            out.println( "Removed because too short:" );
-            for( final Sequence s : too_short ) {
-                out.println( s.toString() );
-            }
-            out.println( "" );
-            out.println( "" );
-            out.println( "initial:" + initial_number );
-            out.println( "ignored because shorter than " + MIN_LENGTH + "aa: " + too_short.size() );
-            out.println( "unique   : " + unique_counter );
-            out.println( "unique   : " + new_seqs_unique.size() );
-            out.println( "duplicate because gn and range same: " + duplicate_gn_ra.size() );
-            out.println( "duplicate because mol seq same     : " + duplicate_mol_seq.size() );
-            out.flush();
-            out.close();
-            System.out.println( "DONE " );
-        }
-        catch ( final Exception e ) {
-            e.printStackTrace();
-        }
-    }
-
-    private static void doit( final List<String> same_protein_seqs, final EasyWriter out ) throws IOException {
-        final int count = same_protein_seqs.size();
-        if ( count == 1 ) {
-            out.println( same_protein_seqs.get( 0 ) );
-        }
-        else {
-            int c = 1;
-            for( final String s : same_protein_seqs ) {
-                out.println( new StringBuffer( s ).insert( s.indexOf( "|" ), "__" + c + "_OF_" + count ).toString() );
-                c++;
-            }
-        }
-    }
-}