2 package org.forester.application;
4 import java.io.FileInputStream;
5 import java.util.ArrayList;
8 import org.forester.io.parsers.FastaParser;
9 import org.forester.msa.Msa;
10 import org.forester.sequence.Sequence;
11 import org.forester.util.ForesterUtil;
15 public static void main( final String args[] ) {
17 System.out.println( "STARTING..." );
18 final List<Sequence> orig = FastaParser
19 .parse( new FileInputStream( "C:\\Users\\zma\\Desktop\\RRMa_domains_ext_20.fasta" ) );
20 final Msa msa = FastaParser.parseMsa( new FileInputStream( "C:\\Users\\zma\\Desktop\\test3_sorted.fasta" ) );
21 for( int i = 0; i < msa.getNumberOfSequences(); ++i ) {
22 final String id = msa.getIdentifier( i );
23 final String id_ = id.substring( 0, id.indexOf( "_" ) );
24 final String range = id.substring( id.indexOf( "[" ) + 1, id.indexOf( "]" ) );
25 //System.out.println( i + ": " + id + "=>" + id_ + " " + range );
26 if ( ForesterUtil.isEmpty( id_ ) ) {
27 System.out.println( "ERROR: id is empty for: " + id );
30 if ( ForesterUtil.isEmpty( range ) ) {
31 System.out.println( "ERROR: range is empty for: " + id );
35 final List<Sequence> found_seqs = new ArrayList<Sequence>();
36 for( final Sequence orig_seq : orig ) {
37 final String orig_seq_id = orig_seq.getIdentifier();
38 if ( orig_seq_id.indexOf( id_ ) >= 0 && orig_seq_id.indexOf( "[" + range + "]" ) >= 0 ) {
40 found_seqs.add( orig_seq );
45 System.out.println( i + ": " + id + "=>" + id_ + " " + range );
46 System.out.println( " found: " + found );
47 for( final Sequence found_seq : found_seqs ) {
48 System.out.println( found_seq.toString() );
53 System.out.println( "ERROR: not found: " + id );
57 System.out.println( "DONE." );
59 catch ( final Exception e ) {