forester/java/src/org/forester/application/aa.java

   1
   2 package org.forester.application;
   3
   4 import java.io.FileInputStream;
   5 import java.util.ArrayList;
   6 import java.util.List;
   7
   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;
  12
  13 public class aa {
  14
  15     public static void main( final String args[] ) {
  16         try {
  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 );
  28                     System.exit( -1 );
  29                 }
  30                 if ( ForesterUtil.isEmpty( range ) ) {
  31                     System.out.println( "ERROR: range is empty for: " + id );
  32                     System.exit( -1 );
  33                 }
  34                 int found = 0;
  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 ) {
  39                         found++;
  40                         found_seqs.add( orig_seq );
  41                     }
  42                 }
  43                 if ( found > 0 ) {
  44                     if ( found > 1 ) {
  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() );
  49                         }
  50                     }
  51                 }
  52                 else {
  53                     System.out.println( "ERROR: not found: " + id );
  54                     System.exit( -1 );
  55                 }
  56             }
  57             System.out.println( "DONE." );
  58         }
  59         catch ( final Exception e ) {
  60             e.printStackTrace();
  61         }
  62     }
  63 }