public int compute(String line){
  this.line=line;
  int count=0;
  if (attemptFirstWord) {
    int a=0;
    while (a < line.length()) {
      if (line.charAt(a) == '>' || Character.isWhitespace(line.charAt(a)))       a++;
 else       break;
    }
    int b=a + 1;
    while (b < line.length()) {
      int ch=line.charAt(b);
      if (Character.isLetterOrDigit(ch) || ch == ':' || ch == '_')       b++;
 else       break;
    }
    if (b - a > 4) {
      pairs[count][0]=a;
      pairs[count++][1]=b;
    }
  }
  if (idTags.length > 0) {
    for (    String tag : idTags) {
      int b;
      for (int a=line.indexOf(tag); a != -1; a=line.indexOf(tag,b + 1)) {
        a+=tag.length();
        b=a + 1;
        while (b < line.length() && (Character.isLetterOrDigit(line.charAt(b)) || line.charAt(b) == '_'))         b++;
        if (b > a) {
          if (count == pairs.length)           pairs=MultiWords.grow(pairs);
          pairs[count][0]=a;
          pairs[count++][1]=b;
        }
      }
    }
  }
  return count;
}

public int compute ( String line ) { this . line = line ; int count = 0 ; if ( attemptFirstWord ) { int a = 0 ; while ( a < line . length ( ) ) { if ( line . charAt ( a ) == '>' || Character . isWhitespace ( line . charAt ( a ) ) ) a ++ ; else break ; } int b = a + 1 ; while ( b < line . length ( ) ) { int ch = line . charAt ( b ) ; if ( Character . isLetterOrDigit ( ch ) || ch == ':' || ch == '_' ) b ++ ; else break ; } if ( b - a > 4 ) { pairs [ count ] [ 0 ] = a ; pairs [ count ++ ] [ 1 ] = b ; } } if ( idTags . length > 0 ) { for ( String tag : idTags ) { int b ; for ( int a = line . indexOf ( tag ) ; a != - 1 ; a = line . indexOf ( tag , b + 1 ) ) { a += tag . length ( ) ; b = a + 1 ; while ( b < line . length ( ) && ( Character . isLetterOrDigit ( line . charAt ( b ) ) || line . charAt ( b ) == '_' ) ) b ++ ; if ( b > a ) { if ( count == pairs . length ) pairs = MultiWords . grow ( pairs ) ; pairs [ count ] [ 0 ] = a ; pairs [ count ++ ] [ 1 ] = b ; } } } } return count ; }
compute all accessions that follow any one of the tags
