Пример #1
0
 /**
  * Simply transfer every header and sequence remaining in the input stream to this output stream
  *
  * @param inputStream the stream to copy to this stream
  * @throws IOException if there was a problem openning or working with either stream
  */
 public void appendRemaining(final DBInputStream inputStream) throws IOException {
   if (inputStream != null) {
     while (inputStream.gotoNextSequence()) {
       this.appendSequence(inputStream.getHeader(), inputStream.getSequence());
     }
   }
 }
Пример #2
0
 /**
  * goes through each header in a fasta file and checks to make sure it is a valid fasta header. If
  * any problems are encountered or a header does not check out then false is returned
  *
  * @param toCheck the file you want to see is a valid FASTA file
  * @return true if the file is a valid fasta file else false
  */
 public static boolean isFASTAFileValid(final File toCheck) {
   DBInputStream in = null;
   try {
     in = new FASTAInputStream(toCheck);
     int sequenceCount = 0;
     in.beforeFirst();
     while (in.gotoNextSequence()) {
       if (isHeader(in.getHeader())) {
         sequenceCount++;
       } else {
         return false;
       }
     }
     return (sequenceCount != 0);
   } catch (Exception e) {
     // SWALLOWED: We just return false as in "not valid"
     LOGGER.warn(e);
     return false;
   } finally {
     FileUtilities.closeQuietly(in);
   }
 }