Bio::SeqIO::phd(3pm)

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next_seq

 Title   : next_seq()
 Usage   : $swq = $stream->next_seq()
 Function: returns the next phred sequence in the stream
 Returns : Bio::Seq::Quality object
 Args    : NONE

write_header

 Title   : write_header()
 Usage   : $seqio->write_header()
 Function: Write out the header (BEGIN_COMMENTS .. END_COMMENT) part of a phd file
 Returns : nothing
 Args    : a Bio::Seq::Quality object
 Notes   : These are the comments that reside in the header of a phd file
           at the present time. If not provided by the Bio::Seq::Quality object,
           the following default values will be used:
     CHROMAT_FILE          : $swq->id()
     ABI_THUMBPRINT        : 0
     PHRED_VERSION         : 0.980904.e
     CALL_METHOD           : phred
     QUALITY_LEVELS        : 99
     TIME                  : <current time>
     TRACE_ARRAY_MIN_INDEX : 0
     TRACE_ARRAY_MAX_INDEX : unknown
     CHEM                  : unknown
     DYE                   : unknown

write_seq

 Title   : write_seq()
 Usage   : $seqio->write_seq($swq);
 Function: Write out a phd file.
 Returns : Nothing.
 Args    : a Bio::Seq::Quality object

attribute

 Title   : attribute()
 Usage   : swq->attribute(name[,value]);
 Function: Get/Set the name attribute.
 Returns : a string if 1 param, nothing else.
 Args    : a name or a pair name, value

chromat_file

 Title   : chromat_file
 Usage   : swq->chromat_file([filename]);
 Function: Get/Set the CHROMAT_FILE attribute.
 Returns : a string if 1 param, nothing else.
 Args    : none or a filename

abi_thumbprint

 Title   : abi_thumbprint
 Usage   : swq->abi_thumbprint([value]);
 Function: Get/Set the ABI_THUMBPRINT attribute.
 Returns : a string if 1 param, nothing else.
 Args    : none or a value

phred_version

 Title   : phred_version
 Usage   : swq->phred_version([value]);
 Function: Get/Set the PHRED_VERSION attribute.
 Returns : a string if 1 param, nothing else.
 Args    : none or a value

call_method

 Title   : call_method
 Usage   : swq->call_method([value]);
 Function: Get/Set the CALL_METHOD attribute.
 Returns : a string if 1 param, nothing else.
 Args    : none or a value

quality_levels

 Title   : quality_levels
 Usage   : swq->quality_levels([value]);
 Function: Get/Set the quality_levels attribute.
 Returns : a string if 1 param, nothing else.
 Args    : none or a value

trace_array_min_index

 Title   : trace_array_min_index
 Usage   : swq->trace_array_min_index([value]);
 Function: Get/Set the trace_array_min_index attribute.
 Returns : a string if 1 param, nothing else.
 Args    : none or a value

trace_array_max_index

 Title   : trace_array_max_index
 Usage   : swq->trace_array_max_index([value]);
 Function: Get/Set the trace_array_max_index attribute.
 Returns : a string if 1 param, nothing else.
 Args    : none or a value

chem

 Title   : chem
 Usage   : swq->chem([value]);
 Function: Get/Set the chem attribute.
 Returns : a string if 1 param, nothing else.
 Args    : none or a value

dye

 Title   : dye
 Usage   : swq->dye([value]);
 Function: Get/Set the dye attribute.
 Returns : a string if 1 param, nothing else.
 Args    : none or a value

time

 Title   : time
 Usage   : swq->time([value]);
 Function: Get/Set the time attribute.
 Returns : a string if 1 param, nothing else.
 Args    : none or a value

touch

 Title   : touch
 Usage   : swq->touch();
 Function: Set the time attribute to current time.
 Returns : nothing
 Args    : none