Mailing Lists¶

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support¶

bioperl-l@bioperl.org

Do not contact the module maintainer directly. Many experienced experts at bioperl-l will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs¶

 http://redmine.open-bio.org/projects/bioperl/

new¶

 Title   : new
 Usage   : my $treebuilder = Bio::Tools::Run::Phylo::FastTree->new();
 Function: Constructor
 Returns : Bio::Tools::Run::Phylo::FastTree
 Args    : -outfile_name => $outname

program_name¶

 Title   : program_name
 Usage   : $factory->program_name()
 Function: holds the program name
 Returns:  string
 Args    : None

program_dir¶

 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory
 Returns:  string
 Args    :

error_string¶

 Title   : error_string
 Usage   : $obj->error_string($newval)
 Function: Where the output from the last analysus run is stored.
 Returns : value of error_string
 Args    : newvalue (optional)

version¶

 Title   : version
 Usage   : exit if $prog->version() < 1.8
 Function: Determine the version number of the program
 Example :
 Returns : float or undef
 Args    : none

run¶

 Title   : run
 Usage   : $factory->run($stockholm_file) OR
           $factory->run($align_object)
 Function: Runs FastTree to generate a tree 
 Returns : Bio::Tree::Tree object
 Args    : File name for your input alignment in stockholm format, OR
           Bio::Align::AlignI compliant object (eg. Bio::SimpleAlign).

_run¶

 Title   : _run
 Usage   : Internal function, not to be called directly
 Function: Runs the application
 Returns : Tree object
 Args    : Alignment file name

_write_alignfile¶

 Title   : _write_alignfile
 Usage   : Internal function, not to be called directly
 Function: Create an alignment file
 Returns : filename
 Args    : Bio::Align::AlignI

_alphabet¶

 Title   : _alphabet
 Usage   : my $alphabet = $self->_alphabet;
 Function: Get the alphabet of the input alignment, defaults to 'dna'
 Returns : 'dna' or 'protein'
 Args    : Alignment file

_setparams¶

 Title   :  _setparams
 Usage   :  Internal function, not to be called directly    
 Function:  Create parameter inputs for FastTree program
 Example :
 Returns : parameter string to be passed to FastTree
 Args    : name of calling object

no_param_checks¶

 Title   : no_param_checks
 Usage   : $obj->no_param_checks($newval)
 Function: Boolean flag as to whether or not we should
           trust the sanity checks for parameter values  
 Returns : value of no_param_checks
 Args    : newvalue (optional)

save_tempfiles¶

 Title   : save_tempfiles
 Usage   : $obj->save_tempfiles($newval)
 Function: 
 Returns : value of save_tempfiles
 Args    : newvalue (optional)

outfile_name¶

 Title   : outfile_name
 Usage   : my $outfile = $FastTree->outfile_name();
 Function: Get/Set the name of the output file for this run
           (if you wanted to do something special)
 Returns : string
 Args    : [optional] string to set value to

tempdir¶

 Title   : tempdir
 Usage   : my $tmpdir = $self->tempdir();
 Function: Retrieve a temporary directory name (which is created)
 Returns : string which is the name of the temporary directory
 Args    : none

cleanup¶

 Title   : cleanup
 Usage   : $FastTree->cleanup();
 Function: Will cleanup the tempdir directory
 Returns : none
 Args    : none

io¶

 Title   : io
 Usage   : $obj->io($newval)
 Function:  Gets a L<Bio::Root::IO> object
 Returns : L<Bio::Root::IO>
 Args    : none