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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Run::Tmhmm 3pm"
.TH Bio::Tools::Run::Tmhmm 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Tools::Run::Tmhmm \- Object for identifying transmembrane helixes
  in a given protein seequence.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  # Build a Tmhmm  factory
\&
\&  # $paramfile is the full path to the seg binary file
\&
\&  my @params = (\*(AqPROGRAM\*(Aq,$paramfile);
\&  my $factory = Bio::Tools::Run::Tmhmm\->new($param);
\&
\&  # Pass the factory a Bio::Seq object
\&  # @feats is an array of Bio::SeqFeature::Generic objects
\&
\&  my @feats = $factory\->run($seq);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Tmhmm is a program for identifying transmembrane helices in proteins.
.PP
You must have the environmental variable \s-1TMHMMDIR\s0 set to the base
directory where \fItmhmm\fR and it's associated data/option files reside
(\s-1NOT\s0 the bin directory where the actual executable resides)
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.PP
head2 Reporting Bugs
.PP
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Bala"
.IX Header "AUTHOR - Bala"
.Vb 1
\& Email savikalpa@fugu\-sg.org
.Ve
.SH "APPENDIX"
.IX Header "APPENDIX"
.Vb 2
\& The rest of the documentation details each of the object
\& methods. Internal methods are usually preceded with a _
.Ve
.SS "program_name"
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory>program_name()
\& Function: holds the program name
\& Returns:  string
\& Args    : None
.Ve
.SS "program_dir"
.IX Subsection "program_dir"
.Vb 7
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable, in this
\&           case it is the tmhmm installation directory, not the location of
\&           the executable.
\& Returns:  string
\& Args    :
.Ve
.SS "program_path"
.IX Subsection "program_path"
.Vb 5
\& Title   : program_path
\& Usage   : my $path = $factory\->program_path();
\& Function: Builds path for executable 
\& Returns : string representing the full path to the exe
\& Args    : none
.Ve
.SS "new"
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Usage   : $rm\->new(@params)
\& Function: creates a new Tmhmm factory
\& Returns:  Bio::Tools::Run::Tmhmm
\& Args    :
.Ve
.SS "predict_protein_features"
.IX Subsection "predict_protein_features"
.Vb 5
\& Title   :   predict_protein_features()
\& Usage   :   DEPRECATED Use $obj\->run($seq) instead
\& Function:   Runs Tmhmm and creates an array of featrues
\& Returns :   An array of Bio::SeqFeature::Generic objects
\& Args    :   A Bio::PrimarySeqI
.Ve
.SS "executable"
.IX Subsection "executable"
.Vb 6
\& Title   : executable
\& Usage   : my $exe = $tmhmm\->executable(\*(Aqtmhmm\*(Aq);
\& Function: Finds the full path to the \*(Aqtmhmm\*(Aq executable
\& Returns : string representing the full path to the exe
\& Args    : [optional] name of executable to set path to
\&           [optional] boolean flag whether or not warn when exe is not found
.Ve
.SS "run"
.IX Subsection "run"
.Vb 5
\& Title   :   run()
\& Usage   :   $obj\->run($seq)
\& Function:   Runs Tmhmm and creates an array of featrues
\& Returns :   An array of Bio::SeqFeature::Generic objects
\& Args    :   A Bio::PrimarySeqI
.Ve
.SS "_input"
.IX Subsection "_input"
.Vb 5
\& Title   :   _input
\& Usage   :   obj\->_input($seqFile)
\& Function:   Internal(not to be used directly)
\& Returns :
\& Args    :
.Ve
.SS "_run"
.IX Subsection "_run"
.Vb 5
\& Title   :   _run
\& Usage   :   $obj\->_run()
\& Function:   Internal(not to be used directly)
\& Returns :   An array of Bio::SeqFeature::Generic objects
\& Args    :
.Ve
.SS "_writeSeqFile"
.IX Subsection "_writeSeqFile"
.Vb 5
\& Title   :   _writeSeqFile
\& Usage   :   obj\->_writeSeqFile($seq)
\& Function:   Internal(not to be used directly)
\& Returns :
\& Args    :
.Ve