Permalink
Browse files

RT #122733: profile has to be renamed to run_profile due to conflict …

…w/ parameter
  • Loading branch information...
1 parent f67ec02 commit c71bab31b6f92a8b4ebfa0d8dd77fce67e5bcfc9 @cjfields cjfields committed Sep 16, 2017
Showing with 18 additions and 18 deletions.
  1. +18 −18 lib/Bio/Tools/Run/Alignment/Muscle.pm
@@ -44,21 +44,21 @@ http://www.drive5.com/muscle
It is recommended you use at least version 3.6. Behaviour with earlier versions
is questionable.
-=head2 Helping the module find your executable
+=head2 Helping the module find your executable
You will need to enable Muscle to find the muscle program. This can be
done in (at least) three ways:
- 1. Make sure the muscle executable is in your path (i.e.
+ 1. Make sure the muscle executable is in your path (i.e.
'which muscle' returns a valid program
- 2. define an environmental variable MUSCLEDIR which points to a
+ 2. define an environmental variable MUSCLEDIR which points to a
directory containing the 'muscle' app:
- In bash
+ In bash
export MUSCLEDIR=/home/progs/muscle or
In csh/tcsh
setenv MUSCLEDIR /home/progs/muscle
- 3. include a definition of an environmental variable MUSCLEDIR
+ 3. include a definition of an environmental variable MUSCLEDIR
in every script that will
BEGIN {$ENV{MUSCLEDIR} = '/home/progs/muscle'; }
use Bio::Tools::Run::Alignment::Muscle;
@@ -74,15 +74,15 @@ of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
-rather than to the module maintainer directly. Many experienced and
-reponsive experts will be able look at the problem and quickly
-address it. Please include a thorough description of the problem
+rather than to the module maintainer directly. Many experienced and
+reponsive experts 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.
=head2 Reporting Bugs
@@ -293,12 +293,12 @@ sub align {
return &_run( $self, $infilename, $param_string );
}
-=head2 profile
+=head2 run_profile
- Title : profile
+ Title : run_profile
Usage : $alnfilename = /t/data/cysprot.msa';
$seqsfilename = 't/data/cysprot.fa';
- $aln = $factory->profile($alnfilename,$seqsfilename);
+ $aln = $factory->run_profile($alnfilename,$seqsfilename);
Function: Perform a profile alignment on a MSA to include more seqs
Returns : Reference to a SimpleAlign object containing the
@@ -312,7 +312,7 @@ sub align {
=cut
-sub profile {
+sub run_profile {
my ( $self, $alnfilename, $seqsfilename ) = @_;
# Create input file pointer
@@ -402,7 +402,7 @@ sub aformat {
=head2 _run
Title : _run
- Usage : Internal function, not to be called directly
+ Usage : Internal function, not to be called directly
Function: makes actual system call to muscle program
Example :
Returns : nothing; muscle output is written to a
@@ -445,7 +445,7 @@ sub _run {
=head2 _setinput
Title : _setinput
- Usage : Internal function, not to be called directly
+ Usage : Internal function, not to be called directly
Function: Create input file for muscle program
Example :
Returns : name of file containing muscle data input AND
@@ -522,7 +522,7 @@ sub _setinput {
=head2 _setparams
Title : _setparams
- Usage : Internal function, not to be called directly
+ Usage : Internal function, not to be called directly
Function: Create parameter inputs for muscle program
Example :
Returns : parameter string to be passed to muscle
@@ -577,7 +577,7 @@ sub _setparams {
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
+ trust the sanity checks for parameter values
Returns : value of no_param_checks
Args : newvalue (optional)
@@ -587,7 +587,7 @@ sub _setparams {
Title : save_tempfiles
Usage : $obj->save_tempfiles($newval)
- Function:
+ Function:
Returns : value of save_tempfiles
Args : newvalue (optional)

0 comments on commit c71bab3

Please sign in to comment.