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Minor updates to the code. Mostly cleanup. #2

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merged 10 commits into from Feb 22, 2012

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neomorphic commented Jan 23, 2012

I have restored all the warnings and strict pragmas and fixed a few warning messages that appeared after restoring said pragmas. I also noticed that one of the methods in the HMM::Profile module was redefining a method exported from PDL (flat), so I renamed it to flatten.

neomorphic added some commits Jan 23, 2012

Restored warnings pragma
We want warnings. Also removed trailing whitespaces.
Fixed printf warnings.
printf in perl does not need the () as it does in C? So removing them
will make the printf behave as expected in the perl community.
Fixed 'redefined sub' warning
The flat subroutine was being imported from PDL::LiteF and then
redefined in the HMM::Profile module. Since I don't think the intention
was to override the PDL function, I renamed the HMM version of the
subroutine to flatten.
Removed META.yml from the manifest.
The META.yml file gets added to the module directory when running 'make
dist', so we don't need to have it in the MANIFEST file that is stored in
source control.
Restored strict and warnings pragma to Utilities
The strict and warning pragmas were removed to get the code to compile.
Fixing the way that variables are created for use with Exporter has
allowed the restoration of the failing pragmas.
Restored strict and warnings pragmas to modules
There were a number of modules where the strict and warnings pragmas
had been removed. I restored these and fixed the warning message in
HMM/Profile (caused by PDL returning the string 'BAD' instead
of a number) by checking the string to make sure it is numeric, before
testing it.
Moved scripts to scripts directory
This stops them from being installed in the lib directory. An EXE_FILES
line was added to the Makefile.PL to tell make which scripts need the
path modified on installation and where to put them.
Added more output options
There are now -data and -fh options in addition to the -file parameter
passed to draw_logo. This allows for the rendered image data to be
placed in an already opened file handle or into a reference to a scalar.

DaGaMs pushed a commit that referenced this pull request Feb 22, 2012

Merge pull request #2 from neomorphic/master
Minor updates to the code. Mostly cleanup.

@DaGaMs DaGaMs merged commit 746b866 into DaGaMs:master Feb 22, 2012

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