From 090a58fe4ce54db906cc24f075704c0788b04570 Mon Sep 17 00:00:00 2001
From: Travis Wheeler <travis@traviswheeler.com>
Date: Thu, 22 Mar 2012 10:11:34 -0400
Subject: [PATCH 1/3] Changing the axis labels in the make_profile.pl script

Adding code to handle the HMMER3/f format (which will eventually see the light of
day in H3.1 release)
---
 HMM/Profile.pm  | 8 +++++---
 make_profile.pl | 9 +++------
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/HMM/Profile.pm b/HMM/Profile.pm
index cf33dc9..10f24a9 100755
--- a/HMM/Profile.pm
+++ b/HMM/Profile.pm
@@ -872,12 +872,14 @@ sub _parseFile3 {
         # Match line
         if ($substate == 0)
         {
-            my ($s, $ascii, $map, $consensus, $rf, $cs);
+            my ($s, $ascii, $map, $consensus, $rf, $mm, $cs);
 
-            if ($self->version =~ /[abcd]$/) {
+            if ($self->version =~ /[abcd]$/) {  # hmm versions a..d or greater
                ($s, $ascii, $map, $rf, $cs)             = $line =~ /^\s*(\d+)\s+(.*)\s+(\S+)\s+(\S)\s+(\S)\s*$/;
-            } else {  # hmm version e or greater
+            } elsif ($self->version =~ /e$/) {  # hmm version e
                ($s, $ascii, $map, $consensus, $rf, $cs) = $line =~ /^\s*(\d+)\s+(.*)\s+(\S+)\s+(\S)\s+(\S)\s+(\S)\s*$/;
+            } else {  # hmm version f or greater
+               ($s, $ascii, $map, $consensus, $rf, $mm, $cs) = $line =~ /^\s*(\d+)\s+(.*)\s+(\S+)\s+(\S)\s+(\S)\s+(\S)\s+(\S)\s*$/;
             }
 
 
diff --git a/make_profile.pl b/make_profile.pl
index f0b2c8d..09faf75 100755
--- a/make_profile.pl
+++ b/make_profile.pl
@@ -21,9 +21,6 @@
 $logo->print_logo_dimensions(
     -xsize          => $xsize,
     -ysize          => $ysize,
-    -x_title        => 'Relative Entropy',
-    -y_title        => 'Contribution',
-    -graph_title    => $graph_title,
     -greyscale      => $greyscale,
     -height_logodds => $height_logodds
   )  or die "Error writing $outfile!\n";
@@ -35,13 +32,13 @@
     -file           => $outfile,
     -xsize          => $xsize,
     -ysize          => $ysize,
-    -x_title        => 'Relative Entropy',
-    -y_title        => 'Contribution',
+    -x_title        => 'Position',
+    -y_title        => 'Contribution (bits)',
     -graph_title    => $graph_title,
     -greyscale      => $greyscale,
     -height_logodds => $height_logodds
   )  or die "Error writing $outfile!\n";
 
-my $data = $logo->flat($height_logodds);
+#my $data = $logo->flat($height_logodds);
 #print STDOUT p( $data);
 print STDOUT "Finished drawing Logo...\n";

From c2172e9e16f7e38e087b3500dec55eef632ebcd5 Mon Sep 17 00:00:00 2001
From: Travis Wheeler <travis@traviswheeler.com>
Date: Wed, 26 Sep 2012 13:28:12 -0400
Subject: [PATCH 2/3] Merge branch 'master' of
 https://github.com/DaGaMs/Logomat

Conflicts:
	scripts/make_profile.pl

From 75951391f021e2bb31983815144a217312fcd7d2 Mon Sep 17 00:00:00 2001
From: Travis Wheeler <travis@traviswheeler.com>
Date: Wed, 26 Sep 2012 13:29:48 -0400
Subject: [PATCH 3/3] Added FindBin module, to allow make_profile to be called
 from other directories

---
 scripts/make_profile.pl | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/scripts/make_profile.pl b/scripts/make_profile.pl
index 57936bd..69b0632 100755
--- a/scripts/make_profile.pl
+++ b/scripts/make_profile.pl
@@ -1,5 +1,8 @@
 #!/usr/bin/env perl
 
+use FindBin;                 # locate this script
+use lib "$FindBin::Bin/..";  # use the parent directory; this is for HMM::Profile, calling from some other directory
+
 use strict;
 use warnings;
 use HMM::Profile;