From d6e95485d08f06bb34354d762b7130540bd25b97 Mon Sep 17 00:00:00 2001
From: Amila_Weerasinghe <amila@wustl.edu>
Date: Wed, 4 Oct 2017 11:59:53 -0500
Subject: [PATCH] filtering vertices by UniProtID and changing the help text

---
 lib/TGI/Mutpro/Main/Cluster.pm | 10 +++++-----
 lib/TGI/Mutpro/Main/Density.pm | 12 ++++++------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/lib/TGI/Mutpro/Main/Cluster.pm b/lib/TGI/Mutpro/Main/Cluster.pm
index da9bdba..61e281f 100644
--- a/lib/TGI/Mutpro/Main/Cluster.pm
+++ b/lib/TGI/Mutpro/Main/Cluster.pm
@@ -563,8 +563,8 @@ sub vertexFilter {
 #TODO if using a different .maf from search step, then some mutations can be missed
 		my $vertexMap = {}; #a hash to map isSameProteinPosition vertices (and others to their selves)-- map=f()
 		my $vfHash = makeVertexFilterHash( $this , $temp_mutations , $temp_distance_matrix ); # a hash with mutationKeys by uniprot id
-		print "vfHash\n";
-		print Dumper $vfHash;
+		# print "vfHash\n";
+		# print Dumper $vfHash;
 
 		foreach my $uniprotID ( keys %{$vfHash} ) {
 			my @mKeys = sort keys %{$vfHash->{$uniprotID}}; #an array to store all the mutation keys corresponding to the uniprotID under consideration
@@ -583,7 +583,7 @@ sub vertexFilter {
 					elsif ( $this->isSameProteinPosition( $temp_mutations , $mutationKey1 , $mutationKey2 ) ) { #if same site
 						$vertexMap->{$mutationKey2} = $mutationKey1;
 						$siteVertexMap->{$mutationKey1}->{$mutationKey2} = $temp_mutations->{$mutationKey2};
-						print "ACSW::VertexFilter::SameSite $mutationKey2 \=\=\> $mutationKey1\n";
+						# print "ACSW::VertexFilter::SameSite $mutationKey2 \=\=\> $mutationKey1\n";
 						delete $temp_mutations->{$mutationKey2};
 					}
 				}
@@ -624,8 +624,8 @@ sub vertexFilter {
 				}
 			}
 		}
-		print "vertex_map\n";
-		print Dumper $vertexMap;
+		# print "vertex_map\n";
+		# print Dumper $vertexMap;
 	} else {
 		%{$mutations} = %{$temp_mutations};
 		%{$distance_matrix} = %{$temp_distance_matrix};
diff --git a/lib/TGI/Mutpro/Main/Density.pm b/lib/TGI/Mutpro/Main/Density.pm
index 196f6ce..7a4375a 100644
--- a/lib/TGI/Mutpro/Main/Density.pm
+++ b/lib/TGI/Mutpro/Main/Density.pm
@@ -104,12 +104,12 @@ sub process {
 		printHash( $mutations, "mutations_hash" );
         printHash( $siteVertexMap, "siteVertexMap_hash" );
 
-        print "mutations\n";
-        print Dumper $mutations;
-        print "distance_matrix\n";
-        print Dumper $distance_matrix;
-        print "siteVertexMap\n";
-        print Dumper $siteVertexMap;
+        # print "mutations\n";
+        # print Dumper $mutations;
+        # print "distance_matrix\n";
+        # print Dumper $distance_matrix;
+        # print "siteVertexMap\n";
+        # print Dumper $siteVertexMap;
 	}
 
     $this->{"siteVertexMap"} = $siteVertexMap; # store the reference to siteVertexMap