promote Types to their own namespace

cjfields · Jun 12, 2010 · bfc97a8 · bfc97a8
1 parent 955ca05
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diff --git a/lib/Biome/Type/Segment.pm b/lib/Biome/Type/Segment.pm
@@ -0,0 +1,106 @@
+# This is a simple package with proposed subtypes; these may end up
+# being split into various packages based on use, namespace, etc.
+
+# TODO:
+# I have tried MooseX::Types and I find it a bit slower that vanilla
+# Moose::Util::TypeParameters, so may revert to the latter if speed becomes an
+# issue
+
+package Biome::Type::Segment;
+
+use MooseX::Types -declare => [qw(
+                               Segment_Pos_Symbol
+                               Segment_Pos_Type
+                               Segment_Symbol
+                               Segment_Type
+                               Split_Segment_Type
+							   )];
+
+use MooseX::Types::Moose qw(Int Str Object CodeRef Any);
+
+my %VALID_SEGMENT_SYMBOL = (
+    '.'          => 'WITHIN',
+    '..'         => 'EXACT',
+    '^'          => 'IN-BETWEEN',
+);
+
+my %VALID_SEGMENT_POS_SYMBOL = (
+    '..'         => 'EXACT',
+    '<'          => 'BEFORE',
+    '>'          => 'AFTER',
+    '.'          => 'WITHIN',
+    '?'          => 'UNCERTAIN'
+);
+
+my %SYMBOL_TYPE = (
+    'EXACT'     => '..',
+    'BEFORE'    => '<',
+    'AFTER'     => '>',
+    'WITHIN'    => '.',
+    'IN-BETWEEN'   => '^',
+    'UNCERTAIN' => '?'
+);
+
+my %TYPE_SYMBOL = map {$SYMBOL_TYPE{$_} => $_} keys %SYMBOL_TYPE;
+
+# WITHIN here is very rare but does occur, ex (122.144)
+my %VALID_SEGMENT_TYPE = map {$_ => 1}
+    qw(EXACT IN-BETWEEN WITHIN);
+
+my %VALID_SEGMENT_POS_TYPE = map {$_ => 1}
+    qw(EXACT BEFORE AFTER WITHIN UNCERTAIN);
+
+# TODO: some of these could probably be redef. as enums, but it makes coercion
+# easier, needs checking
+
+subtype Segment_Symbol,
+    as Str,
+    where {exists $VALID_SEGMENT_SYMBOL{$_}},
+    message {"Unknown Segment symbol $_"};
+
+subtype Segment_Type,
+    as Str,
+    where {exists $VALID_SEGMENT_TYPE{$_}},
+    message {"Unknown Segment type $_"};
+
+subtype Segment_Pos_Symbol,
+    as Str,
+    where {exists $VALID_SEGMENT_POS_SYMBOL{$_}},
+    message {"Unknown Segment positional symbol $_"};
+
+subtype Segment_Pos_Type,
+    as Str,
+    where {exists $VALID_SEGMENT_POS_TYPE{$_}},
+    message {"Unknown Segment positional type $_"};
+
+coerce Segment_Pos_Type,
+    from Segment_Pos_Symbol,
+    via {$TYPE_SYMBOL{$_}};
+
+coerce Segment_Pos_Symbol,
+    from Segment_Pos_Type,
+    via {$SYMBOL_TYPE{$_}};
+
+coerce Segment_Symbol,
+    from Segment_Type,
+    via {$SYMBOL_TYPE{$_}};
+
+coerce Segment_Type,
+    from Segment_Symbol,
+    via {$TYPE_SYMBOL{$_}};
+
+my %VALID_SPLIT_TYPE = map {$_ => 1}
+    qw(JOIN ORDER BOND);
+
+subtype Split_Segment_Type,
+    as Str,
+    where {exists $VALID_SPLIT_TYPE{uc $_}},
+    message {"Unknown Split Location type $_"};
+
+no MooseX::Types;
+no MooseX::Types::Moose;
+
+1;
+
+__END__
+
diff --git a/lib/Biome/Type/Sequence.pm b/lib/Biome/Type/Sequence.pm
@@ -0,0 +1,52 @@
+# This is a simple package with proposed subtypes; these may end up
+# being split into various packages based on use, namespace, etc.
+
+# TODO:
+# I have tried MooseX::Types and I find it a bit slower that vanilla
+# Moose::Util::TypeParameters, so may revert to the latter if speed becomes an
+# issue
+
+package Biome::Type::Sequence;
+
+use MooseX::Types -declare => [qw(
+							   Sequence_Strand
+							   Sequence_Strand_Int
+							   Sequence_Strand_Symbol
+							   Sequence_Alphabet
+							   )];
+
+use MooseX::Types::Moose qw(Int Str Object CodeRef Any);
+
+subtype Sequence_Strand,
+	as Int,
+	where {$_ >= -1 && $_ <= 1},
+	message { "Strand can be -1, 0, or 1, not $_"};
+
+subtype Sequence_Strand_Symbol,
+	as Str,
+	where { /^(?:[\+\-\.])$/},
+	message { "Strand symbol can be one of [-.+], not $_"};
+
+
+my %STRAND_SYMBOL = (
+    '+'     => 1,
+    '.'     => 0,
+    '-'     => -1
+);
+
+coerce Sequence_Strand,
+    from Sequence_Strand_Symbol,
+    via {$STRAND_SYMBOL{$_}};
+
+subtype Sequence_Alphabet,
+	as Str,
+	where { /^(?:dna|rna|protein)$/xism }, # do we want more?
+	message { "Strand must be 'dna', 'rna', or 'protein'"};
+
+no MooseX::Types;
+no MooseX::Types::Moose;
+
+1;
+
+__END__
+