various fixes to Ranges including some test brainos; now passing Rang…

…e tests
cjfields · Sep 4, 2012 · 4df69ff · 4df69ff
1 parent 8b70f83
commit 4df69ff
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diff --git a/lib/Bio/Role/Range.pm b/lib/Bio/Role/Range.pm
@@ -13,32 +13,33 @@ our Int method length {
 }
 
 our Bool method overlaps (Bio::Role::Range $range, :$test = 'ignore') {
-    (self!teststranded($range, test => $test) && !((self.start() > $range.end() || self.end() < $range.start())))
-    ?? True !! False;
+    (self!teststranded($range, test => $test) &&
+        !((self.start() > $range.end() || self.end() < $range.start())))
 }
 
 our Bool method contains (Bio::Role::Range $range, :$test = 'ignore') {
-    (self!teststranded($range, :$test) && $range.start() >= self.start() && $range.end() <= self.end())
-    ?? True !! False;
+    (self!teststranded($range, :$test) &&
+        $range.start() >= self.start() && $range.end() <= self.end())
 }
 
 our Bool method equals (Bio::Role::Range $range, :$test = 'ignore')  {
-    (self!teststranded($range, :$test) && self.start() == $range.start() && self.end() == $range.end())
-    ?? True !! False;
+    (self!teststranded($range, :test($test)) &&
+        (self.start == $range.start && self.end == $range.end))
 }
 
 our Bool method !teststranded (Bio::Role::Range $self: Bio::Role::Range $r, :$test = 'ignore') {
+    my ($s1, $s2) = (self.strand, $r.strand);
     given $test {
         when 'ignore' {
             return True
         }
         when 'weak' {
-            if self.strand == 0 || $r.strand == 0 || self.strand == $r.strand {
+            if $s1 == 0 || $s2 == 0 || $s1 == $s2 {
                 return True
             }
         }
         when 'strong' {
-            if self.strand != 0 && self.strand == $r.strand {
+            if $s1 != 0 && $s1 == $s2 {
                 return True
             }
         }

diff --git a/t/Range.t b/t/Range.t
@@ -33,21 +33,21 @@ use Bio::Role::Range;
 ##m = method, o = overlaps()  c = contains()  e = equals
 ##st = strand tests,  i = ignore, w = weak, s = strong
 ##
-##    r0       r1       r2       r3       r4       r5       r6       r7       r8       r9       r10      r11
-##    o  c  e  o  c  e  o  c  e  o  c  e  o  c  e  o  c  e  o  c  e  o  c  e  o  c  e  o  c  e  o  c  e  o  c  e
-##    iwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiwsiws
-##r0  111111111110110110100100100111111000110110000100100000111000000110000000100000000000000000000000000000000000
-##r1  xxxxxxxxx110110110110110110110110000110110000110110000110000000110000000110000000000000000000000000000000000
-##r2  xxxxxxxxxxxxxxxxxx111111111100100000110110000111111000100000000110000000111000000000000000000000000000000000
-##r3  xxxxxxxxxxxxxxxxxxxxxxxxxxx111111111110110110100100100111000000110000000100000000000000000000000000000000000
-##r4  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx110110110110110110110000000110000000110000000000000000000000000000000000
-##r5  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx111111111100000000110000000111000000000000000000000000000000000
-##r6  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx111111111110110110100100100111000000110000000100000000
-##r7  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx110110110110110110110000000110000000110000000
-##r8  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx111111111100000000110000000111000000
-##r9  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx111111111110110110100100100
-##r10 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx110110110110110110
-##r11 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx111111111
+##    r0       |r1       |r2       |r3       |r4       |r5       |r6       |r7       |r8       |r9       |r10      |r11
+##    o  c  e  |o  c  e  |o  c  e  |o  c  e  |o  c  e  |o  c  e  |o  c  e  |o  c  e  |o  c  e  |o  c  e  |o  c  e  |o  c  e
+##    iwsiwsiws|iwsiwsiws|iwsiwsiws|iwsiwsiws|iwsiwsiws|iwsiwsiws|iwsiwsiws|iwsiwsiws|iwsiwsiws|iwsiwsiws|iwsiwsiws|iwsiwsiws
+##r0  111111111|110110110|100100100|111111000|110110000|100100000|111000000|110000000|100000000|000000000|000000000|000000000
+##r1  xxxxxxxxx|110110110|110110110|110110000|110110000|110110000|110000000|110000000|110000000|000000000|000000000|000000000
+##r2  xxxxxxxxx|xxxxxxxxx|111111111|100100000|110110000|111111000|100000000|110000000|111000000|000000000|000000000|000000000
+##r3  xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|111111111|110110110|100100100|111000000|110000000|100000000|000000000|000000000|000000000
+##r4  xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|110110110|110110110|110000000|110000000|110000000|000000000|000000000|000000000
+##r5  xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|111111111|100000000|110000000|111000000|000000000|000000000|000000000
+##r6  xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|111111111|110110110|100100100|111000000|110000000|100000000
+##r7  xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|110110110|110110110|110000000|110000000|110000000
+##r8  xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|111111111|100000000|110000000|111000000
+##r9  xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|111111111|110110110|100100100
+##r10 xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|110110110|110110110
+##r11 xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|xxxxxxxxx|111111111
 ##
 ##=end Range tests
 
@@ -88,18 +88,18 @@ is(@ranges[11].length, 50);
 # test overlaps, contains, equals, cover all variations
 
 my %map = (
-r0  => '111111111110110110100100100111111000110110000100100000111000000110000000100000000000000000000000000000000000',
-#r1  => '111111000111111000110110000110110000110110000100100000100100000100100000000000000000000000000000000',
-#r2  => '111111111110000000110110000110110110100000000100100000100100100000000000000000000000000000',
-#r3  => '111111111111111000111000000100100100100100000100000000000000000000000000000000000',
-#r4  => '111111000111111000100100000100100000100100000000000000000000000000000000',
-#r5  => '111111111100000000100100000100100100000000000000000000000000000',
-#r6  => '111111111111111000111000000100100100100100000100000000',
-#r7  => '111111000111111000100100000100100000100100000',
-#r8  => '111111111100000000100100000100100100',
-#r9  => '111111111111111000111000000',
-#r10 => '111111000111111000',
-#r11 => '111111111',
+r0  => '111111111|110110110|100100100|111111000|110110000|100100000|111000000|110000000|100000000|000000000|000000000|000000000',
+r1  => '110110110|110110110|110110000|110110000|110110000|110000000|110000000|110000000|000000000|000000000|000000000',
+r2  => '111111111|100100000|110110000|111111000|100000000|110000000|111000000|000000000|000000000|000000000',
+r3  => '111111111|110110110|100100100|111000000|110000000|100000000|000000000|000000000|000000000',
+r4  => '110110110|110110110|110000000|110000000|110000000|000000000|000000000|000000000',
+r5  => '111111111|100000000|110000000|111000000|000000000|000000000|000000000',
+r6  => '111111111|110110110|100100100|111000000|110000000|100000000',
+r7  => '110110110|110110110|110000000|110000000|110000000',
+r8  => '111111111|100000000|110000000|111000000',
+r9  => '111111111|110110110|100100100',
+r10 => '110110110|110110110',
+r11 => '111111111',
 );
 
 for 0..@ranges.end -> $i {
@@ -108,13 +108,11 @@ for 0..@ranges.end -> $i {
     for $i..@ranges.end -> $j {
         my $r1 = @ranges[$i];
         my $r2 = @ranges[$j];
-        for <ignore weak strong> -> $test {
-            my $current = ?@tests.shift;
-            is($r1.overlaps($r2, test => $test ), ?$current, ~$r1 ~ ' overlaps ' ~ $r2 ~ ", $test: "~ $current);
-            $current = ?@tests.shift;
-            is($r1.contains($r2, :test<$test>), ?$current, ~$r1 ~ ' contains ' ~ $r2 ~ ", $test: " ~ $current);
-            $current = ?@tests.shift;
-            is($r1.equals($r2, :test<$test>), ?$current, ~$r1 ~ ' equals ' ~ $r2 ~ ", $test: " ~ $current);
+        for <overlaps contains equals> -> $method {
+            for <ignore weak strong> -> $test {
+                my $current = ?@tests.shift;
+                is($r1."$method"($r2, :test($test) ), $current, "$r1 $method $r2, $test: $current");
+            }
         }
     }
 }
@@ -153,110 +151,110 @@ for 0..@ranges.end -> $i {
 #
 #=end Geometric tests
 
-#my %geo_tests =
-#('0,3,6' => {     #  intersection             union
-#    'strong' => ['(75, 75) strand=1',   '(1, 125) strand=1'],
-#    'weak'   => ['(75, 75) strand=1',   '(1, 125) strand=1'],
-#    'ignore' => ['(75, 75) strand=1',   '(1, 125) strand=1'],
-#            },
-# '6,9'   => {
-#    'strong' => ['(101, 125) strand=1', '(75, 150) strand=1'],
-#    'weak'   => ['(101, 125) strand=1', '(75, 150) strand=1'],
-#    'ignore' => ['(101, 125) strand=1', '(75, 150) strand=1'],
-#            },
-# '6,10'   => {
-#    'strong' => ['',                    '(75, 150) strand=0'],
-#    'weak'   => ['(101, 125) strand=0', '(75, 150) strand=0'],
-#    'ignore' => ['(101, 125) strand=0', '(75, 150) strand=0'],
-#            },
-# '6,11'   => {
-#    'strong' => ['',                    '(75, 150) strand=0'],
-#    'weak'   => ['',                    '(75, 150) strand=0'],
-#    'ignore' => ['(101, 125) strand=0', '(75, 150) strand=0'],
-#            },
-# '0,6,9'   => {
-#    'strong' => ['',                    '(1, 150) strand=1'],
-#    'weak'   => ['',                    '(1, 150) strand=1'],
-#    'ignore' => ['',                    '(1, 150) strand=1'],
-#            },
-#);
+my %geo_tests =
+('0,3,6' => {     #  intersection             union
+    'strong' => ['(75, 75) strand=1',   '(1, 125) strand=1'],
+    'weak'   => ['(75, 75) strand=1',   '(1, 125) strand=1'],
+    'ignore' => ['(75, 75) strand=1',   '(1, 125) strand=1'],
+            },
+ '6,9'   => {
+    'strong' => ['(101, 125) strand=1', '(75, 150) strand=1'],
+    'weak'   => ['(101, 125) strand=1', '(75, 150) strand=1'],
+    'ignore' => ['(101, 125) strand=1', '(75, 150) strand=1'],
+            },
+ '6,10'   => {
+    'strong' => ['',                    '(75, 150) strand=0'],
+    'weak'   => ['(101, 125) strand=0', '(75, 150) strand=0'],
+    'ignore' => ['(101, 125) strand=0', '(75, 150) strand=0'],
+            },
+ '6,11'   => {
+    'strong' => ['',                    '(75, 150) strand=0'],
+    'weak'   => ['',                    '(75, 150) strand=0'],
+    'ignore' => ['(101, 125) strand=0', '(75, 150) strand=0'],
+            },
+ '0,6,9'   => {
+    'strong' => ['',                    '(1, 150) strand=1'],
+    'weak'   => ['',                    '(1, 150) strand=1'],
+    'ignore' => ['',                    '(1, 150) strand=1'],
+            },
+);
+
+for %geo_tests.keys.sort -> $set {
+    my @rest = @ranges[$set.split(',')];
+    my $primary = @rest.shift;
+    for <ignore weak strong> -> $test {
+        my $int = $primary.intersection(@rest, :$test);
+        my $union = $primary.union(@rest, :$test);
+        is(($int.defined ?? $int.Str !! ''), %geo_tests{$set}{$test}[0], "intersection of $set, $test");
+        is(($union.defined ?? $union.Str !! ''), %geo_tests{$set}{$test}[1], "union of $set, $test");
+    }
+}
+
+#=begin Subtraction
 #
-#for %geo_tests.keys.sort -> $set {
-#    my @rest = @ranges[$set.split(',')];
-#    my $primary = @rest.shift;
-#    for <ignore weak strong> -> $test {
-#        my $int = $primary.intersection(@rest, :$test);
-#        my $union = $primary.union(@rest, :$test);
-#        is(($int.defined ?? $int.Str !! ''), %geo_tests{$set}{$test}[0], "intersection of $set, $test");
-#        is(($union.defined ?? $union.Str !! ''), %geo_tests{$set}{$test}[1], "union of $set, $test");
-#    }
-#}
+# r0 |--------->
+# r1 |---------|
+# r2 <---------|
 #
-##=begin Subtraction
-##
-## r0 |--------->
-## r1 |---------|
-## r2 <---------|
-##
-## r3    |-->
-## r4    |--|
-## r5    <--|
-##
-## r6       |-------->
-## r7       |--------|
-## r8       <--------|
-##
-## r9            |-------->
-## r10           |--------|
-## r11           <--------|
-##
-## subtraction of r3 from r0  => two Ranges [1, 24, 1] and [76, 100, 1]
-## subtraction of r0 from r3  => one Range [0,0,1] - empty
-## subtraction of r6 from r0  => one Range [1, 74, 1]
-## subtraction of r0 from r6  => one Range [101,125,1]
-## subtraction of r9 from r6  => one Range [75,100,1]
-## subtraction of r6 from r9  => one Range [126,150,1]
-## subtraction of r9 from r0  => original (or clone?) r0 Range [1, 100, 1]
-## subtraction of r0 from r9  => original (or clone?) r9 Range [101,150,1]
-##
-##=end Subtraction
+# r3    |-->
+# r4    |--|
+# r5    <--|
 #
-#my %subtract_tests = ( # rx->subtract(ry)               ry->subtract(rx)
-# '0,3' =>   {
-#    'strong' =>  ['(1, 24) strand=1,(76, 100) strand=1','(0, 0) strand=0'],
-#    'weak'   =>  ['(1, 24) strand=1,(76, 100) strand=1','(0, 0) strand=0'],
-#    'ignore' =>  ['(1, 24) strand=1,(76, 100) strand=1','(0, 0) strand=0'],
-#            },
-# '0,4' =>   {
-#    'strong' =>  ['(1, 100) strand=1',                  '(25, 75) strand=0'],
-#    'weak'   =>  ['(1, 24) strand=1,(76, 100) strand=1','(0, 0) strand=0'],
-#    'ignore' =>  ['(1, 24) strand=1,(76, 100) strand=1','(0, 0) strand=0'],
-#            },
-# '0,6' =>   {
-#    'strong' =>  ['(1, 74) strand=1',                   '(101, 125) strand=1'],
-#    'weak'   =>  ['(1, 74) strand=1',                   '(101, 125) strand=1'],
-#    'ignore' =>  ['(1, 74) strand=1',                   '(101, 125) strand=1'],
-#            },
-# '6,9' =>   {
-#    'strong' =>  ['(75, 100) strand=1',                 '(126, 150) strand=1'],
-#    'weak'   =>  ['(75, 100) strand=1',                 '(126, 150) strand=1'],
-#    'ignore' =>  ['(75, 100) strand=1',                 '(126, 150) strand=1'],
-#            },
-# '0,9' =>   {
-#    'strong' =>  ['(1, 100) strand=1',                  '(101, 150) strand=1'],
-#    'weak'   =>  ['(1, 100) strand=1',                  '(101, 150) strand=1'],
-#    'ignore' =>  ['(1, 100) strand=1',                  '(101, 150) strand=1'],
-#            },
-#);
+# r6       |-------->
+# r7       |--------|
+# r8       <--------|
 #
-#for %subtract_tests.keys.sort -> $set {
-#    my ($r1, $r2) = @ranges[split(',',$set)];
-#    for <ignore weak strong> -> $st {
-#        my @sub1 = $r1.subtract($r2, test => $st);
-#        my @sub2 = $r2.subtract($r1, test => $st);
-#        is(join(',', @sub1».Str), %subtract_tests{$set}{$st}[0], "subtract" );
-#        is(join(',', @sub2».Str), %subtract_tests{$set}{$st}[1], "subtract");
-#    }
-#}
+# r9            |-------->
+# r10           |--------|
+# r11           <--------|
+#
+# subtraction of r3 from r0  => two Ranges [1, 24, 1] and [76, 100, 1]
+# subtraction of r0 from r3  => one Range [0,0,1] - empty
+# subtraction of r6 from r0  => one Range [1, 74, 1]
+# subtraction of r0 from r6  => one Range [101,125,1]
+# subtraction of r9 from r6  => one Range [75,100,1]
+# subtraction of r6 from r9  => one Range [126,150,1]
+# subtraction of r9 from r0  => original (or clone?) r0 Range [1, 100, 1]
+# subtraction of r0 from r9  => original (or clone?) r9 Range [101,150,1]
+#
+#=end Subtraction
+
+my %subtract_tests = ( # rx->subtract(ry)               ry->subtract(rx)
+ '0,3' =>   {
+    'strong' =>  ['(1, 24) strand=1,(76, 100) strand=1','(0, 0) strand=0'],
+    'weak'   =>  ['(1, 24) strand=1,(76, 100) strand=1','(0, 0) strand=0'],
+    'ignore' =>  ['(1, 24) strand=1,(76, 100) strand=1','(0, 0) strand=0'],
+            },
+ '0,4' =>   {
+    'strong' =>  ['(1, 100) strand=1',                  '(25, 75) strand=0'],
+    'weak'   =>  ['(1, 24) strand=1,(76, 100) strand=1','(0, 0) strand=0'],
+    'ignore' =>  ['(1, 24) strand=1,(76, 100) strand=1','(0, 0) strand=0'],
+            },
+ '0,6' =>   {
+    'strong' =>  ['(1, 74) strand=1',                   '(101, 125) strand=1'],
+    'weak'   =>  ['(1, 74) strand=1',                   '(101, 125) strand=1'],
+    'ignore' =>  ['(1, 74) strand=1',                   '(101, 125) strand=1'],
+            },
+ '6,9' =>   {
+    'strong' =>  ['(75, 100) strand=1',                 '(126, 150) strand=1'],
+    'weak'   =>  ['(75, 100) strand=1',                 '(126, 150) strand=1'],
+    'ignore' =>  ['(75, 100) strand=1',                 '(126, 150) strand=1'],
+            },
+ '0,9' =>   {
+    'strong' =>  ['(1, 100) strand=1',                  '(101, 150) strand=1'],
+    'weak'   =>  ['(1, 100) strand=1',                  '(101, 150) strand=1'],
+    'ignore' =>  ['(1, 100) strand=1',                  '(101, 150) strand=1'],
+            },
+);
+
+for %subtract_tests.keys.sort -> $set {
+    my ($r1, $r2) = @ranges[split(',',$set)];
+    for <ignore weak strong> -> $st {
+        my @sub1 = $r1.subtract($r2, test => $st);
+        my @sub2 = $r2.subtract($r1, test => $st);
+        is(join(',', @sub1».Str), %subtract_tests{$set}{$st}[0], "subtract" );
+        is(join(',', @sub2».Str), %subtract_tests{$set}{$st}[1], "subtract");
+    }
+}
 
 done();