Converted more p5 code in LocationFactory. Uncommented a few more tes…

…ts that now pass and Strand for Split now returns Any instead of Mu when no strand can be found.

lib/Bio/Factory/FTLocationFactory.pm

@@ -26,6 +26,10 @@ method from_string($locstr is copy ,$op?) {
         # convert ABC123:(X..Y) to ABC123:[X..Y]
         # we should never see the above
         #     $locstr =~ s{:\((\d+\.{2}\d+)\)}{:\[$1\]}g;
+        while ($locstr ~~ / \: \( (\d+ \. ** 2 \d+) \)/ ) {
+            $locstr ~~ s/ \: \( (\d+ \. ** 2 \d+) \) /\:\[$0\]/;
+        }
+
     }
 
     # if ($locstr =~ m{(.*?)\(($LOCREG)\)(.*)}o) { # any matching parentheses?
@@ -52,7 +56,6 @@ method from_string($locstr is copy ,$op?) {
 
 #                      && $sub !~~ m{(?:join|order|bond)}) {
                     my @splitlocs = split(',' , $sub);
-
 
                     $loc_obj = Bio::Role::Location::Split.new(#verbose => 1,
                                                         splittype => $oparg);
@@ -109,15 +112,15 @@ method from_string($locstr is copy ,$op?) {
 
 
 
-method !parse_location($locstr) {
+method !parse_location($locstr is copy) {
     my ($loc, $seqid);
     #self.debug( "Location parse, processing $locstr\n");
     # 'remote' location?
-    # if($locstr =~ m{^(\S+):(.*)$}o) {
-    #     # yes; memorize remote ID and strip from location string
-    #     $seqid = $1;
-    #     $locstr = $2;
-    # }
+    if ($locstr ~~ /^(\S+)\:(.*)$/) {
+        # yes; memorize remote ID and strip from location string
+        $seqid = $0;
+        $locstr = $1;
+    }
 
     # split into start and end
     my ($start, $end) = split(/\.\./, $locstr);
@@ -126,7 +129,10 @@ method !parse_location($locstr) {
     # possibly surrounding the entire location the parentheses around start
     # and/or may be asymmetrical
     # Note: these are from X.Y fuzzy locations, which are deprecated!
+
     # $start =~ s/(?:^\[+|\]+$)//g if $start;
+    $start ~~ s/^\[+|\]+// if $start;
+    $end ~~ s/^\[+|\]+// if $end;
     # $end   =~ s/(?:^\[+|\]+$)//g if $end;
 
     # Is this a simple (exact) or a fuzzy location? Simples have exact start
@@ -167,8 +173,6 @@ method !parse_location($locstr) {
     if ( $start_num > $end_num && $loctype ne '?') {
         ($start,$end,$strand) = ($end,$start,-1);
     }
-
-
     # instantiate location and initialize
     $loc = $locclass.new(#verbose => self.verbose,
                                   start   => $start, 

lib/Bio/Role/Location/Split.pm

@@ -213,7 +213,7 @@ multi method strand($value?) {
             if ((! $lstrand) ||
                    ($strand && ($strand != $lstrand)) ||
                        $loc.is_remote()) {
-                $strand = Mu;
+                $strand = Any;
                 last;
             } elsif (! $strand) {
                 $strand = $lstrand;

t/Factory/FTLocationFactory.t

@@ -48,16 +48,16 @@ my %testcases = (
 # 		 2691, 2691, "EXACT", 5163, 5163, "EXACT", "EXACT", 2, -1],
 # 	"complement(34..(122.126))" => [$fuzzy_impl,
 # 		 34, 34, "EXACT", 122, 126, "WITHIN", "EXACT", 1, -1],
-# 	"J00194:100..202" => [$simple_impl,
-# 		 100, 100, "EXACT", 202, 202, "EXACT", "EXACT", 1, 1],
+ 	"J00194:100..202" => [$simple_impl,
+ 		 100, 100, "EXACT", 202, 202, "EXACT", "EXACT", 1, 1],
 # 	# this variant is not really allowed by the FT definition
 # 	# document but we want to be able to cope with it
-# 	"J00194:(100..202)" => [$simple_impl,
-# 		 100, 100, "EXACT", 202, 202, "EXACT", "EXACT", 1, 1],
+ 	"J00194:(100..202)" => [$simple_impl,
+ 		 100, 100, "EXACT", 202, 202, "EXACT", "EXACT", 1, 1],
 # 	"((122.133)..(204.221))" => [$fuzzy_impl,
 # 		 122, 133, "WITHIN", 204, 221, "WITHIN", "EXACT", 1, 1],
-# 	"join(AY016290.1:108..185,AY016291.1:1546..1599)"=> [$split_impl,
-# 		 108, 108, "EXACT", 185, 185, "EXACT", "EXACT", 2, undef],
+ 	"join(AY016290.1:108..185,AY016291.1:1546..1599)"=> [$split_impl,
+ 		 108, 108, "EXACT", 185, 185, "EXACT", "EXACT", 2, Any],
 
 # 	# UNCERTAIN locations and positions (Swissprot)
 #    "?2465..2774" => [$fuzzy_impl,
@@ -85,10 +85,10 @@ my $locfac = Bio::Factory::FTLocationFactory.new();
 ok($locfac ~~ Bio::Factory::FTLocationFactory, 'Is Bio::Location::FTLocationFactory Role');
 
 # sorting is to keep the order constant from one run to the next
-for keys %testcases -> $locstr { 
+for keys %testcases -> $locstr is copy { 
 	my $loc = $locfac.from_string($locstr);
 	if ($locstr eq "join(AY016290.1:108..185,AY016291.1:1546..1599)") {
-		$loc.seq_id("AY016295.1");
+		$loc.seq_id ="AY016295.1";
 	}
         my @res = @(%testcases{$locstr});
 	is($loc.WHAT, @res[0], @res[0]);
@@ -111,6 +111,7 @@ for keys %testcases -> $locstr {
 	is($ftstr, $locstr, "Location String: $locstr");
 	# test strand production
 	is($loc.strand(), @res[9]);
+
 }
 
 # SKIP: {