Merge branch 'master' into issue_76_spatial_randomisation

shawnlaffan · Jun 18, 2016 · c36ae19 · c36ae19
2 parents 32b0b1a + 64da31a
commit c36ae19
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diff --git a/etc/pp/README.txt → etc/pp/README.md b/etc/pp/README.txt → etc/pp/README.md
@@ -1,71 +1,96 @@
-Heavy.pm.patch needs to be applied to
-C:\strawberry\perl\vendor\lib\PAR\Heavy.pm
-It causes DLLs to be extracted with their original names instead of CRCs.
-Needed for GTK modules to work properly.
-
-Also need to add the following lines before the open is attempted.
-This avoids duplicate DLL file names in modules ending in XS.  
-
-near line 153, before the line:
-open $fh, '>', $filename or die $!
-
-### DIRTY HACK 
-if (-e $filename && not $filename =~ /Glib|Gtk2|Gnome|Pango|Cairo/) {
-    $filename .= $member->crc32String; #  kludge workaround
-}
-
-
-To get the Biodiverse icon to properly show the PAR libs need to be updated to use the Biodiverse icon.
-Other solutions using Win32::EXE result in a slew of warnings when first running the program.  
-
-
-Adapt this code as needed (from http://www.zewaren.net/site/?q=node/116).
-It is for a makefile, but seemed to have no effect when run independently using dmake.
-Running each command in sequence did work, though (tweaking as appropriate).
-
-
-PERL_DIR = C:\strawberry_51613_x64\perl
-PAR_PACKER_SRC = C:\strawberry_51613_x64\cpan\build\PAR-Packer-1.018-XUXam8
-
-all:
-    copy /Y C:\shawn\svn\biodiverse_trunk\bin\Biodiverse_icon.ico $(PAR_PACKER_SRC)\myldr\winres\pp.ico
-    #copy /Y medias\jambon.rc $(PAR_PACKER_SRC)\myldr\winres\pp.rc
-    del $(PAR_PACKER_SRC)\myldr\ppresource.coff
-    cd /D $(PAR_PACKER_SRC)\myldr\ && perl Makefile.PL
-    cd /D $(PAR_PACKER_SRC)\myldr\ && dmake boot.exe
-    cd /D $(PAR_PACKER_SRC)\myldr\ && dmake Static.pm
-    attrib -R $(PERL_DIR)\site\lib\PAR\StrippedPARL\Static.pm
-    copy /Y $(PAR_PACKER_SRC)\myldr\Static.pm $(PERL_DIR)\site\lib\PAR\StrippedPARL\Static.pm
-
-
-
-
-Old info below.  The patches are redundant for current versions, and the build script has been updated to copy relevant files across.  
-
-
-Makefile.PL.patch needs to be applied to PAR-Packer-1.013
-This patch doesn't change the behaviour. It is just needed to make it build
-under x86_64.
-Derived from http://www.nntp.perl.org/group/perl.par/2012/03/msg5310.html
-(It has been fixed upstream in PAR-Packer-1.014.)
-
-NOTE: The order is important. PAR-Packer needs to be (re)built/installed
-      after Heavy.pm has been modified, since it gets embedded in some
-      binaries.
-
-= The above is only relevant if you are not using the PPMs in ..\ppm\ppm516*
-
-Run "..\etc\pp\build.bat" when you are in the bin directory to generate
-BiodiverseGUI.exe.
-
-The following DLLs from Strawberry Perl need
-to be distributed with BiodiverseGUI.exe:
-
-libstdc++-6.dll
-libexpat-1__.dll
-
-On 32-bit, libgcc_s_sjlj-1.dll, additionally needs to be distributed.
-
-The win_gtk_builds\etc\win(32|64)\c tree also needs to be distributed as
-"gtk".
+## Packing Gtk2 libs ##
+
+The Heavy.pm.patch needs to be applied to PAR\Heavy.pm
+
+Source is https://rt.cpan.org/Ticket/Attachment/1135201/597366/Heavy.pm.patch
+
+This patch means DLLs will be extracted with their original names instead of CRCs,
+and is needed for GTK modules to work properly.  This is not a perfect approach,
+hence the next step. 
+
+The following lines also need to inserted before the open is attempted.
+This avoids duplicate DLL file names for non-Gtk modules, as otherwise those
+with the same ending would all refer to the same file,
+e.g. List::BinarySearch::XS, YAML::XS and URI::Escape::XS would
+all try to use XS.dll.
+
+Insert the code between START HACK and END HACK near line 153
+ (should make a patch file for this).
+
+```perl
+        ($filename) = $filename =~ /^([\x20-\xff]+)$/;
+
+### START HACK 
+if (-e $filename && not $filename =~ /Glib|Gtk2|Gnome|Pango|Cairo/) {
+    $filename .= $member->crc32String; #  kludge workaround
+}
+### END HACK
+
+        open $fh, '>', $filename or die $!;
+```
+
+## Icon ##
+
+The PAR libs need to be updated to use the Biodiverse icon.
+Other solutions using Win32::EXE result in a slew of warnings
+when first running the program.
+
+Before building PAR, copy the Biodiverse icon file into the PAR build folders 
+as $(PAR_PACKER_SRC)\myldr\winres\pp.ico
+
+
+### Alternate icon approach ###
+
+Adapt this code as needed (from http://www.zewaren.net/site/?q=node/116).
+It is for a makefile, but seemed to have no effect when run independently using dmake.
+Running each command in sequence did work, though (tweaking as appropriate).
+
+
+PERL_DIR = C:\strawberry_51613_x64\perl
+PAR_PACKER_SRC = C:\strawberry_51613_x64\cpan\build\PAR-Packer-1.018-XUXam8
+
+all:
+    copy /Y C:\shawn\svn\biodiverse_trunk\bin\Biodiverse_icon.ico $(PAR_PACKER_SRC)\myldr\winres\pp.ico
+    #copy /Y medias\jambon.rc $(PAR_PACKER_SRC)\myldr\winres\pp.rc
+    del $(PAR_PACKER_SRC)\myldr\ppresource.coff
+    cd /D $(PAR_PACKER_SRC)\myldr\ && perl Makefile.PL
+    cd /D $(PAR_PACKER_SRC)\myldr\ && dmake boot.exe
+    cd /D $(PAR_PACKER_SRC)\myldr\ && dmake Static.pm
+    attrib -R $(PERL_DIR)\site\lib\PAR\StrippedPARL\Static.pm
+    copy /Y $(PAR_PACKER_SRC)\myldr\Static.pm $(PERL_DIR)\site\lib\PAR\StrippedPARL\Static.pm
+
+
+
+## Redundant ##
+
+Old info below.
+
+The patches are redundant for current versions, and the build script has been updated to copy relevant files across.  
+
+
+Makefile.PL.patch needs to be applied to PAR-Packer-1.013
+This patch doesn't change the behaviour. It is just needed to make it build
+under x86_64.
+Derived from http://www.nntp.perl.org/group/perl.par/2012/03/msg5310.html
+(It has been fixed upstream in PAR-Packer-1.014.)
+
+NOTE: The order is important. PAR-Packer needs to be (re)built/installed
+      after Heavy.pm has been modified, since it gets embedded in some
+      binaries.
+
+= The above is only relevant if you are not using the PPMs in ..\ppm\ppm516*
+
+Run "..\etc\pp\build.bat" when you are in the bin directory to generate
+BiodiverseGUI.exe.
+
+The following DLLs from Strawberry Perl need
+to be distributed with BiodiverseGUI.exe:
+
+libstdc++-6.dll
+libexpat-1__.dll
+
+On 32-bit, libgcc_s_sjlj-1.dll, additionally needs to be distributed.
+
+The win_gtk_builds\etc\win(32|64)\c tree also needs to be distributed as
+"gtk".
 The "include" directory can be omitted.
diff --git a/lib/Biodiverse/Indices/Phylogenetic.pm b/lib/Biodiverse/Indices/Phylogenetic.pm
@@ -630,36 +630,37 @@ sub calc_pe_central_lists {
     my $self = shift;
     my %args = @_;
 
-    my %wt_list = %{$args{PE_WTLIST}};    #  need a copy since we will delete from it
+    my $base_wt_list = $args{PE_WTLIST};
     my $c_list  =   $args{PHYLO_C_LIST};  #  those only in nbr set 2
     my $a_list  =   $args{PHYLO_A_LIST};
     my $b_list  =   $args{PHYLO_B_LIST};
-    my (%local_range_list_c, %global_range_list_c);
 
     my $local_range_list  = $args{PE_LOCAL_RANGELIST};
     my $global_range_list = $args{PE_RANGELIST};
 
+    my %results;
+
     #  avoid copies and slices if there are no nodes found only in nbr set 2
     if (scalar keys %$c_list) {
-        #  remove the PE component found only in nbr set 2
-        #  (assuming c_list is shorter than a+b, so this will be the faster approach)
-        delete @wt_list{keys %$c_list};
-
+        my (%wt_list, %local_range_list_c, %global_range_list_c);
         #  Keep any node found in nbr set 1
+        @wt_list{keys %$a_list} = @{$base_wt_list}{keys %$a_list};
+        @wt_list{keys %$b_list} = @{$base_wt_list}{keys %$b_list};
+
         my @keepers = keys %wt_list;
         @local_range_list_c{@keepers}  = @{$local_range_list}{@keepers};
         @global_range_list_c{@keepers} = @{$global_range_list}{@keepers};
+
+        $results{PEC_WTLIST} = \%wt_list;
+        $results{PEC_LOCAL_RANGELIST} = \%local_range_list_c;
+        $results{PEC_RANGELIST}       = \%global_range_list_c;
     }
     else {
-        %local_range_list_c  = %$local_range_list;
-        %global_range_list_c = %$global_range_list;
+        $results{PEC_WTLIST} = $base_wt_list;
+        $results{PEC_LOCAL_RANGELIST} = $local_range_list;
+        $results{PEC_RANGELIST}       = $global_range_list;
     }
 
-    my %results = (
-        PEC_WTLIST => \%wt_list,
-        PEC_LOCAL_RANGELIST  => \%local_range_list_c,
-        PEC_RANGELIST        => \%global_range_list_c,
-    );
 
     return wantarray ? %results : \%results;
 }