in reply to Re^4: Including existing C or CPP library using Inline
in thread Including existing C or CPP library using Inline

Thus my guess is that the issue lies with passing Perl strings to a C++

I think it might have more to do with the way that the string has been passed.
For example, cprintit() works fine if you rewrite it as: 
int cprintit(const char * seq) {
    cout << seq << endl;
    return 10;
}

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That's how you've passed the strings to do_SSW() - the problem with do_SSW() is that you've specified a *return* of type "string".
Perl's typemapping doesn't handle passing of the "string" type (either as argument or as return). You'll need to provide a typemap for "string" if you want to pass that type around.
What happens if you specify a return type of "char *" (instead of "string") for do_SSW() ?

For a solution using a typemap, this works for me: 
#!/usr/bin/perl
use warnings;
use Inline CPP => Config => BUILD_NOISY => 1,
 TYPEMAPS => 'C:/_32/pscrpt/inline-cpp/stringtype.map',
 CLEAN_AFTER_BUILD => 0;

use Inline CPP;

my $seq = "CTGAGCCGGTAAATC";


my $returned = cprintit($seq);
print $returned."\n";


__END__
__CPP__

using namespace std;


int cprintit(string seq) {
    cout << seq << endl;
    return 10;
}

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where 'C:/_32/pscrpt/inline-cpp/stringtype.map' contains the following single line (plus newline): 
string    T_PV

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(Safest to provide a fully qualified path to the typemap file - though a path relative to the cwd should also work.)

Cheers,
Rob

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Re^6: Including existing C or CPP library using Inline
by bontus (Novice) on Mar 23, 2014 at 14:49 UTC
    Hi Rob, This indeed fixed the issue thank you very much! Here's the revised code: 
    #!/usr/bin/perl
use warnings;
use Inline CPP => Config => BUILD_NOISY => 1, CLEAN_AFTER_BUILD => 0,
    TYPEMAPS => './stringtype.map';
use Inline CPP;

my $seq = "CTGAGCCGGTAAATC";
my $ref = "CTGTGCCATGCGACTGGTACAATC";

my $cigar = do_SSW($seq,$ref);
print "$cigar\n";

__END__
__CPP__

using namespace std;
#include <string>
#include "ssw_cpp.h"
#include "ssw_cpp.cpp"
#include "ssw.c"
#include "ssw.h"

char *do_SSW(string queryC, string refC) {
    StripedSmithWaterman::Aligner aligner;
    StripedSmithWaterman::Filter filter;
    StripedSmithWaterman::Alignment alignment;
    aligner.Align(queryC.c_str(), refC.c_str(), refC.size(), filter, &
+alignment);
    string s     = alignment.cigar_string.c_str();
    char *a     = new char[s.size()+1];
    a[s.size()] = 0;
    memcpy(a,s.c_str(),s.size());
    return a;
}

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    Having solved this problem, I am of course facing the next one: since the C++ alignment object contains more information and cannot be fully passed back to Perl right away, I am now trying to find a way to do so. My backup plan is to just concatenate all this information and then split the returned string in Perl.

    Anyhow, again thanks a lot! René
[reply]
[d/l]

      You can always return an SV* containing a reference to an array, hash, or some complex data structure, if that is more useful.

      Since you're using Inline::CPP, you could also encapsulate the data in a class and provide accessors to each component of the data.


      Dave

[reply]

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