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;
}

[download]
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;
}

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

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

Cheers,
Rob

In reply to Re^5: Including existing C or CPP library using Inline by syphilis
in thread Including existing C or CPP library using Inline by bontus

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