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Re: [Seqan-dev] Infix of const String

<-- thread -->
<-- date -->
  • From: Alexander Vowinkel <vowinkel.alexander@gmail.com>
  • To: SeqAn Development <seqan-dev@lists.fu-berlin.de>
  • Date: Wed, 3 Jun 2015 09:56:05 -0500
  • Reply-to: SeqAn Development <seqan-dev@lists.fu-berlin.de>
  • Subject: Re: [Seqan-dev] Infix of const String

Hi Fadhlan,

your example also works for me.
The difference is, that you use as first parameter a DnaString.
I use representative(indexIt), which is according to the error message
a pointer to a Dna5String.
I would say that this should work as well.

Best,
Alexander

2015-06-02 23:42 GMT-05:00 Fadhlan Rizal <fadhlan.fari@gmail.com>:
i don't know, but when i using my program it's work perfectly, of course i using another type (not TBarcodeString).

here my example:

DnaString mySekuens  = "ACGTACGTACGT";

startPosition = 0;
endPosition = startPosition + 5;

Infix<String<Dna> >::Type inf;
inf = infix(mySekuens, startPosition, endPosition);


the output  ACGTA;

2015-06-03 6:46 GMT+07:00 Alexander Vowinkel <vowinkel.alexander@gmail.com>:
Hi Team,

adopting from IndexIterators Tutorial, following problem came up:

When I want to save an Infix of an representative in an Index Iterator:

seqan::Infix<TBarcodeString>::Type referenceIfx = infix(representative(indexIt), parentRepLength(indexIt) + 1, endPos);

the error pops up, that I can't use a const String for this:

/opt/seqan/seqan-src/include/seqan/sequence/segment_infix.h:135:42: error: invalid conversion from ‘seqan::Pointer_<const seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >::Type {aka const seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >*}’ to ‘seqan::Pointer_<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> > >::Type {aka seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >*}’ [-fpermissive]
         data_host(_toPointer(host(_other))),

Solutions?

Best,
Alexander 

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  • Follow-Ups:
    • Re: [Seqan-dev] Infix of const String
      • From: Fadhlan Rizal <fadhlan.fari@gmail.com>
  • References:
    • [Seqan-dev] Infix of const String
      • From: Alexander Vowinkel <vowinkel.alexander@gmail.com>
    • Re: [Seqan-dev] Infix of const String
      • From: Fadhlan Rizal <fadhlan.fari@gmail.com>
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