SecStructGen.cc

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file   core/fragment/picking_old/vall/gen/SecStructGen.cc
/// @brief  default constant length fragment VallExtentGenerator
/// @author Yih-En Andrew Ban (yab@u.washington.edu)

// unit headers
#include <core/fragment/picking_old/vall/gen/SecStructGen.hh>

#include <utility/vector1.hh>



namespace core {
namespace fragment {
namespace picking_old {
namespace vall {
namespace gen {


/// @brief default constructor
SecStructGen::SecStructGen() :
  Super()
{}


/// @brief fragment size constructor
/// @param[in] ss the required secondary structure string of the fragment
SecStructGen::SecStructGen( String const & ss ) :
  Super(),
  ss_( ss )
{}


/// @brief copy constructor
SecStructGen::SecStructGen( SecStructGen const & rval ) :
  Super( rval ),
  ss_( rval.ss_ )
{}


/// @brief default destructor
SecStructGen::~SecStructGen()
{}


/// @brief copy assignment
SecStructGen & SecStructGen::operator =( SecStructGen const & rval ) {
  if ( this != &rval ) {
    Super::operator =( rval );
    ss_ = rval.ss_;
  }
  return *this;
}


/// @brief clone this object
VallFragmentGenOP SecStructGen::clone() const {
  return new SecStructGen( *this );
}


/// @brief return the desired fragment extent w/ length equal to the
///  secondary structure string
/// @return Valid (true) extent if the extent has exactly the required
///  secondary structure string and the end of the extent does not go past
///  section_end.  Invalid (false) extent otherwise.
/// @remarks we assume VallResidueIterator is a type of RandomAccessIterator, such as
///  those used in std::vector
SecStructGen::Extent SecStructGen::operator ()( VallResidueIterator extent_begin, VallResidueIterator section_end ) const {
  Extent extent;
  extent.begin = extent_begin;
  extent.end = extent_begin + ss_.length();
  extent.valid = ( extent.end <= section_end );

  if ( extent.valid ) {

    // check if secondary structure string matches
    Size str_idx = 0;
    for ( VallResidueIterator i = extent.begin; i != extent.end; ++i, ++str_idx ) {
      assert( str_idx != ss_.length() );

      // if secondary structure string doesn't match, set invalid
      // Extent and break out of loop
      if ( i->ss() != ss_.at( str_idx ) ) {
        extent.valid = false;
        break;
      }
    }

  } // if extent.valid

  return extent;
}


} // namespace gen
} // namespace vall
} // namespace picking_old
} // namespace fragment
} // namespace core