alignment_handle.cc

//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2010 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
//------------------------------------------------------------------------------

/*
  Author: Marco Biasini
 */
#include <ost/invalid_handle.hh>
#include <ost/seq/alignment_handle.hh>
#include <ost/seq/impl/sequence_list_impl.hh>
#include <ost/seq/impl/sequence_impl.hh>
#include <ost/seq/sequence_list.hh>
#include <ost/seq/aligned_region.hh>
#include <ost/seq/aligned_column_iterator.hh>
#include <ost/integrity_error.hh>

namespace ost { namespace seq {

AlignmentHandle CreateAlignment()
{
  return AlignmentHandle(impl::SequenceListImplPtr(new impl::SequenceListImpl));
}

AlignmentHandle::AlignmentHandle():
  impl_()
{
}

AlignmentHandle::AlignmentHandle(const impl::SequenceListImplPtr& impl):
  impl_(impl)
{ }


int AlignmentHandle::GetPos(int seq_index, int residue_index) const
{
  this->CheckValidity();
  return impl_->GetPos(seq_index, residue_index);
}

int AlignmentHandle::GetResidueIndex(int seq_index, int pos) const
{
  this->CheckValidity();
  return impl_->GetResidueIndex(seq_index, pos);
}


void AlignmentHandle::AddSequence(const ConstSequenceHandle& sequence)
{
  this->CheckValidity();
  if (impl_->GetCount()>0 && 
      impl_->GetSequence(0)->GetLength()!=sequence.GetLength()) {
    throw InvalidAlignment();
  }
  return impl_->AddSequence(sequence.Impl());
}

ConstSequenceHandle AlignmentHandle::GetSequence(int seq_id) const
{
  this->CheckValidity();
  return impl_->GetSequence(seq_id);
}


String AlignmentHandle::ToString(int width) const
{
  this->CheckValidity();
  return impl_->ToString(width);
}

int AlignmentHandle::GetLength() const
{
  this->CheckValidity();
  if (impl_->GetCount()==0) {
    return 0;
  } else {
    return impl_->GetSequence(0)->GetLength();
  }
}


AlignmentHandle AlignmentHandle::Copy() const
{
  this->CheckValidity();
  return impl_->Copy();
}

bool AlignmentHandle::operator==(const AlignmentHandle& rhs) const
{
  return rhs.impl_==impl_;
}

bool AlignmentHandle::operator!=(const AlignmentHandle& rhs) const
{
    return rhs.impl_!=impl_;
}

void AlignmentHandle::CheckValidity() const
{
  if (!impl_) {
    throw InvalidHandle();
  }
}

int AlignmentHandle::GetCount() const
{
  this->CheckValidity();
  return impl_->GetCount();
}

AlignmentHandle AlignmentFromSequenceList(const SequenceList& seq_list)
{
  if (seq_list.SequencesHaveEqualLength()) {
    return AlignmentHandle(seq_list.Impl());
  }
  throw InvalidAlignment();
}

ConstSequenceList AlignmentHandle::GetSequences() const
{
  this->CheckValidity();
  return ConstSequenceList(impl_);
}


void AlignmentHandle::AttachView(int seq_index, const mol::EntityView& view)
{
  this->CheckValidity();
  impl_->GetSequence(seq_index)->AttachView(view);
}

void AlignmentHandle::AttachView(int seq_index, const mol::EntityView& view, 
                                 const String& chain_name)
{
  this->CheckValidity();
  impl_->GetSequence(seq_index)->AttachView(view, chain_name);
}

ConstSequenceHandle AlignmentHandle::FindSequence(const String& name) const
{
  this->CheckValidity();
  return ConstSequenceHandle(impl_->FindSequence(name));
}


void AlignmentHandle::Cut(int start, int end)
{
  this->CheckValidity();
  for (impl::SequenceListImpl::Iterator i=impl_->Begin(), 
       e=impl_->End(); i!=e; ++i) {
    (*i)->Cut(start, end-start);
  }
}

void AlignmentHandle::Replace(const AlignedRegion& aln_r, int start, int end){
  this->CheckValidity();
  //check that alignment handle and aligned region contain same number of sequences
  if (impl_->GetCount() != aln_r.GetAlignmentHandle().GetCount()) {
    throw IntegrityError("alignment handle and aligned region are required "\
                         "to share the same number of sequences");
  }
  int aln_rStart=aln_r.GetStart();
  int aln_rEnd=aln_r.GetEnd();
  AlignmentHandle aln=aln_r.GetAlignmentHandle();
  //iterate over sequences and replace part of sequences with the substrings
  //from aligned region
  for (int i=0;i<impl_->GetCount() ;++i) {
    this->GetSequence(i).Impl()->Replace(aln.GetSequence(i).GetString().substr(aln_rStart,aln_rEnd), start, end);
  }
}

void AlignmentHandle::ShiftRegion(int start, int end, int amount, 
                                  int master)
{
  this->CheckValidity();
  int cnt=0;
  for (impl::SequenceListImpl::Iterator i=impl_->Begin(), 
       e=impl_->End(); i!=e; ++i, ++cnt) {
    if (master==-1 || cnt==master) {
      (*i)->ShiftRegion(start, end, amount);
    }
  }
}

AlignedRegion AlignmentHandle::MakeRegion(int start, int n, int master) const
{
  this->CheckValidity();
  return AlignedRegion(*this, start, start+n, master);
}

mol::ResidueView AlignmentHandle::GetResidue(int seq_index, int pos) const
{
  this->CheckValidity();
  return impl_->GetSequence(seq_index)->GetResidue(pos);
}

char AlignmentHandle::GetOneLetterCode(int seq_index, int pos) const
{
  this->CheckValidity();
  return impl_->GetSequence(seq_index)->GetOneLetterCode(pos);
}

AlignedColumnIterator AlignmentHandle::begin() const
{
  // no need to check for validity here  
  return AlignedColumnIterator(*this, 0, this->GetLength());
}

AlignedColumnIterator AlignmentHandle::end() const
{
  // no need to check for validity here
  return AlignedColumnIterator(*this, this->GetLength(), this->GetLength());
}

AlignedColumn AlignmentHandle::operator[](int index)
{
  return AlignedColumn(*this, index);
}

void AlignmentHandle::SetSequenceName(int seq_index, const String& name)

{
  this->CheckValidity();
  impl_->GetSequence(seq_index)->SetName(name);
}

void AlignmentHandle::SetSequenceOffset(int seq_index, int offset)
{
  this->CheckValidity();
  impl_->GetSequence(seq_index)->SetSequenceOffset(offset);
}

}}