/// \brief Simple insertion operator for multi_align_builder
///
/// \relates multi_align_builder
ostream & cath::align::detail::operator<<(ostream &arg_os, ///< The ostream to which the multi_align_builder should be output
const multi_align_builder &arg_multi_align_builder ///< The multi_align_builder to output
) {
const size_set active_groups = arg_multi_align_builder.get_active_groups();
arg_os << "multi_align_builder[";
arg_os << active_groups.size();
arg_os << " active groups : ";
for ( const size_t &group_index : active_groups ) {
arg_os << "\n\t";
arg_os << arg_multi_align_builder.get_group_of_index( group_index );
}
arg_os << ( ( ! active_groups.empty() ) ? "\n" : "" );
arg_os << "]";
return arg_os;
}
/// \brief Ctor for alignment_split_mapping
///
/// \todo Consider splitting part of this out into a function that creates a copy of the alignment with any missing residues reinserted
alignment_split_mapping::alignment_split_mapping(const alignment &arg_alignment, ///< TODOCUMENT
const size_set &arg_entries, ///< TODOCUMENT
const size_vec &arg_correct_lengths ///< TODOCUMENT
) : orig_length ( arg_alignment.length() ),
orig_num_entries ( arg_alignment.num_entries() ),
did_insert_entries ( false ),
local_aln ( arg_entries.size() ),
idx_of_orig_aln_idx ( orig_length ),
orig_aln_entries ( common::cbegin( arg_entries ), common::cend( arg_entries ) ),
index_of_pdb_res_index( arg_alignment.num_entries() ) {
// Sanity check the input list of entries
if ( orig_aln_entries.empty() ) {
BOOST_THROW_EXCEPTION(invalid_argument_exception("List of entries is empty"));
}
if ( orig_aln_entries.back() >= orig_num_entries ) {
BOOST_THROW_EXCEPTION(invalid_argument_exception("Entries out of range of the entries in the alignment"));
}
// Loop along the length of the original alignment
for (size_t orig_aln_index = 0; orig_aln_index < orig_length; ++orig_aln_index) {
const alignment_row local_row = get_row_of_entries_of_alignment( arg_alignment, orig_aln_entries, orig_aln_index );
// Only do anything if at least one of the specified entries is present at this index
if ( any_entries_present( local_row ) ) {
// For each entry that's present at this index,
// insert any missing residues into the local_aln, recording where each has gone
for (size_t entry = 0; entry < orig_aln_entries.size(); ++entry) {
// Grab some details for this entry:
// * a reference to the relevant entry of index_of_pdb_res_index
// * the equivalent entry in the original alignment
// * the position for this index/entry in the original alignment
size_vec &pdb_res_indices = index_of_pdb_res_index[ entry ];
const size_t &orig_aln_entry = orig_aln_entries [ entry ];
const aln_posn_opt position = arg_alignment.position_of_entry_of_index( orig_aln_entry, orig_aln_index );
// If there is something present here in the original alignment then add any missing residues
if ( position ) {
// Add any missing residues...
while ( pdb_res_indices.size() < *position ) {
did_insert_entries = true;
pdb_res_indices.push_back( local_aln.length() );
append_row_with_single_value( local_aln, entry, pdb_res_indices.size() - 1 );
}
}
}
// For each entry that's present at this index,
// record where the residue for this index's row will go
for (size_t entry = 0; entry < orig_aln_entries.size(); ++entry) {
// Grab some details for this entry:
// * a reference to the relevant entry of index_of_pdb_res_index
// * the equivalent entry in the original alignment
// * the position for this index/entry in the original alignment
size_vec &pdb_res_indices = index_of_pdb_res_index[ entry ];
const size_t &orig_aln_entry = orig_aln_entries [ entry ];
const aln_posn_opt position = arg_alignment.position_of_entry_of_index( orig_aln_entry, orig_aln_index );
// If there is something present here in the original alignment then store the residue for this index will go
if ( position ) {
// ...and store the residue for this index will go
pdb_res_indices.push_back( local_aln.length() );
}
}
// Store where this alignment row is placed in the local_aln and then put it there
idx_of_orig_aln_idx[ orig_aln_index ] = local_aln.length();
append_row( local_aln, local_row );
}
}
// Append any extra residues that are missing at the end of the original alignment
for (size_t entry = 0; entry < orig_aln_entries.size(); ++entry) {
// Grab some details for this entry:
// * a reference to the relevant entry of index_of_pdb_res_index
// * the equivalent entry in the original alignment
// * the correct length for this entry
size_vec &pdb_res_indices = index_of_pdb_res_index[ entry ];
const size_t &orig_aln_entry = orig_aln_entries [ entry ];
const size_t &correct_length = arg_correct_lengths [ orig_aln_entry ];
// Add any missing residues...
while ( pdb_res_indices.size() < correct_length ) {
did_insert_entries = true;
pdb_res_indices.push_back( local_aln.length() );
append_row_with_single_value( local_aln, entry, pdb_res_indices.size() - 1 );
}
}
// Very basic sanity checks
assert( orig_aln_entries.size() == local_aln.num_entries() );
assert( idx_of_orig_aln_idx.size() == orig_length );
}