void Aligner::BuildDefaultMatrix(void) {
ClearMatrices();
score_matrix_ = new int8_t[score_matrix_size_ * score_matrix_size_];
BuildSwScoreMatrix(match_score_, mismatch_penalty_, score_matrix_);
translation_matrix_ = new int8_t[SizeOfArray(kBaseTranslation)];
memcpy(translation_matrix_, kBaseTranslation, sizeof(int8_t) * SizeOfArray(kBaseTranslation));
}
bool Aligner::ReBuild(
const int8_t* score_matrix,
const int& score_matrix_size,
const int8_t* translation_matrix,
const int& translation_matrix_size) {
ClearMatrices();
score_matrix_ = new int8_t[score_matrix_size_ * score_matrix_size_];
memcpy(score_matrix_, score_matrix, sizeof(int8_t) * score_matrix_size_ * score_matrix_size_);
translation_matrix_ = new int8_t[translation_matrix_size];
memcpy(translation_matrix_, translation_matrix, sizeof(int8_t) * translation_matrix_size);
return true;
}
void Aligner::Clear(void) {
ClearMatrices();
CleanReferenceSequence();
}
void
SILAttributes::SetFromNode(DataNode *parentNode)
{
if(parentNode == 0)
return;
DataNode *searchNode = parentNode->GetNode("SILAttributes");
if(searchNode == 0)
return;
DataNode *node;
DataNode **children;
if((node = searchNode->GetNode("nSets")) != 0)
SetNSets(node->AsInt());
if((node = searchNode->GetNode("setNames")) != 0)
SetSetNames(node->AsStringVector());
if((node = searchNode->GetNode("setIds")) != 0)
SetSetIds(node->AsIntVector());
if((node = searchNode->GetNode("wholeList")) != 0)
SetWholeList(node->AsIntVector());
if((node = searchNode->GetNode("nCollections")) != 0)
SetNCollections(node->AsInt());
if((node = searchNode->GetNode("category")) != 0)
SetCategory(node->AsStringVector());
if((node = searchNode->GetNode("role")) != 0)
SetRole(node->AsIntVector());
if((node = searchNode->GetNode("superset")) != 0)
SetSuperset(node->AsIntVector());
// Clear all the NamespaceAttributess if we got any.
bool clearedNspaces = false;
// Go through all of the children and construct a new
// NamespaceAttributes for each one of them.
children = searchNode->GetChildren();
if(children != 0)
{
for(int i = 0; i < searchNode->GetNumChildren(); ++i)
{
if(children[i]->GetKey() == std::string("NamespaceAttributes"))
{
if (!clearedNspaces)
{
ClearNspaces();
clearedNspaces = true;
}
NamespaceAttributes temp;
temp.SetFromNode(children[i]);
AddNspace(temp);
}
}
}
// Clear all the SILMatrixAttributess if we got any.
bool clearedMatrices = false;
// Go through all of the children and construct a new
// SILMatrixAttributes for each one of them.
children = searchNode->GetChildren();
if(children != 0)
{
for(int i = 0; i < searchNode->GetNumChildren(); ++i)
{
if(children[i]->GetKey() == std::string("SILMatrixAttributes"))
{
if (!clearedMatrices)
{
ClearMatrices();
clearedMatrices = true;
}
SILMatrixAttributes temp;
temp.SetFromNode(children[i]);
AddMatrices(temp);
}
}
}
// Clear all the SILArrayAttributess if we got any.
bool clearedArrays = false;
// Go through all of the children and construct a new
// SILArrayAttributes for each one of them.
children = searchNode->GetChildren();
if(children != 0)
{
for(int i = 0; i < searchNode->GetNumChildren(); ++i)
{
if(children[i]->GetKey() == std::string("SILArrayAttributes"))
{
if (!clearedArrays)
{
ClearArrays();
clearedArrays = true;
}
SILArrayAttributes temp;
temp.SetFromNode(children[i]);
AddArrays(temp);
}
}
}
if((node = searchNode->GetNode("order")) != 0)
SetOrder(node->AsIntVector());
}