/* returns head of the list or NULL on failure. */
OS_Keylist Keylist_Create(
void)
{
struct Keylist *list;
list = KeylistCreate();
if (list)
CheckArraySize(list);
return list;
}
/* inserts a node into its sorted position */
int Keylist_Data_Add(
OS_Keylist list,
KEY key,
void *data)
{
struct Keylist_Node *node; /* holds the new node */
int index = -1; /* return value */
int i; /* counts through the array */
if (list && CheckArraySize(list)) {
/* figure out where to put the new node */
if (list->count) {
(void) FindIndex(list, key, &index);
/* Add to the beginning of the list */
if (index < 0)
index = 0;
/* Add to the end of the list */
else if (index > list->count)
index = list->count;
/* Move all the items up to make room for the new one */
for (i = list->count; i > index; i--) {
list->array[i] = list->array[i - 1];
}
}
else {
index = 0;
}
/* create and add the node */
node = NodeCreate();
if (node) {
list->count++;
node->key = key;
node->data = data;
list->array[index] = node;
}
}
return index;
}
/* returns the data from the node */
void *Keylist_Data_Delete_By_Index(
OS_Keylist list,
int index)
{
struct Keylist_Node *node;
void *data = NULL;
if (list && list->array && list->count && (index >= 0) &&
(index < list->count)) {
node = list->array[index];
if (node)
data = node->data;
/* move the nodes to account for the deleted one */
if (list->count == 1) {
/* There is no node shifting to do */
}
/* We are the last one */
else if (index == (list->count - 1)) {
/* There is no node shifting to do */
}
/* Move all the nodes down one */
else {
int i; /* counter */
int count = list->count - 1;
for (i = index; i < count; i++) {
list->array[i] = list->array[i + 1];
}
}
list->count--;
if (node)
free(node);
/* potentially reduce the size of the array */
(void) CheckArraySize(list);
}
return (data);
}
void RecalibrationModel::InitializeFromJSON(Json::Value &recal_params, string &my_block_key, bool spam_enabled, int over_flow_protect) {
// this needs to signal when it fails in some way
verbose_ = spam_enabled;
int flowStart, flowEnd, flowSpan, xMin, xMax, xSpan, yMin, yMax, ySpan, max_hp_calibrated;
flowStart = rGetParamsInt(recal_params[my_block_key],"flowStart",0);
//cout << flowStart << endl;
flowEnd = rGetParamsInt(recal_params[my_block_key],"flowEnd",0);
if (over_flow_protect>flowEnd)
flowEnd = over_flow_protect; // allocate for combined bam files that need to access flows "past the end" without crashing
//cout << flowEnd << endl;
flowSpan = rGetParamsInt(recal_params[my_block_key],"flowSpan",0);
//cout << flowSpan << endl;
xMin = rGetParamsInt(recal_params[my_block_key],"xMin",0);
//cout << xMin << endl;
xMax =rGetParamsInt(recal_params[my_block_key],"xMax",0);
//cout << xMax << endl;
xSpan =rGetParamsInt(recal_params[my_block_key],"xSpan",0);
//cout << xSpan << endl;
yMin = rGetParamsInt(recal_params[my_block_key],"yMin",0);
//cout << yMin << endl;
yMax =rGetParamsInt(recal_params[my_block_key],"yMax",0);
//cout << yMax << endl;
ySpan = rGetParamsInt(recal_params[my_block_key],"ySpan",0);
//cout << ySpan << endl;
max_hp_calibrated = rGetParamsInt(recal_params[my_block_key],"max_hp_calibrated",0);
stratification.SetupChipRegions(xMin, xMax, xSpan, yMin, yMax, ySpan);
stratification.SetupFlowRegions(flowStart,flowEnd, flowSpan);
//calculate number of partitions and initialize the stratifiedAs and stratifiedBs
SetupStratification(flowStart,flowEnd, flowSpan,xMin,xMax,xSpan,yMin,yMax,ySpan,max_hp_calibrated);
// stratification setup done
// now iterate and obtain each line from the JSON
int iter_size = recal_params[my_block_key]["modelParameters"].size();
for (int i_item=0; i_item<iter_size; i_item++) {
// extract my single line
//model_file >> flowBase >> flowStart >> flowEnd >> xMin >> xMax >> yMin >> yMax >> refHP >> paramA >> paramB;
//flowBase is a special extraction
flowStart = rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"flowStart",0);
flowEnd = rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"flowEnd",0);
xMin = rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"xMin",0);
xMax =rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"xMax",0);
yMin = rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"yMin",0);
yMax =rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"yMax",0);
int refHP;
refHP = rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"refHP",0);
float paramA, paramB;
paramA = rGetParamsDbl(recal_params[my_block_key]["modelParameters"][i_item],"paramA",1.0);
paramB = rGetParamsDbl(recal_params[my_block_key]["modelParameters"][i_item],"paramB",0.0);
//string flowBase = recal_params[my_block_key]["modelParameters"][i_item]["flowBase"].asCString();
char flowBase = (char) rGetParamsInt(recal_params[my_block_key]["modelParameters"][i_item],"flowBase",0);
int nucInd = NuctoInt(flowBase);
// all set with the values
int offsetRegion = stratification.OffsetRegion(xMin,yMin);
// note we only fill >in< flows fit by the recalibration model
FillIndexes(offsetRegion,nucInd, refHP, flowStart, flowEnd, paramA, paramB);
}
// if something bad happened above, how do we find out? - We do some basic sanity checks
CheckArraySize();
// now we're done!
if (verbose_)
cout << "Recalibration: enabled (using recalibration comment " << my_block_key << ") in a "
<< stratification.xCuts << 'x' << stratification.yCuts << 'x' << stratification.flowCuts << " grid." <<endl << endl;
is_enabled_ = true;
}
