int fbs()
{
int head,tail,l;
head=0;tail=1;
b[0][0]=x1;b[0][1]=y1;
while(head!=tail)
{
x1=b[head][0];
y1=b[head++][1];
for(l=0;l<8;l++)
{
x=x1+k[l][0];
y=y1+k[l][1];
if(tru(x,y))
continue;
if(a[x][y])
continue;
b[tail][0]=x;
b[tail++][1]=y;
a[x][y]=a[x1][y1]+1;
if(x==x2&&y==y2)
return a[x][y];
}
}
}
/**
* Helper function to initialize a bitarray from a string
*/
static QBitArray QStringToQBitArray(const QString &str)
{
QBitArray ba;
ba.resize(str.length());
int i;
QChar tru('1');
for (i = 0; i < str.length(); i++)
{
if (str.at(i) == tru)
{
ba.setBit(i, true);
}
}
return ba;
}
MuscleTask::MuscleTask(const MultipleSequenceAlignment &ma, const MuscleTaskSettings& _config)
: Task(tr("MUSCLE alignment"), TaskFlags_FOSCOE | TaskFlag_MinimizeSubtaskErrorText),
config(_config),
inputMA(ma->getExplicitCopy())
{
GCOUNTER( cvar, tvar, "MuscleTask" );
config.nThreads = (config.nThreads == 0 ? AppContext::getAppSettings()->getAppResourcePool()->getIdealThreadCount() : config.nThreads);
SAFE_POINT_EXT(config.nThreads > 0,
setError("Incorrect number of max parallel subtasks"), );
setMaxParallelSubtasks(config.nThreads);
algoLog.info(tr("MUSCLE alignment started"));
ctx = new MuscleContext(config.nThreads);
ctx->params.g_bStable = config.stableMode;
ctx->params.g_uMaxIters = config.maxIterations;
ctx->params.g_ulMaxSecs = config.maxSecs;
parallelSubTask = NULL;
//todo: make more precise estimation, use config.op mode
int aliLen = ma->getLength();
int nSeq = ma->getNumRows();
int memUseMB = qint64(aliLen) * qint64(nSeq) * 200 / (1024 * 1024); //200x per char in alignment
TaskResourceUsage tru(RESOURCE_MEMORY, memUseMB);
QString inputAlName = inputMA->getName();
resultMA->setName(inputAlName);
resultSubMA->setName(inputAlName);
inputSubMA = inputMA->getExplicitCopy();
if (config.alignRegion && config.regionToAlign.length != inputMA->getLength()) {
SAFE_POINT_EXT(config.regionToAlign.length > 0,
setError(tr("Incorrect region to align")), );
inputSubMA = inputMA->mid(config.regionToAlign.startPos, config.regionToAlign.length);
CHECK_EXT(inputSubMA != MultipleSequenceAlignment(), setError(tr("Stopping MUSCLE task, because of error in MultipleSequenceAlignment::mid function")), );
}
