bool CDVDStateSerializer::DVDToXMLState( std::string &xmlstate, const dvd_state_t *state )
{
char buffer[256];
TiXmlDocument xmlDoc("navstate");
TiXmlElement eRoot("navstate");
eRoot.SetAttribute("version", 1);
{ TiXmlElement eRegisters("registers");
for( int i = 0; i < 24; i++ )
{
if( state->registers.SPRM[i] )
{ TiXmlElement eReg("sprm");
eReg.SetAttribute("index", i);
{ TiXmlElement eValue("value");
sprintf(buffer, "0x%hx", state->registers.SPRM[i]);
eValue.InsertEndChild( TiXmlText(buffer) );
eReg.InsertEndChild(eValue);
}
eRegisters.InsertEndChild(eReg);
}
}
for( int i = 0; i < 16; i++ )
{
if( state->registers.GPRM[i] || state->registers.GPRM_mode[i] || state->registers.GPRM_time[i].tv_sec || state->registers.GPRM_time[i].tv_usec )
{ TiXmlElement eReg("gprm");
eReg.SetAttribute("index", i);
{ TiXmlElement eValue("value");
sprintf(buffer, "0x%hx", state->registers.GPRM[i]);
eValue.InsertEndChild( TiXmlText(buffer) );
eReg.InsertEndChild(eValue);
}
{ TiXmlElement eMode("mode");
sprintf(buffer, "0x%c", state->registers.GPRM_mode[i]);
eMode.InsertEndChild( TiXmlText(buffer) );
eReg.InsertEndChild(eMode);
}
{ TiXmlElement eTime("time");
{ TiXmlElement eValue("tv_sec");
sprintf(buffer, "%ld", state->registers.GPRM_time[i].tv_sec);
eValue.InsertEndChild( TiXmlText( buffer ) );
eTime.InsertEndChild( eValue ) ;
}
{ TiXmlElement eValue("tv_usec");
sprintf(buffer, "%ld", (long int)state->registers.GPRM_time[i].tv_usec);
eValue.InsertEndChild( TiXmlText( buffer ) );
eTime.InsertEndChild( eValue ) ;
}
eReg.InsertEndChild(eTime);
}
eRegisters.InsertEndChild(eReg);
}
}
eRoot.InsertEndChild(eRegisters);
}
{ TiXmlElement element("domain");
sprintf(buffer, "%d", state->domain);
element.InsertEndChild( TiXmlText( buffer ) );
eRoot.InsertEndChild(element);
}
{ TiXmlElement element("vtsn");
sprintf(buffer, "%d", state->vtsN);
element.InsertEndChild( TiXmlText( buffer ) );
eRoot.InsertEndChild(element);
}
{ TiXmlElement element("pgcn");
sprintf(buffer, "%d", state->pgcN);
element.InsertEndChild( TiXmlText( buffer ) );
eRoot.InsertEndChild(element);
}
{ TiXmlElement element("pgn");
sprintf(buffer, "%d", state->pgN);
element.InsertEndChild( TiXmlText( buffer ) );
eRoot.InsertEndChild(element);
}
{ TiXmlElement element("celln");
sprintf(buffer, "%d", state->cellN);
element.InsertEndChild( TiXmlText( buffer ) );
eRoot.InsertEndChild(element);
}
{ TiXmlElement element("cell_restart");
sprintf(buffer, "%d", state->cell_restart);
element.InsertEndChild( TiXmlText( buffer ) );
eRoot.InsertEndChild(element);
}
{ TiXmlElement element("blockn");
sprintf(buffer, "%d", state->blockN);
element.InsertEndChild( TiXmlText( buffer ) );
eRoot.InsertEndChild(element);
}
{ TiXmlElement rsm("rsm");
{ TiXmlElement element("vtsn");
sprintf(buffer, "%d", state->rsm_vtsN);
element.InsertEndChild( TiXmlText( buffer ) );
rsm.InsertEndChild(element);
}
{ TiXmlElement element("blockn");
sprintf(buffer, "%d", state->rsm_blockN);
element.InsertEndChild( TiXmlText( buffer ) );
rsm.InsertEndChild(element);
}
{ TiXmlElement element("pgcn");
sprintf(buffer, "%d", state->rsm_pgcN);
element.InsertEndChild( TiXmlText( buffer ) );
rsm.InsertEndChild(element);
}
{ TiXmlElement element("celln");
sprintf(buffer, "%d", state->rsm_cellN);
element.InsertEndChild( TiXmlText( buffer ) );
rsm.InsertEndChild(element);
}
{ TiXmlElement regs("registers");
for( int i = 0; i < 5; i++ )
{
TiXmlElement reg("sprm");
reg.SetAttribute("index", i);
{ TiXmlElement element("value");
sprintf(buffer, "0x%hx", state->rsm_regs[i]);
element.InsertEndChild( TiXmlText(buffer) );
reg.InsertEndChild(element);
}
regs.InsertEndChild(reg);
}
rsm.InsertEndChild(regs);
}
eRoot.InsertEndChild(rsm);
}
xmlDoc.InsertEndChild(eRoot);
std::stringstream stream;
stream << xmlDoc;
xmlstate = stream.str();
return true;
}
//This function uses the contents of m_blastOutput (the raw output from the
//BLAST search) to construct the BlastHit objects.
//It looks at the filters to possibly exclude hits which fail to meet user-
//defined thresholds.
void BlastSearch::buildHitsFromBlastOutput()
{
QStringList blastHitList = m_blastOutput.split("\n", QString::SkipEmptyParts);
for (int i = 0; i < blastHitList.size(); ++i)
{
QString hitString = blastHitList[i];
QStringList alignmentParts = hitString.split('\t');
if (alignmentParts.size() < 12)
continue;
QString queryName = alignmentParts[0];
QString nodeLabel = alignmentParts[1];
double percentIdentity = alignmentParts[2].toDouble();
int alignmentLength = alignmentParts[3].toInt();
int numberMismatches = alignmentParts[4].toInt();
int numberGapOpens = alignmentParts[5].toInt();
int queryStart = alignmentParts[6].toInt();
int queryEnd = alignmentParts[7].toInt();
int nodeStart = alignmentParts[8].toInt();
int nodeEnd = alignmentParts[9].toInt();
SciNot eValue(alignmentParts[10]);
double bitScore = alignmentParts[11].toDouble();
//Only save BLAST hits that are on forward strands.
if (nodeStart > nodeEnd)
continue;
QString nodeName = getNodeNameFromString(nodeLabel);
DeBruijnNode * node;
if (g_assemblyGraph->m_deBruijnGraphNodes.contains(nodeName))
node = g_assemblyGraph->m_deBruijnGraphNodes[nodeName];
else
continue;
BlastQuery * query = g_blastSearch->m_blastQueries.getQueryFromName(queryName);
if (query == 0)
continue;
QSharedPointer<BlastHit> hit(new BlastHit(query, node, percentIdentity, alignmentLength,
numberMismatches, numberGapOpens, queryStart, queryEnd,
nodeStart, nodeEnd, eValue, bitScore));
//Check the user-defined filters.
if (g_settings->blastAlignmentLengthFilterOn &&
alignmentLength < g_settings->blastAlignmentLengthFilterValue)
continue;
if (g_settings->blastQueryCoverageFilterOn)
{
if (100.0 * hit->getQueryCoverageFraction() <= g_settings->blastQueryCoverageFilterValue)
continue;
}
if (g_settings->blastIdentityFilterOn &&
percentIdentity < g_settings->blastIdentityFilterValue)
continue;
if (g_settings->blastEValueFilterOn &&
eValue > g_settings->blastEValueFilterValue)
continue;
if (g_settings->blastBitScoreFilterOn &&
bitScore < g_settings->blastBitScoreFilterValue)
continue;
m_allHits.push_back(hit);
query->addHit(hit);
}
}
