Region* Instrument::GetFirstRegion() {
if (!pRegions) LoadRegions();
if (!pRegions) return NULL;
RegionsIterator = pRegions->begin();
return (RegionsIterator != pRegions->end()) ? *RegionsIterator : NULL;
}
void CConsole::Process( int c )
{
char outputline[128], temp[1024];
bool kill = false;
int indexcount = 0;
int j;
int keyresp;
CSocket *tSock = NULL;
if( c == '*' )
{
if( cwmWorldState->GetSecure() )
messageLoop << "Secure mode disabled. Press ? for a commands list";
else
messageLoop << "Secure mode re-enabled";
cwmWorldState->SetSecure( !cwmWorldState->GetSecure() );
return;
}
else
{
if( cwmWorldState->GetSecure() )
{
messageLoop << "Secure mode prevents keyboard commands! Press '*' to disable";
return;
}
JSCONSOLEKEYMAP_ITERATOR toFind = JSKeyHandler.find( c );
if( toFind != JSKeyHandler.end() )
{
if( toFind->second.isEnabled )
{
cScript *toExecute = JSMapping->GetScript( toFind->second.scriptID );
if( toExecute != NULL )
{ // All commands that execute are of the form: command_commandname (to avoid possible clashes)
#if defined( UOX_DEBUG_MODE )
Print( "Executing JS keystroke %c %s\n", c, toFind->second.cmdName.c_str() );
#endif
toExecute->CallParticularEvent( toFind->second.cmdName.c_str(), NULL, 0 );
}
return;
}
}
switch( c )
{
case '!':
// Force server to save accounts file
messageLoop << "CMD: Saving Accounts... ";
Accounts->Save();
messageLoop << MSG_PRINTDONE;
break;
case '@':
// Force server to save all files.(Manual save)
messageLoop << MSG_WORLDSAVE;
break;
case 'Y':
std::cout << "System: ";
while( !kill )
{
keyresp = cl_getch();
switch( keyresp )
{
case -1: // no key pressed
case 0:
break;
case 0x1B:
memset( outputline, 0x00, sizeof( outputline ) );
indexcount = 0;
kill = true;
std::cout << std::endl;
messageLoop << "CMD: System broadcast canceled.";
break;
case 0x08:
--indexcount;
if( indexcount < 0 )
indexcount = 0;
else
std::cout << "\b \b";
break;
case 0x0A:
case 0x0D:
outputline[indexcount] = 0;
messageLoop.NewMessage( MSG_CONSOLEBCAST, outputline );
indexcount = 0;
kill = true;
std::cout << std::endl;
sprintf( temp, "CMD: System broadcast sent message \"%s\"", outputline );
memset( outputline, 0x00, sizeof( outputline ) );
messageLoop << temp;
break;
default:
if( static_cast<size_t>(indexcount) < sizeof( outputline ) )
{
outputline[indexcount++] = (UI08)(keyresp);
std::cout << (char)keyresp;
}
break;
}
keyresp = 0x00;
}
break;
case '[':
{
// We want to group all the contents of the multimap container numerically by group. We rely on the self ordering in the multimap implementation to do this.
messageLoop << " ";
messageLoop << "Auto-AddMenu Statistics";
messageLoop << " ";
char szBuffer[128];
// We need to get an iteration into the map first of all the top level ULONGs then we can get an equal range.
std::map< UI32, UI08 > localMap;
localMap.clear();
for( ADDMENUMAP_CITERATOR CJ = g_mmapAddMenuMap.begin(); CJ != g_mmapAddMenuMap.end(); CJ++ )
{
// check to see if the group id has been checked already
if( localMap.find( CJ->first ) == localMap.end() )
{
localMap.insert( std::make_pair( CJ->first, 0 ) );
memset( szBuffer, 0x00, sizeof( szBuffer ) );
sprintf( szBuffer, "AddMenuGroup %lu:", CJ->first );
messageLoop << szBuffer;
std::pair< ADDMENUMAP_CITERATOR, ADDMENUMAP_CITERATOR > pairRange = g_mmapAddMenuMap.equal_range( CJ->first );
int count = 0;
for( ADDMENUMAP_CITERATOR CI=pairRange.first;CI != pairRange.second; CI++ )
{
count++;
}
memset( szBuffer, 0x00, sizeof( szBuffer ) );
sprintf( szBuffer, " Found %i Auto-AddMenu Item(s).", count );
messageLoop << szBuffer;
}
}
messageLoop << MSG_SECTIONBEGIN;
break;
}
case '<':
messageLoop << "Function not implemented.";
break;
case '>':
messageLoop << "Function not implemented.";
break;
case 0x1B:
case 'Q':
messageLoop << MSG_SECTIONBEGIN;
messageLoop << "CMD: Immediate Shutdown initialized!";
messageLoop << MSG_SHUTDOWN;
break;
case '0':
if( !cwmWorldState->GetReloadingScripts() )
{
cwmWorldState->SetReloadingScripts( true );
// Reload all the files. If there are issues with these files change the order reloaded from here first.
cwmWorldState->ServerData()->Load();
messageLoop << "CMD: Loading All";
messageLoop << " Server INI... ";
// Reload accounts, and update Access.adm if new accounts available.
messageLoop << " Loading Accounts... ";
Accounts->Load();
messageLoop << MSG_PRINTDONE;
// Reload Region Files
messageLoop << " Loading Regions... ";
UnloadRegions();
LoadRegions();
messageLoop << MSG_PRINTDONE;
// Reload the serve spawn regions
messageLoop << " Loading Spawn Regions... ";
UnloadSpawnRegions();
LoadSpawnRegions();
messageLoop << MSG_PRINTDONE;
// Reload the server command list
messageLoop << " Loading commands... ";
Commands->Load();
messageLoop << MSG_PRINTDONE;
// Reload DFN's
messageLoop << " Loading Server DFN... ";
FileLookup->Reload();
LoadTeleportLocations();
messageLoop << MSG_PRINTDONE;
// messageLoop access is REQUIRED, as this function is executing in a different thread, so we need thread safety
messageLoop << " Loading JSE Scripts... ";
// Reload the current Spells
messageLoop << " Loading spells... ";
Magic->LoadScript();
messageLoop << MSG_PRINTDONE;
// Reload the HTML output templates
messageLoop << " Loading HTML Templates... ";
HTMLTemplates->Unload();
HTMLTemplates->Load();
cwmWorldState->SetReloadingScripts( false );
messageLoop << MSG_PRINTDONE;
}
else
messageLoop << "Server can only load one script at a time";
break;
case 'T':
// Timed shut down(10 minutes)
messageLoop << "CMD: 10 Minute Server Shutdown Announced(Timed)";
cwmWorldState->SetEndTime( BuildTimeValue( 600 ) );
endmessage(0);
break;
case 'D':
// Disconnect account 0 (useful when client crashes)
for( tSock = Network->LastSocket(); tSock != NULL; tSock = Network->PrevSocket() )
{
if( tSock->AcctNo() == 0 )
Network->Disconnect( tSock );
}
messageLoop << "CMD: Socket Disconnected(Account 0).";
break;
case 'K':
{
for( tSock = Network->FirstSocket(); !Network->FinishedSockets(); tSock = Network->NextSocket() )
{
Network->Disconnect( tSock );
}
messageLoop << "CMD: All Connections Closed.";
}
break;
case 'P':
{
UI32 networkTimeCount = cwmWorldState->ServerProfile()->NetworkTimeCount();
UI32 timerTimeCount = cwmWorldState->ServerProfile()->TimerTimeCount();
UI32 autoTimeCount = cwmWorldState->ServerProfile()->AutoTimeCount();
UI32 loopTimeCount = cwmWorldState->ServerProfile()->LoopTimeCount();
// 1/13/2003 - Dreoth - Log Performance Information enhancements
LogEcho( true );
Log( "--- Starting Performance Dump ---", "performance.log");
Log( "\tPerformace Dump:", "performance.log");
Log( "\tNetwork code: %.2fmsec [%i samples]", "performance.log", (R32)((R32)cwmWorldState->ServerProfile()->NetworkTime()/(R32)networkTimeCount), networkTimeCount);
Log( "\tTimer code: %.2fmsec [%i samples]", "performance.log", (R32)((R32)cwmWorldState->ServerProfile()->TimerTime()/(R32)timerTimeCount), timerTimeCount);
Log( "\tAuto code: %.2fmsec [%i samples]", "performance.log", (R32)((R32)cwmWorldState->ServerProfile()->AutoTime()/(R32)autoTimeCount), autoTimeCount);
Log( "\tLoop Time: %.2fmsec [%i samples]", "performance.log", (R32)((R32)cwmWorldState->ServerProfile()->LoopTime()/(R32)loopTimeCount), loopTimeCount);
ObjectFactory *ourFac = ObjectFactory::getSingletonPtr();
Log( "\tCharacters: %i/%i - Items: %i/%i (Dynamic)", "performance.log", ourFac->CountOfObjects( OT_CHAR ), ourFac->SizeOfObjects( OT_CHAR ), ourFac->CountOfObjects( OT_ITEM ), ourFac->SizeOfObjects( OT_ITEM ) );
Log( "\tSimulation Cycles: %f per sec", "performance.log", (1000.0*(1.0/(R32)((R32)cwmWorldState->ServerProfile()->LoopTime()/(R32)loopTimeCount))));
Log( "\tBytes sent: %i", "performance.log", cwmWorldState->ServerProfile()->GlobalSent());
Log( "\tBytes Received: %i", "performance.log", cwmWorldState->ServerProfile()->GlobalReceived());
Log( "--- Performance Dump Complete ---", "performance.log");
LogEcho( false );
break;
}
case 'W':
// Display logged in chars
messageLoop << "CMD: Current Users in the World:";
j = 0;
CSocket *iSock;
Network->PushConn();
for( iSock = Network->FirstSocket(); !Network->FinishedSockets(); iSock = Network->NextSocket() )
{
++j;
CChar *mChar = iSock->CurrcharObj();
sprintf( temp, " %i) %s [%x %x %x %x]", j - 1, mChar->GetName().c_str(), mChar->GetSerial( 1 ), mChar->GetSerial( 2 ), mChar->GetSerial( 3 ), mChar->GetSerial( 4 ) );
messageLoop << temp;
}
Network->PopConn();
sprintf( temp, " Total users online: %i", j );
messageLoop << temp;
break;
case 'M':
size_t tmp, total;
total = 0;
tmp = 0;
messageLoop << "CMD: UOX Memory Information:";
messageLoop << " Cache:";
sprintf( temp, " Tiles: %u bytes", Map->GetTileMem() );
messageLoop << temp;
sprintf( temp, " Multis: %u bytes", Map->GetMultisMem() );
messageLoop << temp;
size_t m, n;
m = ObjectFactory::getSingleton().SizeOfObjects( OT_CHAR );
total += tmp = m + m*sizeof( CTEffect ) + m*sizeof(char) + m*sizeof(int)*5;
sprintf( temp, " Characters: %u bytes [%u chars ( %u allocated )]", tmp, ObjectFactory::getSingleton().CountOfObjects( OT_CHAR ), m );
messageLoop << temp;
n = ObjectFactory::getSingleton().SizeOfObjects( OT_ITEM );
total += tmp = n + n * sizeof( int ) * 4;
sprintf( temp, " Items: %u bytes [%u items ( %u allocated )]", tmp, ObjectFactory::getSingleton().CountOfObjects( OT_ITEM ), n );
messageLoop << temp;
sprintf( temp, " You save I: %i & C: %i bytes!", m * sizeof(CItem) - ObjectFactory::getSingleton().CountOfObjects( OT_ITEM ), m * sizeof( CChar ) - ObjectFactory::getSingleton().CountOfObjects( OT_CHAR ) );
total += tmp = 69 * sizeof( SpellInfo );
sprintf( temp, " Spells: %i bytes", tmp );
messageLoop << " Sizes:";
sprintf( temp, " CItem : %i bytes", sizeof( CItem ) );
messageLoop << temp;
sprintf( temp, " CChar : %i bytes", sizeof( CChar ) );
messageLoop << temp;
sprintf( temp, " TEffect: %i bytes (%i total)", sizeof( CTEffect ), sizeof( CTEffect ) * cwmWorldState->tempEffects.Num() );
messageLoop << temp;
total += tmp = Map->GetTileMem() + Map->GetMultisMem();
sprintf( temp, " Approximate Total: %i bytes", total );
messageLoop << temp;
break;
case '?':
messageLoop << MSG_SECTIONBEGIN;
messageLoop << "Console commands:";
messageLoop << MSG_SECTIONBEGIN;
messageLoop << " ShardOP:";
messageLoop << " * - Lock/Unlock Console ? - Commands list(this)";
messageLoop << " C - Configuration H - Unused";
messageLoop << " Y - Console Broadcast Q - Quit/Exit ";
messageLoop << " Load Commands:";
messageLoop << " 1 - Ini 2 - Accounts";
messageLoop << " 3 - Regions 4 - Spawn Regions";
messageLoop << " 5 - Spells 6 - Commands";
messageLoop << " 7 - Dfn's 8 - JavaScript";
messageLoop << " 9 - HTML Templates 0 - ALL(1-9)";
messageLoop << " Save Commands:";
messageLoop << " ! - Accounts @ - World(w/AccountImport)";
messageLoop << " # - Unused $ - Unused";
messageLoop << " % - Unused ^ - Unused";
messageLoop << " & - Unused ( - Unused";
messageLoop << " ) - Unused";
messageLoop << " Server Maintenence:";
messageLoop << " P - Performance W - Characters Online";
messageLoop << " M - Memory Information T - 10 Minute Shutdown";
messageLoop << " V - Dump Lookups(Devs) F - Display Priority Maps";
messageLoop << " Network Maintenence:";
messageLoop << " D - Disconnect Acct0 K - Disconnect All";
messageLoop << " Z - Socket Logging ";
messageLoop << MSG_SECTIONBEGIN;
break;
case 'v':
case 'V':
// Dump look up data to files so developers working with extending the ini will have a table to use
messageLoop << "| CMD: Creating Server.scp and Uox3.ini Tag Lookup files(For Developers)....";
cwmWorldState->ServerData()->dumpLookup( 0 );
cwmWorldState->ServerData()->save( "./uox.tst.ini" );
messageLoop << MSG_PRINTDONE;
break;
case 'z':
case 'Z':
{
// Log socket activity
Network->PushConn();
bool loggingEnabled = false;
CSocket *snSock = Network->FirstSocket();
if( snSock != NULL )
loggingEnabled = !snSock->Logging();
for( ; !Network->FinishedSockets(); snSock = Network->NextSocket() )
{
if( snSock != NULL )
snSock->Logging( !snSock->Logging() );
}
Network->PopConn();
if( loggingEnabled )
messageLoop << "CMD: Network Logging Enabled.";
else
messageLoop << "CMD: Network Logging Disabled.";
break;
}
case 'c':
case 'C':
// Shows a configuration header
DisplaySettings();
break;
case 'f':
case 'F':
FileLookup->DisplayPriorityMap();
break;
default:
sprintf( temp, "Key \'%c\' [%i] does not perform a function", (char)c, c );
messageLoop << temp;
break;
}
}
}
void GCContent::OutputGCContent(String & reference, int windowSize, String &gcContentFile, String ®ionFile, bool invertRegion)
{
GenomeSequence genome;
bool memoryMap = false;
genome.setReferenceName(reference.c_str());
if (genome.open())
{
fprintf(stderr, "Failed to open reference index and is creating one...\n");
if(genome.create())
error("Failed to create reference index!\n");
}
genome.useMemoryMap(memoryMap);
if(genome.open())
error("Open reference failed...!\n");
LoadRegions(regionFile, genome, invertRegion);
if (regionIndicator.size() == 0) {
printf("Calculate GC file for whole genome; ");
} else {
printf("Calculate GC file for specified region ( %u bp ); ",
(unsigned int) regionIndicator.size());
}
printf("reference genome has %u bp\n", genome.sequenceLength());
FILE * fh = fopen(gcContentFile.c_str(), "wb");
int gccnt = 0;
int atcnt = 0;
uint8_t gc = 0;
uint32_t gcContentDist[101];
for(int i=0; i<101; i++) gcContentDist[i] = 0;
for(int i=0; i<windowSize; i++)
{
if(toupper((genome)[i]) == 'G' || toupper((genome)[i]) == 'C')
gccnt++;
if(toupper((genome)[i]) == 'A' || toupper((genome)[i]) == 'T')
atcnt++;
}
for(int i=0; i<windowSize/2; i++)
{
fwrite(&gc, 1, sizeof(uint8_t), fh);
gcContentDist[gc]++;
}
for(uint32_t i=windowSize; i<genome.sequenceLength(); i++)
{
if(toupper((genome)[i])=='G' || toupper((genome)[i]) == 'C')
gccnt++;
if(toupper((genome)[i-windowSize]) == 'G' ||toupper((genome)[i-windowSize]) == 'C')
gccnt--;
if(toupper((genome)[i])=='A' || toupper((genome)[i]) == 'T')
atcnt++;
if(toupper((genome)[i-windowSize]) == 'A' ||toupper((genome)[i-windowSize]) == 'T')
atcnt--;
if(gccnt+atcnt<windowSize) gc = 0;
else gc = floor(double(gccnt)/(gccnt+atcnt)*100+0.5);
fwrite(&gc, 1, sizeof(uint8_t), fh);
if(regionIndicator.size() > 0 && regionIndicator[i]==false) gc = 0;
gcContentDist[gc]++;
}
gc = 0;
for(int i=0; i<windowSize/2; i++)
{
fwrite(&gc, 1, sizeof(uint8_t), fh);
gcContentDist[gc]++;
}
fwrite(&gcContentDist, 1, sizeof(gcContentDist), fh);
printf("GCPercentage\tFrequency\n");
for(int i=0; i<101; i++) printf("%d\t%u\n", i, gcContentDist[i]);
fclose(fh);
}
int
Process(etPMode PMode, // processing mode
etFMode FMode, // output format mode
int MovAvgFilter, // apply this moving average window size filter
int BaselineFilter, // baseline normalisation window size
char *pszTrackName, // UCSC track name
double DyadratioThres, // dyad grooves must be at least this ratio to background
double Dyad2ratioThres, // immediately flanking grooves must be at least this ratio to background
double Dyad3ratioThres, // remainder of flanking grooves must be at least this ration to background
char *pszInGenomefile, // bioseq genome file
char *pszInConfFile, // file containing conformation characteristics
char *pszOutFile, // where to write nucleosome predictions
char *pszInclRegionFile, // only report predicted nucleosomes if intersecting with regions in this file
int OfsLoci, // offset region start loci by this many nt
int DeltaLen, // change region length by this many nt
int TruncLength) // truncate regions to be a maximum of this length
{
int Rslt = 0;
bool bRegionFilter; // set true if region filtering
int SeqIdx;
int WindLen = 147; // nucleosomes are this length - agreed :-)
int ChkGroove[13]; // to hold dyad (ChkGroove[6]) and +/- 6 at approx decimer (depends on twist) offsets
int DecIdx; // index into ChkGroove, incr/decr every 360 degree twist
int GrooveCnt; // to hold number of groove values contributing to current ChkGroove[DecIdx] so average can be calculated
int AccumTwist; // to hold accumulated twist relative to dyad
int ChkTwist; // AccumTwist % 360 used to determine if minor groove back on same plane as at dyad
int BaseLineValueSum;
double BaseLineAv;
double ChromBaseLineSum;
int NumBaseLines;
Init();
m_PMode = PMode;
m_FMode = FMode;
strcpy(m_szTrackName,pszTrackName);
m_DyadratioThres = DyadratioThres;
m_Dyad2ratioThres = Dyad2ratioThres;
m_Dyad3ratioThres = Dyad3ratioThres;
if((m_pszOutBuff = new char [cAllocOutBuff])==NULL)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Unable to alloc memory (%d bytes requested) for bufering output results",cAllocOutBuff);
Reset();
return(eBSFerrMem);
}
m_AllocdOutBuff = cAllocOutBuff;
if((m_pBioSeqFile = new CBioSeqFile) == NULL)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Unable to instantiate CBioSeqFile object");
Reset();
return(eBSFerrObj);
}
if((Rslt = m_pBioSeqFile->Open(pszInGenomefile))!=eBSFSuccess)
{
while(m_pBioSeqFile->NumErrMsgs())
gDiagnostics.DiagOut(eDLFatal,gszProcName,m_pBioSeqFile->GetErrMsg());
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Unable to open genome assembly sequence file '%s'",pszInGenomefile);
Reset();
return(Rslt);
}
if(pszInclRegionFile != NULL && pszInclRegionFile[0] != '\0')
{
if((Rslt = LoadRegions(pszInclRegionFile,OfsLoci,DeltaLen,TruncLength))!=eBSFSuccess)
{
Reset();
return(Rslt);
}
bRegionFilter = true;
}
else
bRegionFilter = false;
if((m_pTwister = new CTwister)==NULL)
{
gDiagnostics.DiagOut(eDLFatal,"ProcessFastaStruct","Unable to create CTwister object");
Reset();
return(eBSFerrObj);
}
if((Rslt = m_pTwister->LoadStructParams(pszInConfFile)) < eBSFSuccess)
{
while(m_pTwister->NumErrMsgs())
gDiagnostics.DiagOut(eDLFatal,gszProcName,m_pTwister->GetErrMsg());
gDiagnostics.DiagOut(eDLFatal,"ProcessFastaStruct","LoadStructParams(%s) failed",pszInConfFile);
Reset();
return(Rslt);
}
#ifdef _WIN32
if((m_hOutFile = open(pszOutFile, _O_RDWR | _O_BINARY | _O_SEQUENTIAL | _O_CREAT | _O_TRUNC, _S_IREAD | _S_IWRITE ))==-1)
#else
if((m_hOutFile = open(pszOutFile, O_RDWR | O_CREAT | O_TRUNC, S_IREAD | S_IWRITE ))==-1)
#endif
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Unable to create predicted nucleosome output file: %s - %s",pszOutFile,strerror(errno));
Reset();
return(eBSFerrCreateFile);
}
if(FMode == eFMbedGraphDyads || FMode == eFMbedGraphNucs)
{
m_UsedOutBuff = sprintf(m_pszOutBuff,
"track type=bedGraph name=\"%s\" description=\"%s\" visibility=full color=200,100,0 altColor=0,100,200 priority=20 autoScale=on alwaysZero=on graphType=bar smoothingWindow=4\n",
pszTrackName,pszTrackName);
CUtility::SafeWrite(m_hOutFile,m_pszOutBuff,m_UsedOutBuff);
m_UsedOutBuff = 0;
}
// iterate over chromosomes
tBSFEntryID ChromID = 0;
while((ChromID = m_pBioSeqFile->Next(ChromID))>0)
{
m_pBioSeqFile->GetName(ChromID,sizeof(m_szCurChrom),m_szCurChrom);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Processing %s...",m_szCurChrom);
m_ChromSeqLen = m_pBioSeqFile->GetDataLen(ChromID);
if(m_pChromSeq == NULL || m_ChromSeqLen > m_AllocdChromSeq)
{
if(m_pChromSeq != NULL)
{
delete m_pChromSeq;
m_pChromSeq = NULL;
}
int AllocLen = m_ChromSeqLen + m_ChromSeqLen/10;
if((m_pChromSeq = new unsigned char [AllocLen])==NULL)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Unable to alloc memory (%d requested) for holding raw sequence data",AllocLen);
Reset();
return(eBSFerrMem);
}
m_AllocdChromSeq = AllocLen;
if(m_pScores != NULL)
{
delete m_pScores;
m_pScores = NULL;
}
if((m_pScores = new int [AllocLen])==NULL)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Unable to allocate memory (%d bytes) for holding scores",AllocLen);
Reset();
return(eBSFerrMem);
}
if(m_pConfGroove != NULL)
{
delete m_pConfGroove;
m_pConfGroove = NULL;
}
if((m_pConfGroove = new int [AllocLen])==NULL)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Unable to allocate memory (%d bytes) for holding minor groove conformation values",AllocLen);
Reset();
return(eBSFerrMem);
}
if(m_pConfTwist != NULL)
{
delete m_pConfTwist;
m_pConfTwist = NULL;
}
if((m_pConfTwist = new int [AllocLen])==NULL)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Unable to allocate memory (%d bytes) for holding rotational twist conformation values",AllocLen);
Reset();
return(eBSFerrMem);
}
}
if((Rslt=m_pBioSeqFile->GetData(ChromID,eSeqBaseType,0,m_pChromSeq,m_ChromSeqLen)) != m_ChromSeqLen)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Loading sequence of length %d failed from chrom: %s file: '%s'",m_ChromSeqLen,m_szCurChrom,pszInGenomefile);
Reset();
return(Rslt);
}
// remove any repeat masking and randomly substitute bases for eBaseN's - not expecting too many of these say's he hopefully!
etSeqBase *pSeq = m_pChromSeq;
for(SeqIdx = 0; SeqIdx < m_ChromSeqLen; SeqIdx++,pSeq++)
if((*pSeq &= ~cRptMskFlg) > eBaseT)
*pSeq = rand() % 4;
if((Rslt = m_pTwister->GetSequenceConformation(eSSminorgroove, // process for this conformational parameter
0, // initial starting offset (0..n) in pSeq
0, // number of steps (0 for all) to process starting at pSeq[iStartPsn]|pSeq[iStartPsn+1]
m_ChromSeqLen, // total length of sequence
m_pChromSeq, // sequence to be processed
m_pConfGroove))!=eBSFSuccess) // where to return step conformational values
{
gDiagnostics.DiagOut(eDLFatal,"GetSequenceConformation","minor groove failed");
Reset();
return(Rslt);
}
if((Rslt = m_pTwister->GetSequenceConformation(eSStwist, // process for this conformational parameter
0, // initial starting offset (0..n) in pSeq
0, // number of steps (0 for all) to process starting at pSeq[iStartPsn]|pSeq[iStartPsn+1]
m_ChromSeqLen, // total length of sequence
m_pChromSeq, // sequence to be processed
m_pConfTwist))!=eBSFSuccess) // where to return step conformational values
{
gDiagnostics.DiagOut(eDLFatal,"GetSequenceConformation","rotational twist failed");
Reset();
return(Rslt);
}
memset(m_pScores,0,m_ChromSeqLen * sizeof(int)); // reset all scores back to minimum
// establish the baseline conformational characteristic value over initial window which is centered around the WindLen window
// the baseline will be updated as the putative dyad is slid along the chromosome
int *pConfGroove;
int *pBaseLineWin5;
int *pBaseLineWin3;
int *pConfTwist;
int BaseLineWin = min(5 * WindLen,m_ChromSeqLen);
BaseLineValueSum = 0;
pBaseLineWin3 = m_pConfGroove;
for(SeqIdx = 0; SeqIdx < BaseLineWin; SeqIdx++)
BaseLineValueSum += *pBaseLineWin3++;
double BestMaxRatio = 0.0f;
double BestMinRatio = 10000.0f;
int DyadFirstOfs = 73;
int DyadLastOfs = m_ChromSeqLen - 73;
m_ChromPutDyads = 0;
ChromBaseLineSum = 0.0;
NumBaseLines = 0;
pBaseLineWin5 = m_pConfGroove;
for(SeqIdx = DyadFirstOfs; SeqIdx < DyadLastOfs; SeqIdx++)
{
if(SeqIdx > BaseLineWin/2 && SeqIdx < (m_ChromSeqLen - (BaseLineWin+1)/2))
{
BaseLineValueSum -= *pBaseLineWin5++;
BaseLineValueSum += *pBaseLineWin3++;
}
BaseLineAv = (double)BaseLineValueSum/BaseLineWin;
ChromBaseLineSum += BaseLineAv/10000.0f;
NumBaseLines += 1;
if(bRegionFilter && !InAnyRegion(ChromID,SeqIdx-74,SeqIdx+73,0))
continue;
DecIdx = 6;
pConfGroove = &m_pConfGroove[SeqIdx];
ChkGroove[DecIdx++] = *pConfGroove++;
m_DyadRatio = (double)ChkGroove[6]/BaseLineAv;
if(m_DyadRatio < DyadratioThres)
continue;
pConfTwist = &m_pConfTwist[SeqIdx+1];
AccumTwist = *pConfTwist;
ChkGroove[DecIdx] = 0;
GrooveCnt = 0;
// iterate over bases to right of putative dyad and every rotation of the dsDNA get the minor groove
int Bases = 1;
while(DecIdx <= 12)
{
Bases += 1;
pConfTwist += 1;
pConfGroove += 1;
AccumTwist += *pConfTwist;
ChkTwist = AccumTwist % 3600000;
if(ChkTwist >= 3300000 || ChkTwist <= 300000)
{
ChkGroove[DecIdx] += *pConfGroove;
GrooveCnt += 1;
}
else
{
if(GrooveCnt > 0)
{
ChkGroove[DecIdx] /= GrooveCnt;
GrooveCnt = 0;
if(DecIdx++ < 12)
ChkGroove[DecIdx]= 0;
}
}
}
// now iterate over bases to left of putative dyad and every rotation of the dsDNA get the minor groove
DecIdx = 5;
pConfGroove = &m_pConfGroove[SeqIdx-1];
pConfTwist = &m_pConfTwist[SeqIdx-1];
AccumTwist = *pConfTwist;
ChkGroove[DecIdx] = 0;
GrooveCnt = 0;
Bases = 1;
while(DecIdx >= 0)
{
Bases += 1;
pConfTwist -= 1;
pConfGroove -= 1;
AccumTwist += *pConfTwist;
ChkTwist = AccumTwist % 3600000;
if(ChkTwist >= 3300000 || ChkTwist <= 300000)
{
ChkGroove[DecIdx] += *pConfGroove;
GrooveCnt += 1;
}
else
{
if(GrooveCnt > 0)
{
ChkGroove[DecIdx] /= GrooveCnt;
GrooveCnt = 0;
if(DecIdx-- > 0)
ChkGroove[DecIdx] = 0;
}
}
}
m_Dyad2Ratio = (double)(ChkGroove[5] + ChkGroove[7])/(2*BaseLineAv);
m_Dyad3Ratio = (double)(ChkGroove[0] + ChkGroove[1] + ChkGroove[2] + ChkGroove[3] + ChkGroove[4] +
ChkGroove[8] + ChkGroove[9] + ChkGroove[10] + ChkGroove[11] + ChkGroove[12])/(10*BaseLineAv);
if(m_Dyad2Ratio < Dyad2ratioThres || m_Dyad3Ratio < Dyad3ratioThres)
continue;
if(bRegionFilter)
InAnyRegion(ChromID,SeqIdx-74,SeqIdx+73,1);
int LocScore = (int)(1000 * ((m_DyadRatio - 1.0f) + ((m_Dyad2Ratio - 1.0f) * 0.85) + ((m_Dyad3Ratio - 1.0f) * 0.75)));
if(LocScore < 0)
printf("\nHave an issue!");
m_pScores[SeqIdx] = LocScore;
}
OutputDyads(m_hOutFile, // results file
FMode, // output format mode
MovAvgFilter, // apply this width moving average filter
BaselineFilter, // use this window size when normalising for baseline
pszTrackName, // track name
m_szCurChrom, // dyads on this chromosome
m_ChromSeqLen, // last dyad loci
m_pScores); // dyad scores
gDiagnostics.DiagOut(eDLInfo,gszProcName,"On chromosome '%s' (length %d), %d putative nucleosome dyads were identified - running total: %d",m_szCurChrom,m_ChromSeqLen,m_ChromPutDyads,m_NumPutDyads);
gDiagnostics.DiagOut(eDLInfo,gszProcName,"On chromosome '%s' (length %d), averaged minor groove baseline was %1.6f",m_szCurChrom,m_ChromSeqLen,ChromBaseLineSum/NumBaseLines);
}
if(m_UsedOutBuff)
{
if((Rslt=write(m_hOutFile,m_pszOutBuff,m_UsedOutBuff))!=m_UsedOutBuff)
Rslt = eBSFerrWrite;
m_UsedOutBuff = 0;
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"After processing a total of %d putative nucleosome dyads have been identified",m_NumPutDyads);
DumpRegionHitStats();
Reset();
return(Rslt);
}
