int FILE_IO::getNextMidiMsg(int channel, int tick)
{
MidiEvent event;
while((event = midiFile.getEvent(0, index)).tick == tick){
//if() continue; //cases to ignore
printf("0\n");
MidiMessage msg;
msg.setSize(event.getSize());
for(int i=0; i < event.getSize(); i++){
msg[i] = event[i];
}
writeInMidiMsg(channel, msg);
index++;
if (index == midiFile.getNumEvents(0)){
resetIndex();
return 0;
}
}
return 1;
}
void wingReset()
{
/* 970910 mina 実際に動かして得た値
eye = (-1.639130, 1.000000, -0.271015), to = (-0.773105, 0.500000, -0.271014)
*/
eye_x = -1.639130; eye_y = 1.0; eye_z = -0.271015;
to_x = -0.773105; to_y = 0.5; to_z = -0.271014;
phy = 900, theta = 300;
calcLookAtPoint(lookAt, FALSE);
glutSetWindow(mapwindow);
glutPostRedisplay();
resetTOC();
resetIndex();
}
int RepSetIterator::do_reset_increment( int i, bool initial ) {
bool emptyDomain = false;
for( unsigned ii=(i+1); ii<d_index.size(); ii++ ){
int ri_res = resetIndex( ii, initial );
if( ri_res==-1 ){
//failed
d_index.clear();
d_incomplete = true;
break;
}else if( ri_res==0 ){
emptyDomain = true;
}
//force next iteration if currently an empty domain
if( emptyDomain ){
d_index[ii] = domainSize(ii)-1;
}
}
if( emptyDomain ){
Trace("rsi-debug") << "This is an empty domain, increment." << std::endl;
return increment();
}else{
return i;
}
}
void Horus::Commons::TestsHelper::ExpectedStrings::reset()
{
m_expectedStrings.clear();
resetIndex();
}
// Read & parse the specified index file.
StatGenStatus::Status Tabix::readIndex(const char* filename)
{
// Reset the index from anything that may previously be set.
resetIndex();
IFILE indexFile = ifopen(filename, "rb");
// Failed to open the index file.
if(indexFile == NULL)
{
return(StatGenStatus::FAIL_IO);
}
// read the tabix index structure.
// Read the magic string.
char magic[4];
if(ifread(indexFile, magic, 4) != 4)
{
// Failed to read the magic
return(StatGenStatus::FAIL_IO);
}
// If this is not an index file, set num references to 0.
if (magic[0] != 'T' || magic[1] != 'B' || magic[2] != 'I' || magic[3] != 1)
{
// Not a Tabix Index file.
return(StatGenStatus::FAIL_PARSE);
}
// It is a tabix index file.
// Read the number of reference sequences.
if(ifread(indexFile, &n_ref, 4) != 4)
{
// Failed to read.
return(StatGenStatus::FAIL_IO);
}
// Size the references.
myRefs.resize(n_ref);
// Read the Format configuration.
if(ifread(indexFile, &myFormat, sizeof(myFormat)) != sizeof(myFormat))
{
// Failed to read.
return(StatGenStatus::FAIL_IO);
}
// Read the length of the chromosome names.
uint32_t l_nm;
if(ifread(indexFile, &l_nm, sizeof(l_nm)) != sizeof(l_nm))
{
// Failed to read.
return(StatGenStatus::FAIL_IO);
}
// Read the chromosome names.
myChromNamesBuffer = new char[l_nm];
if(ifread(indexFile, myChromNamesBuffer, l_nm) != l_nm)
{
return(StatGenStatus::FAIL_IO);
}
myChromNamesVector.resize(n_ref);
// Parse out the chromosome names.
bool prevNull = true;
int chromIndex = 0;
for(uint32_t i = 0; i < l_nm; i++)
{
if(chromIndex >= n_ref)
{
// already set the pointer for the last chromosome name,
// so stop looping.
break;
}
if(prevNull == true)
{
myChromNamesVector[chromIndex++] = myChromNamesBuffer + i;
prevNull = false;
}
if(myChromNamesBuffer[i] == '\0')
{
prevNull = true;
}
}
for(int refIndex = 0; refIndex < n_ref; refIndex++)
{
// Read each reference.
Reference* ref = &(myRefs[refIndex]);
// Resize the bins so they can be indexed by bin number.
ref->bins.resize(MAX_NUM_BINS + 1);
// Read the number of bins.
if(ifread(indexFile, &(ref->n_bin), 4) != 4)
{
// Failed to read the number of bins.
// Return failure.
return(StatGenStatus::FAIL_PARSE);
}
// Read each bin.
for(int binIndex = 0; binIndex < ref->n_bin; binIndex++)
{
uint32_t binNumber;
// Read in the bin number.
if(ifread(indexFile, &(binNumber), 4) != 4)
{
// Failed to read the bin number.
// Return failure.
return(StatGenStatus::FAIL_IO);
}
// Add the bin to the reference and get the
// pointer back so the values can be set in it.
Bin* binPtr = &(ref->bins[binNumber]);
binPtr->bin = binNumber;
// Read in the number of chunks.
if(ifread(indexFile, &(binPtr->n_chunk), 4) != 4)
{
// Failed to read number of chunks.
// Return failure.
return(StatGenStatus::FAIL_IO);
}
// Read in the chunks.
// Allocate space for the chunks.
uint32_t sizeOfChunkList = binPtr->n_chunk * sizeof(Chunk);
binPtr->chunks = (Chunk*)malloc(sizeOfChunkList);
if(ifread(indexFile, binPtr->chunks, sizeOfChunkList) != sizeOfChunkList)
{
// Failed to read the chunks.
// Return failure.
return(StatGenStatus::FAIL_IO);
}
}
// Read the number of intervals.
if(ifread(indexFile, &(ref->n_intv), 4) != 4)
{
// Failed to read, set to 0.
ref->n_intv = 0;
// Return failure.
return(StatGenStatus::FAIL_IO);
}
// Allocate space for the intervals and read them.
uint32_t linearIndexSize = ref->n_intv * sizeof(uint64_t);
ref->ioffsets = (uint64_t*)malloc(linearIndexSize);
if(ifread(indexFile, ref->ioffsets, linearIndexSize) != linearIndexSize)
{
// Failed to read the linear index.
// Return failure.
return(StatGenStatus::FAIL_IO);
}
}
// Successfully read teh bam index file.
return(StatGenStatus::SUCCESS);
}
// Read & parse the specified index file.
SamStatus::Status BamIndex::readIndex(const char* filename)
{
// Reset the index from anything that may previously be set.
resetIndex();
IFILE indexFile = ifopen(filename, "rb");
// Failed to open the index file.
if(indexFile == NULL)
{
return(SamStatus::FAIL_IO);
}
// generate the bam index structure.
// Read the magic string.
char magic[4];
if(ifread(indexFile, magic, 4) != 4)
{
// Failed to read the magic
ifclose(indexFile);
return(SamStatus::FAIL_IO);
}
// If this is not an index file, set num references to 0.
if (magic[0] != 'B' || magic[1] != 'A' || magic[2] != 'I' || magic[3] != 1)
{
// Not a BAM Index file.
ifclose(indexFile);
return(SamStatus::FAIL_PARSE);
}
// It is a bam index file.
// Read the number of reference sequences.
if(ifread(indexFile, &n_ref, 4) != 4)
{
// Failed to read.
ifclose(indexFile);
return(SamStatus::FAIL_IO);
}
// Size the references.
myRefs.resize(n_ref);
for(int refIndex = 0; refIndex < n_ref; refIndex++)
{
// Read each reference.
Reference* ref = &(myRefs[refIndex]);
// Read the number of bins.
if(ifread(indexFile, &(ref->n_bin), 4) != 4)
{
// Failed to read the number of bins.
// Return failure.
ifclose(indexFile);
return(SamStatus::FAIL_PARSE);
}
// If there are no bins, then there are no
// mapped/unmapped reads.
if(ref->n_bin == 0)
{
ref->n_mapped = 0;
ref->n_unmapped = 0;
}
// Resize the bins so they can be indexed by bin number.
ref->bins.resize(ref->n_bin + 1);
// Read each bin.
for(int binIndex = 0; binIndex < ref->n_bin; binIndex++)
{
uint32_t binNumber;
// Read in the bin number.
if(ifread(indexFile, &(binNumber), 4) != 4)
{
// Failed to read the bin number.
// Return failure.
ifclose(indexFile);
return(SamStatus::FAIL_IO);
}
// Add the bin to the reference and get the
// pointer back so the values can be set in it.
Bin* binPtr = &(ref->bins[binIndex]);
binPtr->bin = binNumber;
// Read in the number of chunks.
if(ifread(indexFile, &(binPtr->n_chunk), 4) != 4)
{
// Failed to read number of chunks.
// Return failure.
ifclose(indexFile);
return(SamStatus::FAIL_IO);
}
// Read in the chunks.
// Allocate space for the chunks.
uint32_t sizeOfChunkList = binPtr->n_chunk * sizeof(Chunk);
binPtr->chunks = (Chunk*)malloc(sizeOfChunkList);
if(ifread(indexFile, binPtr->chunks, sizeOfChunkList) != sizeOfChunkList)
{
// Failed to read the chunks.
// Return failure.
ifclose(indexFile);
return(SamStatus::FAIL_IO);
}
// Determine the min/max for this bin if it is not the max bin.
if(binPtr->bin != MAX_NUM_BINS)
{
for(int i = 0; i < binPtr->n_chunk; i++)
{
if(binPtr->chunks[i].chunk_beg < ref->minChunkOffset)
{
ref->minChunkOffset = binPtr->chunks[i].chunk_beg;
}
if(binPtr->chunks[i].chunk_end > ref->maxChunkOffset)
{
ref->maxChunkOffset = binPtr->chunks[i].chunk_end;
}
if(binPtr->chunks[i].chunk_end > maxOverallOffset)
{
maxOverallOffset = binPtr->chunks[i].chunk_end;
}
}
}
else
{
// Mapped/unmapped are the last chunk of the
// MAX BIN
ref->n_mapped = binPtr->chunks[binPtr->n_chunk - 1].chunk_beg;
ref->n_unmapped = binPtr->chunks[binPtr->n_chunk - 1].chunk_end;
}
}
// Read the number of intervals.
if(ifread(indexFile, &(ref->n_intv), 4) != 4)
{
// Failed to read, set to 0.
ref->n_intv = 0;
// Return failure.
ifclose(indexFile);
return(SamStatus::FAIL_IO);
}
// Allocate space for the intervals and read them.
uint32_t linearIndexSize = ref->n_intv * sizeof(uint64_t);
ref->ioffsets = (uint64_t*)malloc(linearIndexSize);
if(ifread(indexFile, ref->ioffsets, linearIndexSize) != linearIndexSize)
{
// Failed to read the linear index.
// Return failure.
ifclose(indexFile);
return(SamStatus::FAIL_IO);
}
}
int32_t numUnmapped = 0;
if(ifread(indexFile, &numUnmapped, sizeof(int32_t)) == sizeof(int32_t))
{
myUnMappedNumReads = numUnmapped;
}
// Successfully read the bam index file.
ifclose(indexFile);
return(SamStatus::SUCCESS);
}
FileFilterIndex::~FileFilterIndex()
{
resetIndex();
}
void push_back( QList<QConsoleWidgetCommand> cmd ){
commandBuffers.push_front(cmd);
resetIndex();
}
