unsigned int getSize()
{
unsigned int totalSize = 0;
// Start with the size of the contents
// (don't use seek as we don't know if the client still wants to write stuff)
totalSize += static_cast<unsigned int>(contents.size());
if (!subChunks.empty())
{
// Sum up the size of the subchunks
for (Chunk& chunk : subChunks)
{
totalSize += 4; // ID (4 bytes)
totalSize += chunk.chunkSizeBytes; // Subchunk Size Info (can be 4 or 2 bytes)
// While the child chunk size itself doesn't include padding, we need to respect
// it when calculating the size of this parent chunk
unsigned int childChunkSize = chunk.getSize();
totalSize += childChunkSize + (childChunkSize % 2); // add 1 padding byte if odd
}
}
else
{
totalSize += rawData.size();
}
return totalSize;
}
void MSDigestSearch::printProteinCoverage ( ostream& os, const CharVector& aaCovered ) const
{
int protLen = aaCovered.size ();
if ( protLen ) {
int coverCount = 0;
for ( int m = 0; m < protLen ; m++ ) {
if ( aaCovered [m] > 0 ) coverCount++;
}
os << "The matched peptides cover <b>" << 100 * coverCount / protLen << "%</b>";
os << " ";
os << "(" << coverCount << "/" << protLen << " AA's) of the protein.";
os << "<p />";
}
}
void SQLiteAATable::insert ()
{
v1 [3] = "";
v1 [4] = "1";
v1 [5] = "0";
CharVector cv = AAInfo::getInfo ().getAminoAcids ();
for ( StringVectorSizeType i = 0 ; i < cv.size () ; i++ ) {
char c = cv [i];
v1 [0] = AAInfo::getInfo ().getLongName ( c );
v1 [1] = "one_letter_code";
v1 [2] = string ( 1, c );
insertTable ( tableName, n1, v1 );
v1 [1] = "formula";
v1 [2] = AAInfo::getInfo ().getElementalString ( c );
insertTable ( tableName, n1, v1 );
v1 [1] = "dw_substituent_a";
string subA = AAInfo::getInfo ().getSubstituentA ( c );
if ( subA != "0" ) {
v1 [2] = subA;
insertTable ( tableName, n1, v1 );
}
v1 [1] = "dw_substituent_b";
string subB = AAInfo::getInfo ().getSubstituentB ( c );
if ( subB != "0" ) {
v1 [2] = subB;
insertTable ( tableName, n1, v1 );
}
v1 [1] = "pk_c_term";
string ctpk = AAInfo::convert_pk ( AAInfo::getInfo ().getCTermPK ( c ) );
if ( ctpk != "n/a" ) {
v1 [2] = ctpk;
insertTable ( tableName, n1, v1 );
}
v1 [1] = "pk_n_term";
string ntpk = AAInfo::convert_pk ( AAInfo::getInfo ().getNTermPK ( c ) );
if ( ntpk != "n/a" ) {
v1 [2] = ntpk;
insertTable ( tableName, n1, v1 );
}
v1 [1] = "pk_acidic_sc";
string ascpk = AAInfo::convert_pk ( AAInfo::getInfo ().getAcidicSCPK ( c ) );
if ( ascpk != "n/a" ) {
v1 [2] = ascpk;
insertTable ( tableName, n1, v1 );
}
v1 [1] = "pk_basic_sc";
string bscpk = AAInfo::convert_pk ( AAInfo::getInfo ().getBasicSCPK ( c ) );
if ( bscpk != "n/a" ) {
v1 [2] = bscpk;
insertTable ( tableName, n1, v1 );
}
}
}
void parseFromStream(CharVector& buffer, int level, Chunk& parsedChunk)
{
VectorBuffer<char> tempBuf(buffer);
std::istream stream(&tempBuf);
if (parsedChunk.id == "SURF")
{
std::string surfName = parseString0(stream);
std::string parentName = parseString0(stream);
addStringToContents(parsedChunk.contents, surfName);
addStringToContents(parsedChunk.contents, parentName);
}
if (parsedChunk.id == "IMAP")
{
std::string ordinal = parseString0(stream);
addStringToContents(parsedChunk.contents, ordinal);
}
while (!stream.eof())
{
// Read header
Chunk chunk;
char id[5];
stream.read(id, 4);
id[4] = '\0';
chunk.id = id;
if (stream.eof()) break;
if (parsedChunk.id == "SURF" || parsedChunk.id == "BLOK" ||
parsedChunk.id == "IMAP" || parsedChunk.id == "TMAP")
{
uint16_t size;
stream.read((char*)&size, 2);
size = reverse(size);
chunk.size = size;
chunk.chunkSizeBytes = 2;
}
else
{
uint32_t size;
stream.read((char*)&size, 4);
size = reverse(size);
chunk.size = size;
chunk.chunkSizeBytes = 4;
}
assert(!stream.fail());
//std::string indent(level * 2, ' ');
//std::cout << indent << id << " with size " << chunk.size << " bytes" << std::endl;
// Check size restrictions
assert(4 + chunk.chunkSizeBytes + chunk.size <= buffer.size());
uint32_t dataSize = chunk.size;
if (chunk.id == "FORM")
{
// LWO doesn't have the correct size?
if (dataSize + 4 + 4 != buffer.size())
{
std::cout << "ERROR: FORM Size Value + 8 Bytes is not the same as the file size." << std::endl;
assert(false);
}
// Read the LWO2 tag
char lwo2[5];
stream.read(lwo2, 4);
lwo2[4] = '\0';
assert(std::string(lwo2) == "LWO2");
chunk.contents.push_back('L');
chunk.contents.push_back('W');
chunk.contents.push_back('O');
chunk.contents.push_back('2');
dataSize -= 4;
}
assert(!stream.fail());
chunk.rawData.resize(dataSize);
stream.read(&chunk.rawData.front(), dataSize);
#if 0
if (chunk.id == "COLR")
{
uint32_t colr1Raw = *((uint32_t*)&chunk.rawData[0]);
colr1Raw = reverse(colr1Raw);
float colr1 = *((float*)&colr1Raw);
std::cout << colr1;
}
#endif
assert(!stream.fail());
// Fill bit if size is odd
if (dataSize % 2 == 1)
{
char temp;
stream.read(&temp, 1);
assert(temp == '\0');
assert(!stream.fail());
}
parsedChunk.subChunks.push_back(chunk);
}
// Try to parse the subchunks
for (Chunk& chunk : parsedChunk.subChunks)
{
if (chunk.id == "FORM" || chunk.id == "SURF" || chunk.id == "BLOK" ||
chunk.id == "IMAP" || chunk.id == "TMAP")
{
parseFromStream(chunk.rawData, level + 1, chunk);
}
}
}
virtual std::size_t size () const
{
return m_char_vector.size();
}