static void loadFile(huffTableEntry **table, const char *filename)
{
char buf[1024];
char *from;
char *to;
char *binary;
char *colon;
CFile fp(filename, "r");
if ( fp )
{
while ( fgets(buf,sizeof(buf),fp) != NULL )
{
// Tokenize string "in place"
from = buf;
colon = strchr(buf, ':');
if (colon == NULL)
continue;
binary = colon + 1;
*colon = 0;
colon = strchr(binary, ':');
if (colon == NULL)
continue;
*colon = 0;
to = colon + 1;
colon = strchr(to, ':');
if (colon != NULL)
*colon = 0;
{
int bin_len = strlen(binary);
int from_char = resolveChar(from);
char to_char = resolveChar(to);
unsigned long bin = decodeBinary(binary);
// Add entry to end of bucket
huffTableEntry **pCurrent = &table[from_char];
while ( *pCurrent != NULL )
{
pCurrent = &((*pCurrent)->nextEntry);
}
*pCurrent = new huffTableEntry(bin, bin_len, to_char);
}
}
}
#ifdef FREESATV2_DEBUG
else
{
eDebug("[FREESAT] Cannot load '%s'",filename);
}
#endif
}
void parseSequenceLine(){
if(fastdist){
parseSequenceLineFastDist();
return;
}
if(firstSequence){
// find the length of the sequence
parseSequenceName();
while (curChar != 10){
if(curChar > 32) {
charBuffer.push_back(curChar);
}
curChar = getNextChar();
}
// We have the length. Use char arrays to store the char data in.
sequenceLength = charBuffer.size();
char* data = new char[sequenceLength];
sequences->push_back(data);
for(unsigned int i = 0; i < sequenceLength; i++){
data[i] = resolveChar(charBuffer[i]);
}
charBuffer.clear();
discoverInputType(sequences->at(0));
firstSequence = false;
} else {
parseSequenceName();
unsigned int counter = 0;
char* data = new char[sequenceLength];
sequences->push_back(data);
while (curChar != 10){
if(curChar > 32){
data[counter] = resolveChar(curChar);
counter++;
}
curChar = getNextChar();
}
if(counter != sequenceLength){
cerr << "ERROR: Sequence " << sequenceCount << " has length " << counter << " while the preceding sequences in the alignment has length " << sequenceLength << "." << endl;
exit(1);
}
}
sequenceCount++;
}
inline void encodeProteinSequence(unsigned int* bitString, vector<char>& data){
for(unsigned int i = 0; i < sequenceLength+paddingLength; i++) {
int offset = i % 4;
unsigned int bitStringIdx = i / 4;
if(offset == 0){
bitString[bitStringIdx] = 0;
}
char c = resolveChar(data[i]);
bitString[bitStringIdx] += (c << (offset*8));
}
}