void TLexer::ReadNumber(std::string &value) {
States state = State_Int;
while (true) {
if (FileEOF()) {
throw new ExceptionLexerEOF(value, PosLine, PosColumn);
break;
}
char c = GetChar();
if (isdigit(c)) {
value += c;
} else if (c == '.' && state == State_Int) {
state = State_Double;
value += c;
} else if (c == 'e' && state == State_Double) {
char c_temp = GetChar();
char c_temp2 = GetChar();
if ((c_temp == '+' || c_temp == '-') && isdigit(c_temp2)) {
value += c;
value += c_temp;
value += c_temp2;
} else {
throw new ExceptionLexerIncorrectChar(value, PosLine, PosColumn);
break;
}
} else {
IsCorrectToken(c, value, state);
break;
}
}
}
void TLexer::Read() {
char c;
std::string value = "";
while (true) {
c = GetChar();
if (FileEOF()) {
break;
}
value += c;
switch (c) {
case 34: {
ReadString(value);
break;
}
case 39: {
ReadSymbol(value);
break;
}
case '.' : {
FindToken(State_Point, value);
break;
}
case '(': {
FindToken(State_Lbkt,value);
break;
}
case ')': {
FindToken(State_Rbkt,value);
break;
}
case '#': {
ReadSharp(value);
break;
}
default: {
if (isspecial(c) || isalpha(c)) {
ReadIdent(value);
} else if (isdigit(c)) {
ReadNumber(value);
} else if (IsEndToken(c)) {
value.erase(value.size() - 1, value.size());
}
break;
}
}
}
value = "EOF";
FindToken(State_EOF, value);
}
void FileGetS (char *buffer, int length, FileBuffer buf){
int a;
for (a = 0; a < length && !FileEOF (buf); a++){
buffer[a] = FilePeekC (buf);
buf->head++;
if (a + 1 < length && buffer[a] == '\n'){
buffer[a + 1] = '\0';
break;
}
}
}
char TLexer::GetChar() {
char c;
fin.get(c);
if (FileEOF()) {
return c;
}
if (c == '\n') {
PosLine += 1;
PosColumn = 1;
} else {
PosColumn += 1;
}
return c;
}
void TLexer::ReadIdent(std::string &value) {
while (true) {
if (FileEOF()) {
throw new ExceptionLexerEOF(value, PosLine, PosColumn);
break;
}
char c = GetChar();
if (isspecial(c) || isdigit(c) || isalpha(c)) {
value += c;
} else {
IsCorrectToken(c, value, State_Ident);
break;
}
}
}
void ROFile::ReadBuffer(void* pBuffer, unsigned int uiBufferSize)
{
if(!m_File)
{
throw FileError("NULL File pointer", EL_BAD, "ROFile::ReadBuffer", "File hasn't been opened!");
}
unsigned int rc = fread(pBuffer, uiBufferSize, 1, m_File);
if(feof(m_File))
{
throw FileEOF(m_sFilename.c_str(), rc);
}
else if(ferror(m_File))
{
throw FileReadError(m_sFilename.c_str(), EL_BAD, "ROFile::ReadBuffer", "Error while reading file:\r\n" + m_sFilename);
}
}
char *FileGetLine (FileBuffer buf){
int a = 0, length = 1;
char *buffer = (char *) malloc (1 * sizeof(char));
assert (buffer);
while (!FileEOF (buf)){
buffer[a] = FilePeekC (buf);
buf->head++;
if (buffer[a] == '\n'){
buffer[a] = '\0';
break;
}
a++;
if (a == length){
buffer = (char *) realloc (buffer, (length *= 2) * sizeof(char));
assert (buffer);
}
}
return buffer;
}
void TLexer::ReadString(std::string &value) {
bool IsSpecialForString = false;
while(true) {
if (FileEOF()) {
throw new ExceptionLexerEOF(value, PosLine, PosColumn);
break;
}
char c = GetChar();
value += c;
if (c == '\\' && !IsSpecialForString) {
IsSpecialForString = true;
} else if ((c == '\\' || c == '\"') && IsSpecialForString) {
IsSpecialForString = false;
continue;
} else if (c == '\"' && !IsSpecialForString) {
c = GetChar();
IsCorrectToken(c, value, State_String);
break;
} else if (IsSpecialForString) {
throw new ExceptionLexerIncorrectChar(value, PosLine, PosColumn);
break;
}
}
}
seq* FileRead (FileBuffer buf, int start, int finish, int version){
char* res = (char*) malloc(sizeof(char));
int ressize = 1, numread = 0, i, numNs = 0;
char *tempname, temp[256], currchar, *curr, *resend;
seq* myseq = (seq*) malloc(sizeof(seq));
if (FileEOF(buf))
return 0;
if (start == 1 && finish == 0) {
start = buf->startpos;
finish = buf->endpos;
if (start == 0)
start = 1;
}
tempname = FileGetLine (buf);
if (tempname[0] != '>') {
fprintf(stderr, "File is not in FASTA format!!\n");
exit(1);
}
myseq->name = (char*) malloc((strlen(tempname))*sizeof(char));
strcpy(myseq->name, tempname+1);
if (strchr(myseq->name, '\n'))
*(char *)(strchr(myseq->name, '\n')) = 0;
free (tempname);
for (i = 0; i < 256; i++){
temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ?
toupper((char) i) : 'N';
}
FileUpdate (buf);
curr = res;
resend = res + ressize;
if (version == VER_ORDER || version == VER_MLAGAN){
ressize = 2;
numread = 1;
if (version == VER_ORDER)
res[0] = 0;
else
res[0] = 'N';
curr++;
}
while (buf->head < buf->tail || !feof (buf->data)){
while (buf->head < buf->tail){
currchar = *(buf->head);
if (currchar == '>') goto outer;
if (currchar != ' ' && currchar != '\n' && currchar != '\r' &&
currchar != '\t' && currchar != '\t' && currchar != '\v') {
if (currchar == 'N') numNs++;
*curr++ = temp[(int) currchar];
if (curr >= resend) {
numread = curr - res;
res = (char *) realloc (res, sizeof(char) * (ressize *= 2));
curr = res + numread;
resend = res + ressize;
}
}
buf->head++;
}
buf->tail = buf->buffer + fread (buf->buffer, sizeof(char), BUFFER_SIZE, buf->data);
buf->head = buf->buffer;
}
outer:
numread = curr - res;
res[numread]=0;
myseq->rptr = res;
if (version == VER_FCHAOS){
if (start > 0) {
res[finish] = 0;
res = &res[start-1];
numread = finish-start+1;
}
myseq->numlets = numread;
}
else if (version == VER_ORDER){
if (start > 0){
res = &res[start-1];
res[0] = 0;
res[finish-start+2] = 0;
numread = finish-start+2;
}
myseq->numlets = numread-1;
}
else if (version == VER_MLAGAN){
if (start > 0 || finish > 0) {
res[finish] = 0;
res = &res[start-1];
numread = finish-start+1;
}
myseq->numlets = numread;
myseq->leftbound = start;
myseq->rightbound = finish;
}
myseq->numsiglets = numread - numNs;
myseq->lets = res;
return myseq;
}
/*============================================================================
Description: See documentation for standard C library feof
==========================================================================*/
short palm_feof( PALM_FILE* io_pSF )
{
ChASSERT(io_pSF->volRef == ((UInt16)-1));
return ( fileErrEOF == FileEOF( io_pSF->file.fh ) ) ? EOF : 0;
}
