// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
void Properties::load(istream& in)
{
setDefaults();
// Loop reading properties
string key, value;
for(;;)
{
// Get the key associated with this property
key = readQuotedString(in);
// Make sure the stream is still okay
if(!in)
return;
// A null key signifies the end of the property list
if(key == "")
break;
// Get the value associated with this property
value = readQuotedString(in);
// Make sure the stream is still okay
if(!in)
return;
// Set the property
PropertyType type = getPropertyType(key);
set(type, value);
}
}
void Parser::readBlock(Block& block)
{
do {
std::string str = readKeyword();
switch (nextToken()) {
case Parser::Error:
return;
case Parser::Begin:
readBegin();
readBlock(block.addBlock(str));
readEnd();
break;
case Parser::Equal:
readEqual();
if (nextToken() == QuoteStr) {
block.addString(str, readQuotedString());
while (nextToken() == Parser::Comma) {
readComma();
block.addString(str, readQuotedString());
}
} else if (nextToken() == Real) {
block.addReal(str, readReal());
while (nextToken() == Parser::Comma) {
readComma();
block.addReal(str, readReal());
}
} else if (nextToken() == RelativeReal) {
block.addRelativeReal(str, readRelativeReal());
while (nextToken() == Parser::Comma) {
readComma();
block.addRelativeReal(str, readRelativeReal());
}
} else if (nextToken() == Str) {
block.addString(str, readString());
while (nextToken() == Parser::Comma) {
readComma();
block.addString(str, readString());
}
} else {
throw utils::InternalError();
}
readSemicolon();
break;
default:
throw utils::InternalError("bad file");
};
} while (nextToken() != Parser::End and mStream);
}
bool ParserStringLiteral::parseImpl(Pos & pos, Pos end, ASTPtr & node, Pos & max_parsed_pos, Expected & expected)
{
Pos begin = pos;
String s;
if (pos == end || *pos != '\'')
{
expected = "opening single quote";
return false;
}
ReadBuffer in(const_cast<char *>(pos), end - pos, 0);
try
{
readQuotedString(s, in);
}
catch (const Exception & e)
{
expected = "string literal";
return false;
}
pos += in.count();
node = std::make_shared<ASTLiteral>(StringRange(begin, pos), s);
return true;
}
void DataTypeAggregateFunction::deserializeTextQuoted(IColumn & column, ReadBuffer & istr) const
{
String s;
readQuotedString(s, istr);
deserializeFromString(function, column, s);
}
short Scanner::getToken( YYSTYPE & lval )
//---------------------------------------
// get the next token from the input stream.
// at each call, the next character should be
// in _current.
{
const int MaxBufLen = 512;
char buffer[ MaxBufLen ];
int bufPos; // position in buffer
char special;
gobble();
if( isEOF() ) {
return 0;
}
if( isSpecial() ) {
special = (char) _current;
get(); // set up for next call
return special; // <-------- early return
}
if( isQuote() ) {
readQuotedString( lval );
return T_String; // <-------- early return
}
if( _current == '0' ) {
get();
if( toupper( _current ) == 'X' ) {
readHex( lval );
} else {
if( isDigit() ) {
readDecimal( lval );
} else {
lval = 0;
}
}
return T_Number; // <-------- early return
}
if( isDigit() ) {
readDecimal( lval );
return T_Number; // <-------- early return
}
for( bufPos = 0; bufPos < MaxBufLen; bufPos += 1 ) {
buffer[ bufPos ] = (char) _current;
get();
if( isEOF() || isSpace() || isSpecial() ) break;
}
bufPos += 1;
assert( bufPos < MaxBufLen );
buffer[ bufPos ] = '\0';
return tokenValue( buffer, lval );
}
XmlElement* XmlDocument::readNextElement (const bool alsoParseSubElements)
{
XmlElement* node = nullptr;
skipNextWhiteSpace();
if (outOfData)
return nullptr;
if (*input == '<')
{
++input;
String::CharPointerType endOfToken (XmlIdentifierChars::findEndOfToken (input));
if (endOfToken == input)
{
// no tag name - but allow for a gap after the '<' before giving an error
skipNextWhiteSpace();
endOfToken = XmlIdentifierChars::findEndOfToken (input);
if (endOfToken == input)
{
setLastError ("tag name missing", false);
return node;
}
}
node = new XmlElement (input, endOfToken);
input = endOfToken;
LinkedListPointer<XmlElement::XmlAttributeNode>::Appender attributeAppender (node->attributes);
// look for attributes
for (;;)
{
skipNextWhiteSpace();
const juce_wchar c = *input;
// empty tag..
if (c == '/' && input[1] == '>')
{
input += 2;
break;
}
// parse the guts of the element..
if (c == '>')
{
++input;
if (alsoParseSubElements)
readChildElements (*node);
break;
}
// get an attribute..
if (XmlIdentifierChars::isIdentifierChar (c))
{
String::CharPointerType attNameEnd (XmlIdentifierChars::findEndOfToken (input));
if (attNameEnd != input)
{
const String::CharPointerType attNameStart (input);
input = attNameEnd;
skipNextWhiteSpace();
if (readNextChar() == '=')
{
skipNextWhiteSpace();
const juce_wchar nextChar = *input;
if (nextChar == '"' || nextChar == '\'')
{
XmlElement::XmlAttributeNode* const newAtt
= new XmlElement::XmlAttributeNode (attNameStart, attNameEnd);
readQuotedString (newAtt->value);
attributeAppender.append (newAtt);
continue;
}
}
else
{
setLastError ("expected '=' after attribute '"
+ String (attNameStart, attNameEnd) + "'", false);
return node;
}
}
}
else
{
if (! outOfData)
setLastError ("illegal character found in " + node->getTagName() + ": '" + c + "'", false);
}
break;
}
}
return node;
}
XmlElement* XmlDocument::readNextElement (const bool alsoParseSubElements)
{
XmlElement* node = nullptr;
skipNextWhiteSpace();
if (outOfData)
return nullptr;
const int openBracket = input.indexOf ((juce_wchar) '<');
if (openBracket >= 0)
{
input += openBracket + 1;
int tagLen = findNextTokenLength();
if (tagLen == 0)
{
// no tag name - but allow for a gap after the '<' before giving an error
skipNextWhiteSpace();
tagLen = findNextTokenLength();
if (tagLen == 0)
{
setLastError ("tag name missing", false);
return node;
}
}
node = new XmlElement (String (input, (size_t) tagLen));
input += tagLen;
LinkedListPointer<XmlElement::XmlAttributeNode>::Appender attributeAppender (node->attributes);
// look for attributes
for (;;)
{
skipNextWhiteSpace();
const juce_wchar c = *input;
// empty tag..
if (c == '/' && input[1] == '>')
{
input += 2;
break;
}
// parse the guts of the element..
if (c == '>')
{
++input;
if (alsoParseSubElements)
readChildElements (node);
break;
}
// get an attribute..
if (XmlIdentifierChars::isIdentifierChar (c))
{
const int attNameLen = findNextTokenLength();
if (attNameLen > 0)
{
const String::CharPointerType attNameStart (input);
input += attNameLen;
skipNextWhiteSpace();
if (readNextChar() == '=')
{
skipNextWhiteSpace();
const juce_wchar nextChar = *input;
if (nextChar == '"' || nextChar == '\'')
{
XmlElement::XmlAttributeNode* const newAtt
= new XmlElement::XmlAttributeNode (String (attNameStart, (size_t) attNameLen),
String::empty);
readQuotedString (newAtt->value);
attributeAppender.append (newAtt);
continue;
}
}
}
}
else
{
if (! outOfData)
setLastError ("illegal character found in " + node->getTagName() + ": '" + c + "'", false);
}
break;
}
}
return node;
}
bool MenuConf::readItemCaption(FILE* f, Item* item)
{
eatWhitespace(f);
return readQuotedString(f, item->data->caption, ItemData::CaptionSize);
}
void DataTypeEnum<Type>::deserializeTextQuoted(IColumn & column, ReadBuffer & istr) const
{
std::string name;
readQuotedString(name, istr);
static_cast<ColumnType &>(column).getData().push_back(getValue(StringRef(name)));
}
static void parseGtfEnd(char *s, struct gffFile *gff, struct gffLine *gl,
char *fileName, int lineIx)
/* Read the semi-colon separated end bits of a GTF line into gl and
* hashes. */
{
char *type, *val;
struct hashEl *hel;
bool gotSemi;
for (;;)
{
gotSemi = FALSE;
if ((type = nextWord(&s)) == NULL)
break;
s = skipLeadingSpaces(s);
if (NULL == s || s[0] == 0)
errAbort("Unpaired type(%s)/val on end of gtf line %d of %s", type, lineIx, fileName);
if (s[0] == '"' || s[0] == '\'')
{
val = s;
readQuotedString(fileName, lineIx, s, val, &s);
}
else
{
int len;
val = nextWord(&s);
len = strlen(val) - 1;
if (val[len] == ';')
{
val[len] = 0;
len -= 1;
gotSemi = TRUE;
}
if (len < 0)
errAbort("Empty value for %s line %d of %s", type, lineIx, fileName);
}
if (s != NULL && !gotSemi)
{
s = strchr(s, ';');
if (s != NULL)
++s;
}
/* only use the first occurance of gene_id and transcript_id */
if (sameString("gene_id", type) && (gl->geneId == NULL))
{
struct gffGeneId *gg;
if ((hel = hashLookup(gff->geneIdHash, val)) == NULL)
{
AllocVar(gg);
hel = hashAdd(gff->geneIdHash, val, gg);
gg->name = hel->name;
slAddHead(&gff->geneIdList, gg);
}
else
{
gg = hel->val;
}
gl->geneId = gg->name;
}
else if (sameString("transcript_id", type) && (gl->group == NULL))
{
struct gffGroup *gg;
if ((hel = hashLookup(gff->groupHash, val)) == NULL)
{
AllocVar(gg);
hel = hashAdd(gff->groupHash, val, gg);
gg->name = hel->name;
gg->seq = gl->seq;
gg->source = gl->source;
slAddHead(&gff->groupList, gg);
}
else
{
gg = hel->val;
}
gl->group = gg->name;
}
else if (sameString("exon_id", type))
gl->exonId = gffFileGetStr(gff, val);
else if (sameString("exon_number", type))
{
if (!isdigit(val[0]))
errAbort("Expecting number after exon_number, got %s line %d of %s", val, lineIx, fileName);
gl->exonNumber = atoi(val);
}
else if (sameString("intron_id", type))
gl->intronId = gffFileGetStr(gff, val);
else if (sameString("intron_status", type))
gl->intronStatus = gffFileGetStr(gff, val);
else if (sameString("protein_id", type))
gl->proteinId = gffFileGetStr(gff, val);
else if (sameString("gene_name", type))
gl->geneName = gffFileGetStr(gff, val);
else if (sameString("transcript_name", type))
gl->transcriptName = gffFileGetStr(gff, val);
}
if (gl->group == NULL)
{
if (gl->geneId == NULL)
warn("No gene_id or transcript_id line %d of %s", lineIx, fileName);
}
}