bool open_weights(
const char *weight_file,
s_motif *motifs[],
int num_motifs )
{
// open the file
ifstream ifs;
_CALL(
_open_input( ifs, weight_file, ".txt" )
);
// find the EOL character
char this_EOL = _find_EOL( ifs );
if( !this_EOL )
// no EOL character was identified
{
cout << "ERROR: The file has no EOL character." << endl;
return false;
}
// read the file
cout << "Reading the weights..." << endl;
_CALL(
read_weights( ifs, motifs, num_motifs, this_EOL )
);
ifs.close();
return true;
}
bool read_FASTA(
ifstream &ifs,
s_gene *genes[],
int *num_genes,
char this_EOL )
// reads sequences from &ifs
// returns true if successful, false otherwise
//
// ifs: input file stream
// genes: the list of genes whose sequences are to be read
// num_genes: will contain the number of genes that are in the list
// this_EOL: the end of line character. this character is determined separately in another function for this file stream
{
// A line cannot be longer than MAX_LINE_LENGTH characters
char string[ MAX_LINE_LENGTH + 1 ];
char gene_name[ MAX_LINE_LENGTH + 1 ] = "";
char gene_seq[ MAX_SEQ_LENGTH + 1 ] = "";
// read the file line by line
_line_number = 0; // reset the line number
while( true )
{
// read the line
ifs.getline( string, MAX_LINE_LENGTH, this_EOL );
if( !ifs || ifs.eof() ) // the end of the file has reached
{
// add the last read gene to the list
_CALL(
_add_gene( gene_name, gene_seq, genes, num_genes )
);
break;
}
_line_number ++; // update the line number that was just read
if( string[ 0 ] == '>' ) // this is a header
{
// add the last read gene to the list
_CALL(
_add_gene( gene_name, gene_seq, genes, num_genes )
);
// store the name of the new gene
strcpy( gene_name, string + 1 );
gene_seq[ 0 ] = 0; // reset the gene sequence
}
else // this line contains sequence information
strcat( gene_seq, string );
}
return true;
}
bool open_FASTA(
const char *file,
s_seq *seqs[],
int *num_seqs )
// opens a file and reads its content
// returns true if successful, false otherwise
//
{
// open the file
ifstream ifs;
_CALL(
_open_input( ifs, file, ".fasta" )
);
// find the EOL character
char this_EOL = _find_EOL( ifs );
if( !this_EOL )
// no EOL character was identified
{
cout << "ERROR: The file has no EOL character." << endl;
return false;
}
// read the file
cout << "Reading the sequences..." << endl;
_CALL(
read_FASTA( ifs, seqs, num_seqs, this_EOL )
);
// count the number of positive instances
int num_pos = 0;
int i;
for( i = 0; i < *num_seqs; i ++ )
num_pos += seqs[ i ] ->positive;
cout << *num_seqs << " sequences were read, including " << num_pos << " positive and "
<< *num_seqs - num_pos << " negatives." << endl << endl;
if( num_pos < 10 || *num_seqs - num_pos < 10 )
{
cout << "ERROR: At least 10 positive and 10 negative sequences are required." << endl;
return false;
}
// close the input file stream
ifs.close();
return true;
}
tree::Exp *
X86Frame::externalCall(const std::string &func, const tree::ExpList &args)
{
Label *flabel = gcnew(Label, (func));
tree::NAME *name = _NAME(flabel);
tree::CALL *call = _CALL(name, args);
return call;
}
bool open_rndforest(
const char *file,
s_motif *motifs[],
int *num_motifs,
char const *filter )
// opens a file and reads its content
// returns true if successful, false otherwise
{
// open the file
ifstream ifs;
_CALL(
_open_input( ifs, file, ".txt" )
);
// find the EOL character
char this_EOL = _find_EOL( ifs );
if( !this_EOL )
// no EOL character was identified
{
cout << "ERROR: The file has no EOL character." << endl;
return false;
}
// read the file
cout << "Reading RF results..." << endl;
_CALL(
read_rndforest( ifs, motifs, num_motifs, filter, this_EOL )
);
if( *num_motifs )
cout << *num_motifs << " motifs were read." << endl << endl;
else
{
cout << "ERROR: No motifs were read. The input protein possibly does not have canonical C2H2-ZFs." << endl;
return false;
}
// close the input file stream
ifs.close();
return true;
}
/// Add a link to another object.
virtual STATUS linkObject(OBJECT* from, CSTR& objPath, OBJECT* to) {
return _CALL(m_current.dataProvider, linkObject, (from, objPath, to));
}
/// Add a link to another object.
virtual STATUS linkObject(CSTR& fullPath, OBJECT* to) {
return _CALL(m_current.dataProvider, linkObject, (fullPath, to));
}
/// IDataManagerSvc: Analyze by traversing all data objects in the data store.
virtual STATUS traverseTree( AGENT* pAgent ) {
return _CALL(m_current.dataManager, traverseTree, (pAgent));
}
/// Find object in the data store.
virtual STATUS findObject(OBJECT* parent, int item, OBJECT*& pObject) {
return _CALL(m_current.dataProvider, findObject, (parent, item, pObject));
}
/// Update object.
virtual STATUS updateObject(OBJECT* parent, CSTR& updatePath) {
return _CALL(m_current.dataProvider, updateObject, (parent, updatePath));
}
/// Remove all data objects below the sub tree identified
virtual STATUS clearSubTree(CSTR& path) {
return _CALL(m_current.dataManager, clearSubTree, (path));
}
/// Unregister object from the data store.
virtual STATUS unregisterObject(OBJECT* pObj, CSTR& path) {
return _CALL(m_current.dataProvider, unregisterObject, (pObj, path));
}
/// Update object.
virtual STATUS updateObject(CSTR& path) {
return _CALL(m_current.dataProvider, updateObject, (path));
}
/// Register object with the data store.
virtual STATUS registerObject(OBJECT* parent, int obj, OBJECT* pObj) {
return _CALL(m_current.dataProvider, registerObject, (parent, obj, pObj));
}
/// Unregister object from the data store.
virtual STATUS unregisterObject(CSTR& parent, int obj) {
return _CALL(m_current.dataProvider, unregisterObject, (parent, obj));
}
/// Register object with the data store.
virtual STATUS registerObject(CSTR& parent, int item, OBJECT* pObj) {
return _CALL(m_current.dataProvider, registerObject, (parent, item, pObj));
}
/// Add an item to the preload list
virtual STATUS removePreLoadItem(CSTR& item) {
return _CALL(m_current.dataProvider, removePreLoadItem, (item));
}
/// Remove an item from the preload list
virtual STATUS removePreLoadItem(const DataStoreItem& item) {
return _CALL(m_current.dataProvider, removePreLoadItem, (item));
}
/// Remove a link to another object.
virtual STATUS unlinkObject(OBJECT* from, CSTR& objPath) {
return _CALL(m_current.dataProvider, unlinkObject, (from, objPath));
}
/// Unregister object from the data store.
virtual STATUS unregisterObject(OBJECT* pObj, int item ) {
return _CALL(m_current.dataProvider, unregisterObject, (pObj, item));
}
/// Update object identified by its directory entry.
virtual STATUS updateObject(IRegistry* pDirectory ) {
return _CALL(m_current.dataProvider, updateObject, (pDirectory));
}
/// Analyze by traversing all data objects below the sub tree
virtual STATUS traverseSubTree(CSTR& path, AGENT* pAgent) {
return _CALL(m_current.dataManager, traverseSubTree, (path, pAgent));
}
/// Update object.
virtual STATUS updateObject(OBJECT* pObj ) {
return _CALL(m_current.dataProvider, updateObject, (pObj));
}
/// IDataManagerSvc: Explore the object store: retrieve the object's parent
virtual STATUS objectParent(const IRegistry* pObject, IRegistry*& refpParent) {
return _CALL(m_current.dataManager, objectParent, (pObject, refpParent));
}
/// Remove all data objects below the sub tree identified
virtual STATUS clearSubTree(OBJECT* pObject) {
return _CALL(m_current.dataManager, clearSubTree, (pObject));
}
/// Find object in the data store.
virtual STATUS findObject(OBJECT* parent, CSTR& path, OBJECT*& pObject) {
return _CALL(m_current.dataProvider, findObject, (parent, path, pObject));
}
/// Retrieve object from data store.
virtual STATUS retrieveObject(OBJECT* parent, int item, OBJECT*& pObj ) {
return _CALL(m_current.dataProvider, retrieveObject, (parent, item, pObj));
}
/// IDataManagerSvc: Analyze by traversing all data objects below the sub tree
virtual STATUS traverseSubTree(OBJECT* pObject, AGENT* pAgent) {
return _CALL(m_current.dataManager, traverseSubTree, (pObject, pAgent));
}
/// Find object in the data store.
virtual STATUS findObject(CSTR& parent, CSTR& path, OBJECT*& pObj) {
return _CALL(m_current.dataProvider, retrieveObject, (parent, path, pObj));
}
/// Explore the object store: retrieve all leaves attached to the object
virtual STATUS objectLeaves(const IRegistry* pObject, std::vector<IRegistry*>& leaves) {
return _CALL(m_current.dataManager, objectLeaves, (pObject, leaves));
}