void testAt(IntVector& test)
{
cout << "First position" << endl;
cout << test.at(0) << endl << endl;
cout << "Last position" << endl;
cout << test.at(test.size() - 1) << endl << endl;
cout << "Front position" << endl;
cout << test.front() << endl << endl;
cout << "Back position" << endl;
cout << test.back() << endl << endl;
cout << "First pos changed to last pos" << endl;
test.at(0) = test.back();
testValues(test);
}
FeedForwardNetwork& addActivationNode()
{
int size = (int)mNodeSizes.back();
// Ensure ActivationType is derived from ActivationNode
ActivationNode *node = new ActivationType(size);
return addNodePtr(node);
}
void printout(const IntVector &deck) {
int lastCard = deck.back();
for ( auto card: deck)
cout << card << ( card == lastCard ? "" : ", " );
cout << endl << endl;
}
inline size_t IndexedList::front() const {
return _list.back();
}
FeedForwardNetwork& addLinearNode(const int size, const float spread = 0.05)
{
return addNodePtr(new LinearNode(mNodeSizes.back(), size, spread));
}
bool MSProductParameters::getSequenceElements ( ParameterList* params, const string& num, string& sequence, string& nTermName, string& cTermName, string& neutralLossName )
{
sequence = params->getStrippedStringValue ( "sequence" + num, "" );
if ( sequence.empty () ) return false;
nTermName = params->getStringValue ( "nterm" + num, "" );
cTermName = params->getStringValue ( "cterm" + num, "" );
neutralLossName = params->getStringValue ( "nloss" + num, "" );
if ( nTermName.empty () && cTermName.empty () && neutralLossName.empty () ) {
static StringVector nTermNames = ConstMod::getNTermNames ();
static StringVector cTermNames = ConstMod::getCTermNames ();
static StringVector nLossNames = ConstMod::getNLossNames ();
IntVector plusIdx;
IntVector minusIdx;
for ( StringSizeType i = 0 ; i < sequence.length () ; i++ ) {
char p = sequence [i];
if ( p == '+' ) plusIdx.push_back ( i );
else if ( p == '-' )minusIdx.push_back ( i );
else if ( p == '(' ) {
int bracket = 0;
for ( ; i < sequence.length () ; i++ ) {
char a = sequence [i];
if ( a == '(' ) bracket++;
if ( a == ')' ) bracket--;
if ( bracket == 0 ) break;
}
}
}
if ( !plusIdx.empty () ) {
for ( int i = 0 ; i < nLossNames.size () ; i++ ) {
string nL = nLossNames [i];
if ( isSuffix ( sequence, "+" + nL ) ) {
sequence = sequence.substr ( 0, sequence.length () - 1 - nL.length () );
neutralLossName = nL;
break;
}
}
if ( neutralLossName.empty () ) {
string possNLoss = sequence.substr ( plusIdx.back () + 1 ); // Add 1 to the last +
if ( genStringIsFloat ( possNLoss ) ) { // Check if number
sequence = sequence.substr ( 0, plusIdx.back () );
neutralLossName = possNLoss;
}
}
while ( !minusIdx.empty () && minusIdx.back () >= sequence.length () ) minusIdx.pop_back ();
}
if ( !minusIdx.empty () ) {
for ( int i = 0 ; i < cTermNames.size () ; i++ ) {
string nC = cTermNames [i];
if ( nC.empty () ) continue;
if ( isSuffix ( sequence, "-" + nC ) ) {
sequence = sequence.substr ( 0, sequence.length () - 1 - nC.length () );
cTermName = nC;
break;
}
}
if ( cTermName.empty () ) {
int idx = minusIdx.back ();
if ( sequence [idx-1] != '-' ) idx += 1;
string possCTerm = sequence.substr ( idx ); // Add 1 to the last -
if ( genStringIsFloat ( possCTerm ) ) { // Check if number
sequence = sequence.substr ( 0, idx - 1 );
cTermName = possCTerm;
}
}
while ( minusIdx.back () >= sequence.length () ) minusIdx.pop_back ();
}
if ( !minusIdx.empty () ) {
for ( int j = 0 ; j < nTermNames.size () ; j++ ) {
string nN = nTermNames [j];
if ( nN.empty () ) continue;
if ( isPrefix ( sequence, nN + "-" ) ) {
sequence = sequence.substr ( nN.length () + 1 );
nTermName = nN;
break;
}
}
if ( nTermName.empty () ) {
int idx = ( sequence [0] == '-' ) ? minusIdx [1] : minusIdx [0];
string possNTerm = sequence.substr ( 0, idx );
if ( genStringIsFloat ( possNTerm ) ) { // Check if number
sequence = sequence.substr ( idx + 1 );
nTermName = possNTerm;
}
}
}
params->addOrReplaceName ( "sequence" + num, sequence );
params->addOrReplaceName ( "nterm" + num, nTermName );
params->addOrReplaceName ( "cterm" + num, cTermName );
params->addOrReplaceName ( "nloss" + num, neutralLossName );
}
return true;
}
