void picPunto::drawLine()
{
QPointF prevP, nextP;
int i;
for (i = 0; i < dataList.size(); ++i) {
pointData *pd = dataList.at(i);
if (!pd->x.isEmpty() && !pd->y.isEmpty()){
prevP.setX(getPValue(pd->x));
prevP.setY(getPValue(pd->y));
i++;
break;
} else {
QMessageBox::information(this, "Info", QString(tr("picPunto drawLine: first point is empty %1")).arg(i));
}
}
for (; i < dataList.size(); ++i) {
pointData *pd = dataList.at(i);
if (!pd->x.isEmpty() && !pd->y.isEmpty()){
nextP.setX(getPValue(pd->x));
nextP.setY(getPValue(pd->y));
currDoc->addLine(&prevP, &nextP);
// QMessageBox::information(this, "Info", QString(tr("picPunto drawLine: addLine %1 %2,%3 %4,%5")).arg(i).arg(prevP.x()).arg(prevP.y()).arg(nextP.x()).arg(nextP.y()));
prevP = nextP;
cnt++;
} else {
QMessageBox::information(this, "Info", QString(tr("picPunto drawLine: next point is empty %1")).arg(i));
}
}
while (!dataList.isEmpty())
delete dataList.takeFirst();
}
void picPunto::drawCircle(QString x, QString y, QString radius)
{
QPointF center;
qreal rad;
center.setX(getPValue(x));
center.setY(getPValue(y));
rad = getPValue(radius);
currDoc->addCircle(¢er, rad);
cnt++;
}
void picPunto::drawText(QString x, QString y, QString txt, QString align)
{
DPI::VAlign va = DPI::VAlignBottom;
DPI::HAlign ha;
QString sty = "txt";
double height = 0.05 * scale;
ha = (align == "ljust") ? DPI::HAlignLeft : (align == "rjust") ? DPI::HAlignRight : DPI::HAlignCenter;
QPointF pt(getPValue(x), getPValue(y));
currDoc->addText(txt, sty, &pt, height, 0.0, ha, va);
cnt++;
}
JsonObject*
SamiUnitConversion::asJsonObject() {
JsonObject *pJsonObject = new JsonObject();
pJsonObject->Construct();
JsonString *pUnit_idKey = new JsonString(L"unit_id");
pJsonObject->Add(pUnit_idKey, toJson(getPUnitId(), "Integer", ""));
JsonString *pStep_numberKey = new JsonString(L"step_number");
pJsonObject->Add(pStep_numberKey, toJson(getPStepNumber(), "Boolean", ""));
JsonString *pOperationKey = new JsonString(L"operation");
pJsonObject->Add(pOperationKey, toJson(getPOperation(), "Boolean", ""));
JsonString *pValueKey = new JsonString(L"value");
pJsonObject->Add(pValueKey, toJson(getPValue(), "Float", ""));
JsonString *pCreated_atKey = new JsonString(L"created_at");
pJsonObject->Add(pCreated_atKey, toJson(getPCreatedAt(), "DateTime", ""));
JsonString *pUpdated_atKey = new JsonString(L"updated_at");
pJsonObject->Add(pUpdated_atKey, toJson(getPUpdatedAt(), "DateTime", ""));
return pJsonObject;
}
vector_t LinearModel::getPVals()
{
int tmp = testParameter;
vector_t res;
for (testParameter = 1; testParameter < np; testParameter++)
res.push_back( getPValue() );
testParameter = tmp;
return res;
}
JsonObject*
SamiMeasurementValue::asJsonObject() {
JsonObject *pJsonObject = new JsonObject();
pJsonObject->Construct();
JsonString *pStart_timeKey = new JsonString(L"start_time");
pJsonObject->Add(pStart_timeKey, toJson(getPStartTime(), "Long", ""));
JsonString *pValueKey = new JsonString(L"value");
pJsonObject->Add(pValueKey, toJson(getPValue(), "Float", ""));
return pJsonObject;
}
JsonObject*
SamiNAMeasureBodyElem::asJsonObject() {
JsonObject *pJsonObject = new JsonObject();
pJsonObject->Construct();
JsonString *pBeg_timeKey = new JsonString(L"beg_time");
pJsonObject->Add(pBeg_timeKey, toJson(getPBegTime(), "Integer", ""));
JsonString *pStep_timeKey = new JsonString(L"step_time");
pJsonObject->Add(pStep_timeKey, toJson(getPStepTime(), "Integer", ""));
JsonString *pValueKey = new JsonString(L"value");
pJsonObject->Add(pValueKey, toJson(getPValue(), "IList", "array"));
return pJsonObject;
}
void picPunto::drawBox(QString posx, QString posy, QString width, QString height)
{
QPointF prevP, nextP;
prevP.setX(getPValue(posx));
prevP.setY(getPValue(posy));
nextP.setX(getPValue(posx)+getPValue(width));
nextP.setY(prevP.y());
currDoc->addLine(&prevP, &nextP);
prevP=nextP;
nextP.setY(prevP.y()+getPValue(height));
currDoc->addLine(&prevP, &nextP);
prevP=nextP;
nextP.setX(getPValue(posx));
currDoc->addLine(&prevP, &nextP);
prevP=nextP;
nextP.setY(getPValue(posy));
currDoc->addLine(&prevP, &nextP);
cnt++;
}
SEXP getExceptional( int *G_edges, int G_nnodes,
int M_Min_nnodes, int M_Max_nnodes,
int *NodeToClass, double *Pi, int NbrClasses,
double PValue, int Directed,
int &n_prot) {
//
// Get all occurrences of size k = M_nnodes
//
//
// Find all motif with size k
//
FindMotif find( StoreMode, 0);
FindMotif f( CountMode, 0);
vector<int*> *list;
SparseAdjacency G( G_edges, G_nnodes, true );
// G.print( "G");
SparseAdjacency H( G_edges, G_nnodes, ! Directed );
// H.print( "H");
SEXP S_ReturnList;
// All components are store even if they are NULL
PROTECT( S_ReturnList = allocVector( VECSXP,
M_Max_nnodes - M_Min_nnodes + 1)); n_prot++;
// Index in the Returned list
int i_k = 0;
/// Previous non NULL value of k index
int prev_k_index = -1;
for ( int k= M_Min_nnodes; k <= M_Max_nnodes; k++, i_k++) {
// To optimize the motifs
// int perm_0[k-1];
int *perm_0 = new int[k];
int *perm_1 = new int[k];
SEXP S_Result;
// Occurence list 'list' must be deallocated"
// Doesn't belong to 'find'
// TODO To improve
find.clearFoundList();
list = find.findAllMotifs( G, k );
S_Result = sort_m_mp_u( H, G_nnodes, k, list,
Pi, NodeToClass, NbrClasses,
0, -1,
PValue,
n_prot, false );
if ( S_Result != R_NilValue ) {
// Store k value
SEXP S_k;
PROTECT( S_k = allocVector( INTSXP, 1) ); n_prot++;
int *p_k = INTEGER_POINTER( S_k );
p_k[0] = k;
SEXP S_Struct;
PROTECT( S_Struct = allocVector( VECSXP, 2 )); n_prot++;;
SET_VECTOR_ELT( S_Struct, 0, S_k );
SET_VECTOR_ELT( S_Struct, 1, S_Result );
SET_VECTOR_ELT( S_ReturnList, i_k, S_Struct );
SEXP S_Adj_1 = VECTOR_ELT( S_Result, 0 );
int MotifNbr_1 = LENGTH( S_Adj_1 );
// Skip First motif
// if ( prev_k_index != -1 ) {
for ( int k_index = 0; k_index <= (prev_k_index); k_index++ ) {
SEXP S_k_value = VECTOR_ELT(
VECTOR_ELT( S_ReturnList,
k_index ),
0 );
int prev_k_value = INTEGER_POINTER( S_k_value ) [0];
// Get Adjacency matrix with i-1 nodes
SEXP S_Adj_0 = VECTOR_ELT(
VECTOR_ELT(
VECTOR_ELT( S_ReturnList,
k_index ),
1 ),
0);
// Get M_list
SEXP S_m_0 = VECTOR_ELT(
VECTOR_ELT(
VECTOR_ELT( S_ReturnList,
k_index ),
1 ),
1);
int MotifNbr_0 = LENGTH( S_Adj_0 );
for(int m = 0; m < MotifNbr_0; m++ ) {
// Test NULL SEXP
if( VECTOR_ELT(S_Adj_0, m) != R_NilValue ) {
// int debug = LENGTH( VECTOR_ELT(S_Adj_0, m) );
int *adj_0 = INTEGER_POINTER( VECTOR_ELT(S_Adj_0, m) );
// printList( "canonic ", adj_0, adj_0+ (k-1)*(k-1), " ", true);
SparseAdjacency motif0( adj_0, prev_k_value, "dense", (Directed == 0) );
SparseAdjacency motif0_canon( motif0 );
motif0.optimizeConnexity( perm_0 );
// motif0.print( "motif opt 0" );
// printList( " perm 0 ", perm_0, perm_0 + (k-1), true );
// Number of Del class
SEXP S_m_mp_0 = VECTOR_ELT( S_m_0, m );
int m_mp_len_0 = LENGTH( S_m_mp_0 );
int *del_class_0 = new int[ m_mp_len_0 ];
// get the first node ID of the del class
getDelClassNode( S_m_mp_0, m_mp_len_0, del_class_0 );
// printList( "Del class 0 ", del_class_0,
// del_class_0 + m_mp_len_0, " ", true);
// Get Degree of delete node
// int deg_in_0 = 0;
// int deg_out_0 = 0;
for(int p = 0; p < MotifNbr_1; p++ ) {
// Test NULL SEXP
if( VECTOR_ELT(S_Adj_1, p) != R_NilValue ) {
// int debug_1 = LENGTH( VECTOR_ELT(S_Adj_1, p) );
int *adj_1 = INTEGER_POINTER( VECTOR_ELT(S_Adj_1, p) );
#if ( MSG > 0 )
printList( "canonic 1 ", adj_1, adj_1 + (k)*(k), " ", true);
#endif
SparseAdjacency motif1( adj_1, k, "dense", (Directed == 0) );
SparseAdjacency motif1_canonic( motif1 );
motif1.optimizeConnexity( perm_1 );
// get M List
SEXP S_m_1 = VECTOR_ELT(
VECTOR_ELT(
VECTOR_ELT( S_ReturnList,
i_k ),
1 ),
1);
// Number of Del class
SEXP S_m_mp_1 = VECTOR_ELT( S_m_1, p );
int m_mp_len_1 = LENGTH( S_m_mp_1 ) ;
int *del_class_1 = new int [ m_mp_len_1 ];
// get the first node ID of the del class
getDelClassNode( S_m_mp_1, m_mp_len_1, del_class_1 );
// printList( "Del class 1 ", del_class_1,
// del_class_1 + m_mp_len_1, " ", true);
// printList( "canonic ", adj_0, adj_0 + (k-1)*(k-1), " ", true);
// printList( "canonic ", adj_1, adj_1 + (k)*(k), " ", true);
for( int del_0 = 0; del_0 < m_mp_len_0; del_0++) {
if( del_class_0[del_0] >= 0 ) {
// Get Degree of delete node
int deg_in_0 = 0;
int deg_out_0 = 0;
if ( Directed ) {
deg_in_0 = motif0_canon.getRowSize( del_class_0[ del_0 ] );
deg_out_0 = motif0_canon.getColSize( del_class_0[ del_0] );
} else {
deg_in_0 = motif0_canon.getAllRowSize( del_class_0[ del_0 ] );
}
for( int del_1 = 0; del_1 < m_mp_len_1; del_1++) {
if( del_class_1[ del_1 ] >= 0 ) {
if( getPValue( S_m_mp_1, del_1 ) <= PValue ) {
if( getPValue( S_m_mp_0, del_0 ) <= PValue ) {
// Get Degree of delete node
int deg_in_1 = 0;
int deg_out_1 = 0;
if ( Directed ) {
deg_in_1 = motif1_canonic.getRowSize( del_class_1[ del_1 ] );
deg_out_1 = motif1_canonic.getColSize( del_class_1[ del_1 ] );
} else {
deg_in_1 = motif1_canonic.getAllRowSize( del_class_1[ del_1 ] );
}
// cout << "del_0 :" << del_0 << ", del_1 :" << del_1 << endl;
if ( ( deg_in_0 == deg_in_1 ) && (deg_out_0 == deg_out_1 ) ) {
int *color_0 = new int [ prev_k_value ];
int *color_1 = new int [ k ];
for( int *ptr=color_0,
*ptr_end= color_0 + (prev_k_value);
ptr != ptr_end; ptr++ ) {
*ptr=0;
}
for( int *ptr=color_1, *ptr_end= color_1 + (k);
ptr != ptr_end; ptr++ ) {
*ptr=0;
}
color_0[ perm_0[ del_class_0[ del_0 ] ]] = 1;
color_1[ perm_1[ del_class_1[ del_1 ] ]] = 1;
// printList( " color_0 ", color_0,color_0+ (k-1), true);
// printList( " color_1 ", color_1,color_1+ (k), true);
bool incl = f.isExactlyIncluded( motif0, motif1, color_0, color_1 );
if( incl ) {
setMotifFilter( S_m_mp_1, del_1, 0, 1, m, del_class_0[ del_0 ] );
} else {
setMotifFilter( S_m_mp_1, del_1, 1, 0, 0, 0 );
}
// cout << "( k=" << k-1 << ", motif=" << m << ", del="
// << del_class_0[ del_0 ] << ") ";
// cout << "( k=" << k << ", motif=" << p << ", del="
// << del_class_1[ del_1 ] << ") : " << incl << endl ;
delete [] color_0;
delete [] color_1;
} else {
// Different degrees => over-represented
setMotifFilter( S_m_mp_1, del_1, 1, 0, 0, 0);
}
} else {
// Parent motif not over-represented
setMotifFilter( S_m_mp_1, del_1, 1, 0, 0, 0);
}
} else {
// motif not over-represented
setMotifFilter( S_m_mp_1, del_1, 0, 0, 0, 0);
}
} // Valid DelClass - if( del_class_1[del_1] >= 0 )
} // for( int del_1 = 0; ...
} // Valid DelClass - if( del_class_0[del_0] >= 0 )
} // for( int del_0 = 0; ...
delete [] del_class_1;
} // if( VECTOR_ELT(S_Adj_1, p) != R_NilValue ) {
} // for(int p = 0; p < MotifNbr_1; p++ )
delete [] del_class_0;
} // if( VECTOR_ELT(S_Adj_0, m) != R_NilValue ) {
} // for(int m = 0; m < MotifNbr_0; m++ ) {
}
if ( prev_k_index == -1 ) {
// First value of k
SEXP S_m_0 = VECTOR_ELT(
VECTOR_ELT(
VECTOR_ELT( S_ReturnList, i_k ),
1 ),
1);
int MotifNbr_0 = LENGTH( S_m_0 );
for(int m = 0; m < MotifNbr_0; m++ ) {
SEXP S_m_mp_0 = VECTOR_ELT( S_m_0, m );
if ( S_m_mp_0 != R_NilValue ) {
int m_mp_len_0 = LENGTH( S_m_mp_0 );
for( int del_0 = 0; del_0 < m_mp_len_0; del_0++) {
if ( VECTOR_ELT( S_m_mp_0, del_0) != R_NilValue ) {
if( getPValue( S_m_mp_0, del_0 ) < PValue ) {
setMotifFilter( S_m_mp_0, del_0, 1, 0, 0, 0);
} else {
setMotifFilter( S_m_mp_0, del_0, 0, 0, 0, 0);
}
}
}
}
} // for(int m = 0; m < MotifNbr_0; m++ )
}
prev_k_index = i_k;
} else {
// S_Result NULL
}
// for ( vector<int*>::iterator it = list->begin(),
// it_end=list->end();it != it_end; it++ ) {
// delete [] *it;
// }
FindMotif::deallocateFoundList( list );
delete [] perm_0;
delete [] perm_1;
}
return S_ReturnList;
}
