static void domainsPrint(struct section *section,
struct sqlConnection *conn, char *geneId)
/* Print out protein domains. */
{
char *db = sqlGetDatabase(conn);
struct slName *el, *list;
list = spExtDbAcc1List(spConn, swissProtAcc, "Interpro");
if (list != NULL)
{
char query[256], **row, **row2;
struct sqlResult *sr, *sr2;
hPrintf("<B>InterPro Domains: </B> ");
hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/protein/%s\" TARGET=_blank>",
swissProtAcc);
hPrintf("Graphical view of domain structure</A><BR>");
sqlSafef(query, sizeof(query),
"select extAcc1,extAcc2 from extDbRef,extDb"
" where extDbRef.acc = '%s'"
" and extDb.val = 'Interpro' and extDb.id = extDbRef.extDb"
, swissProtAcc);
sr = sqlGetResult(spConn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
//hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/entry/%s\" TARGET=_blank>", row[0]);
//hPrintf("%s</A> - %s<BR>\n", row[0], row[1]);
char interPro[256];
char *pdb = hPdbFromGdb(db);
safef(interPro, 128, "%s.interProXref", pdb);
if (hTableExists(db, interPro))
{
sqlSafef(query, sizeof(query),
"select description from %s where accession = '%s' and interProId = '%s'",
interPro, swissProtAcc, row[0]);
sr2 = sqlGetResult(conn, query);
if ((row2 = sqlNextRow(sr2)) != NULL)
{
hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/entry/%s\" TARGET=_blank>", row[0]);
hPrintf("%s</A> - %s <BR>\n", row[0], row2[0]);
}
sqlFreeResult(&sr2);
}
else
{
hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/entry/%s\" TARGET=_blank>", row[0]);
hPrintf("%s</A> - %s<BR>\n", row[0], row[1]);
}
}
hPrintf("<BR>\n");
slFreeList(&list);
}
if (kgVersion == KG_III)
{
/* Do Pfam domains here. */
list = getPfamDomainList(conn, geneId);
if (list != NULL)
{
hPrintf("<B>Pfam Domains:</B><BR>");
for (el = list; el != NULL; el = el->next)
{
char query[256];
char *description;
sqlSafef(query, sizeof(query),
"select description from pfamDesc where pfamAC='%s'", el->name);
description = sqlQuickString(conn, query);
if (description == NULL)
description = cloneString("n/a");
hPrintf("<A HREF=\"http://pfam.xfam.org/family?acc=%s\" TARGET=_blank>",
el->name);
hPrintf("%s</A> - %s<BR>\n", el->name, description);
freez(&description);
}
slFreeList(&list);
hPrintf("<BR>\n");
}
/* Do SCOP domains here */
list = getDomainList(conn, geneId, "Scop");
if (list != NULL)
{
hPrintf("<B>SCOP Domains:</B><BR>");
for (el = list; el != NULL; el = el->next)
{
char query[256];
char *description;
sqlSafef(query, sizeof(query),
"select description from scopDesc where acc='%s'", el->name);
description = sqlQuickString(conn, query);
if (description == NULL)
description = cloneString("n/a");
hPrintf("<A HREF=\"http://scop.berkeley.edu/sunid=%s\" TARGET=_blank>",
el->name);
hPrintf("%s</A> - %s<BR>\n", el->name, description);
freez(&description);
}
slFreeList(&list);
hPrintf("<BR>\n");
}
}
else
{
list = spExtDbAcc1List(spConn, swissProtAcc, "Pfam");
if (list != NULL)
{
char *pfamDescSql = genomeSetting("pfamDescSql");
hPrintf("<B>Pfam Domains:</B><BR>");
for (el = list; el != NULL; el = el->next)
{
char query[256];
char *description;
sqlSafef(query, sizeof(query), pfamDescSql, el->name);
description = sqlQuickString(conn, query);
if (description == NULL)
description = cloneString("n/a");
hPrintf("<A HREF=\"http://pfam.xfam.org/family?acc=%s\" TARGET=_blank>",
el->name);
hPrintf("%s</A> - %s<BR>\n", el->name, description);
freez(&description);
}
slFreeList(&list);
hPrintf("<BR>\n");
}
}
list = spExtDbAcc1List(spConn, swissProtAcc, "PDB");
if (list != NULL)
{
struct sqlConnection *conn2 = sqlConnect(db);
char query[256], **row;
struct sqlResult *sr;
int column = 0, maxColumn=3, rowCount=0;
hPrintf("<B>Protein Data Bank (PDB) 3-D Structure</B><BR>");
sqlSafef(query, sizeof(query),
"select extAcc1,extAcc2 from extDbRef,extDb"
" where extDbRef.acc = '%s'"
" and extDb.val = 'PDB' and extDb.id = extDbRef.extDb"
, swissProtAcc);
sr = sqlGetResult(spConn, query);
hPrintf("<TABLE><TR>\n");
while ((row = sqlNextRow(sr)) != NULL)
{
if (++column > maxColumn)
{
hPrintf("</TR><TR>");
column = 1;
if (rowCount == 0)
{
hPrintf("<TD ALIGN=CENTER COLSPAN=4><I>To conserve bandwidth, only the images from the first %d structures are shown.</I>", maxColumn);
hPrintf("</TR><TR>");
}
++rowCount;
}
hPrintf("<TD>");
hPrintf("<A HREF=\"http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=%s\" TARGET=_blank>", row[0]);
if (rowCount < 1)
hPrintf("<IMG SRC=\"http://www.rcsb.org/pdb/images/%s_asym_r_250.jpg\"><BR>", row[0]);
hPrintf("%s</A> - %s ", row[0], row[1]);
// include links LS-SNP and to launch viewer in PDB chimera
struct tempName chimerax;
lsSnpPdbChimeraSnpAnn(conn, row[0], NULL, &chimerax);
hPrintf(" <A HREF=\"%s\">Chimera</A>", chimerax.forHtml);
if (lsSnpPdbHasPdb(conn2, row[0]))
hPrintf(" <A HREF=\"%s\" TARGET=_blank>LS-SNP</A>", lsSnpPdbGetUrlPdbSnp(row[0], NULL));
hPrintf("</TD>\n");
}
hPrintf("</TR></TABLE>\n");
hPrintf("<A href=\"../goldenPath/help/chimera.html\" TARGET=_blank>Chimera help</A>\n");
hPrintf("<BR><BR>\n");
slFreeList(&list);
sqlDisconnect(&conn2);
}
/* Do modBase link. */
{
hPrintf("<B>ModBase Predicted Comparative 3D Structure on ");
modBaseAnchor(swissProtAcc);
hPrintf("%s", swissProtAcc);
hPrintf("</A></B><BR>\n");
hPrintf("<TABLE><TR>");
hPrintf("<TD>");
modBaseAnchor(swissProtAcc);
hPrintf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s\"></A></TD>", swissProtAcc);
hPrintf("<TD>");
modBaseAnchor(swissProtAcc);
hPrintf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s&axis=x°ree=90\"></A></TD>", swissProtAcc);
hPrintf("<TD>");
modBaseAnchor(swissProtAcc);
hPrintf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s&axis=y°ree=90\"></A></TD>", swissProtAcc);
hPrintf("</TR><TR>\n");
hPrintf("<TD ALIGN=CENTER>Front</TD>");
hPrintf("<TD ALIGN=CENTER>Top</TD>");
hPrintf("<TD ALIGN=CENTER>Side</TD>");
hPrintf("</TR></TABLE>\n");
hPrintf("<I>The pictures above may be empty if there is no "
"ModBase structure for the protein. The ModBase structure "
"frequently covers just a fragment of the protein. You may "
"be asked to log onto ModBase the first time you click on the "
"pictures. It is simplest after logging in to just click on "
"the picture again to get to the specific info on that model.</I>");
}
}
void GeomData::mappingNodesIds(pMesh theMesh){
int ndom = getNumDomains();
const int* domainList = getDomainList();
std::map<int,int> mapIDtoIndex, mapBdryIDtoIndex, mapIDtoIndex_global;
std::set<int> setID, setBdryID;
int i, j, k, id, id0, id1;
pEntity node, edge, face, tetra;
i = 0;
// set a sequential numbering for each vertex ID: from 0 to n-1, where n is the number of vertices
VIter vit = M_vertexIter(theMesh);
while ( (node=VIter_next(vit))){
mapIDtoIndex_global[EN_id(node)] = i++;
}
VIter_delete(vit);
pEntity v1,v2,v3;
bool extElem = true;// PERFORME ONLY ONCE
// STEP1: get all vertices ID from domain "dom" and its boundary.
// All IDs are stored into setID and setBdryID set containers.
for (k=0; k<ndom; k++){
int dom = domainList[k];
if (dim==2){
FIter fit = M_faceIter(theMesh);
while ( (face=FIter_next(fit) )){
int faceflag = getFaceFlag(face);
if (faceflag==domainList[k]){
for(i=0; i<3; i++){
setID.insert( EN_id(face->get(0,i)) ); // nodes domain
}
for(i=0; i<3; i++){
if (getVertexFlag(face->get(0,i))!=faceflag){
setBdryID.insert(EN_id(face->get(0,i))); // boundary nodes
}
}
}
}
FIter_delete(fit);
}
else{
RIter rit = M_regionIter(theMesh);
while ( (tetra = RIter_next(rit) )){
int tetraflag = getTetraFlag(tetra);
if (tetraflag==domainList[k]){
for(i=0; i<4; i++){
setID.insert( EN_id(tetra->get(0,i)) ); // nodes domain
}
for(i=0; i<4; i++){
if (getVertexFlag(tetra->get(0,i))!=tetraflag){
setBdryID.insert(EN_id(tetra->get(0,i))); // boundary nodes
}
}
}
}
RIter_delete(rit);
}
// get external boundary edges/faces only: It's for saturation gradient calculation
if (extElem){
i = 0;
if (dim==2){
EIter eit = M_edgeIter(theMesh);
while ( (edge=EIter_next(eit)) ){
/* ONLY EXTERNAL EDGES */
if (E_numFaces(edge)==1){
v1 = edge->get(0,0);
v2 = edge->get(0,1);
external_bdry_elem[0].setValue(i,0,mapIDtoIndex_global[EN_id(v1)]);
external_bdry_elem[0].setValue(i,1,mapIDtoIndex_global[EN_id(v2)]);
external_bdry_elem[0].setValue(i,2,GEN_tag(v1->getClassification()));
external_bdry_elem[0].setValue(i,3,GEN_tag(v2->getClassification()));
i++;
}
}
EIter_delete(eit);
}
else{
FIter fit = M_faceIter(theMesh);
while ( (face = FIter_next(fit)) ){
/* ONLY EXTERNAL FACES */
if ( F_numRegions(face)==1 ){
v1 = face->get(0,0);
v2 = face->get(0,1);
v3 = face->get(0,2);
external_bdry_elem[0].setValue(i,0,mapIDtoIndex_global[EN_id(v1)]);
external_bdry_elem[0].setValue(i,1,mapIDtoIndex_global[EN_id(v2)]);
external_bdry_elem[0].setValue(i,2,mapIDtoIndex_global[EN_id(v3)]);
external_bdry_elem[0].setValue(i,3,GEN_tag(v1->getClassification()));
external_bdry_elem[0].setValue(i,4,GEN_tag(v2->getClassification()));
external_bdry_elem[0].setValue(i,5,GEN_tag(v3->getClassification()));
i++;
}
}
FIter_delete(fit);
}
extElem = false;
}
// STEP2: map IDs from step1 like this:
// id0 = 0;
// id1 = 1;
// id2 = 2;
// ...
// idn = n;
if (setID.size() > this->getNumNodesPerDomain(k)){
char msg[256]; sprintf(msg,"NUmber of elements collected [%d] is greater than the max [%d]",(int)setID.size(),this->getNumNodesPerDomain(k));
throw Exception(__LINE__,__FILE__,msg);
}
// domain
i = 0;
pVertex node;
for (std::set<int>::iterator iter=setID.begin(); iter!= setID.end(); iter++){
int id = *iter; // vertex ID
mapIDtoIndex[id] = i; // gives a sequential numbering (0,1,2,...) for all vertices ID for domain k
ID[k].setValue(i,id);
node = theMesh->getVertex(id);
volume[k].setValue(i,getVolume(node,dom) );
nodes[k].setValue(i,mapIDtoIndex_global[id]);
i++;
}
setID.clear();
// boundary
i = 0;
for (std::set<int>::iterator iter=setBdryID.begin(); iter!= setBdryID.end(); iter++){
int id = *iter; // boundary vertex ID
mapBdryIDtoIndex[id] = i; // gives a sequential numbering (0,1,2,...) for all boundary vertices ID for domain k
ID_bdry[k].setValue(i,id);
node = theMesh->getVertex(id);
volume_bdry[k].setValue(i,getVolume(node,dom) );
i++;
}
setBdryID.clear();
// STEP3: use mapped ID to initialize edge struct, where:
// edge_id0 = index_mapped
// edge_id1 = index_mapped
// ALL EDGES
i = 0;
EIter eit = M_edgeIter(theMesh);
while ( (edge=EIter_next(eit)) ){
if ( edgeBelongToDomain(edge,domainList[k]) ){
v1 = edge->get(0,0);
v2 = edge->get(0,1);
id0 = EN_id( v1 );
id1 = EN_id( v2 );
edges[k].setValue(i,0,mapIDtoIndex[id0]); // index number for vertex ID for domain k
edges[k].setValue(i,1,mapIDtoIndex[id1]); // index number for vertex ID for domain k
edges[k].setValue(i,2,mapIDtoIndex_global[id0]); // global index number for vertex ID
edges[k].setValue(i,3,mapIDtoIndex_global[id1]); // global index number for vertex ID
edges[k].setValue(i,4,GEN_tag(v1->getClassification()));
edges[k].setValue(i,5,GEN_tag(v2->getClassification()));
i++;
}
}
if (!i){
throw Exception(__LINE__,__FILE__,"Any edge detected!");
}
i = 0;
bool bdryElem_detected = false;
if (dim==2){
// BOUNDARY EDGES PER DOMAIN
eit = M_edgeIter(theMesh);
while ( (edge=EIter_next(eit)) ){
if ( edgeBelongToDomain(edge,domainList[k]) ){
if (belongsToBoundary(edge)){
bdryElem_detected = true;
for (j=0;j<2;j++){
id = EN_id( edge->get(0,j) );
edges_bdry[k].setValue(i,j,mapBdryIDtoIndex[id]); // index number for boundary vertex ID for domain k
edges_bdry[k].setValue(i,j+2,mapIDtoIndex[id]); // index number for vertex ID for domain k
edges_bdry[k].setValue(i,j+4,mapIDtoIndex_global[id]); // global index number for vertex ID
}
i++;
}
}
}
}
else{
// BOUNDARY FACES PER DOMAIN
FIter fit = M_faceIter(theMesh);
while ( (face = FIter_next(fit)) ){
if ( faceBelongToDomain(face,domainList[k]) ){
if ( belongsToBoundary(face) ){
bdryElem_detected = true;
for (j=0;j<3;j++){
id = EN_id( face->get(0,j) );
faces_bdry[k].setValue(i,j,mapBdryIDtoIndex[id]); // index number for boundary vertex ID for domain k
faces_bdry[k].setValue(i,j+3,mapIDtoIndex[id]); // index number for vertex ID for domain k
faces_bdry[k].setValue(i,j+6,mapIDtoIndex_global[id]); // global index number for vertex ID
}
i++;
}
}
}
FIter_delete(fit);
if (!bdryElem_detected){
throw Exception(__LINE__,__FILE__,"Any boundary element detected! You must use Physical command in .geo Gmsh to define them.");
}
}
mapBdryIDtoIndex.clear();
mapIDtoIndex.clear();
}
mapIDtoIndex_global.clear();
}
static std::error_code loadTrigger(ExecState& exec, const JSObject& ruleObject, Trigger& trigger)
{
VM& vm = exec.vm();
auto scope = DECLARE_THROW_SCOPE(vm);
const JSValue triggerObject = ruleObject.get(&exec, Identifier::fromString(&exec, "trigger"));
if (!triggerObject || scope.exception() || !triggerObject.isObject())
return ContentExtensionError::JSONInvalidTrigger;
const JSValue urlFilterObject = triggerObject.get(&exec, Identifier::fromString(&exec, "url-filter"));
if (!urlFilterObject || scope.exception() || !urlFilterObject.isString())
return ContentExtensionError::JSONInvalidURLFilterInTrigger;
String urlFilter = urlFilterObject.toWTFString(&exec);
if (urlFilter.isEmpty())
return ContentExtensionError::JSONInvalidURLFilterInTrigger;
trigger.urlFilter = urlFilter;
const JSValue urlFilterCaseValue = triggerObject.get(&exec, Identifier::fromString(&exec, "url-filter-is-case-sensitive"));
if (urlFilterCaseValue && !scope.exception() && urlFilterCaseValue.isBoolean())
trigger.urlFilterIsCaseSensitive = urlFilterCaseValue.toBoolean(&exec);
const JSValue resourceTypeValue = triggerObject.get(&exec, Identifier::fromString(&exec, "resource-type"));
if (!scope.exception() && resourceTypeValue.isObject()) {
auto typeFlagsError = getTypeFlags(exec, resourceTypeValue, trigger.flags, readResourceType);
if (typeFlagsError)
return typeFlagsError;
} else if (!resourceTypeValue.isUndefined())
return ContentExtensionError::JSONInvalidTriggerFlagsArray;
const JSValue loadTypeValue = triggerObject.get(&exec, Identifier::fromString(&exec, "load-type"));
if (!scope.exception() && loadTypeValue.isObject()) {
auto typeFlagsError = getTypeFlags(exec, loadTypeValue, trigger.flags, readLoadType);
if (typeFlagsError)
return typeFlagsError;
} else if (!loadTypeValue.isUndefined())
return ContentExtensionError::JSONInvalidTriggerFlagsArray;
const JSValue ifDomain = triggerObject.get(&exec, Identifier::fromString(&exec, "if-domain"));
if (!scope.exception() && ifDomain.isObject()) {
auto ifDomainError = getDomainList(exec, asObject(ifDomain), trigger.domains);
if (ifDomainError)
return ifDomainError;
if (trigger.domains.isEmpty())
return ContentExtensionError::JSONInvalidDomainList;
ASSERT(trigger.domainCondition == Trigger::DomainCondition::None);
trigger.domainCondition = Trigger::DomainCondition::IfDomain;
} else if (!ifDomain.isUndefined())
return ContentExtensionError::JSONInvalidDomainList;
const JSValue unlessDomain = triggerObject.get(&exec, Identifier::fromString(&exec, "unless-domain"));
if (!scope.exception() && unlessDomain.isObject()) {
if (trigger.domainCondition != Trigger::DomainCondition::None)
return ContentExtensionError::JSONUnlessAndIfDomain;
auto unlessDomainError = getDomainList(exec, asObject(unlessDomain), trigger.domains);
if (unlessDomainError)
return unlessDomainError;
if (trigger.domains.isEmpty())
return ContentExtensionError::JSONInvalidDomainList;
trigger.domainCondition = Trigger::DomainCondition::UnlessDomain;
} else if (!unlessDomain.isUndefined())
return ContentExtensionError::JSONInvalidDomainList;
return { };
}
