int SlaterDetBuilder::putDeterminant(xmlNodePtr cur, int firstIndex) {
string basisName("invalid");
string detname("NONE"), refname("NONE");
OhmmsAttributeSet aAttrib;
aAttrib.add(basisName,basisset_tag);
aAttrib.add(detname,"id");
aAttrib.add(refname,"ref");
aAttrib.put(cur);
xmlNodePtr c_ptr = NULL, o_ptr=NULL;
Det_t* adet=0;
//index of the last SlaterDeterminant
int dIndex=DetSet.size();
if(refname == "NONE") { //create one and use detname
if(detname =="NONE") { //no id is given, assign one
char newname[8];
sprintf(newname,"det%d",dIndex);
detname=newname;
}
}
map<string,SPOSetBasePtr>::iterator lit(SPOSet.find(detname));
SPOSetBasePtr psi;
if(lit == SPOSet.end()) {
#if defined(ENABLE_SMARTPOINTER)
psi.reset(myBasisSetFactory->createSPOSet(cur));
#else
psi = myBasisSetFactory->createSPOSet(cur);
#endif
psi->put(cur);
psi->checkObject();
SPOSet[detname]=psi;
} else {
psi = (*lit).second;
}
if(psi->getOrbitalSetSize()) {
map<string,Det_t*>::iterator dit(DetSet.find(detname));
if(dit == DetSet.end()) {
adet = new Det_t(psi,firstIndex);
adet->set(firstIndex,psi->getOrbitalSetSize());
DetSet[detname]=adet;
} else {
adet = (*dit).second;
}
firstIndex += psi->getOrbitalSetSize();
}
//only if a determinant is not 0
if(adet) SlaterDetSet.back()->add(adet);
return firstIndex;
}
bool validateGffRec(GffObj* gffrec, GList<GffObj>* gfnew) {
if (reftbl.Count()>0) { //check if we need to reject by ref seq filter
GStr refname(gffrec->getRefName());
RefTran* rt=reftbl.Find(refname.chars());
if (rt==NULL && refname.length()>2 && refname[-2]=='.' && isdigit(refname[-1])) {
//try removing the version suffix
refname.cut(-2);
//GMessage("[DEBUG] Trying ref name '%s'...\n", refname.chars());
rt=reftbl.Find(refname.chars());
}
if (rt) {
gffrec->setRefName(rt->new_name);
}
else return false; //discard, ref seq not in the given translation table
}
if (mRNAOnly && gffrec->isDiscarded()) {
//discard generic "locus" features with no other detailed subfeatures
//GMessage("Warning: discarding %s GFF generic gene/locus container %s\n",gffrec->getID());
return false;
}
if (rfltGSeq!=NULL) { //filter by gseqName
if (strcmp(gffrec->getGSeqName(),rfltGSeq)!=0) {
return false;
}
}
if (rfltStrand>0 && gffrec->strand !=rfltStrand) {
return false;
}
//check coordinates
if (rfltStart!=0 || rfltEnd!=MAX_UINT) {
if (rfltWithin) {
if (gffrec->start<rfltStart || gffrec->end>rfltEnd) {
return false; //not within query range
}
}
else {
if (gffrec->start>rfltEnd || gffrec->end<rfltStart) {
return false;
}
}
}
if (multiExon && gffrec->exons.Count()<=1) {
return false;
}
if (wCDSonly && gffrec->CDstart==0) {
return false;
}
if (ensembl_convert && startsWith(gffrec->getID(), "ENS")) {
//keep track of chr|gene_id data -- coordinate range
char* geneid=gffrec->getGeneID();
if (geneid!=NULL) {
GeneInfo* ginfo=gene_ids.Find(geneid);
if (ginfo==NULL) {//first time seeing this gene ID
GeneInfo* geneinfo=new GeneInfo(gffrec, ensembl_convert);
gene_ids.Add(geneid, geneinfo);
if (gfnew!=NULL)
gfnew->Add(geneinfo->gf); //FIXME: do I really need this?
}
else ginfo->update(gffrec);
}
}
return true;
}
void PeepsWindow::MessageReceived(BMessage *msg)
{
switch(msg->what)
{
case B_ABOUT_REQUESTED:
{
be_app->PostMessage(msg);
break;
}
case M_RUN_TOOL:
{
BString sig;
if(msg->FindString("signature",&sig)==B_OK)
{
if(strcmp(sig.String(),"application/x-vnd.wgp-PeopleMover")==0)
{
be_roster->Launch(sig.String());
break;
}
// Get the filename for the currently-selected person
int32 selection=fPeopleList->CurrentSelection();
if(selection<0)
break;
PeepsListItem *peepsitem=(PeepsListItem*)fPeopleList->ItemAt(selection);
if(!peepsitem || peepsitem->IsGroup())
break;
PersonItem *personitem=(PersonItem*)peepsitem;
PersonData *persondata=personitem->GetData();
if(!persondata)
break;
entry_ref ref=persondata->FileRef();
BPath path(&ref);
char *launchv[1];
launchv[0]=new char[255];
sprintf(launchv[0],"%s",path.Path());
be_roster->Launch(sig.String(),1,launchv,NULL);
delete [] launchv[0];
}
break;
}
case M_SHOW_ACTIONS:
{
uint32 buttons;
BPoint pt;
fPeopleList->GetMouse(&pt,&buttons,false);
pt.x=(pt.x>5)?pt.x-5:0;
pt.y=(pt.y>5)?pt.y-5:0;
fPeopleList->ShowContextMenu(fPeopleList->ConvertToScreen(pt));
break;
}
case M_BITMAP_REMOVED:
case M_PHOTO_MODIFIED:
{
fPeopleList->SaveImageData();
break;
}
case B_REFS_RECEIVED:
case B_SIMPLE_DATA:
{
entry_ref ref;
if(msg->FindRef("refs",0,&ref)==B_OK)
{
if(!IsPerson(ref))
{
// Might be an image dropped on the photo view. find out which child is the
// target
BPoint pt;
if(msg->FindPoint("_drop_offset",&pt)!=B_OK)
break;
BView *target=FindView(pt);
if(!target || strcmp(target->Name(),"photoview")!=0)
break;
// This will set the image, if possible
target->MessageReceived(msg);
// Save the image data to a real file and attach the Person attributes
// to it
fPeopleList->SaveImageData();
}
// Offer to move/copy file if not in People directory
BDirectory dir,peopledir("/boot/home/people");
BEntry entry(&ref);
entry.GetParent(&dir);
if(dir!=peopledir)
{
BString refname(ref.name);
BString errstr=TRANSLATE("%s is not currently stored in the People folder. Mr. Peeps! will not"
" see it on startup unless it is stored there. Would you like to move it"
" there?");
char errmsg[errstr.CountChars() - 2 + refname.CountChars() + 1];
sprintf(errmsg,errstr.String(),refname.String());
BAlert *alert=new BAlert("Mr. Peeps!",errmsg,TRANSLATE("Move"),TRANSLATE("Don't Move"));
if(alert->Go()==0)
{
entry.MoveTo(&peopledir);
entry.GetRef(&ref);
}
}
if(!SelectPerson(ref))
AddPerson(ref,true);
}
break;
}
case M_PREV_ITEM:
{
if(fPeopleList->CountItems()==0)
break;
int32 selection=fPeopleList->CurrentSelection();
if(!fPeopleList->IsFocus())
{
fPeopleList->MakeFocus(true);
PeepsListItem *pitem=(PeepsListItem*)fPeopleList->ItemAt(selection);
if(!pitem->IsGroup())
{
fPeopleList->SyncData((PersonItem*)pitem);
// fPeopleList->SaveData();
}
fPeopleList->SaveData();
}
if(selection>=0)
{
if(selection>0)
fPeopleList->Select(selection-1);
}
else
{
fPeopleList->Select(0L);
}
break;
}
case M_NEXT_ITEM:
{
if(fPeopleList->CountItems()==0)
break;
int32 selection=fPeopleList->CurrentSelection();
if(!fPeopleList->IsFocus())
{
fPeopleList->MakeFocus(true);
PeepsListItem *pitem=(PeepsListItem*)fPeopleList->ItemAt(selection);
if(!pitem->IsGroup())
{
fPeopleList->SyncData((PersonItem*)pitem);
// fPeopleList->SaveData();
}
fPeopleList->SaveData();
}
if(selection==fPeopleList->CountItems()-1 || selection<0)
fPeopleList->Select(fPeopleList->CountItems()-1);
else
fPeopleList->Select(selection+1);
break;
}
case M_MOD_DATA:
case M_SAVE:
{
fPeopleList->SyncData(NULL);
fPeopleList->SaveData();
break;
}
case M_ADD_PERSON:
{
entry_ref ref;
status_t stat=CreatePerson(&ref);
if(stat==B_FILE_EXISTS)
{
for(int32 i=0;i<gPeopleData.CountItems(); i++)
{
PersonData *pdata=(PersonData*)gPeopleData.ItemAt(i);
if(BString(TRANSLATE("New Person")).ICompare(pdata->Name())==0)
{
int32 selection=fPeopleList->CurrentSelection();
if(selection>=0)
{
PeepsListItem *peepsitem=(PeepsListItem*)fPeopleList->ItemAt(selection);
if(peepsitem && !peepsitem->IsGroup())
fPeopleList->Collapse(fPeopleList->Superitem(peepsitem));
}
PersonItem *pitem=pdata->InstanceAt(0);
GroupItem *gitem=(GroupItem*)fPeopleList->Superitem(pitem);
if(!gitem->IsExpanded())
fPeopleList->Expand(gitem);
fPeopleList->Select(fPeopleList->IndexOf(pitem));
fPeopleList->ScrollToSelection();
break;
}
}
}
else
{
// Add the current group to the New Person's file so that we end up staying
// in the current group.
if(stat==B_OK)
{
int32 selection=fPeopleList->CurrentSelection();
BString groupstr(TRANSLATE("Ungrouped"));
if(selection>=0)
{
PeepsListItem *currentitem=(PeepsListItem*)fPeopleList->ItemAt(selection);
if(currentitem->IsGroup())
groupstr=currentitem->Name();
else
groupstr=((PersonItem*)currentitem)->Group();
}
PersonData *pdata=new PersonData(ref);
pdata->SetGroup(groupstr.String());
pdata->SetName(TRANSLATE("New Person"));
pdata->SaveToFile();
delete pdata;
AddPerson(ref,true);
SortList();
SelectPerson(TRANSLATE("New Person"));
dataview->SetFirstFieldFocus();
}
}
break;
}
case M_DELETE_PERSON:
{
int32 selection=fPeopleList->CurrentSelection();
if(selection<0)
break;
PeepsListItem *item=(PeepsListItem*)fPeopleList->ItemAt(selection);
if(item->IsGroup())
DeleteGroup((GroupItem*)item);
else
{
DeletePerson(((PersonItem*)item)->GetData());
}
break;
}
case M_DISABLE_DELETE:
{
BMenuItem *item=fPeopleMenu->FindItem(TRANSLATE("Move To Trash"));
if(item)
item->SetEnabled(false);
break;
}
case M_ENABLE_DELETE:
{
BMenuItem *item=fPeopleMenu->FindItem(TRANSLATE("Move To Trash"));
if(item)
item->SetEnabled(true);
break;
}
case M_SET_LANGUAGE:
{
// Restart MrPeeps!
gRestartApp=true;
int32 language;
if(msg->FindInt32("index",&language)!=B_OK)
break;
BMenuItem *item = fLanguageMenu->ItemAt(language);
if(!item)
break;
fLocale = item->Label();
WriteLocaleSettings();
be_app->PostMessage(B_QUIT_REQUESTED);
break;
}
case M_HANDLE_NO_SELECTION:
{
// This is the initial case. No selection means quite a few different
// menu items are disabled.
fTabMenu->SetEnabled(false);
fEditMenu->SetEnabled(false);
if(fToolPeopleAtAGlance)
fToolPeopleAtAGlance->SetEnabled(false);
if(fToolVCardExport)
fToolVCardExport->SetEnabled(false);
UpdateActions(true);
break;
}
case M_HANDLE_GROUP_SELECTION:
{
// This is the initial case. No selection means quite a few different
// menu items are disabled.
fTabMenu->SetEnabled(false);
fEditMenu->SetEnabled(true);
if(fToolPeopleAtAGlance)
fToolPeopleAtAGlance->SetEnabled(false);
if(fToolVCardExport)
fToolVCardExport->SetEnabled(false);
UpdateActions(true);
break;
}
case M_HANDLE_PERSON_SELECTION:
{
// This is the initial case. No selection means quite a few different
// menu items are disabled.
fTabMenu->SetEnabled(true);
fEditMenu->SetEnabled(true);
if(fToolPeopleAtAGlance)
fToolPeopleAtAGlance->SetEnabled(true);
if(fToolVCardExport)
fToolVCardExport->SetEnabled(true);
UpdateActions(false);
break;
}
case M_SEND_PERSONAL_EMAIL:
{
if(dataview->Email())
{
BMessage *emailmsg=new BMessage(M_SEND_EMAIL);
emailmsg->AddString("address",dataview->Email());
be_app->PostMessage(emailmsg);
}
break;
}
case M_SEND_WORK_EMAIL:
{
if(dataview->WorkEmail())
{
BMessage *emailmsg=new BMessage(M_SEND_EMAIL);
emailmsg->AddString("address",dataview->WorkEmail());
be_app->PostMessage(emailmsg);
}
break;
}
case M_SEND_ALT_EMAIL:
{
if(dataview->Email3())
{
BMessage *emailmsg=new BMessage(M_SEND_EMAIL);
emailmsg->AddString("address",dataview->Email3());
be_app->PostMessage(emailmsg);
}
break;
}
case M_BROWSE_WWW_HOME:
{
if(dataview->URL())
{
BMessage *wwwmsg=new BMessage(M_LAUNCH_BROWSER);
wwwmsg->AddString("address",dataview->URL());
be_app->PostMessage(wwwmsg);
}
break;
}
case M_BROWSE_WWW_WORK:
{
if(dataview->WorkURL())
{
BMessage *wwwmsg=new BMessage(M_LAUNCH_BROWSER);
wwwmsg->AddString("address",dataview->WorkURL());
be_app->PostMessage(wwwmsg);
}
break;
}
case M_BROWSE_WWW_ALT:
{
if(dataview->OtherURL())
{
BMessage *wwwmsg=new BMessage(M_LAUNCH_BROWSER);
wwwmsg->AddString("address",dataview->OtherURL());
be_app->PostMessage(wwwmsg);
}
break;
}
case M_TAB_1:
{
fPeopleList->SyncData();
fPeopleList->SaveData();
dataview->ShowTab(0);
if(!fPeopleList->IsFocus())
dataview->SetFirstFieldFocus();
break;
}
case M_TAB_2:
{
fPeopleList->SyncData();
fPeopleList->SaveData();
dataview->ShowTab(1);
if(!fPeopleList->IsFocus())
dataview->SetFirstFieldFocus();
break;
}
case M_TAB_3:
{
fPeopleList->SyncData();
fPeopleList->SaveData();
dataview->ShowTab(2);
if(!fPeopleList->IsFocus())
dataview->SetFirstFieldFocus();
break;
}
case M_TAB_4:
{
fPeopleList->SyncData();
fPeopleList->SaveData();
dataview->ShowTab(3);
if(!fPeopleList->IsFocus())
dataview->SetFirstFieldFocus();
break;
}
case M_TAB_5:
{
fPeopleList->SyncData();
fPeopleList->SaveData();
dataview->ShowTab(4);
if(!fPeopleList->IsFocus())
dataview->SetFirstFieldFocus();
break;
}
case M_UNDO:
{
dataview->UndoField();
break;
}
case M_CUT:
{
dataview->CutField();
break;
}
case M_COPY:
{
dataview->CopyField();
break;
}
case M_PASTE:
{
dataview->PasteField();
break;
}
case B_NODE_MONITOR:
{
HandleNodeMonitoring(msg);
break;
}
default:
{
BWindow::MessageReceived(msg);
break;
}
}
}
