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; } } }