cdd_annot_dialog.cpp

ncbi源码

            throw "no MMDB ID found in annotation";
        int mmdbID = annot.GetId().front()->GetMmdb_id().Get();

        // map object to aligned molecule ID and interval of alignment on that chain
        typedef map < const StructureObject * , ChainInfo > ObjectMap;
        ObjectMap annotObjects;

        // first find all objects with the annotation's mmdbID; fill out chain id and interval
        const BlockMultipleAlignment *alignment = set->alignmentManager->GetCurrentMultipleAlignment();
        if (!alignment) throw "no alignment";
        BlockMultipleAlignment::UngappedAlignedBlockList alignedBlocks;
        alignment->GetUngappedAlignedBlocks(&alignedBlocks);
        if (alignedBlocks.size() == 0) throw "no aligned blocks";
        for (int row=0; row<alignment->NRows(); ++row) {
            const StructureObject *object;
            const Sequence *seq = alignment->GetSequenceOfRow(row);
            if (!seq->molecule || seq->molecule->identifier->mmdbID != mmdbID ||
                !seq->molecule->GetParentOfType(&object))
                continue;
            ChainInfo& ci = annotObjects[object];
            ci.alignedMoleculeID = seq->molecule->id;
            ci.from = alignedBlocks.front()->GetRangeOfRow(row)->from;
            ci.to = alignedBlocks.back()->GetRangeOfRow(row)->to;
            ci.hits = 0;
        }
        if (annotObjects.size() == 0)
            throw "no chain of annotation's MMDB ID in the alignment";

        GlobalMessenger()->RemoveAllHighlights(true);
        CCn3d_style_settings globalStyleSettings;
        set->styleManager->GetGlobalStyle().SaveSettingsToASN(&globalStyleSettings);

        // iterate over molecule/residue intervals
        if (annot.GetFeatures().size() > 0 &&
            annot.GetFeatures().front()->GetFeatures().size() > 0 &&
            annot.GetFeatures().front()->GetFeatures().front()->IsSetLocation() &&
            annot.GetFeatures().front()->GetFeatures().front()->GetLocation().IsSubgraph() &&
            annot.GetFeatures().front()->GetFeatures().front()->GetLocation().
                GetSubgraph().IsResidues() &&
            annot.GetFeatures().front()->GetFeatures().front()->GetLocation().
                GetSubgraph().GetResidues().IsInterval() &&
            annot.GetFeatures().front()->GetFeatures().front()->GetLocation().
                GetSubgraph().GetResidues().GetInterval().size() > 0)
        {

            ObjectMap::iterator o, oe = annotObjects.end();
            CResidue_pntrs::TInterval::const_iterator i, ie =
                annot.GetFeatures().front()->GetFeatures().front()->GetLocation().
                    GetSubgraph().GetResidues().GetInterval().end();
            for (i=annot.GetFeatures().front()->GetFeatures().front()->GetLocation().
                    GetSubgraph().GetResidues().GetInterval().begin(); i!=ie; ++i)
            {
                // for each object
                for (o=annotObjects.begin(); o!=oe; ++o) {

                    // find molecule with annotation's moleculeID
                    ChemicalGraph::MoleculeMap::const_iterator
                        m = o->first->graph->molecules.find((*i)->GetMolecule_id().Get());
                    if (m == o->first->graph->molecules.end())
                        throw "molecule with annotation's specified molecule ID not found in object";

                        // make sure this stuff is visible in global style
                        if (m->second->IsProtein()) {
                            if (globalStyleSettings.GetProtein_backbone().GetType() == eCn3d_backbone_type_off &&
                                !globalStyleSettings.GetProtein_sidechains().GetIs_on())
                            {
                                globalStyleSettings.SetProtein_backbone().SetType(eCn3d_backbone_type_trace);
                            }
                        } else if (m->second->IsNucleotide()) {
                            if (globalStyleSettings.GetNucleotide_backbone().GetType() == eCn3d_backbone_type_off &&
                                !globalStyleSettings.GetNucleotide_sidechains().GetIs_on())
                            {
                                globalStyleSettings.SetNucleotide_backbone().SetType(eCn3d_backbone_type_trace);
                            }
                        } else if (m->second->IsSolvent()) {
                            globalStyleSettings.SetSolvents().SetIs_on(true);
                        } else if (m->second->IsHeterogen()) {
                            globalStyleSettings.SetHeterogens().SetIs_on(true);
                        }

                        for (int r=(*i)->GetFrom().Get(); r<=(*i)->GetTo().Get(); ++r) {
                        // highlight residues in interval
                        if (o == annotObjects.begin()) {
                            if (r >= 1 && r <= m->second->NResidues())
                                GlobalMessenger()->ToggleHighlight(m->second, r);
                            else
                                throw "annotation's residue ID out of molecule's residue range";
                        }

                        // count hits of annotated residues in aligned chain+interval
                        if (o->second.alignedMoleculeID == m->second->id &&
                                r >= o->second.from && r <= o->second.to)
                            (o->second.hits)++;
                    }
                }
            }

            set->styleManager->SetGlobalStyle(globalStyleSettings);

            // return object with most hits of annotation to aligned chain region
            const StructureObject *bestObject = NULL;
            for (o=annotObjects.begin(); o!=oe; ++o)
                if (!bestObject || o->second.hits > annotObjects[bestObject].hits)
                    bestObject = o->first;
            return bestObject;

        } else
            throw "unrecognized annotation structure";

    } catch (const char *err) {
        ERRORMSG("HighlightResidues() - " << err);
    }
    return NULL;
}

void CDDAnnotateDialog::ShowEvidence(void)
{
    // get selected evidence
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(evids, ID_L_EVID, wxListBox)
    if (evids->GetCount() == 0 || evids->GetSelection() < 0) return;
    CFeature_evidence *selectedEvidence =
        reinterpret_cast<CFeature_evidence*>(evids->GetClientData(evids->GetSelection()));
    if (!selectedEvidence) {
        ERRORMSG("CDDAnnotateDialog::ShowEvidence() - error getting evidence pointer");
        return;
    }

    // launch URL given PMID
    if (selectedEvidence->IsReference() && selectedEvidence->GetReference().IsPmid()) {
        wxString url;
        url.Printf("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?"
            "cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=%i",
            selectedEvidence->GetReference().GetPmid().Get());
        LaunchWebPage(url);
    }

    // highlight residues if structure evidence
    else if (IS_STRUCTURE_EVIDENCE_BSANNOT(*selectedEvidence)) {
        const StructureObject *bestObject = HighlightResidues(structureSet, selectedEvidence->GetBsannot());
        if (bestObject) {

            // first, set show/hide to make only objects of this mmdb id visible
            structureSet->showHideManager->MakeAllVisible();
            StructureSet::ObjectList::const_iterator o, oe = structureSet->objects.end();
            for (o=structureSet->objects.begin(); o!=oe; ++o)
                if ((*o)->mmdbID != bestObject->mmdbID)
                    structureSet->showHideManager->Show(*o, false);
            // now force redrawing of structures, so the frames that contains
            // these objects aren't empty (otherwise, renderer won't show selected frame)
            GlobalMessenger()->ProcessRedraws();

            // now show the frame containing the "best" object (get display list from first molecule)
            unsigned int displayList = bestObject->graph->molecules.find(1)->second->displayLists.front();
            for (int frame=0; frame<structureSet->frameMap.size(); ++frame) {
                StructureSet::DisplayLists::const_iterator d, de = structureSet->frameMap[frame].end();
                for (d=structureSet->frameMap[frame].begin(); d!=de; ++d) {
                    if (*d == displayList) { // is display list in this frame?
                        structureSet->renderer->ShowFrameNumber(frame);
                        frame = structureSet->frameMap.size(); // to exit out of next-up loop
                        break;
                    }
                }
            }

            wxMessageBox(
                selectedEvidence->GetBsannot().GetFeatures().front()->GetDescr().front()->GetName().c_str(),
                "Structure Evidence", wxOK | wxCENTRE, this);
        }
    }

    else if (selectedEvidence->IsComment()) {
        wxMessageBox(selectedEvidence->GetComment().c_str(), "Comment", wxOK | wxCENTRE, this);
    }

    else {
        ERRORMSG("CDDAnnotateDialog::ShowEvidence() - can't show that evidence type");
    }
}

void CDDAnnotateDialog::MoveEvidence(bool moveUp)
{
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(annots, ID_L_ANNOT, wxListBox)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(evids, ID_L_EVID, wxListBox)

    // get selected annotation
    if (annots->GetCount() == 0 || annots->GetSelection() < 0) return;
    CAlign_annot *selectedAnnot =
        reinterpret_cast<CAlign_annot*>(annots->GetClientData(annots->GetSelection()));
    if (!selectedAnnot) {
        ERRORMSG("CDDAnnotateDialog::MoveEvidence() - error getting annotation pointer");
        return;
    }

    // get selected evidence
    if (evids->GetCount() == 0 || evids->GetSelection() < 0) return;
    CFeature_evidence *selectedEvidence =
        reinterpret_cast<CFeature_evidence*>(evids->GetClientData(evids->GetSelection()));
    if (!selectedEvidence) {
        ERRORMSG("CDDAnnotateDialog::MoveEvidence() - error getting evidence pointer");
        return;
    }

    CAlign_annot::TEvidence::iterator e, ee = selectedAnnot->SetEvidence().end(), ePrev = ee, eSwap = ee;
    CRef < CFeature_evidence > tmp;
    for (e=selectedAnnot->SetEvidence().begin(); e!=ee; ++e) {

        if (*e == selectedEvidence) {
            // figure out which (prev or next) evidence field to swap with
            if (moveUp && ePrev != ee)
                eSwap = ePrev;
            else if (!moveUp && (++(eSwap = e)) != ee)
                ;
            else
                return;

            // do the swap and update GUI
            tmp = *eSwap;
            *eSwap = *e;
            *e = tmp;
            structureSet->SetDataChanged(StructureSet::eUserAnnotationData);
            SetupGUIControls(annots->GetSelection(), evids->GetSelection() + (moveUp ? -1 : 1));
            return;
        }

        ePrev = e;
    }
}


///// CDDEvidenceDialog stuff /////

BEGIN_EVENT_TABLE(CDDEvidenceDialog, wxDialog)
    EVT_CLOSE       (       CDDEvidenceDialog::OnCloseWindow)
    EVT_BUTTON      (-1,    CDDEvidenceDialog::OnButton)
    EVT_RADIOBUTTON (-1,    CDDEvidenceDialog::OnChange)
    EVT_TEXT        (-1,    CDDEvidenceDialog::OnChange)
END_EVENT_TABLE()

CDDEvidenceDialog::CDDEvidenceDialog(wxWindow *parent, const ncbi::objects::CFeature_evidence& initial) :
    wxDialog(parent, -1, "CDD Annotations", wxPoint(400, 100), wxDefaultSize,
        wxCAPTION | wxSYSTEM_MENU), // not resizable
    changed(false), rerange(false)
{
    // construct the panel
    wxPanel *panel = new wxPanel(this, -1);
    wxSizer *topSizer = SetupEvidenceDialog(panel, false);

    // call sizer stuff
    topSizer->Fit(this);
    topSizer->Fit(panel);
    topSizer->SetSizeHints(this);

    // set initial states
    if (initial.IsComment()) {
        DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(rComment, ID_R_COMMENT, wxRadioButton)
        DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(tComment, ID_T_COMMENT, wxTextCtrl)
        rComment->SetValue(true);
        tComment->SetValue(initial.GetComment().c_str());
        tComment->SetFocus();
    } else if (initial.IsReference() && initial.GetReference().IsPmid()) {
        DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(rPMID, ID_R_PMID, wxRadioButton)
        DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(tPMID, ID_T_PMID, wxTextCtrl)
        rPMID->SetValue(true);
        wxString pmid;
        pmid.Printf("%i", initial.GetReference().GetPmid().Get());
        tPMID->SetValue(pmid);
        tPMID->SetFocus();
    } else if (IS_STRUCTURE_EVIDENCE_BSANNOT(initial)) {
        DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(rSTRUCTURE, ID_R_STRUCTURE, wxRadioButton)
        DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(tSTRUCTURE, ID_T_STRUCTURE, wxTextCtrl)
        rSTRUCTURE->SetValue(true);
        tSTRUCTURE->SetValue(
            initial.GetBsannot().GetFeatures().front()->GetDescr().front()->GetName().c_str());
    } else {
        ERRORMSG("CDDEvidenceDialog::CDDEvidenceDialog() - "
            "don't (yet) know how to edit this evidence type");
    }
    SetupGUIControls();
}

// same as hitting cancel button
void CDDEvidenceDialog::OnCloseWindow(wxCloseEvent& event)
{
    EndModal(wxCANCEL);
}

void CDDEvidenceDialog::OnButton(wxCommandEvent& event)
{
    switch (event.GetId()) {
        case ID_B_EDIT_OK: {
            EndModal(wxOK);
            break;
        }
        case ID_B_EDIT_CANCEL:
            EndModal(wxCANCEL);
            break;
        case ID_B_RERANGE:
            rerange = changed = true;
            break;
        default:
            event.Skip();
    }
}

void CDDEvidenceDialog::OnChange(wxCommandEvent& event)
{
    changed = true;
    SetupGUIControls();
}

void CDDEvidenceDialog::SetupGUIControls(void)
{
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(rComment, ID_R_COMMENT, wxRadioButton)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(stComment, ID_ST_COMMENT, wxStaticText)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(tComment, ID_T_COMMENT, wxTextCtrl)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(rPMID, ID_R_PMID, wxRadioButton)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(stPMID, ID_ST_PMID, wxStaticText)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(tPMID, ID_T_PMID, wxTextCtrl)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(rStructure, ID_R_STRUCTURE, wxRadioButton)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(stStructure, ID_ST_STRUCTURE, wxStaticText)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(tStructure, ID_T_STRUCTURE, wxTextCtrl)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(bStructure, ID_B_RERANGE, wxButton)

//    stComment->Enable(rComment->GetValue());
    tComment->Enable(rComment->GetValue());
//    stPMID->Enable(rPMID->GetValue());
    tPMID->Enable(rPMID->GetValue());
//    stStructure->Enable(rStructure->GetValue());
    tStructure->Enable(rStructure->GetValue());
    bStructure->Enable(rStructure->GetValue());
}

bool CDDEvidenceDialog::GetData(ncbi::objects::CFeature_evidence *evidence)
{
    DECLARE_AND_FIND_WINDOW_RETURN_FALSE_ON_ERR(rComment, ID_R_COMMENT, wxRadioButton)
    DECLARE_AND_FIND_WINDOW_RETURN_FALSE_ON_ERR(rPMID, ID_R_PMID, wxRadioButton)
    DECLARE_AND_FIND_WINDOW_RETURN_FALSE_ON_ERR(rSTRUCTURE, ID_R_STRUCTURE, wxRadioButton)

    if (rComment->GetValue()) {
        DECLARE_AND_FIND_WINDOW_RETURN_FALSE_ON_ERR(tComment, ID_T_COMMENT, wxTextCtrl)
        if (tComment->GetValue().size() > 0) {
            evidence->SetComment(tComment->GetValue().c_str());
            return true;
        } else {
            ERRORMSG("CDDEvidenceDialog::GetData() - comment must not be zero-length");
            return false;
        }