cdd_annot_dialog.cpp

ncbi源码

                    (*e)->GetBsannot().GetFeatures().front()->GetDescr().front()->GetName().c_str());
            else
                evidTitle = "(unknown type)";
            evids->Append(evidTitle, e->GetPointer());
        }
        if (selectEvidence < evids->GetCount())
            evids->SetSelection(selectEvidence);
        else if (evids->GetCount() > 0)
            evids->SetSelection(0);
        if (evids->GetCount() > 0)
            selectedEvid = reinterpret_cast<CFeature_evidence*>(evids->GetClientData(evids->GetSelection()));
    }

    // set button states
    bNewAnnot->Enable(!readOnly);
    bDelAnnot->Enable(selectedAnnot != NULL && !readOnly);
    bEditAnnot->Enable(selectedAnnot != NULL && !readOnly);
    bHighlight->Enable(selectedAnnot != NULL);
    bAnnotUp->Enable(annots->GetSelection() > 0 && !readOnly);
    bAnnotDown->Enable(annots->GetSelection() < annots->GetCount() - 1 && !readOnly);
    bNewEvid->Enable(selectedAnnot != NULL && !readOnly);
    bDelEvid->Enable(selectedEvid != NULL && !readOnly);
    bEditEvid->Enable(selectedEvid != NULL && !readOnly);
    bShow->Enable(selectedEvid != NULL &&
        ((selectedEvid->IsReference() && selectedEvid->GetReference().IsPmid()) ||
         IS_STRUCTURE_EVIDENCE_BSANNOT(*selectedEvid) || selectedEvid->IsComment()));
    bEvidUp->Enable(evids->GetSelection() > 0 && !readOnly);
    bEvidDown->Enable(evids->GetSelection() < evids->GetCount() - 1 && !readOnly);
}

void CDDAnnotateDialog::NewAnnotation(void)
{
    IntervalList intervals;
    GetCurrentHighlightedIntervals(&intervals);
    if (intervals.size() == 0) {
        ERRORMSG("No aligned+highlighted master residues!");
        return;
    }

    // get description from user
    wxString descr = wxGetTextFromUser(
        "Enter a description for the new annotation:", "Description");
    if (descr.size() == 0) return;

    // create a new annotation
    CRef < CAlign_annot > annot(new CAlign_annot());
    annot->SetDescription(descr.c_str());

    // fill out location
    if (intervals.size() == 1) {
        annot->SetLocation().SetInt(*(intervals.front()));
    } else {
        CPacked_seqint *packed = new CPacked_seqint();
        packed->Set() = intervals;  // copy list
        annot->SetLocation().SetPacked_int(*packed);
    }

    // add to annotation list
    annotSet->Set().push_back(annot);
    structureSet->SetDataChanged(StructureSet::eUserAnnotationData);

    // update GUI
    SetupGUIControls(annotSet->Get().size() - 1, 0);
}

void CDDAnnotateDialog::DeleteAnnotation(void)
{
    // get selection
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(annots, ID_L_ANNOT, wxListBox)
    if (annots->GetCount() == 0 || annots->GetSelection() < 0) return;
    CAlign_annot *selectedAnnot =
        reinterpret_cast<CAlign_annot*>(annots->GetClientData(annots->GetSelection()));
    if (!selectedAnnot) {
        ERRORMSG("CDDAnnotateDialog::DeleteAnnotation() - error getting annotation pointer");
        return;
    }

    // confirm with user
    int confirm = wxMessageBox("This will remove the selected annotation and all the\n"
        "evidence associated with it. Is this correct?", "Confirm", wxOK | wxCANCEL | wxCENTRE, this);
    if (confirm != wxOK) return;

    // actually delete the annotation
    CAlign_annot_set::Tdata::iterator a, ae = annotSet->Set().end();
    for (a=annotSet->Set().begin(); a!=ae; ++a) {
        if (*a == selectedAnnot) {
            annotSet->Set().erase(a);
            structureSet->SetDataChanged(StructureSet::eUserAnnotationData);
            break;
        }
    }

    // update GUI
    SetupGUIControls(0, 0);
}

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

    IntervalList intervals;
    GetCurrentHighlightedIntervals(&intervals);
    if (intervals.size() > 0) {
        // move the annotation?
        int move = wxMessageBox("Do you want to move the annotation to the currently\n"
            "highlighted and aligned residues?", "Move?", wxYES_NO | wxCANCEL | wxCENTRE, this);
        if (move == wxCANCEL)
            return;
        else if (move == wxYES) {
            // change location
            if (intervals.size() == 1) {
                selectedAnnot->SetLocation().SetInt(*(intervals.front()));
            } else {
                CPacked_seqint *packed = new CPacked_seqint();
                packed->Set() = intervals;  // copy list
                selectedAnnot->SetLocation().SetPacked_int(*packed);
            }
            structureSet->SetDataChanged(StructureSet::eUserAnnotationData);
        }
    }

    // edit description
    wxString initial;
    if (selectedAnnot->IsSetDescription()) initial = selectedAnnot->GetDescription().c_str();
    wxString descr = wxGetTextFromUser(
        "Enter a description for the new annotation:", "Description", initial);
    if (descr.size() > 0 && descr != selectedAnnot->GetDescription().c_str()) {
        selectedAnnot->SetDescription(descr.c_str());
        structureSet->SetDataChanged(StructureSet::eUserAnnotationData);
    }

    // update GUI
    SetupGUIControls(annots->GetSelection(), evids->GetSelection());
}

bool CDDAnnotateDialog::HighlightInterval(const ncbi::objects::CSeq_interval& interval)
{
    const BlockMultipleAlignment *alignment = structureSet->alignmentManager->GetCurrentMultipleAlignment();
    const Sequence *master = alignment->GetMaster();

    // make sure annotation sequence matches master sequence
    if (!master->identifier->MatchesSeqId(interval.GetId())) {
        ERRORMSG("CDDAnnotateDialog::HighlightInterval() - interval Seq-id/master sequence mismatch");
        return false;
    }

    // do the highlighting
    return alignment->HighlightAlignedColumnsOfMasterRange(interval.GetFrom(), interval.GetTo());
}

void CDDAnnotateDialog::HighlightAnnotation(void)
{
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(annots, ID_L_ANNOT, wxListBox)

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

    // highlight annotation's intervals
    GlobalMessenger()->RemoveAllHighlights(true);
    bool okay = true;
    if (selectedAnnot->GetLocation().IsInt()) {
        okay = HighlightInterval(selectedAnnot->GetLocation().GetInt());
    } else if (selectedAnnot->GetLocation().IsPacked_int()) {
        CPacked_seqint::Tdata::iterator s,
            se = selectedAnnot->SetLocation().SetPacked_int().Set().end();
        for (s=selectedAnnot->SetLocation().SetPacked_int().Set().begin(); s!=se; ++s) {
            if (!HighlightInterval(**s))
                okay = false;
        }
    }
    if (!okay)
        wxMessageBox("WARNING: this annotation specifies master residues outside the aligned blocks;"
            " see the message log for details.", "Annotation Error",
            wxOK | wxCENTRE | wxICON_ERROR, this);
}

void CDDAnnotateDialog::MoveAnnotation(bool moveUp)
{
    // get selection
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(annots, ID_L_ANNOT, wxListBox)
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(evids, ID_L_EVID, wxListBox)
    if (annots->GetCount() == 0 || annots->GetSelection() < 0) return;
    CAlign_annot *selectedAnnot =
        reinterpret_cast<CAlign_annot*>(annots->GetClientData(annots->GetSelection()));
    if (!selectedAnnot) {
        ERRORMSG("CDDAnnotateDialog::MoveAnnotation() - error getting annotation pointer");
        return;
    }

    CAlign_annot_set::Tdata::iterator a, ae = annotSet->Set().end(), aPrev = ae, aSwap = ae;
    CRef < CAlign_annot > tmp;
    for (a=annotSet->Set().begin(); a!=ae; ++a) {

        if (*a == selectedAnnot) {
            // figure out which (prev or next) annot field to swap with
            if (moveUp && aPrev != ae)
                aSwap = aPrev;
            else if (!moveUp && (++(aSwap = a)) != ae)
                ;
            else
                return;

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

        aPrev = a;
    }

    ERRORMSG("CDDAnnotateDialog::MoveAnnotation() - error finding selected annotation");
}

void CDDAnnotateDialog::NewEvidence(void)
{
    DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(annots, ID_L_ANNOT, 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::NewEvidence() - error getting annotation pointer");
        return;
    }

    // create default comment evidence
    CRef < CFeature_evidence > newEvidence(new CFeature_evidence());
    newEvidence->SetComment("");

    // bring up evidence editor
    CDDEvidenceDialog dialog(this, *newEvidence);
    int result = dialog.ShowModal();

    // add new evidence
    if (result == wxOK) {
        if (dialog.GetData(newEvidence.GetPointer())) {
            selectedAnnot->SetEvidence().push_back(newEvidence);
            SetupGUIControls(annots->GetSelection(), selectedAnnot->GetEvidence().size() - 1);
            structureSet->SetDataChanged(StructureSet::eUserAnnotationData);
        } else
            ERRORMSG("CDDAnnotateDialog::NewEvidence() - error getting dialog data");
    }
}

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

    // 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::DeleteEvidence() - error getting evidence pointer");
        return;
    }

    // confirm with user
    int confirm = wxMessageBox("This will remove the selected evidence from\n"
        "the selected annotation. Is this correct?", "Confirm", wxOK | wxCANCEL | wxCENTRE, this);
    if (confirm != wxOK) return;

    // delete evidence from annotation's list
    CAlign_annot::TEvidence::iterator e, ee = selectedAnnot->SetEvidence().end();
    for (e=selectedAnnot->SetEvidence().begin(); e!=ee; ++e) {
        if (*e == selectedEvidence) {
            selectedAnnot->SetEvidence().erase(e);
            structureSet->SetDataChanged(StructureSet::eUserAnnotationData);
            break;
        }
    }
    if (e == ee) {
        ERRORMSG("CDDAnnotateDialog::DeleteEvidence() - evidence pointer not found in annotation");
        return;
    }

    // update GUI
    SetupGUIControls(annots->GetSelection(), 0);
}

void CDDAnnotateDialog::EditEvidence(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::DeleteEvidence() - error getting evidence pointer");
        return;
    }

    // bring up evidence editor
    CDDEvidenceDialog dialog(this, *selectedEvidence);
    int result = dialog.ShowModal();

    // update evidence
    if (result == wxOK && dialog.HasDataChanged()) {
        if (dialog.GetData(selectedEvidence)) {
            DECLARE_AND_FIND_WINDOW_RETURN_ON_ERR(annots, ID_L_ANNOT, wxListBox)
            structureSet->SetDataChanged(StructureSet::eUserAnnotationData);
            SetupGUIControls(annots->GetSelection(), evids->GetSelection());
        } else
            ERRORMSG("CDDAnnotateDialog::EditEvidence() - error getting dialog data");
    }
}

typedef struct {
    int alignedMoleculeID;
    int from, to;
    int hits;
} ChainInfo;

static const StructureObject * HighlightResidues(const StructureSet *set, const CBiostruc_annot_set& annot)
{
    try {
        if (!annot.IsSetId() || annot.GetId().size() == 0 || !annot.GetId().front()->IsMmdb_id())