data_manager.cpp

ncbi源码

{
    if (mimeData.NotEmpty())
        return WriteASNToFile(filename, mimeData.GetObject(), isBinary, err, fixNonPrint);
    else
        return WriteASNToFile(filename, cddData.GetObject(), isBinary, err, fixNonPrint);
}

ncbi::objects::CCdd * ASNDataManager::GetInternalCDDData(void)
{
    if (cddData.NotEmpty()) return cddData.GetPointer();
    else if (mimeData.NotEmpty() && mimeData->IsGeneral() &&
             mimeData->GetGeneral().GetSeq_align_data().IsCdd())
        return &(mimeData->SetGeneral().SetSeq_align_data().SetCdd());
    else
        return NULL;
}

const ncbi::objects::CCdd * ASNDataManager::GetInternalCDDData(void) const
{
    if (cddData.NotEmpty()) return cddData.GetPointer();
    else if (mimeData.NotEmpty() && mimeData->IsGeneral() &&
             mimeData->GetGeneral().GetSeq_align_data().IsCdd())
        return &(mimeData->GetGeneral().GetSeq_align_data().GetCdd());
    else
        return NULL;
}

bool ASNDataManager::IsCDD(void) const
{
    return (GetInternalCDDData() != NULL);
}

bool ASNDataManager::IsCDDInMime(void) const
{
    return (GetInternalCDDData() != NULL && mimeData.NotEmpty());
}

const string& ASNDataManager::GetCDDName(void) const
{
    static const string empty = "";
    const CCdd *cdd = GetInternalCDDData();
    if (cdd)
        return cdd->GetName();
    else
        return empty;
}

bool ASNDataManager::SetCDDName(const string& name)
{
    CCdd *cdd = GetInternalCDDData();
    if (!cdd || name.size() == 0) return false;
    cdd->SetName(name);
    SetDataChanged(StructureSet::eCDDData);
    return true;
}

const string& ASNDataManager::GetCDDDescription(void) const
{
    static const string empty = "";
    const CCdd *cdd = GetInternalCDDData();
    if (!cdd) return empty;

    // find first 'comment' in Cdd-descr-set, assume this is the "long description"
    if (!cdd->IsSetDescription() || cdd->GetDescription().Get().size() == 0) return empty;
    CCdd_descr_set::Tdata::const_iterator d, de = cdd->GetDescription().Get().end();
    for (d=cdd->GetDescription().Get().begin(); d!=de; ++d)
        if ((*d)->IsComment())
            return (*d)->GetComment();

    return empty;
}

bool ASNDataManager::SetCDDDescription(const string& descr)
{
    CCdd *cdd = GetInternalCDDData();
    if (!cdd || descr.size() == 0) return false;

    if (cdd->IsSetDescription() && cdd->GetDescription().Get().size() >= 0) {
        // find first 'comment' in Cdd-descr-set, assume this is the "long description"
        CCdd_descr_set::Tdata::iterator d, de = cdd->SetDescription().Set().end();
        for (d=cdd->SetDescription().Set().begin(); d!=de; ++d) {
            if ((*d)->IsComment()) {
                if ((*d)->GetComment() != descr) {
                    (*d)->SetComment(descr);
                    SetDataChanged(StructureSet::eCDDData);
                }
                return true;
            }
        }
    }

    // add new comment if not yet present
    CRef < CCdd_descr > comment(new CCdd_descr);
    comment->SetComment(descr);
    cdd->SetDescription().Set().push_front(comment);
    SetDataChanged(StructureSet::eCDDData);
    return true;
}

bool ASNDataManager::GetCDDNotes(TextLines *lines) const
{
    const CCdd *cdd = GetInternalCDDData();
    if (!lines || !cdd) return false;
    lines->clear();

    if (!cdd->IsSetDescription() || cdd->GetDescription().Get().size() == 0)
        return true;

    // find scrapbook item
    CCdd_descr_set::Tdata::const_iterator d, de = cdd->GetDescription().Get().end();
    for (d=cdd->GetDescription().Get().begin(); d!=de; ++d) {
        if ((*d)->IsScrapbook()) {

            // fill out lines from scrapbook string list
            lines->resize((*d)->GetScrapbook().size());
            CCdd_descr::TScrapbook::const_iterator l, le = (*d)->GetScrapbook().end();
            int i = 0;
            for (l=(*d)->GetScrapbook().begin(); l!=le; ++l)
                (*lines)[i++] = *l;
            return true;
        }
    }
    return true;
}

bool ASNDataManager::SetCDDNotes(const TextLines& lines)
{
    CCdd *cdd = GetInternalCDDData();
    if (!cdd) return false;

    CCdd_descr::TScrapbook *scrapbook = NULL;

    // find an existing scrapbook item
    if (cdd->IsSetDescription()) {
        CCdd_descr_set::Tdata::iterator d, de = cdd->SetDescription().Set().end();
        for (d=cdd->SetDescription().Set().begin(); d!=de; ++d) {
            if ((*d)->IsScrapbook()) {
                if (lines.size() == 0) {
                    cdd->SetDescription().Set().erase(d);   // if empty, remove scrapbook item
                    SetDataChanged(StructureSet::eCDDData);
                    TRACEMSG("removed scrapbook");
                } else
                    scrapbook = &((*d)->SetScrapbook());
                break;
            }
        }
    }
    if (lines.size() == 0) return true;

    // create a scrapbook item if doesn't exist already
    if (!scrapbook) {
        CRef < CCdd_descr > descr(new CCdd_descr());
        scrapbook = &(descr->SetScrapbook());
        cdd->SetDescription().Set().push_back(descr);
    }

    // fill out scrapbook lines
    scrapbook->clear();
    for (int i=0; i<lines.size(); ++i)
        scrapbook->push_back(lines[i]);
    SetDataChanged(StructureSet::eCDDData);

    return true;
}

ncbi::objects::CCdd_descr_set * ASNDataManager::GetCDDDescrSet(void)
{
    CCdd *cdd = GetInternalCDDData();
    if (cdd) {
        // make a new descr set if not present
        if (!cdd->IsSetDescription()) {
            CRef < CCdd_descr_set > ref(new CCdd_descr_set());
            cdd->SetDescription(*ref);
        }
        return &(cdd->SetDescription());
    } else
        return NULL;
}

ncbi::objects::CAlign_annot_set * ASNDataManager::GetCDDAnnotSet(void)
{
    CCdd *cdd = GetInternalCDDData();
    if (cdd) {
        // make a new annot set if not present
        if (!cdd->IsSetAlignannot()) {
			CRef < CAlign_annot_set > ref(new CAlign_annot_set());
            cdd->SetAlignannot(*ref);
        }
        return &(cdd->SetAlignannot());
    } else
        return NULL;
}

const ncbi::objects::CSeq_id * ASNDataManager::GetCDDMaster3d(void) const
{
    const CCdd *cdd = GetInternalCDDData();
    if (cdd && cdd->IsSetMaster3d())
        return cdd->GetMaster3d().front().GetPointer(); // just return the first one...
    else
        return NULL;
}

void ASNDataManager::AddReject(ncbi::objects::CReject_id *reject)
{
    CCdd *cdd = GetInternalCDDData();
    if (!cdd) return;

    cdd->SetRejects().push_back(CRef < CReject_id > (reject));
    dataChanged |= StructureSet::eCDDData;
}

const StructureSet::RejectList * ASNDataManager::GetRejects(void) const
{
    const CCdd *cdd = GetInternalCDDData();
    if (!cdd || !cdd->IsSetRejects())
        return NULL;
    return &(cdd->GetRejects());
}

END_SCOPE(Cn3D)

/*
* ---------------------------------------------------------------------------
* $Log: data_manager.cpp,v $
* Revision 1000.2  2004/06/01 18:28:33  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.23
*
* Revision 1.23  2004/05/21 21:41:39  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.22  2004/05/21 17:29:51  thiessen
* allow conversion of mime to cdd data
*
* Revision 1.21  2004/03/15 18:25:36  thiessen
* prefer prefix vs. postfix ++/-- operators
*
* Revision 1.20  2004/02/19 17:04:55  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.19  2003/08/21 18:02:01  thiessen
* change header order for Mac compilation
*
* Revision 1.18  2003/02/03 19:20:03  thiessen
* format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
*
* Revision 1.17  2003/01/27 15:52:22  thiessen
* merge after highlighted row; show rejects; trim rejects from new reject list
*
* Revision 1.16  2002/11/22 19:48:14  thiessen
* one more fix for const changes in objects API
*
* Revision 1.15  2002/11/19 21:19:44  thiessen
* more const changes for objects; fix user vs default style bug
*
* Revision 1.14  2002/11/18 19:48:40  grichenk
* Removed "const" from datatool-generated setters
*
* Revision 1.13  2002/11/06 00:18:10  thiessen
* fixes for new CRef/const rules in objects
*
* Revision 1.12  2002/10/27 22:23:51  thiessen
* save structure alignments from vastalign.cgi imports
*
* Revision 1.11  2002/07/03 13:39:39  thiessen
* fix for redundant sequence removal
*
* Revision 1.10  2002/06/05 17:50:08  thiessen
* title tweaks
*
* Revision 1.9  2002/03/19 18:47:58  thiessen
* small bug fixes; remember PSSM weight
*
* Revision 1.8  2002/02/27 16:29:41  thiessen
* add model type flag to general mime type
*
* Revision 1.7  2002/02/19 14:59:39  thiessen
* add CDD reject and purge sequence
*
* Revision 1.6  2002/02/12 17:19:21  thiessen
* first working structure import
*
* Revision 1.5  2002/01/19 02:34:40  thiessen
* fixes for changes in asn serialization API
*
* Revision 1.4  2001/12/15 03:15:59  thiessen
* adjustments for slightly changed object loader Set...() API
*
* Revision 1.3  2001/12/06 23:13:45  thiessen
* finish import/align new sequences into single-structure data; many small tweaks
*
* Revision 1.2  2001/11/30 14:02:05  thiessen
* progress on sequence imports to single structures
*
* Revision 1.1  2001/11/27 16:26:08  thiessen
* major update to data management system
*
*/