// ----------------------------------------------------------------------------
void CFeatTableEdit::GenerateLocusTags()
// ----------------------------------------------------------------------------
{
CRef<CGb_qual> pLocusTag;
SAnnotSelector selGenes;
selGenes.IncludeFeatSubtype(CSeqFeatData::eSubtype_gene);
CFeat_CI itGenes(mHandle, selGenes);
for ( ; itGenes; ++itGenes) {
string locusTagVal = itGenes->GetNamedQual("locus_tag");
if (!locusTagVal.empty()) {
continue;
}
CSeq_feat_EditHandle feh(mpScope->GetObjectHandle(
(itGenes)->GetOriginalFeature()));
feh.AddQualifier("locus_tag", xNextLocusTag());
}
SAnnotSelector selOther;
selOther.ExcludeFeatSubtype(CSeqFeatData::eSubtype_gene);
CFeat_CI itOther(mHandle, selOther);
for ( ; itOther; ++itOther) {
const CSeq_feat& feat = itOther->GetOriginalFeature();
CSeq_feat_EditHandle feh(mpScope->GetObjectHandle(
(itOther)->GetOriginalFeature()));
feh.RemoveQualifier("locus_tag");
CConstRef<CSeq_feat> pGeneParent = xGetGeneParent(feat);
if (!pGeneParent) {
continue;
}
string locusTag = pGeneParent->GetNamedQual("locus_tag");
feh.AddQualifier("locus_tag", locusTag);
}
}
// ----------------------------------------------------------------------------
void CFeatTableEdit::GenerateOrigProteinAndOrigTranscriptIds()
// ----------------------------------------------------------------------------
{
// that's for cds's.
SAnnotSelector sel;
sel.IncludeFeatSubtype(CSeqFeatData::eSubtype_cdregion);
CFeat_CI it(mHandle, sel);
for ( ; it; ++it) {
const CSeq_feat& cds = it->GetOriginalFeature();
string proteinId = cds.GetNamedQual("protein_id");
string transcriptId = cds.GetNamedQual("transcript_id");
CConstRef<CSeq_feat> pParentRna = xGetMrnaParent(cds);
if (!pParentRna) {
continue;
}
CRef<CSeq_feat> pEditedRna(new CSeq_feat);
pEditedRna->Assign(*pParentRna);
CRef<CGb_qual> pOrigProteinId(new CGb_qual);
pOrigProteinId->SetQual("orig_protein_id");
pOrigProteinId->SetVal(proteinId);
pEditedRna->SetQual().push_back(pOrigProteinId);
CRef<CGb_qual> pOrigTranscriptId(new CGb_qual);
pOrigTranscriptId->SetQual("orig_transcript_id");
pOrigTranscriptId->SetVal(transcriptId);
pEditedRna->SetQual().push_back(pOrigTranscriptId);
CSeq_feat_EditHandle feh(mpScope->GetObjectHandle(*pParentRna));
feh.Replace(*pEditedRna);
}
}
// ----------------------------------------------------------------------------
void CFeatTableEdit::GenerateProteinAndTranscriptIds()
// ----------------------------------------------------------------------------
{
// that's for cds's.
SAnnotSelector sel;
sel.IncludeFeatSubtype(CSeqFeatData::eSubtype_cdregion);
CFeat_CI it(mHandle, sel);
for ( ; it; ++it) {
const CSeq_feat& cds = it->GetOriginalFeature();
string proteinId = xNextProteinId(cds);
string transcriptId = xCurrentTranscriptId(cds);
if (proteinId.empty()) {
continue;
}
CRef<CSeq_feat> pEditedCds(new CSeq_feat);
pEditedCds->Assign(cds);
CRef<CGb_qual> pProteinId(new CGb_qual);
pProteinId->SetQual("protein_id");
pProteinId->SetVal(proteinId);
pEditedCds->SetQual().push_back(pProteinId);
CRef<CGb_qual> pTranscriptId(new CGb_qual);
pTranscriptId->SetQual("transcript_id");
pTranscriptId->SetVal(transcriptId);
pEditedCds->SetQual().push_back(pTranscriptId);
CSeq_feat_EditHandle feh(mpScope->GetObjectHandle(cds));
feh.Replace(*pEditedCds);
}
}
// ----------------------------------------------------------------------------
void CFeatTableEdit::EliminateBadQualifiers()
// ----------------------------------------------------------------------------
{
typedef CSeq_feat::TQual QUALS;
CFeat_CI it(mHandle);
for ( ; it; ++it) {
CSeq_feat_EditHandle feh(mpScope->GetObjectHandle(
(it)->GetOriginalFeature()));
const QUALS& quals = (*it).GetQual();
vector<string> badQuals;
for (QUALS::const_iterator qual = quals.begin(); qual != quals.end();
++qual) {
string qualVal = (*qual)->GetQual();
CSeqFeatData::EQualifier qualType = CSeqFeatData::GetQualifierType(qualVal);
if (qualType == CSeqFeatData::eQual_bad) {
badQuals.push_back(qualVal);
}
}
for (vector<string>::const_iterator badIt = badQuals.begin();
badIt != badQuals.end(); ++badIt) {
feh.RemoveQualifier(*badIt);
}
}
}
int main (){
int start,end,lamda;
int i,c;
for(;;)
{printf("1.input data\n2.Print data\n3.Quit\n\tYour Choice : ");
scanf("%d",&c);
switch(c) {
case 1:
printf("start point : ");scanf("%d",&start);
printf("end point : ");scanf("%d",&end);
printf("lamda : ");scanf("%d",&lamda);
break;
case 2:
printf("%c %c\n",'C','F');
for (i = start ; i <= end; i += lamda) printf("%d %.2f\n",i,feh(i));
break;
case 3:return;}
}
return 0;}
// -------------------------------------------------------------------------
void CFeatTableEdit::InferParentMrnas()
// -------------------------------------------------------------------------
{
SAnnotSelector sel;
sel.IncludeFeatSubtype(CSeqFeatData::eSubtype_cdregion);
CFeat_CI it(mHandle, sel);
for ( ; it; ++it) {
const CSeq_feat& cds = it->GetOriginalFeature();
CRef<CSeq_feat> pRna = edit::MakemRNAforCDS(cds, *mpScope);
if (!pRna) {
continue;
}
//find proper name for rna
string rnaId(xNextFeatId());
pRna->SetId().SetLocal().SetStr(rnaId);
//add rna xref to cds
CSeq_feat_EditHandle feh(mpScope->GetObjectHandle(cds));
feh.AddFeatXref(rnaId);
//add new rna to feature table
mEditHandle.AddFeat(*pRna);
}
}
// ----------------------------------------------------------------------------
void CFeatTableEdit::InferPartials()
// ----------------------------------------------------------------------------
{
edit::CLocationEditPolicy editPolicy(
edit::CLocationEditPolicy::ePartialPolicy_eSetForBadEnd,
edit::CLocationEditPolicy::ePartialPolicy_eSetForBadEnd,
false, //extend 5'
false, //extend 3'
edit::CLocationEditPolicy::eMergePolicy_NoChange);
SAnnotSelector sel;
sel.IncludeFeatSubtype(CSeqFeatData::eSubtype_cdregion);
CFeat_CI it(mHandle, sel);
for ( ; it; ++it) {
const CSeq_feat& cds = it->GetOriginalFeature();
CRef<CSeq_feat> pEditedCds(new CSeq_feat);
pEditedCds->Assign(cds);
editPolicy.ApplyPolicyToFeature(*pEditedCds, *mpScope);
CSeq_feat_EditHandle feh(mpScope->GetObjectHandle(cds));
feh.Replace(*pEditedCds);
}
}
// ---------------------------------------------------------------------------
void CFeatTableEdit::InferParentGenes()
// ---------------------------------------------------------------------------
{
SAnnotSelector sel;
sel.IncludeFeatSubtype(CSeqFeatData::eSubtype_mRNA);
CFeat_CI it(mHandle, sel);
for ( ; it; ++it) {
const CSeq_feat& rna = it->GetOriginalFeature();
CRef<CSeq_feat> pGene = xMakeGeneForMrna(rna);
if (!pGene) {
continue;
}
//find proper name for gene
string geneId(xNextFeatId());
pGene->SetId().SetLocal().SetStr(geneId);
//add gene xref to rna
CSeq_feat_EditHandle feh(mpScope->GetObjectHandle(rna));
feh.AddFeatXref(geneId);
//add new gene to feature table
mEditHandle.AddFeat(*pGene);
}
}
