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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuCdFamily_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/structure/cd_utils/cuCdFamily.cpp Source File

(cDIterator ==

())

(it->cd->GetAccession() == acc) {

(it->cd->GetAccession() == acc) {

(sit != pit.

())

cds.push_back(sit->cd);

(sit != pit.

())

vector<CCdCore*> tmpCds;

(

= 0;

< tmpCds.size(); ++

) {

cds.push_back(tmpCds[

]);

vector<CCdCore*> tmpCds;

(

= 0;

< tmpCds.size(); ++

) {

vector<CCdCore*> cds;

cds.push_back(cit->cd);

vector<CDFamily*> families;

subfam = families[0];

(find(cds.begin(), cds.end(), fit->cd) != cds.end())

fit->selected =

;

fit->selected =

;

fit->selected =

;

cds.push_back(fit->cd);

(; cit !=

(); ++cit)

cds.push_back(cit->cd);

* parentCd = initialCD;

currentCd = parentCd;

path.push_back(currentCd);

vector<CCdCore*> pathToRoot1, pathToRoot2;

vector<CCdCore*>::reverse_iterator rit1 = pathToRoot1.rbegin();

vector<CCdCore*>::reverse_iterator rit2 = pathToRoot2.rbegin();

vector<CCdCore*>::reverse_iterator lastConvergedIt1, lastConvergedIt2;

( (rit1 == pathToRoot1.rend()) || (rit2 == pathToRoot2.rend()))

((*rit1) = (*rit2));

* lastConvergedPoint = *rit1;

(; rit1 != pathToRoot1.rend() && rit2 != pathToRoot2.rend(); rit1++, rit2++)

(*rit1 == *rit2) {

lastConvergedPoint = *rit1;

lastConvergedIt1 = rit1;

lastConvergedIt2 = rit2;

(rit1 = lastConvergedIt1; rit1 != pathToRoot1.rend(); ++rit1) {

path1.push_back(*rit1);

reverse(path1.begin(), path1.end());

(rit2 = lastConvergedIt2; rit2 != pathToRoot2.rend(); ++rit2) {

path2.push_back(*rit2);

reverse(path2.begin(), path2.end());

(lastConvergedPoint);

vector<CCdCore*> path1, path2;

vector<CCdCore*>::reverse_iterator rit1 = path1.rbegin();

vector<CCdCore*>::reverse_iterator rit2 = path2.rbegin();

( (rit1 == path1.rend()) || (rit2 == path2.rend()))

((*rit1) = (*rit2));

* lastConvergedPoint = *rit1;

(; rit1 != path1.rend() && rit2 != path2.rend(); rit1++, rit2++)

((!byAccession && *rit1 == *rit2) || (byAccession && (*rit1)->GetAccession() == (*rit2)->GetAccession()))

lastConvergedPoint = *rit1;

(cds.

() == 0)

* lastConvergedPoint = *cit;

(fit ==

() || fit ==

())

(; cit != cds.

(); cit++)

fit =

(lastConvergedPoint, *cit, byAccession);

(fit ==

() || fit ==

())

lastConvergedPoint = fit->cd;

notOnPath.push_back(cit->cd);

notOnPath.push_back(cit->cd);

notOnPath.size();

isAncestor =

;

(cd && potentialAncestorCd && cd != potentialAncestorCd) {

(potentialAncestorCd ==

()) {

(

&& !isAncestor) {

(

== potentialAncestorCd) {

hasError =

;

err.append(

);

err.append(

);

err.append(

);

(; fit !=

(); ++fit)

acc = fit->cd->GetAccession();

* cd = one.getRootCD();

(

= 0;

<

.size();

++)

occurrence > 1;

(

= 0;

< families.size();

++)

(families[

].

(cd) != families[

].

())

&(families[

]);

vector<CCdCore*>::iterator cdIterator = cds.begin();

(cdIterator != cds.end())

cds.erase(cdIterator);

families.push_back(cdFamily);

cdIterator = cds.begin();

families.size();

cdFamily.

(cds[*sit], parentCD);

vector<CCdCore*>

(cds);

(

= 0;

<

.size();

++)

(children.

(

) == children.

())

cds.push_back(

[

]);

(

= 0;

< cds.size();

++)

(acc.compare(cds[

]->GetAccession()) == 0)

(

= 0;

< (

) cds.size();

++)

(acc.compare(cds[

]->GetClassicalParentAccession()) == 0)

children.

() > 0;

underscore(

);

;

isRoot = (cursor ==

());

(sib != cursor.

()) {

string GetAccession(int &Version) const

string GetClassicalParentAccession(int &Version) const

CCdCore * getClassicalParent(CCdCore *childCD) const

static bool findParent(CCdCore *cd, vector< CCdCore * > &cds)

bool isDescendant(CCdCore *cd, CCdCore *potentialDescendantCd) const

int getCdsNotOnPathToRoot(CCdCore *initialCD, vector< CCdCore * > &notOnPath) const

CDFamilyIterator convergeTo(CCdCore *cd1, CCdCore *cd2, bool byAccession=false) const

void getDescendants(vector< CCdCore * > &cds, CCdCore *parentCD) const

int getPathToRoot(CCdCore *initialCD, vector< CCdCore * > &path) const

int getAllCD(vector< CCdCore * > &cds) const

string getNewickRepresentation() const

static void extractFamily(CCdCore *parentCD, CDFamily &cdFamily, vector< CCdCore * > &cds)

CDFamilyIterator setRootCD(CCdCore *rootCD)

static bool findChildren(CCdCore *cd, vector< CCdCore * > &cds, set< int > &children)

CCdCore * getRootCD() const

static int createFamilies(vector< CCdCore * > &cds, vector< CDFamily * > &families)

CDFamilyIterator findCDByAccession(CCdCore *cd) const

void selectCDs(const vector< CCdCore * > &cds)

void subfamily(CDFamilyIterator cit, CDFamily *&subfam, bool childrenOnly=false)

CDFamilyIterator findCD(CCdCore *cd) const

bool removeChild(CCdCore *cd)

int getSelectedCDs(vector< CCdCore * > &cds)

CDFamilyIterator addChild(CCdCore *cd, CCdCore *parentCD)

bool isDirectAncestor(CCdCore *cd, CCdCore *potentialAncestorCd) const

static bool IsFamilyValid(const CDFamily *family, string &err)

static CDFamily * findFamily(CCdCore *cd, vector< CDFamily > &families)

static bool isDup(CDFamily &one, vector< CDFamily > &all)

void getChildren(vector< CCdCore * > &cds, CCdCore *parentCD) const

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

sibling_iterator end() const

unsigned int number_of_children() const

sibling_iterator begin() const

iter append_child(iter position)

pre_order_iterator begin() const

iter insert(iter position, const T &x)

unsigned int number_of_siblings(const iterator_base &) const

pre_order_iterator end() const

CDFamilyBase::iterator CDFamilyIterator

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

static const char label[]

unsigned int

A callback function used to compare two keys in a database.

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is smart and slim</td> n<td> orig</td> n</tr> n<tr> n<td> last_modified</td> n<td> optional</td> n<td> Integer</td> n<td class=\"description\"> The blob last modification If provided then the exact match will be requested with n the Cassandra storage corresponding field value</td> n<td> Positive integer Not provided means that the most recent match will be selected</td> n<td></td> n</tr> n<tr> n<td> use_cache</td> n<td> optional</td> n<td> String</td> n<td class=\"description\"> The option controls if the Cassandra LMDB cache and or database should be used It n affects the seq id resolution step and the blob properties lookup step The following n options are BIOSEQ_INFO and BLOB_PROP at all

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