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NCBI C++ ToolKit: src/objtools/align/alngraphic.cpp Source File

*

[] = {

,

,

,

,

,

,

,

,

,

};

}

(bits < 50) {

}

(bits < 80) {

}

(bits < 200) {

}

(bits < 50) {

}

(bits < 80) {

}

(bits < 200) {

(num_str.size() > 2) {

trail_zero (num_str.size() - 2,

);

mid_num_str =

+ trail_zero;

(!alninfo_list.empty()){

alninfo_list.back()->range->GetTo());

TAlnInfoListList::iterator iter_temp;

list<CRange<TSeqPos>* > effective_range_list;

effective_range_list.push_back(temp_range);

overlap =

;

(effective_range){

effective_range_list){

min_to =

(effective_range->

(),

temp_range2->

());

max_from =

(effective_range->

(),

((

)((max_from - min_to)*pixel_factor) <=

){

(*iter)->merge(**iter_temp);

effective_range_list.push_back(effective_range);

effective_range;

effective_range_list.clear();

TAlnInfoList::iterator prev_iter;

(

> 0 && (*prev_iter)->range->IntersectingWith(*((*iter)->range))){

(*iter)->range->Set(

((*prev_iter)->range->GetFrom(),

(*iter)->range->GetFrom()),

((*prev_iter)->range->GetTo(),

(*iter)->range->GetTo()));

((*iter)->bits < (*prev_iter)->bits){

(*iter)->bits = (*prev_iter)->bits;

(*iter)->info = (*prev_iter)->info;

(*prev_iter)->range;

alninfo_list.erase(prev_iter);

<

container>

hasScore =

;

(

container, iter, scoreList) {

(

.GetStr()==

){

score = (*iter)->GetValue().GetInt();

}

(

.GetStr()==

){

bits = (*iter)->GetValue().GetReal();

}

(

.GetStr()==

||

.GetStr()==

) {

evalue = (*iter)->GetValue().GetReal();

hasScore =

;

score, bits, evalue);

score, bits, evalue);

bit_str, evalue_str;

ostream << setprecision (2) << evalue;

+=

+ bit_str +

+ formatted_evalue;

aln_info->

= bits;

aln_info->

= bit_str;

aln_info->

= formatted_evalue;

:m_AlnSet(&seqalign),

(&scope), m_MasterRange(master_range) {

(*iter2)->range;

is_first_aln =

;

center =

CHTML_center;

tbl_box->SetCellSpacing(0)->SetCellPadding(10)->SetAttribute(

,

);

tbl_box->SetAttribute(

,

);

tbl_box->SetAttribute(

,

);

(CSeq_align_set::Tdata::const_iterator iter =

->

().begin();

iter++, num_align++){

subid = &((*iter)->GetSeq_id(1));

master_id = &((*iter)->GetSeq_id(0));

(!is_first_aln && !subid->

(*previous_id)) {

alninfo->

= seq_range;

alninfo_list->push_back(alninfo);

is_first_aln =

;

pixel_factor = ((double)

)/master_len;

textbox->SetAttribute(

,

);

textbox->SetAttribute(

,

);

tbl->SetCellSpacing(1)->SetCellPadding(0)->SetAttribute(

,

);

score_margin_img->SetAttribute(

,

);

tc = tbl->InsertAt(0, 0, score_margin_img);

score->SetAttribute(

,

);

tc = tbl->InsertAt(0, 1, score);

tbl_box_tc = tbl_box->

(0, 0, tbl);

tbl->SetCellSpacing(1)->SetCellPadding(0)->SetAttribute(

,

);

master->SetAttribute(

,

);

tc = tbl->InsertAt(0, 0, master);

(&(*center), &(*tbl_box), tbl_box_tc);

tbl->SetCellSpacing(0)->SetCellPadding(0)->SetAttribute(

,

);

image->SetAttribute(

,

);

tc = tbl->InsertAt(0,

, image);

image->SetAttribute(

,

);

tc = tbl->InsertAt(0,

, image);

scale_unit = ((float)(master_len))/(

- 1);

pixel_factor = ((double)

)/master_len;

(

= 1;

*round_number <= master_len;

++) {

spacer_length = (

)(pixel_factor*round_number) -

;

image->SetAttribute(

,

);

tc = tbl->InsertAt(0,

, image);

image->SetAttribute(

,

);

tc = tbl->InsertAt(0,

, image);

digit_str, previous_digitstr, first_digit_str;

image->SetAttribute(

,

);

tbl->SetCellSpacing(0)->SetCellPadding(0)->SetAttribute(

,

);

tc = tbl->InsertAt(0,

, image);

(

j = 0; j < first_digit_str.size(); j ++){

one_digit(1, first_digit_str[j]);

image->SetAttribute(

,

);

tc = tbl->InsertAt(0,

, image);

previous_digitstr = first_digit_str;

(

= 1; (

)

*round_number <= master_len;

++) {

spacer_length = (

)(pixel_factor*round_number)

- previous_digitstr.size()/2))

previous_digitstr = digit_str;

image->SetAttribute(

,

);

tc = tbl->InsertAt(0,

, image);

(

j = 0; j < digit_str.size(); j ++){

one_digit(1, digit_str[j]);

image->SetAttribute(

,

);

tc = tbl->InsertAt(0,

, image);

pixel_factor = ((double)

)/master_len;

temp_value, temp_value2 ;

previous_end = -1;

front_margin = 0;

prev_round = 0;

(!(*iter)->empty()){

tbl->SetCellSpacing(0)->SetCellPadding(0)->SetAttribute(

,

);

image->SetAttribute(

,

);

tc = tbl->InsertAt(0,

, image);

is_first_segment =

;

current_id = (*iter2)->id;

from = (*iter2)->range->GetFrom();

stop = (*iter2)->range->GetTo();

(from <= previous_end) {

(stop > previous_end) {

from = previous_end + 1;

(*iter2)->range->SetFrom(from);

break_len = from - (previous_end + 1);

break_len_added =

;

temp_value = break_len*pixel_factor + prev_round;

front_margin = (

)(temp_value + (temp_value < 0.0 ? -0.5 : 0.5));

(front_margin > 0) {

prev_round = temp_value - front_margin;

prev_round = temp_value;

temp_value2 = (*iter2)->range->GetLength()*pixel_factor +

bar_length = (

)(temp_value2 + (temp_value2 < 0.0 ? -0.5 : 0.5));

(bar_length == 0 && (*iter2)->range->GetLength()*pixel_factor >= 0.50){

(bar_length > 0) {

prev_round = temp_value2 - bar_length;

prev_round = temp_value2;

(!is_first_segment && front_margin == 0 && bar_length > 1) {

break_len_added =

;

(front_margin > 0) {

&& previous_id->

(*current_id)){

(break_len_added) {

image->SetAttribute(

,

);

tc = tbl->InsertAt(0,

, image);

previous_id = current_id;

is_first_segment =

;

image->SetAttribute(

, 0);

image->SetAttribute(

,

+

image->SetAttribute(

,

);

seqid = (*iter2)->gi ==

ad =

(

+ seqid, image);

tc = tbl->InsertAt(0,

, ad);

tc = tbl->InsertAt(0,

, image);

image->SetAttribute(

,

);

tbl->SetCellSpacing(0)->SetCellPadding(0)->SetAttribute(

,

);

tbl->InsertAt(0, 0, image);

defline =

,

is_first_aln =

;

(CSeq_align_set::Tdata::const_iterator iter =

->

().begin();

iter++, num_align++){

subid = &((*iter)->GetSeq_id(1));

master_id = &((*iter)->GetSeq_id(0));

(!is_first_aln && !subid->

(*previous_id)) {

alninfo->

= seq_range;

alninfo_list->push_back(alninfo);

is_first_aln =

;

grScaleDigits;

spacer = (

== 0) ? 0 : spacer_length;

digit_str, previous_digitstr, first_digit_str;

first_digit = 0;

previous_digitstr = first_digit_str;

- previous_digitstr.size()/2))

previous_digitstr = digit_str;

grScale + grScaleDigits;

temp_value, temp_value2 ;

previous_end = -1;

front_margin = 0;

prev_round = 0;

(!(*iter)->empty()){

is_first_segment =

;

current_id = (*iter2)->id;

from = (*iter2)->range->GetFrom();

stop = (*iter2)->range->GetTo();

(from <= previous_end) {

(stop > previous_end) {

from = previous_end + 1;

(*iter2)->range->SetFrom(from);

break_len = from - (previous_end + 1);

break_len_added =

;

front_margin = (

)(temp_value + (temp_value < 0.0 ? -0.5 : 0.5));

(front_margin > 0) {

prev_round = temp_value - front_margin;

prev_round = temp_value;

bar_length = (

)(temp_value2 + (temp_value2 < 0.0 ? -0.5 : 0.5));

(bar_length == 0 && (*iter2)->range->GetLength()*

>= 0.50){

(bar_length > 0) {

prev_round = temp_value2 - bar_length;

prev_round = temp_value2;

(!is_first_segment && front_margin == 0 && bar_length > 1) {

break_len_added =

;

connectingBar;

(front_margin > 0) {

imgWidth = front_margin;

imgClass,imgFile;

&& previous_id->

(*current_id)){

(break_len_added) {

oneAlign += connectingBar;

previous_end = stop;

previous_id = current_id;

(bar_length > 0){

is_first_segment =

;

seqid,defline,eval,acc,score;

defline = (*iter2)->info;

acc = (*iter2)->accession;

eval = (*iter2)->eval;

score =(*iter2)->score;

graph_seq_popup;

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

User-defined methods of the data storage class.

const TSeqPos kScoreLength

const TSeqPos kDigitHeight

const TSeqPos kScoreHeight

static string s_MapSeqInfoTemplate(string seqTemplate, string score, string seq, string defline, string acc, string eval)

const TSeqPos kScaleWidth

const TSeqPos kScoreMargin

const TSeqPos kDigitWidth

static bool s_GetBlastScore(const container &scoreList, int &score, double &bits, double &evalue)

static string s_GetScoreColor(int bits)

static string s_GetGif(int bits)

static const int kOverlapDiff

const TSeqPos kMasterBarLength

const TSeqPos kMasterPixel

const TSeqPos kGreakHeight

const TSeqPos kBlankBarHeight

static void s_GetAlnScores(const CSeq_align &aln, int &score, double &bits, double &evalue)

const TSeqPos kScaleMarginAdj

static int s_GetRoundNumber(int number)

const TSeqPos kScaleHeight

static string s_MapBarTemplate(string imageTemplate, int width, string imgType, string cssClass, string score="", string seq="", string defline="", string acc="", string eval="")

const TSeqPos kMasterHeight

static string MapTemplate(string inpString, string tmplParamName, Int8 templParamVal)

Replace template tags by real data.

void x_DisplayMaster(int master_len, CNCBINode *center, CHTML_table *tbl_box, CHTML_tc *&tbl_box_tc)

string x_FormatScaleDigit(string digitString, int spacer_length)

CAlnGraphic(const CSeq_align_set &seqalign, CScope &scope, CRange< TSeqPos > *master_range=NULL)

void x_MergeDifferentSeq(double pixel_factor)

static bool FromRangeAscendingSort(SAlignInfo *const &info1, SAlignInfo *const &info2)

CRange< TSeqPos > * m_MasterRange

CConstRef< CSeq_align_set > m_AlnSet

TAlnInfoListList m_AlninfoListList

void x_MergeSameSeq(TAlnInfoList &alninfo_list)

string m_MouseOverFormName

void x_FormatGraphOverview(CNcbiOstream &out)

void Display(CNcbiOstream &out)

list< SAlignInfo * > TAlnInfoList

CRange< TSeqPos > * x_GetEffectiveRange(TAlnInfoList &alninfo_list)

SAlignGraphTemplates * m_AlignGraphTemplates

void x_PrintTop(CNCBINode *center, CHTML_table *tbl_box, CHTML_tc *&tbl_box_tc)

list< TAlnInfoList * > TAlnInfoListList

void AlnGraphicDisplay(CNcbiOstream &out)

void x_BuildHtmlTable(int master_len, CHTML_table *tbl_box, CHTML_tc *&tbl_box_tc)

string x_FormatScale(void)

void x_GetAlnInfo(const CSeq_align &aln, const CSeq_id &id, SAlignInfo *aln_info)

Class for computing sequences' titles ("definitions").

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

API (CDeflineGenerator) for computing sequences' titles ("definitions").

std::ofstream out("events_result.xml")

main entry point for tests

static const char * column

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

static string HTMLEncode(const string &str, THTMLEncodeFlags flags=fEncodeAll)

HTML encodes a string. E.g. <.

CNCBINode * AppendChild(CNCBINode *child)

virtual CNcbiOstream & Print(CNcbiOstream &out, TMode mode=eHTML)

CHTML_tc * InsertAt(TIndex row, TIndex column, CNCBINode *node)

void SetAttribute(const string &name, const string &value)

TGi FindGi(const container &ids)

Return gi from id list if exists, return 0 otherwise.

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

static int WorstRank(const CRef< CSeq_id > &id)

@ eContent

Untagged human-readable accession or the like.

string GenerateDefline(const CBioseq_Handle &bsh, TUserFlags flags=0)

Main method.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

TSeqPos GetBioseqLength(void) const

CConstRef< TObject > GetObjectCore(void) const

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

position_type GetLength(void) const

TThisType & Set(position_type from, position_type to)

#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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

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

Convert int to string.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static string JavaScriptEncode(const CTempString str)

Encode a string for JavaScript.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

TId GetId(void) const

Get the variant data.

const TDenseg & GetDenseg(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

const TStd & GetStd(void) const

Get the variant data.

const TDendiag & GetDendiag(void) const

Get the variant data.

const TScore & GetScore(void) const

Get the Score member data.

const TScores & GetScores(void) const

Get the Scores member data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_id > > TId

unsigned int

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

static SLJIT_INLINE sljit_ins br(sljit_gpr target)

CRange< TSeqPos > * range

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