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)

146

, m_IsDryRun(

)

152

: m_RemoveDuplicates(

)

153

, m_IsDryRun(

)

161 static const char

*sc_Functions[] = {

177

vector<string> func_vec;

178 for

(

const char

** func = sc_Functions; func && *func; ++func) {

179

func_vec.push_back(*func);

250 const

objects::CSeq_id_Handle& subj,

289 if

(

Match

(**iter)) {

290

aligns_out.push_back(*iter);

383 bool

compart_match =

true

;

402

compart_match =

false

;

419 if

(cit != qit->second.end()) {

432 return

compart_match;

466

ostr <<

"Parse Tree:"

<< endl;

486 md5

.GetChecksum().GetMD5Digest(md5_str);

491 const

objects::CSeq_align& align,

492 bool

throw_if_not_found)

498

(*m_DryRunOutput) << score_name <<

": " 506 if

( throw_if_not_found)

510 _TRACE

(

Trace

"score "

<< score_name <<

" not found"

);

513 return

numeric_limits<double>::quiet_NaN();

519 double

this_val = numeric_limits<double>::quiet_NaN();

520 string function

= node.

().GetStrValue();

530 "invalid number of nodes: expected 2, got 1"

);

536 "invalid number of nodes: " 537 "expected 2, got more than 2"

);

543

this_val = val1 * val2;

555 "invalid number of nodes: expected 2, got 1"

);

561 "invalid number of nodes: " 562 "expected 2, got more than 2"

);

571 if

(val1 !=

round

(val1)) {

573 "MOD() function requires an integral operand: " 579 if

(val2 !=

round

(val2)) {

581 "MOD() function requires an integral base: " 590 "MOD() requires a positive base"

);

605 "invalid number of nodes: expected 2, got 1"

);

611 "invalid number of nodes: " 612 "expected 2, got more than 2"

);

618

this_val = val1 / val2;

629 "invalid number of nodes: expected 2, got 1"

);

635 "invalid number of nodes: " 636 "expected 2, got more than 2"

);

642

this_val = val1 + val2;

653 "invalid number of nodes: expected 2, got 1"

);

659 "invalid number of nodes: " 660 "expected 2, got more than 2"

);

666

this_val = val1 - val2;

676 for

( ; iter != end; ++iter) {

700 "invalid number of nodes: expected 1, got more than 1"

);

706 "invalid seg type - expected string"

);

708 const string

& s = node1.

().GetStrValue();

746 "invalid seg type: "

+ s);

755 const string

& which = node1.

().GetStrValue();

756 if

(which !=

"query"

&& which !=

"subject"

) {

758 "Invalid first argument to HAS_DESC_KEYWORD; must be " 759 "either 'query' or 'subject'"

);

765 "invalid number of nodes: expected 2, got 1"

);

768 const string

& keyword = node2.

().GetStrValue();

772 "invalid number of nodes: " 773 "expected 2, got more than 2"

);

776 bool

found_keyword =

false

;

785

desc_ci && !found_keyword; ++desc_ci)

788 switch

(desc_ci->Which()) {

790 if

(desc_ci->GetGenbank().IsSetKeywords()) {

791

keywords = &desc_ci->GetGenbank().GetKeywords();

796 if

(desc_ci->GetPir().IsSetKeywords()) {

797

keywords = &desc_ci->GetPir().GetKeywords();

802 if

(desc_ci->GetSp().IsSetKeywords()) {

803

keywords = &desc_ci->GetSp().GetKeywords();

808 if

(desc_ci->GetEmbl().IsSetKeywords()) {

809

keywords = &desc_ci->GetEmbl().GetKeywords();

814 if

(desc_ci->GetPrf().IsSetKeywords()) {

815

keywords = &desc_ci->GetPrf().GetKeywords();

826

found_keyword =

true

;

834 return

found_keyword ? 1 : 0;

842 const string

& which = node1.

().GetStrValue();

843 if

(which !=

"query"

&& which !=

"subject"

) {

845 "Invalid first argument to OVERLAPS_ANNOTS; must be " 846 "either 'query' or 'subject'"

);

854 "invalid number of nodes: expected 2, got 1"

);

857 const string

& regions_file = node2.

().GetStrValue();

861 "invalid number of nodes: " 862 "expected 2, got more than 2"

);

865 if

(!regions.count(idh)) {

871 return

overlap.

Empty

() ? 0 : 1;

875 "function not understood: "

function

);

885 if

(region_map.

empty

()) {

899 while

(!is->EndOfData()) {

904

regions_file +

" does not contain feature tables"

);

908

*feat->GetLocation().GetId());

909

region_map[idh] += feat->GetLocation().GetTotalRange();

933 bool

throw_if_not_found)

938 return

term_node.

().GetInt();

940 return

term_node.

().GetDouble();

961 "unexpected expression"

);

976 string

s = l_node.

().GetStrValue();

987

constant_seqid =

false

;

992

constant_seqid =

false

;

995

constant_seqid =

true

;

999 if

(constant_seqid) {

1000

(*m_DryRunOutput) <<

val

": SeqId, "

;

1003

(*m_DryRunOutput) <<

"No synonyms"

;

1005

(*m_DryRunOutput) <<

"synonyms "

;

1007 if

(syn_it != syns->begin()) {

1008

(*m_DryRunOutput) <<

","

;

1013

(*m_DryRunOutput) << endl;

1026 if

(other_idh == idh) {

1053 "Should reach this point only with equality"

);

1056 if

( !syns || syns->empty() ) {

1059 return

(syns->ContainsSynonym(other_idh) == !is_not);

1073

}

else if

(

val

.size() != 1) {

1075 "Valid strand values are '+', '-', 'b' and '?'"

);

1097 "Valid strand values are '+', '-, 'b'' and '?'"

);

1112 return

other_strand == strand ? !is_not : is_not;

1115 "unhandled parse node in expression"

);

1134 string

status_string =

"MODEL"

;

1152 "unhandled parse node in expression"

);

1169 return

((l_val == r_val) == !is_not);

1172 return

((l_val < r_val) == !is_not);

1175 return

((l_val <= r_val) == !is_not);

1178 return

((l_val > r_val) == !is_not);

1181 return

((l_val >= r_val) == !is_not);

1206 bool

between = (val1 <= this_val) && (this_val <= val2);

1207 return

(between == !is_not);

1241 switch

(node.

().GetType()) {

1256 "invalid number of nodes: expected 2, got 1"

);

1262 "invalid number of nodes: " 1263 "expected 2, got more than 2"

);

1283 "invalid number of nodes: expected 3, got 1"

);

1289 "invalid number of nodes: " 1290 "expected 3, got 2"

);

1297 "invalid number of nodes: " 1298 "expected 3, got more than 3"

);

1303 "unexpected expression"

);

1307

node2, node3, align);

1317

res =

(**iter, align);

1326

res &=

(**iter, align);

1338

res = !

(**iter, align);

1350

res =

(**iter, align);

1359

res |=