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(parent,

wxT

(

"Import file"

), wxEmptyString, wxEmptyString,

60 if

(

.ShowModal() != wxID_OK) {

75 if

(dlg.ShowModal() == wxID_OK) {

96 for

(

size_t

index = 0; index <

m_Ids

.size(); ++index) {

100

}

catch

(exception &) {

106 for

(

CBioseq_CI

bi(tse); bi && !found; ++bi) {

107 for

(

auto

&& id_it : bi->GetId()) {

109 if

(id2 && id1->

Match

(*id2)) {

133

wxArrayString choices;

134

choices.Add(

(

"All unmatched sequences are far pointers"

));

135

choices.Add(

(

"Remove all unmatched sequences from the alignment"

));

136

choices.Add(

(

"Read in a file that maps alignment IDs to sequence IDs"

));

143 msg

" from alignment in set"

;

145 int

answer = wxGetSingleChoiceIndex(

msg

(

"Unmatched sequences found"

), choices);

149 else if

(answer == 1) {

152 else if

(answer == 2) {

156 return

(answer != -1);

163

SFind_ID(

const string

& id_name) : m_IdName(id_name) {}

165 bool

operator() (

const

pair<string, string>& str_pair)

const 175 for

(CUpdateAlign::TIdToRowVec::iterator it = nonPresentIDs.begin();

176

it != nonPresentIDs.end(); ++it) {

177 if

(it->second == index) {

181 return

nonPresentIDs.end();

184 string

s_GetIDLabel(

const string

& initial_val)

186 string

id_label = initial_val;

187 size_t

pos = id_label.find(

"|"

);

188 if

(pos != string::npos) {

189

id_label = id_label.substr(pos + 1, string::npos);

205 int

dim =

static_cast<int>

(dense_seg.

().size());

209

rows.push_back(it.second);

218 auto

starts_it = dense_seg.

GetStarts

().begin();

220 for

(

int

seg = 0; seg < numseg; ++seg) {

221 for

(

int

index = 0; index < dim; ++index) {

222 if

(find(rows.begin(), rows.end(), index) == rows.end()) {

223

new_starts.push_back(*starts_it);

228

dense_seg.

SetStarts

().swap(new_starts);

234 auto

strand_it = dense_seg.

GetStrands

().begin();

236 for

(

int

seg = 0; seg < numseg; ++seg) {

237 for

(

int

index = 0; index < dim; ++index) {

238 if

(find(rows.begin(), rows.end(), index) == rows.end()) {

239

new_strands.push_back(*strand_it);

250 for

(

size_t

index = 0; index < dense_seg.

().size(); ++index) {

251 if

(find(rows.begin(), rows.end(), (

int

)index) == rows.end()) {

252

new_ids.push_back(dense_seg.

()[index]);

258

dense_seg.

().swap(new_ids);

274 size_t

previous_ids = dense_seg.

().size();

277 for

(

size_t

index = 0; index < dense_seg.

().

size

(); ++index) {

280 if

((

int

)index == it.second) {

281 string

farptrID =

"acc"

+ s_GetIDLabel(it.first);

283

new_ids.push_back(new_id);

290

new_ids.push_back(dense_seg.

()[index]);

294

dense_seg.

().swap(new_ids);

308

vector<pair<string, string>> oldId_toNewId;

309

wxFileDialog

(parent,

wxT

(

"Import ID map from file"

), wxEmptyString, wxEmptyString,

311

wxFD_OPEN | wxFD_FILE_MUST_EXIST);

312 if

(

.ShowModal() != wxID_OK) {

316

wxString path =

.GetPath();

317 if

(!path.IsEmpty()) {

322 string str

= *++line_reader;

326

list<string> row_values;

328 if

(row_values.size() == 2) {

329

oldId_toNewId.emplace_back(*row_values.begin(), *row_values.rbegin());

331

}

while

(!line_reader.

AtEOF

());

335 size_t

previous_ids = dense_seg.

().size();

338 string

unmapped_ids =

"("

;

341 for

(

size_t

index = 0; index < dense_seg.

().

size

(); ++index) {

344

new_ids.push_back(dense_seg.

()[index]);

347

std::function<

bool

(

const

pair<string, string>& str_pair)> tester = SFind_ID(id_it->first);

348 auto

map_it = find_if(begin(oldId_toNewId), end(oldId_toNewId), tester);

349 if

(map_it == oldId_toNewId.end()) {

351

unmapped_ids += id_it->first;

352

unmapped_ids +=

", "

;

353

new_ids.push_back(dense_seg.

()[index]);

357

new_ids.push_back(new_id);

362

dense_seg.