~ubuntu-branches/ubuntu/saucy/ncbi-tools6/saucy-proposed

ErrPostEx(SEV_ERROR, 0, 0, "Dramatic Suggest failure: Please check reverse\n on both aa and DNA sequences.\nPlease check that the proper sequences selected.\n");

1420

1173

if (min_exon_from_form > -1 || Min_val > 0 || Max_val < dna_len){

1421

1174

ErrPostEx(SEV_ERROR, 0, 0, "Since Parameters were set, also check them on the verify form.\n");

1422

1175

}

1176

#endif

1423

1177

}

1424

1178

1425

1179

if (Min_val <=0)

1437

1191

#ifdef CdCycle

1438

1192

ErrPostEx(SEV_INFO, 0, 0, "Ending Suggest");

1439

1193

#endif

1440

return 0;

1194

return rsult;

1441

1195

Error:

1442

1196

cleanup();

1443

1197

#ifdef CdCycle

1596

1350

1597

1351

*****************************************************************************/

1598

1352

1599

static void Suggest_Intervals (SuggestRecPtr sugrp,

1600

SuggestOutputPtr pSuggestOut, Int4 num_nuc)

1353

static Int2 Suggest_Intervals (SuggestRecPtr sugrp, SuggestOutputPtr pSuggestOut, Int4 num_nuc)

1601

1354

{

1602

1355

Boolean goOn;

1603

1356

Int4 i;

1607

1360

SeqRecPtr nucleotide;

1608

1361

SeqRecPtr protein;

1609

1362

Int4 tripdex;

1363

Int2 rsult = 0;

1610

1364

struct trip_node *h, *oh;

1611

1365

1612

1366

if (sugrp != NULL) {

1616

1370

geneticCode = sugrp->geneticCode;

1617

1371

if (nucleotide != NULL && protein != NULL && geneticCode != NULL) {

1618

1372

if ((nucleotide->length +1) / 3 < protein->length) {

1373

#ifdef DEBUG_TOO_SHORT

1619

1374

ReportSuggestIntervalsError (nucleotide, "Nucleotide is too short to encode protein");

1375

#endif

1376

rsult = 2;

1620

1377

goOn = FALSE;

1621

1378

}

1622

1379

if (nucleotide->length < 18) {

1380

#ifdef DEBUG_TOO_SHORT

1623

1381

ReportSuggestIntervalsError (nucleotide, "Nucleotide length is too short");

1382

#endif

1383

rsult = 3;

1624

1384

goOn = FALSE;

1625

1385

}

1626

1386

if (protein->length < 6) {

1387

#ifdef DEBUG_TOO_SHORT

1627

1388

ReportSuggestIntervalsError (protein, "Protein length is too short");

1389

#endif

1390

rsult = 4;

1628

1391

goOn = FALSE;

1629

1392

}

1630

1393

1686

1449

nt_id_seq[nt] = nt;

1687

1450

}

1688

1451

1689

APT_suggest (pSuggestOut, num_nuc);

1452

if (APT_suggest (pSuggestOut, num_nuc) != 0) {

1453

rsult = 1;

1454

}

1690

1455

1691

1456

m_stk = MemFree (m_stk);

1692

1457

1717

1482

1718

1483

}

1719

1484

}

1485

return rsult;

1720

1486

}

1721

1487

1722

1488

/* default code (code 0) means use the standard code (code 1) */

1747

1513

1748

1514

*****************************************************************************/

1749

1515

1750

Int4 Get_Genetic_Code (Int4 code, SuggestRecPtr sugrp)

1516

extern Int4 Get_Genetic_Code (Int4 code, SuggestRecPtr sugrp)

1751

1517

1752

1518

{

1753

1519

GeneticCodePtr codes;

1815

1581

* FALSE otherwise

1816

1582

1817

1583

\*----------------------------------------------------------------------------*/

1818

Boolean

1819

InitSuggest(void)

1584

extern Boolean InitSuggest (void)

1820

1585

{

1821

1586

if (!AllObjLoad ()) {

1822

1587

Message (MSG_FATAL, "AllObjLoad failed");

1866

1631

* FALSE - otherwise;

1867

1632

1868

1633

\*----------------------------------------------------------------------------*/

1869

Boolean

1870

ProcessData(SuggestOutputPtr pSuggestOut, Boolean clearNucSeqRec)

1634

1635

Int2 ProcessData (SuggestOutputPtr pSuggestOut, Boolean clearNucSeqRec)

1871

1636

{

1872

1637

Int4 num_nuc;

1873

1638

Int4 num_prt;

1874

1639

Int4 len;

1875

1640

Int4 i;

1641

Int2 rsult = 0;

1876

1642

1877

1643

suggestRec.protein.sequence = MemFree(suggestRec.protein.sequence);

1878

1644

suggestRec.protein.length = 0;

1882

1648

BSSeek(suggestRec.protein.rawSeq, 0L, 0);

1883

1649

1884

1650

for (i = 0; i < num_prt; i++) {

1885

OutProteinID(pSuggestOut, i);

1651

OutProteinID (pSuggestOut, i);

1886

1652

BSRead(suggestRec.protein.segLens, &len, sizeof(len));

1887

1653

suggestRec.protein.sequence = MemNew((len + 1) * sizeof(Uint1));

1888

1654

len = BSRead(suggestRec.protein.rawSeq,

1889

1655

suggestRec.protein.sequence, len);

1890

1656

suggestRec.protein.length = len;

1891

Suggest_Intervals(&suggestRec, pSuggestOut, num_nuc);

1657

rsult = Suggest_Intervals(&suggestRec, pSuggestOut, num_nuc);

1892

1658

suggestRec.minVal = 0L;

1893

1659

suggestRec.maxVal = 0L;

1894

1660

suggestRec.tooShort = 0L;

1904

1670

suggestRec.geneticCode = (CharPtr)MemFree(suggestRec.geneticCode);

1905

1671

genetic_code = NULL;

1906

1672

1907

return TRUE;

1673

return rsult;

1908

1674

}

1909

1675

1910

1676

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