Changeset 6287 for branches/stable_5.0/READSEQ/ureadseq.c
- Timestamp:
- 01/12/09 11:10:13 (2 years ago)
- Files:
-
- 1 modified
-
branches/stable_5.0/READSEQ/ureadseq.c (modified) (30 diffs)
Legend:
- Unmodified
- Added
- Removed
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branches/stable_5.0/READSEQ/ureadseq.c
r5155 r6287 70 70 71 71 #ifndef Local 72 # define Local static/* local functions */72 # define Local static /* local functions */ 73 73 #endif 74 74 … … 144 144 } 145 145 146 Local void getline(struct ReadSeqVars *V)146 Local void GetLine(struct ReadSeqVars *V) 147 147 { 148 148 readline(V->f, V->s, &V->linestart); 149 149 } 150 150 151 Local void un getline(struct ReadSeqVars *V)151 Local void unGetLine(struct ReadSeqVars *V) 152 152 { 153 153 fseek(V->f, V->linestart, 0); … … 227 227 if (addfirst) addseq(V->s, V); 228 228 do { 229 getline(V);229 GetLine(V); 230 230 V->done = feof(V->f); 231 231 V->done |= (*endTest)( &addend, &ungetend, V); … … 238 238 else { 239 239 V->allDone = (V->nseq >= V->choice); 240 if (V->allDone && ungetend) un getline(V);240 if (V->allDone && ungetend) unGetLine(V); 241 241 } 242 242 } … … 258 258 while (!V->allDone) { 259 259 do { 260 getline(V);260 GetLine(V); 261 261 for (si= V->s; *si != 0 && *si < ' '; si++) *si= ' '; /* drop controls */ 262 262 if (*si == 0) *V->s= 0; /* chop line to empty */ … … 284 284 285 285 while (!V->allDone) { 286 getline(V);286 GetLine(V); 287 287 if (strstr(V->s,"; DNA sequence ") == V->s) 288 288 strcpy(V->seqid, (V->s)+16); … … 290 290 strcpy(V->seqid, (V->s)+1); 291 291 while ((!feof(V->f)) && (*V->s == ';')) { 292 getline(V);292 GetLine(V); 293 293 } 294 294 if (feof(V->f)) V->allDone = true; … … 310 310 while (!V->allDone) { 311 311 while (! (feof(V->f) || strstr(V->s,"ENTRY") || strstr(V->s,"SEQUENCE")) ) 312 getline(V);312 GetLine(V); 313 313 strcpy(V->seqid, (V->s)+16); 314 314 while (! (feof(V->f) || strstr(V->s,"SEQUENCE") == V->s)) 315 getline(V);315 GetLine(V); 316 316 readLoop(0, false, endPIR, V); 317 317 … … 319 319 while (! (feof(V->f) || ((*V->s != 0) 320 320 && (strstr( V->s,"ENTRY") == V->s)))) 321 getline(V);321 GetLine(V); 322 322 } 323 323 if (feof(V->f)) V->allDone = true; … … 342 342 strcpy(V->seqid, (V->s)+12); 343 343 while (! (feof(V->f) || strstr(V->s,"ORIGIN") == V->s)) 344 getline(V);344 GetLine(V); 345 345 readLoop(0, false, endGB, V); 346 346 … … 348 348 while (! (feof(V->f) || ((*V->s != 0) 349 349 && (strstr( V->s, "LOCUS") == V->s)))) 350 getline(V);350 GetLine(V); 351 351 } 352 352 if (feof(V->f)) V->allDone = true; … … 382 382 while (!V->allDone) { 383 383 strcpy(V->seqid, (V->s)+4); 384 getline(V); /*skip title-junk line*/384 GetLine(V); /*skip title-junk line*/ 385 385 readLoop(0, false, endNBRF, V); 386 386 if (!V->allDone) { 387 387 while (!(feof(V->f) || (*V->s != 0 && *V->s == '>'))) 388 getline(V);388 GetLine(V); 389 389 } 390 390 if (feof(V->f)) V->allDone = true; … … 408 408 if (!V->allDone) { 409 409 while (!(feof(V->f) || ((*V->s != 0) && (*V->s == '>')))) 410 getline(V);410 GetLine(V); 411 411 } 412 412 if (feof(V->f)) V->allDone = true; … … 428 428 strcpy(V->seqid, (V->s)+5); 429 429 do { 430 getline(V);430 GetLine(V); 431 431 } while (!(feof(V->f) | (strstr(V->s,"SQ ") == V->s))); 432 432 … … 435 435 while (!(feof(V->f) | 436 436 ((*V->s != '\0') & (strstr(V->s,"ID ") == V->s)))) 437 getline(V);437 GetLine(V); 438 438 } 439 439 if (feof(V->f)) V->allDone = true; … … 455 455 456 456 while (!V->allDone) { 457 getline(V); /*s == "seqLen seqid string..."*/457 GetLine(V); /*s == "seqLen seqid string..."*/ 458 458 strcpy(V->seqid, (V->s)+6); 459 459 readLoop(0, false, endZuker, V); … … 461 461 while (!(feof(V->f) | 462 462 ((*V->s != '\0') & (*V->s == '(')))) 463 getline(V);463 GetLine(V); 464 464 } 465 465 if (feof(V->f)) V->allDone = true; … … 504 504 addseq(V->s, V); 505 505 V->done = feof(V->f); 506 getline(V);506 GetLine(V); 507 507 } while (!V->done); 508 508 if (V->choice == kListSequences) addinfo(V->seqid, V); … … 516 516 10nov91: Reading GCG files casued duplication of last line when 517 517 EOF followed that line !!! 518 fix: getline now sets *V->s = 0518 fix: GetLine now sets *V->s = 0 519 519 */ 520 520 char *si; … … 530 530 do { 531 531 V->done = feof(V->f); 532 getline(V);532 GetLine(V); 533 533 if (!V->done) addseq((V->s), V); 534 534 } while (!V->done); … … 549 549 rewind(V->f); V->nseq= 0; 550 550 do { 551 getline(V);551 GetLine(V); 552 552 V->done = feof(V->f); 553 553 … … 632 632 rewind(V->f); V->nseq= 0; 633 633 do { 634 getline(V);634 GetLine(V); 635 635 V->done = feof(V->f); 636 636 … … 703 703 704 704 do { 705 getline(V);705 GetLine(V); 706 706 V->done = feof(V->f); 707 707 … … 784 784 indata= true; /* call here after we find "matrix" */ 785 785 do { 786 getline(V);786 GetLine(V); 787 787 V->done = feof(V->f); 788 788 … … 869 869 870 870 do { 871 getline(V);871 GetLine(V); 872 872 V->done = feof(V->f); 873 873 … … 922 922 skipwhitespace(si); 923 923 V->topseqlen= atol(si); 924 getline(V);924 GetLine(V); 925 925 while (!V->allDone) { 926 926 V->seqlencount= 0; … … 953 953 else { 954 954 955 for (l = skiplines_; l > 0; l--) getline( V);955 for (l = skiplines_; l > 0; l--) GetLine( V); 956 956 957 957 do { 958 getline( V);958 GetLine( V); 959 959 for (l= strlen(V->s); (l > 0) && (V->s[l] == ' '); l--) ; 960 960 } while ((l == 0) && !feof(V->f)); … … 981 981 /* rewind(V->f); V->nseq= 0; ?? assume it is at top ?? skiplines ... */ 982 982 while (!done) { 983 getline( V);983 GetLine( V); 984 984 tolowerstr( V->s); 985 985 if (strstr( V->s, "matrix")) done= true; … … 1013 1013 1014 1014 case kFitch : 1015 strcpy(V->seqid, V->s); getline(V);1015 strcpy(V->seqid, V->s); GetLine(V); 1016 1016 readFitch(V); 1017 1017 break; … … 1021 1021 gotuw = (strstr(V->s,"..") != NULL); 1022 1022 if (gotuw) readUWGCG(V); 1023 getline(V);1023 GetLine(V); 1024 1024 } while (!(feof(V->f) || V->allDone)); 1025 1025 break;
