void test_online_fetchhead__colon_only_dst_refspec_creates_no_branch(void)
{
int refs;
fetchhead_test_clone();
refs = count_references();
fetchhead_test_fetch("refs/heads/first-merge:", FETCH_HEAD_EXPLICIT_DATA);
cl_assert_equal_i(refs, count_references());
}
void test_online_fetchhead__empty_dst_refspec_creates_no_branch(void)
{
git_reference *ref;
int refs;
fetchhead_test_clone();
refs = count_references();
fetchhead_test_fetch("refs/heads/first-merge", FETCH_HEAD_EXPLICIT_DATA);
cl_git_fail(git_branch_lookup(&ref, g_repo, "first-merge", GIT_BRANCH_ALL));
cl_assert_equal_i(refs, count_references());
}
void test_online_fetchhead__explicit_dst_refspec_creates_branch(void)
{
git_reference *ref;
int refs;
fetchhead_test_clone();
refs = count_references();
fetchhead_test_fetch("refs/heads/first-merge:refs/heads/explicit-refspec", FETCH_HEAD_EXPLICIT_DATA);
cl_git_pass(git_branch_lookup(&ref, g_repo, "explicit-refspec", GIT_BRANCH_ALL));
cl_assert_equal_i(refs + 1, count_references());
git_reference_free(ref);
}
extern void Tempest::search_fasta_database()
{
int i;
int iProtein;
int iLengthProtein;
int iLengthBuffer;
int iProteinBuffer = INITIAL_PROTEIN_BUFFER;
char sLineBuffer[LENGTH_INPUT_BUFFER+1];
char sProteinReference[MAX_LENGTH_REFERENCE+1];
char *sProteinSequence;
FILE *fp;
eObj *e;
float fProgress;
// Setup
// allocate working memory
if (0 == (sProteinSequence = (char*) malloc(iProteinBuffer*sizeof(char)))) {
fprintf(stderr, "\nERROR\tUnable to allocate memory for the active protein sequence.\n");
Tempest::tempest_exit(EXIT_FAILURE);
}
// calculate peptide mass range
// TODO: change if we allow negative mod masses
float fMaxAAModMass = 0.0f;
for (i=0; i<Tempest::params.iNumMods; i++) {
if (Tempest::params.tMods[i].cSymbol && Tempest::params.tMods[i].dMassDiff > fMaxAAModMass)
fMaxAAModMass = Tempest::params.tMods[i].dMassDiff;
}
float fMaxNtermModMass = 0.0f;
for (i=0; i<Tempest::params.numNtermModSites; i++)
if (Tempest::params.ntermModMasses[i] > fMaxNtermModMass)
fMaxNtermModMass = Tempest::params.ntermModMasses[i];
float fMaxCtermModMass = 0.0f;
for (i=0; i<Tempest::params.numCtermModSites; i++)
if (Tempest::params.ctermModMasses[i] > fMaxCtermModMass)
fMaxCtermModMass = Tempest::params.ctermModMasses[i];
float maxMaxTermModMass = fMaxNtermModMass > fMaxCtermModMass ? fMaxNtermModMass : fMaxCtermModMass;
float minMaxTermModMass = fMaxNtermModMass < fMaxCtermModMass ? fMaxNtermModMass : fMaxCtermModMass;
float fMaxMassDiff = 0.0;
int remainingMods = Tempest::params.iModificationsMax;
if (remainingMods && maxMaxTermModMass > fMaxAAModMass) {
fMaxMassDiff += maxMaxTermModMass;
remainingMods -= 1;
}
if (remainingMods && minMaxTermModMass > fMaxAAModMass) {
fMaxMassDiff += minMaxTermModMass;
remainingMods -= 1;
}
fMaxMassDiff += fMaxAAModMass * remainingMods;
if (Tempest::params.bPrecursorTolerancePPM) {
Tempest::data.fMinPrecursorMass -= Tempest::data.fMinPrecursorMass*Tempest::params.fPrecursorTolerance/1000000.0f;
Tempest::data.fMaxPrecursorMass += Tempest::data.fMaxPrecursorMass*Tempest::params.fPrecursorTolerance/1000000.0f;
}
else {
Tempest::data.fMinPrecursorMass -= Tempest::params.fPrecursorTolerance;
Tempest::data.fMaxPrecursorMass += Tempest::params.fPrecursorTolerance;
}
Tempest::data.dMinPeptideMass = Tempest::data.fMinPrecursorMass - fMaxMassDiff;
Tempest::data.dMaxPeptideMass = Tempest::data.fMaxPrecursorMass;
// open fasta file
// command line overrides param file
char* fastaFile = Tempest::args.sFasta == NULL ? Tempest::params.sFasta : Tempest::args.sFasta;
if (0 == (fp = (FILE *) fopen(fastaFile, "r"))) {
fprintf(stderr, "\nERROR\tUnable to open fasta database: %s\n", fastaFile);
Tempest::tempest_exit(EXIT_FAILURE);
}
// count proteins
Tempest::data.iNumProteins = count_references(fp);
if (Tempest::data.iNumProteins == 0) {
fprintf(stderr, "\nERROR\tNo proteins found in fasta database: %s\n", Tempest::args.sFasta);
Tempest::tempest_exit(EXIT_FAILURE);
}
// progress
if (Tempest::args.iPrintLevel && !Tempest::args.bPrintCandidates) {
printf(" » Digesting %d proteins... ", Tempest::data.iNumProteins);
}
// Get memory for the protein references
if (0 == (Tempest::data.sProteinReferences = (char *) malloc(Tempest::data.iNumProteins * MAX_LENGTH_REFERENCE * sizeof(char)))) {
fprintf(stderr, "\nERROR\tUnable to allocate memory for protein references.\n");
Tempest::tempest_exit(EXIT_FAILURE);
}
// parse fasta line by line
iProtein = 0;
iLengthProtein = 0;
sProteinSequence[0] = '\0';
while (fgets(sLineBuffer, LENGTH_INPUT_BUFFER, fp)) {
if (strlen(sLineBuffer) <= 0) continue;
// reference line
if ('>' == sLineBuffer[0]) {
// check for previous protein
if (iLengthProtein > 0) {
// process
strcpy(&Tempest::data.sProteinReferences[iProtein * MAX_LENGTH_REFERENCE * sizeof(char)], sProteinReference);
digest_protein(iProtein++, iLengthProtein, sProteinSequence);
if (Tempest::args.iPrintLevel && !Tempest::args.bPrintCandidates) {
fProgress = (100.0f * iProtein) / Tempest::data.iNumProteins;
if (fProgress - floor(fProgress) < 0.01f) printf("\b\b\b\b%*d%%", 3, (int) fProgress);
fflush(0);
}
// reset
iLengthProtein = 0;
sProteinSequence[0] = '\0';
}
// get next reference
parse_reference(sLineBuffer, sProteinReference);
}
// protein sequence line
else {
//get length
iLengthBuffer = (int) strlen(sLineBuffer);
//strip newlines
while(iLengthBuffer>0 && !isalnum(sLineBuffer[iLengthBuffer-1])) {
iLengthBuffer--;
}
if (iLengthBuffer <= 0)
continue;
// check new sequence length against buffer size
if (iLengthProtein + iLengthBuffer > iProteinBuffer) {
//grow protein sequence buffer
iProteinBuffer *= 2;
if (0 == (sProteinSequence = (char*) realloc(sProteinSequence, iProteinBuffer*sizeof(char)))) {
fprintf(stderr, "\nERROR\tCould not allocate memory for protein %s (length %d)\n", sProteinReference, iProteinBuffer);
Tempest::tempest_exit(EXIT_FAILURE);
}
}
// concatenate to sequence
strncat(sProteinSequence,sLineBuffer,iLengthBuffer);
iLengthProtein += iLengthBuffer;
}
}
// check for errors
if (ferror(fp)) {
fprintf(stderr, "\nERROR\tUnable to read from %s, while reading database.\n", Tempest::args.sFasta);
Tempest::tempest_exit(EXIT_FAILURE);
}
// Final protein
strncpy(&Tempest::data.sProteinReferences[iProtein * MAX_LENGTH_REFERENCE],sProteinReference,MAX_LENGTH_REFERENCE);
digest_protein(iProtein++, iLengthProtein, sProteinSequence);
if (Tempest::args.iPrintLevel && !Tempest::args.bPrintCandidates) {
fProgress = (100.0f * iProtein) / Tempest::data.iNumProteins;
printf("\b\b\b\b%*d%%", 3, (int) fProgress);
}
// Score Remaining Candidates
for(i=0;i<Tempest::data.iNumPrecursorBins;i++) {
for (e = Tempest::data.eScanIndex[i]; e; e = e->next) {
//printf("%d\t%d\n", gpu_info.iNumScoringKernels, i);
if (e->iNumBufferedCandidates > 0)
e->device->scoreCandidates(e);
}
}
// close fasta
fclose(fp);
// summary
if (Tempest::args.iPrintLevel && !Tempest::args.bPrintCandidates) {
printf("\n");
}
//cleanup
free(sProteinSequence);
}
