/**
* @brief synchronize a container
*
* @param[in] container The container to synchronize.
*
* @param[in] state The partial state to synch this container to.
*
* Synchronizes the container @a container and it's desired children to be as written down in
* the WindowStateBase @a state.
*
* The process involves 3 steps:
* 1. find or create any View or ContainerWidget objects required to fill the container.
* This will recurse into sub containers.
* 2. remove anything that is left over in the @a container.
* 3. add the found objects to @a container.
*/
void ModeSwitcher::synchronizeContainer(ContainerWidget* container, XmlState* state) {
QList< AbstractViewWidget* > newContents;
// We start by creating a list of what shall be inside the container. Thus we call the
// grabXXX methods which will search anything existing and give it to us (in case it is
// reusable). If grabXXX won't find anything, it will create something new.
// During this run, we recurse into sub-containers.
foreach (const XmlState::Ptr& ws, state->children()) {
AbstractViewWidget* next = NULL;
switch(ws->type()) {
case XmlState::WSView:
next = grabView(static_cast<XmlStateView*>(ws.data()));
break;
case XmlState::WSSplitter:
next = grabSplitter(static_cast<XmlStateSplitter*>(ws.data()));
synchronizeContainer(next->asContainerWidget(), ws.data());
break;
case XmlState::WSTab:
next = grabTab(static_cast<XmlStateTab* >(ws.data()));
synchronizeContainer(next->asContainerWidget(), ws.data());
break;
default:
break;
}
Q_ASSERT_X(next,
"synchronizeContainer",
qPrintable(
QString(QLatin1String("Invalid window state (%1) for child "
"\"%2\" of container \"%3\""))
.arg(ws->type())
.arg(ws->identifier().toString())
.arg(container->identifier().toString())
));
associateViewContainer(next, ws.data());
newContents.append(next);
}
// We have now taken all views that we want to reuse "out" of the container, leaving only
// the ones which are referenced by mExistingViews but shall no longer be inside this
// container. If they will not be reused until the end of this run, killUnsed() will take
// care of conserving their content and delete the views.
// So, all we need to do here is to take anything that's still inside the container away.
while(container->count()) {
container->takeAt(container->count() - 1);
}
// Insert all Views/Containers we want into the ContainerWidget
foreach (AbstractViewWidget* viewToAdd, newContents) {
container->add(viewToAdd);
}
int clean(const char *devFile, const char *logFile, const char *strR1, const char *strR2, const char *strSE, int tmpforcePairs, int tmpPolyATTrim) {
int forcePairs = tmpforcePairs;
FILE *f = fopen(devFile, "r");
//FILE *f = stderr;
FILE *R1 = NULL;
FILE *R2 = NULL;
FILE *SE = NULL;
FILE *log = NULL;
struct reads r;
struct stats s;
int sum = 0, R1_len = 0, R2_len = 0, SE_len = 0;
statsConstruct(&s);
PolyATTrim = tmpPolyATTrim;
while (grabTab(f, &r, &s)) {
if ((r.r2).r_header != NULL && (r.r1).r_header != NULL) {
s.pe_kept++;
if (R1 == NULL) {
R1 = fopen(strR1, "a");
}
if (R2 == NULL) {
R2 = fopen(strR2, "a");
}
if ((r.r1).r_header[0] == '@') {
if ((r.r1).r_header[strlen((r.r1).r_header)-1] == '1') {
fprintf(R1, "%s\n%s\n+\n%s\n", (r.r1).r_header, (r.r1).r_seq, (r.r1).r_qual);
(r.r2).r_header[strlen((r.r2).r_header)-1] = '2';
fprintf(R2, "%s\n%s\n+\n%s", (r.r2).r_header, (r.r2).r_seq, (r.r2).r_qual);
} else {
fprintf(R1, "%s/1\n%s\n+\n%s\n", (r.r1).r_header, (r.r1).r_seq, (r.r1).r_qual);
fprintf(R2, "%s/2\n%s\n+\n%s", (r.r2).r_header, (r.r2).r_seq, (r.r2).r_qual);
}
} else {
fprintf(R1, "@%s/1\n%s\n+\n%s\n", (r.r1).r_header, (r.r1).r_seq, (r.r1).r_qual);
fprintf(R2, "@%s/2\n%s\n+\n%s", (r.r2).r_header, (r.r2).r_seq, (r.r2).r_qual);
}
} else if (forcePairs && (r.r1).r_header != NULL) {
s.numForcedPairs++;
int loc = (strlen((r.r1).r_seq))/2;
char cSeq = (r.r1).r_seq[loc];
char cQual = (r.r1).r_qual[loc];
if (R1 == NULL) {
R1 = fopen(strR1, "a");
}
if (R2 == NULL) {
R2 = fopen(strR2, "a");
}
if ((r.r1).r_header[0] == '@') {
(r.r1).r_seq[loc] = '\0';
(r.r1).r_qual[loc] = '\0';
fprintf(R1, "%s/1\n%s\n+\n%s\n", (r.r1).r_header, (r.r1).r_seq, (r.r1).r_qual);
(r.r1).r_seq[loc] = cSeq;
(r.r1).r_qual[loc] = cQual;
fprintf(R2, "%s/2\n%s\n+\n%s", (r.r1).r_header, reverseComp(&((r.r1).r_seq)[loc]), reverse(&((r.r1).r_qual)[loc]));
} else {
(r.r1).r_seq[loc] = '\0';
(r.r1).r_qual[loc] = '\0';
fprintf(R1, "@%s/1\n%s\n+\n%s\n", (r.r1).r_header, (r.r1).r_seq, (r.r1).r_qual);
(r.r1).r_seq[loc] = cSeq;
(r.r1).r_qual[loc] = cQual;
fprintf(R2, "@%s/2\n%s\n+\n%s", (r.r1).r_header, reverseComp(&((r.r1).r_seq)[loc]), reverse(&((r.r1).r_qual)[loc]));
}
} else if ((r.r1).r_header != NULL) {
if (SE == NULL) {
SE = fopen(strSE, "a");
}
s.se_kept++;
if ((r.r1).r_header[0] == '@') {
fprintf(SE, "%s\n%s\n+\n%s", (r.r1).r_header, (r.r1).r_seq, (r.r1).r_qual);
} else {
fprintf(SE, "@%s\n%s\n+\n%s", (r.r1).r_header, (r.r1).r_seq, (r.r1).r_qual);
}
if ((r.r1).r_qual[strlen((r.r1).r_qual)-1] != '\n') {
fprintf(SE, "\n");
}
}
}
if (log == NULL) {
log = fopen(logFile, "a");
}
for (sum = 0; sum < 700; sum++) {
R1_len += (s.R1_length[sum] * sum);
R2_len += (s.R2_length[sum] * sum);
SE_len += (s.SE_length[sum] * sum);
}
fprintf(log, "A\tT\tG\tC\tN\tPolyA_Removed_Reads\tPolyT_Removed_Reads\tShort_discarded\tPE_Kept\tSE_Kept\tForced_Pairs\tR1_Ave_Len\tR2_Ave_Len\tSE_Ave_Len\tAverageQual\n");
fprintf(log, "%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t%llu\t\
%.2f\t%.2f\t%.2f\t%.2f\n",
s.A, s.T, s.G, s.C, s.N, s.polyATrimmed, s.polyTTrimmed, s.r1_discarded + s.r2_discarded + s.se_discarded, s.pe_kept, s.se_kept, s.numForcedPairs,
(float)R1_len/(float)(s.pe_kept), (float)R2_len/(float)(s.pe_kept), (float)SE_len/(float)(s.se_kept), (float)((float)(s.qualTotal)/(float)(s.A + s.T + s.C + s.G + s.N)));
if (f != NULL) {
fclose(f);
}
if (R1 != NULL) {
fclose(R1);
fclose(R2);
}
if (SE != NULL) {
fclose(SE);
}
if (log != NULL) {
fclose(log);
}
return 1;
}
