DuplicateMerger::DuplicateMerger(QWidget *parent) : QDialog(parent)
{
setAttribute(Qt::WA_DeleteOnClose);
resize(800,600);
QWidget* top = new QWidget(this);
QVBoxLayout* topLayout = new QVBoxLayout(top);
setLayout(topLayout);
topLayout->addWidget(top);
QString txt = i18n("<p>Below is a list of all images that are duplicate in your database.<br/>"
"Select which you want merged, and which of the duplicates should be kept.<br/>"
"The tag and description from the deleted images will be transferred to the kept image</p>");
QLabel* label = new QLabel(txt);
QFont fnt = font();
fnt.setPixelSize(18);
label->setFont(fnt);
topLayout->addWidget(label);
m_trash = new QRadioButton(i18n("Move to &trash"));
m_deleteFromDisk = new QRadioButton(i18n("&Delete from disk"));
QRadioButton* blockFromDB = new QRadioButton(i18n("&Block from database"));
m_trash->setChecked(true);
topLayout->addSpacing(10);
topLayout->addWidget(m_trash);
topLayout->addWidget(m_deleteFromDisk);
topLayout->addWidget(blockFromDB);
topLayout->addSpacing(10);
QScrollArea* scrollArea = new QScrollArea;
topLayout->addWidget(scrollArea);
scrollArea->setWidgetResizable(true);
m_container = new QWidget(scrollArea);
m_scrollLayout = new QVBoxLayout(m_container);
scrollArea->setWidget(m_container);
m_selectionCount = new QLabel;
topLayout->addWidget(m_selectionCount);
QDialogButtonBox* buttonBox = new QDialogButtonBox();
m_selectAllButton = buttonBox->addButton(i18n("Select &All"), QDialogButtonBox::YesRole);
m_selectNoneButton = buttonBox->addButton(i18n("Select &None"), QDialogButtonBox::NoRole);
m_okButton = buttonBox->addButton(QDialogButtonBox::Ok);
m_cancelButton = buttonBox->addButton(QDialogButtonBox::Cancel);
connect(m_selectAllButton, SIGNAL(clicked()), this, SLOT(selectAll()));
connect(m_selectNoneButton, SIGNAL(clicked()), this, SLOT(selectNone()));
connect(m_okButton, SIGNAL(clicked()), this, SLOT(go()));
connect(m_cancelButton, SIGNAL(clicked()), this, SLOT(reject()));
topLayout->addWidget(buttonBox);
findDuplicates();
}
int main(void)
{
int Input[] = {4,3,2,7,8,2,3,1};
int InputSize = sizeof(Input)/sizeof(int);
printf("The input is:\n");
printArray(Input, InputSize);
int returnSize;
int *result = findDuplicates(Input, InputSize, &returnSize);
printf("The duplicated numbers are:\n");
printArray(result, returnSize);
return 0;
}
void ContactWidget::silentSetId(const int pId)
{
disconnect(_first, SIGNAL(lostFocus()), this, SLOT(findDuplicates()));
disconnect(_last, SIGNAL(lostFocus()), this, SLOT(findDuplicates()));
if (pId == -1 || pId == 0)
{
_id = -1;
_valid = false;
connect(_first, SIGNAL(lostFocus()), this, SLOT(findDuplicates()));
connect(_last, SIGNAL(lostFocus()), this, SLOT(findDuplicates()));
clear();
}
else if (pId == _id)
return;
else
{
XSqlQuery idQ;
idQ.prepare(_query + " WHERE cntct_id = :id;");
idQ.bindValue(":id", pId);
idQ.exec();
if (idQ.first())
{
_ignoreSignals = true;
_id = pId;
_valid = true;
_number->setText(idQ.value("cntct_number").toString());
_honorific->setEditText(idQ.value("cntct_honorific").toString());
_first->setText(idQ.value("cntct_first_name").toString());
_middle->setText(idQ.value("cntct_middle").toString());
_last->setText(idQ.value("cntct_last_name").toString());
_suffix->setText(idQ.value("cntct_suffix").toString());
_initials->setText(idQ.value("cntct_initials").toString());
_crmAcct->setId(idQ.value("cntct_crmacct_id").toInt());
_title->setText(idQ.value("cntct_title").toString());
_phone->setText(idQ.value("cntct_phone").toString());
_phone2->setText(idQ.value("cntct_phone2").toString());
_fax->setText(idQ.value("cntct_fax").toString());
_email->setText(idQ.value("cntct_email").toString());
_webaddr->setText(idQ.value("cntct_webaddr").toString());
_address->setId(idQ.value("cntct_addr_id").toInt());
_active->setChecked(idQ.value("cntct_active").toBool());
_notes = idQ.value("cntct_notes").toString();
_owner->setUsername(idQ.value("cntct_owner_username").toString());
if (_mapper->model())
{
_mapper->model()->setData(_mapper->model()->index(_mapper->currentIndex(),_mapper->mappedSection(_number)), _number->text()); _mapper->model()->setData(_mapper->model()->index(_mapper->currentIndex(),_mapper->mappedSection(_number)), _number->text());
_mapper->model()->setData(_mapper->model()->index(_mapper->currentIndex(),_mapper->mappedSection(_honorific)), _honorific->currentText());
_mapper->model()->setData(_mapper->model()->index(_mapper->currentIndex(),_mapper->mappedSection(_first)), _first->text());
_mapper->model()->setData(_mapper->model()->index(_mapper->currentIndex(),_mapper->mappedSection(_last)), _last->text());
_mapper->model()->setData(_mapper->model()->index(_mapper->currentIndex(),_mapper->mappedSection(_initials)), _initials->text());
_mapper->model()->setData(_mapper->model()->index(_mapper->currentIndex(),_mapper->mappedSection(this)), _number->text());
_mapper->model()->setData(_mapper->model()->index(_mapper->currentIndex(),_mapper->mappedSection(_title)), _title->text());
_mapper->model()->setData(_mapper->model()->index(_mapper->currentIndex(),_mapper->mappedSection(_phone)), _phone->text());
_mapper->model()->setData(_mapper->model()->index(_mapper->currentIndex(),_mapper->mappedSection(_phone2)), _phone2->text());
_mapper->model()->setData(_mapper->model()->index(_mapper->currentIndex(),_mapper->mappedSection(_fax)), _fax->text());
_mapper->model()->setData(_mapper->model()->index(_mapper->currentIndex(),_mapper->mappedSection(_email)), _email->text());
_mapper->model()->setData(_mapper->model()->index(_mapper->currentIndex(),_mapper->mappedSection(_webaddr)), _webaddr->text());
}
_ignoreSignals = false;
}
else if (idQ.lastError().type() != QSqlError::NoError)
QMessageBox::critical(this, tr("A System Error Occurred at %1::%2.")
.arg(__FILE__)
.arg(__LINE__),
idQ.lastError().databaseText());
_valid = true;
}
_changed=false;
// _parsed = TRUE;
}
void ContactWidget::init()
{
_ignoreSignals = false;
_titleSingular = tr("Contact");
_titlePlural = tr("Contacts");
_query = "SELECT cntct.*, crmacct_name "
"FROM cntct LEFT OUTER JOIN crmacct ON (cntct_crmacct_id = crmacct_id) ";
_layoutDone = false;
_minimalLayout = false;
_searchAcctId = -1;
_list = new QPushButton(tr("..."), this);
_list->setObjectName("_list");
_list->setSizePolicy(QSizePolicy::Fixed, QSizePolicy::Fixed);
#ifndef Q_WS_MAC
_list->setMaximumWidth(25);
#else
_list->setMinimumWidth(60);
_list->setMinimumHeight(32);
#endif
_grid->removeWidget(_label); // will be reinserted
_grid->removeWidget(_description);
delete _description;
_description = 0;
_grid->setMargin(0);
_grid->setSpacing(2);
_nameBox = new QHBoxLayout;
_nameBox->setSpacing(2);
_initialsBox = new QHBoxLayout;
_initialsBox->setSpacing(2);
_titleBox = new QHBoxLayout;
_titleBox->setSpacing(2);
_change = new XLineEdit(this);
_numberLit = new QLabel(tr("Number:"), this);
_numberLit->setObjectName("_numberLit");
_number = new XLineEdit(this, "_number");
_change->hide();
_number->hide();
_numberLit->hide();
_nameLit = new QLabel(tr("Name:"), this);
_nameLit->setObjectName("_nameLit");
_honorific = new XComboBox(this, "_honorific");
_first = new XLineEdit(this, "_first");
_middle = new XLineEdit(this, "_middle");
_middle->setFixedWidth(20);
_last = new XLineEdit(this, "_last");
_suffix = new XLineEdit(this, "_suffix");
_suffix->setFixedWidth(30);
_initialsLit = new QLabel(tr("Initials:"), this);
_initialsLit->setObjectName("_initialsLit");
_initials = new XLineEdit(this, "_initials");
_initials->setFixedWidth(_initials->size().width() / 3);
_titleLit = new QLabel(tr("Job Title:"), this);
_titleLit->setObjectName("_titleLit");
_title = new XLineEdit(this, "_title");
_mapper = new XDataWidgetMapper(this);
//_nameBox->addWidget(_nameLit, 0);
_nameBox->addWidget(_honorific, 0);
_nameBox->addWidget(_first, 1);
_nameBox->addWidget(_middle, 0);
_nameBox->addWidget(_last, 2);
_nameBox->addWidget(_suffix, 0);
_nameBox->addWidget(_list, 0, Qt::AlignRight);
//_initialsBox->addWidget(_initialsLit, 0);
_initialsBox->addWidget(_initials, 0);
_initialsBox->addStretch(0);
//_titleBox->addWidget(_titleLit, 0);
_titleBox->addWidget(_title, 2);
_buttonBox = new QGridLayout;
_crmAcct = new CRMAcctCluster(this, "_crmAcct");
_active = new QCheckBox(tr("Active"), this);
_active->setObjectName("_active");
_owner = new UsernameCluster(this, "_owner");
_buttonBox->addWidget(_crmAcct, 0, 1, Qt::AlignTop);
_buttonBox->addWidget(_owner, 0, 2, Qt::AlignTop);
_phoneLit = new QLabel(tr("Voice:"), this);
_phoneLit->setObjectName("_phoneLit");
_phone = new XLineEdit(this, "_phone");
_phone2Lit = new QLabel(tr("Alternate:"), this);
_phone2Lit->setObjectName("_phone2Lit");
_phone2 = new XLineEdit(this, "_phone2");
_faxLit = new QLabel(tr("Fax:"), this);
_faxLit->setObjectName("_faxLit");
_fax = new XLineEdit(this, "_fax");
_emailLit = new QLabel(tr("E-Mail:"), this);
_emailLit->setObjectName("_emailLit");
_email = new XLineEdit(this, "_email");
_webaddrLit = new QLabel(tr("Web:"), this);
_webaddrLit->setObjectName("_webaddrLit");
_webaddr = new XLineEdit(this, "_webaddr");
_address = new AddressCluster(this, "_address");
#if defined Q_OS_MAC
_honorific->setMinimumHeight(26);
_first->setMinimumHeight(22);
_middle->setMinimumHeight(22);
_last->setMinimumHeight(22);
_suffix->setMinimumHeight(22);
_phone->setMinimumWidth(140);
_crmAcct->setMinimumHeight(72);
#endif
QPalette p = _email->palette();
p.setColor(QPalette::Text, Qt::blue);
_email->setPalette(p);
_webaddr->setPalette(p);
QFont newFont = _email->font();
newFont.setUnderline(TRUE);
_email->setFont(newFont);
_webaddr->setFont(newFont);
_numberLit->setAlignment(Qt::AlignRight | Qt::AlignVCenter);
_label->setAlignment(Qt::AlignLeft | Qt::AlignVCenter);
_nameLit->setAlignment(Qt::AlignRight | Qt::AlignVCenter);
_titleLit->setAlignment(Qt::AlignRight | Qt::AlignVCenter);
_phoneLit->setAlignment(Qt::AlignRight | Qt::AlignVCenter);
_phone2Lit->setAlignment(Qt::AlignRight | Qt::AlignVCenter);
_faxLit->setAlignment(Qt::AlignRight | Qt::AlignVCenter);
_emailLit->setAlignment(Qt::AlignRight | Qt::AlignVCenter);
_initialsLit->setAlignment(Qt::AlignRight | Qt::AlignVCenter);
_webaddrLit->setAlignment(Qt::AlignRight | Qt::AlignVCenter);
_honorific->setEditable(true);
_honorific->setType(XComboBox::Honorifics);
_crmAcct->setLabel(tr("CRM Account:"));
_owner->setLabel(tr("Owner:"));
layout();
connect(_list, SIGNAL(clicked()), this, SLOT(sEllipses()));
connect(_honorific, SIGNAL(newID(int)), this, SIGNAL(changed()));
connect(_first, SIGNAL(textChanged(const QString&)), this, SIGNAL(changed()));
connect(_middle, SIGNAL(textChanged(const QString&)), this, SIGNAL(changed()));
connect(_last, SIGNAL(textChanged(const QString&)), this, SIGNAL(changed()));
connect(_suffix, SIGNAL(textChanged(const QString&)), this, SIGNAL(changed()));
connect(_initials, SIGNAL(textChanged(const QString&)), this, SIGNAL(changed()));
connect(_crmAcct, SIGNAL(newId(int)), this, SIGNAL(changed()));
connect(_title, SIGNAL(textChanged(const QString&)), this, SIGNAL(changed()));
connect(_phone, SIGNAL(textChanged(const QString&)), this, SIGNAL(changed()));
connect(_phone2, SIGNAL(textChanged(const QString&)), this, SIGNAL(changed()));
connect(_fax, SIGNAL(textChanged(const QString&)), this, SIGNAL(changed()));
connect(_email, SIGNAL(textChanged(const QString&)), this, SIGNAL(changed()));
connect(_webaddr, SIGNAL(textChanged(const QString&)), this, SIGNAL(changed()));
connect(_address, SIGNAL(changed()), this, SIGNAL(changed()));
connect(this, SIGNAL(changed()), this, SLOT(setChanged()));
connect(_honorific, SIGNAL(newID(int)), this, SLOT(sCheck()));
connect(_first, SIGNAL(lostFocus()), this, SLOT(sCheck()));
connect(_middle, SIGNAL(lostFocus()), this, SLOT(sCheck()));
connect(_last, SIGNAL(lostFocus()), this, SLOT(sCheck()));
connect(_suffix, SIGNAL(lostFocus()), this, SLOT(sCheck()));
connect(_initials, SIGNAL(lostFocus()), this, SLOT(sCheck()));
connect(_crmAcct, SIGNAL(newId(int)), this, SLOT(sCheck()));
connect(_title, SIGNAL(lostFocus()), this, SLOT(sCheck()));
connect(_phone, SIGNAL(lostFocus()), this, SLOT(sCheck()));
connect(_phone2, SIGNAL(lostFocus()), this, SLOT(sCheck()));
connect(_fax, SIGNAL(lostFocus()), this, SLOT(sCheck()));
connect(_email, SIGNAL(lostFocus()), this, SLOT(sCheck()));
connect(_webaddr, SIGNAL(lostFocus()), this, SLOT(sCheck()));
connect(_address, SIGNAL(changed()), this, SLOT(sCheck()));
connect(_email, SIGNAL(doubleClicked()), this, SLOT(sLaunchEmail()));
connect(_webaddr, SIGNAL(doubleClicked()), this, SLOT(sLaunchWebaddr()));
setListVisible(true);
connect(_first, SIGNAL(lostFocus()), this, SLOT(findDuplicates()));
connect(_last, SIGNAL(lostFocus()), this, SLOT(findDuplicates()));
connect(_crmAcct, SIGNAL(newId(int)), this, SLOT(setSearchAcct(int)));
setFocusPolicy(Qt::StrongFocus);
setFocusProxy(_honorific);
setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Fixed);
setLabel("");
_limits = 0;
silentSetId(-1);
setOwnerVisible(false);
_mode = Edit;
}
void driver(){
Integer A[]={1,2,3,4,2,2,2,4};
cout<<"duplicates are"<<findDuplicates(A,ARRAYSIZE(A))<<endl;
}
void
processArray(int argc, char **argv) {
int arg = 1;
while (arg < argc) {
if ((strcmp(argv[arg], "-f") == 0) ||
(strcmp(argv[arg], "-F") == 0)) {
delete fasta;
fasta = new seqCache(argv[++arg]);
} else if (strcmp(argv[arg], "-i") == 0) {
failIfNoSource();
++arg;
if ((argv[arg] == 0L) || (argv[arg][0] == '-'))
fprintf(stderr, "ERROR: next arg to -i should be 'name', I got '%s'\n",
(argv[arg] == 0L) ? "(nullpointer)" : argv[arg]), exit(1);
for (uint32 s=0; s<fasta->getNumberOfSequences(); s++)
fprintf(stdout, "G\tseq\t%s:"F_U32"\t"F_U32"\t%s\n",
argv[arg], s, fasta->getSequenceLength(s), ">unimplemented");
} else if (strcmp(argv[arg], "-d") == 0) {
failIfNoSource();
printf(F_U32"\n", fasta->getNumberOfSequences());
} else if (strcmp(argv[arg], "-L") == 0) {
uint32 small = strtouint32(argv[++arg]);
uint32 large = strtouint32(argv[++arg]);
failIfNoSource();
for (uint32 s=0; s<fasta->getNumberOfSequences(); s++)
if ((small <= fasta->getSequenceLength(s)) && (fasta->getSequenceLength(s) < large))
printSequence(s);
} else if (strcmp(argv[arg], "-N") == 0) {
double small = atof(argv[++arg]);
double large = atof(argv[++arg]);
failIfNoSource();
for (uint32 s=0; s<fasta->getNumberOfSequences(); s++) {
seqInCore *S = fasta->getSequenceInCore(s);
uint32 Ns = 0;
uint32 len = S->sequenceLength();
char *seq = S->sequence();
for (uint32 i=begPos; i<len && i<endPos; i++)
if ((seq[i] == 'n') || (seq[i] == 'N'))
Ns++;
double Np = 100.0 * Ns / len;
if ((small <= Np) && (Np < large))
printSequence(S);
delete S;
}
} else if (strcmp(argv[arg], "-W") == 0) {
failIfNoSource();
for (uint32 s=0; s<fasta->getNumberOfSequences(); s++)
printSequence(s);
} else if (strcmp(argv[arg], "-G") == 0) {
uint32 n = strtouint32(argv[++arg]);
uint32 s = strtouint32(argv[++arg]);
uint32 l = strtouint32(argv[++arg]);
char bases[4] = {'A', 'C', 'G', 'T'};
char *def = new char [1024];
char *seq = new char [l + 1];
if (s == 0)
s = 1;
if (s > l)
fprintf(stderr, "leaff: usage: -G num-seqs min-length max-length\n"), exit(1);
for (uint32 i=0; i<n; i++) {
uint32 j = s + ((l-s == 0) ? 0 : (MT.mtRandom32() % (l-s)));
uint32 p = 0;
while (p < j)
seq[p++] = bases[MT.mtRandom32() & 0x3];
seq[p] = 0;
sprintf(def, "random%06"F_U32P, i);
printSequence(def, seq, 0, j);
}
delete [] seq;
delete [] def;
} else if (strcmp(argv[arg], "-s") == 0) {
failIfNoSource();
failIfNotRandomAccess(); // Easy to fix, just read the first N sequences
printSequence(argv[++arg]);
} else if (strcmp(argv[arg], "-S") == 0) {
failIfNoSource();
failIfNotRandomAccess(); // Easy to fix, just read the first N sequences
uint32 lowID = fasta->getSequenceIID(argv[++arg]);
uint32 highID = fasta->getSequenceIID(argv[++arg]);
if (lowID > highID) {
uint32 t = lowID;
lowID = highID;
highID = t;
}
for (uint32 s=lowID; (s <= highID) && (s <= fasta->getNumberOfSequences()); s++)
printSequence(s);
} else if (strcmp(argv[arg], "-r") == 0) {
uint32 num = strtouint32(argv[++arg]);
failIfNoSource();
failIfNotRandomAccess(); // Impossible to fix, or load whole thing into memory
if (num >= fasta->getNumberOfSequences())
num = fasta->getNumberOfSequences();
uint32 *seqs = new uint32 [fasta->getNumberOfSequences()];
for (uint32 i=0; i<fasta->getNumberOfSequences(); i++)
seqs[i] = i;
for (uint32 i=0; i<fasta->getNumberOfSequences(); i++) {
uint32 j = MT.mtRandom32() % (fasta->getNumberOfSequences() - i) + i;
uint32 t = seqs[j];
seqs[j] = seqs[i];
seqs[i] = t;
}
for (uint32 i=0; i<num; i++)
printSequence(seqs[i]);
delete [] seqs;
} else if (strcmp(argv[arg], "-q") == 0) {
failIfNoSource();
failIfNotRandomAccess(); // Impossible to fix, or load whole thing into memory
printIDsFromFile(argv[++arg]);
} else if (strcmp(argv[arg], "-6") == 0) {
withLineBreaks = 60;
if ((argv[arg+1] != 0L) && (argv[arg+1][0] != '-'))
withLineBreaks = strtouint32(argv[++arg]);
} else if (strcmp(argv[arg], "-w") == 0) {
toUppercase = !toUppercase;
for (int z=0; z<256; z++)
translate[z] = (toUppercase) ? alphabet.toUpper(z) : (char)z;
} else if (strcmp(argv[arg], "-R") == 0) {
doReverse = !doReverse;
} else if (strcmp(argv[arg], "-C") == 0) {
doComplement = !doComplement;
} else if (strcmp(argv[arg], "-H") == 0) {
withDefLine = !withDefLine;
specialDefLine = 0L;
} else if (strcmp(argv[arg], "-h") == 0) {
withDefLine = true;
specialDefLine = argv[++arg];
} else if (strcmp(argv[arg], "-e") == 0) {
begPos = strtouint32(argv[++arg]);
endPos = strtouint32(argv[++arg]);
} else if (strcmp(argv[arg], "-ends") == 0) {
endExtract = strtouint32(argv[++arg]);
} else if (strcmp(argv[arg], "-A") == 0) {
processFile(argv[++arg]);
} else if (strcmp(argv[arg], "--findduplicates") == 0) {
findDuplicates(argv[++arg]);
exit(0);
} else if (strcmp(argv[arg], "--mapduplicates") == 0) {
mapDuplicates(argv[arg+1], argv[arg+2]);
exit(0);
} else if (strcmp(argv[arg], "--md5") == 0) {
md5_s md5;
char sum[33];
fasta = new seqCache(argv[++arg]);
for (uint32 s=0; s<fasta->getNumberOfSequences(); s++) {
seqInCore *S = fasta->getSequenceInCore(s);
fprintf(stdout, "%s %s\n",
md5_toascii(md5_string(&md5, S->sequence(), S->sequenceLength()), sum),
S->header());
delete S;
}
delete fasta;
exit(0);
} else if ((strcmp(argv[arg], "--partition") == 0) ||
(strcmp(argv[arg], "--partitionmap") == 0)) {
char *prefix = 0L;
if (strcmp(argv[arg], "--partition") == 0)
prefix = argv[++arg];
// does the next arg end with gbp, mbp, kbp or bp? If so,
// partition by length, else partition into buckets.
//
int al = strlen(argv[arg+1]);
uint64 ps = strtouint64(argv[arg+1]);
char a3 = (al<3) ? '0' : alphabet.toLower(argv[arg+1][al-3]);
char a2 = (al<2) ? '0' : alphabet.toLower(argv[arg+1][al-2]);
char a1 = (al<1) ? '0' : alphabet.toLower(argv[arg+1][al-1]);
// partition!
if (!isdigit(a1) || !isdigit(a2) || !isdigit(a3)) {
if ((a3 == 'g') && (a2 == 'b') && (a1 == 'p')) {
ps *= 1000000000;
} else if ((a3 == 'm') && (a2 == 'b') && (a1 == 'p')) {
ps *= 1000000;
} else if ((a3 == 'k') && (a2 == 'b') && (a1 == 'p')) {
ps *= 1000;
} else if (isdigit(a3) && (a2 == 'b') && (a1 == 'p')) {
ps *= 1;
} else {
fprintf(stderr, "Unknown partition size option '%s'\n", argv[arg+1]), exit(1);
}
if (ps == 0)
fprintf(stderr, "Unknown or zero partition size '%s'\n", argv[arg+1]), exit(1);
partitionBySize(prefix, ps, argv[arg+2]);
} else {
if (ps == 0)
fprintf(stderr, "Unknown or zero partition size '%s'\n", argv[arg+1]), exit(1);
partitionByBucket(prefix, ps, argv[arg+2]);
}
exit(0);
} else if (strcmp(argv[arg], "--segment") == 0) {
partitionBySegment(argv[arg+1], strtouint32(argv[arg+2]), argv[arg+3]);
exit(0);
} else if (strcmp(argv[arg], "--gccontent") == 0) {
computeGCcontent(argv[++arg]);
exit(0);
} else if (strcmp(argv[arg], "--dumpblocks") == 0) {
dumpBlocks(argv[++arg]);
exit(0);
} else if (strcmp(argv[arg], "--stats") == 0) {
stats(argv[arg+1], (argv[arg+2] != 0L) ? strtouint64(argv[arg+2]) : 0);
exit(0);
} else if (strcmp(argv[arg], "--errors") == 0) {
int L = strtouint32(argv[++arg]); // Desired length
int l = 0; // min of desired length, length of sequence
int N = strtouint32(argv[++arg]); // number of copies per sequence
int C = strtouint32(argv[++arg]); // number of mutations per copy
double P = atof(argv[++arg]); // probability of mutation
uint32 i = 0;
fasta = new seqCache(argv[++arg]);
seqInCore *S = fasta->getSequenceInCore(i++);
while (S) {
char *seq = S->sequence();
char *hdr = S->header();
int len = S->sequenceLength();
l = len;
if ((L > 0) && (L < len))
l = L;
simseq(seq, hdr, len, N, l, C, P);
delete S;
S = fasta->getSequenceInCore(i++);
}
delete fasta;
exit(0);
} else if (strcmp(argv[arg], "--seqstore") == 0) {
constructSeqStore(argv[++arg], fasta);
exit(0);
} else if (strcmp(argv[arg], "-help") == 0) {
if ((argv[arg+1]) && (strcmp(argv[arg+1], "analysis") == 0))
helpAnalysis(argv[0]);
else if ((argv[arg+1]) && (strcmp(argv[arg+1], "examples") == 0))
helpExamples(argv[0]);
else
helpStandard(argv[0]);
exit(0);
} else {
helpStandard(argv[0]);
fprintf(stderr, "Unknown option '%s'\n", argv[arg]);
exit(1);
}
arg++;
}
delete fasta;
fasta = 0L;
}
