void InvokeMethod::on_comboMethods_activated(const QString &method)
{
if (!activex)
return;
listParameters->clear();
const QMetaObject *mo = activex->metaObject();
const QMetaMethod slot = mo->method(mo->indexOfSlot(method.toLatin1()));
QString signature = QString::fromLatin1(slot.signature());
signature = signature.mid(signature.indexOf(QLatin1Char('(')) + 1);
signature.truncate(signature.length()-1);
QList<QByteArray> pnames = slot.parameterNames();
QList<QByteArray> ptypes = slot.parameterTypes();
for (int p = 0; p < ptypes.count(); ++p) {
QString ptype(QString::fromLatin1(ptypes.at(p)));
if (ptype.isEmpty())
continue;
QString pname(QString::fromLatin1(pnames.at(p).constData()));
if (pname.isEmpty())
pname = QString::fromLatin1("<unnamed %1>").arg(p);
QTreeWidgetItem *item = new QTreeWidgetItem(listParameters);
item->setText(0, pname);
item->setText(1, ptype);
}
if (listParameters->topLevelItemCount())
listParameters->setCurrentItem(listParameters->topLevelItem(0));
editReturn->setText(QString::fromLatin1(slot.typeName()));
}
//**********************************************************************************************************************
vector<string> ChopSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","qfile",false,false,true); parameters.push_back(pqfile);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pnumbases("numbases", "Number", "", "0", "", "", "","",false,true,true); parameters.push_back(pnumbases);
CommandParameter pcountgaps("countgaps", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcountgaps);
CommandParameter pshort("short", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pshort);
CommandParameter pkeep("keep", "Multiple", "front-back", "front", "", "", "","",false,false); parameters.push_back(pkeep);
CommandParameter pkeepn("keepn", "Boolean", "", "f", "", "", "","",false,false); parameters.push_back(pkeepn);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "ChopSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> ClusterCommand::setParameters(){
try {
CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","list",false,false,true); parameters.push_back(pphylip);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","rabund-sabund",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pcount);
CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","list",false,false,true); parameters.push_back(pcolumn);
CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "","",false,false,true); parameters.push_back(pmethod);
CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshowabund);
CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming);
CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim);
CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
//CommandParameter padjust("adjust", "String", "", "F", "", "", "","",false,false); parameters.push_back(padjust);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "ClusterCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> MGClusterCommand::setParameters(){
try {
CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pblast);
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
CommandParameter plength("length", "Number", "", "5", "", "", "",false,false); parameters.push_back(plength);
CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "",false,false); parameters.push_back(ppenalty);
CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
CommandParameter pmethod("method", "Multiple", "furthest-nearest-average", "average", "", "", "",false,false); parameters.push_back(pmethod);
CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
CommandParameter pmin("min", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmin);
CommandParameter pmerge("merge", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmerge);
CommandParameter phcluster("hcluster", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phcluster);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "MGClusterCommand", "setParameters");
exit(1);
}
}
static at *generic_listeval(at *p, at *q)
{
if (LISTP(p))
error("eval", "not a function call", q);
else
error(pname(p), "can't evaluate this list", NIL);
}
//**********************************************************************************************************************
vector<string> TreeGroupCommand::setParameters(){
try {
CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","tree",false,false,true); parameters.push_back(pshared);
CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","tree",false,false); parameters.push_back(pphylip);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","",false,false); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "countcolumn","",false,false); parameters.push_back(pcount);
CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName-countcolumn","tree",false,false); parameters.push_back(pcolumn);
CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson-jsd-rjsd", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
//CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "TreeGroupCommand", "setParameters");
exit(1);
}
}
/* psymbol - parse a symbol name */
LOCAL LVAL psymbol(LVAL fptr)
{
int escflag;
LVAL val;
pname(fptr,&escflag);
return (escflag || !isnumber(buf,&val) ? xlenter(buf) : val);
}
void AddClusterSelectionTask(TString name = "ClusterSelectionTask")
{
gSystem->AddIncludePath("-I$ALICE_ROOT/include");
AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
if (!mgr) {
::Error("AddTaskPHOSPi0Flow", "No analysis manager to connect to");
return NULL;
}
if (!mgr->GetInputEventHandler()) {
::Error("AddTaskPHOSPi0Flow", "This task requires an input event handler");
return NULL;
}
gROOT->LoadMacro("ClusterSelectionTask.cxx+g");
ClusterSelectionTask * task = new ClusterSelectionTask(name);
mgr->AddTask(task);
mgr->ConnectInput(task, 0, mgr->GetCommonInputContainer() );
TString cname(Form("HistList", name));
TString pname(Form("%s:%s", AliAnalysisManager::GetCommonFileName(), name));
AliAnalysisDataContainer *coutput1 = mgr->CreateContainer(cname.Data(), TList::Class(), AliAnalysisManager::kOutputContainer, pname.Data());
mgr->ConnectOutput(task, 1, coutput1);
cname = Form("SelectedPhotons", name);
AliAnalysisDataContainer *cexchange2 = mgr->CreateContainer(cname.Data(), TList::Class(), AliAnalysisManager::kExchangeContainer, pname.Data());
mgr->ConnectOutput(task, 2, cexchange2);
return task;
}
//**********************************************************************************************************************
vector<string> GetSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false,true); parameters.push_back(pfasta);
CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "FNGLT", "none","fastq",false,false,true); parameters.push_back(pfastq);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none","count",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none","group",false,false,true); parameters.push_back(pgroup);
CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false,true); parameters.push_back(plist);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none","alignreport",false,false); parameters.push_back(palignreport);
CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none","qfile",false,false); parameters.push_back(pqfile);
CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
CommandParameter pdups("dups", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pdups);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos2);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "setParameters");
exit(1);
}
}
static PyObject* py_glGetVertexAttrib(PyObject *, PyObject *args) {
CHECK_ARG_COUNT(args, 2);
PyObject *rv = 0;
Uint attrib(PyTuple_GetItem(args, 0));
Enum pname(PyTuple_GetItem(args, 1));
switch (pname) {
case GL_VERTEX_ATTRIB_ARRAY_BUFFER_BINDING:
case GL_VERTEX_ATTRIB_ARRAY_ENABLED:
case GL_VERTEX_ATTRIB_ARRAY_SIZE:
case GL_VERTEX_ATTRIB_ARRAY_STRIDE:
case GL_VERTEX_ATTRIB_ARRAY_TYPE:
case GL_VERTEX_ATTRIB_ARRAY_NORMALIZED: {
GLint value;
glGetVertexAttribiv(attrib, pname, &value);
rv = PyInt_FromLong(value);
break;
}
case GL_CURRENT_VERTEX_ATTRIB: {
Array1D<Float> values(4);
glGetVertexAttribfv(attrib, pname, values);
rv = values.toPy();
break;
}
default:
PyErr_SetString(PyExc_RuntimeError, "gl.GetVertexAttrib: invalid parameter name");
}
return rv;
}
//**********************************************************************************************************************
vector<string> PreClusterCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
CommandParameter pdiffs("diffs", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pdiffs);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "","",false,false); parameters.push_back(palign);
CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
CommandParameter ptopdown("topdown", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(ptopdown);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "PreClusterCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> ClassifyOtuCommand::setParameters(){
try {
CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(plist);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","constaxonomy",false,true,true); parameters.push_back(ptaxonomy);
CommandParameter preftaxonomy("reftaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(preftaxonomy);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ppersample);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter pbasis("basis", "Multiple", "otu-sequence", "otu", "", "", "","",false,false); parameters.push_back(pbasis);
CommandParameter pcutoff("cutoff", "Number", "", "51", "", "", "","",false,true); parameters.push_back(pcutoff);
CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pprobs);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "ClassifyOtuCommand", "setParameters");
exit(1);
}
}
void InputConfigDialog::UpdateProfileComboBox()
{
std::string pname(File::GetUserPath(D_CONFIG_IDX));
pname += PROFILES_PATH;
pname += m_plugin.profile_name;
CFileSearch::XStringVector exts;
exts.push_back("*.ini");
CFileSearch::XStringVector dirs;
dirs.push_back(pname);
CFileSearch cfs(exts, dirs);
const CFileSearch::XStringVector& sv = cfs.GetFileNames();
wxArrayString strs;
CFileSearch::XStringVector::const_iterator si = sv.begin(),
se = sv.end();
for (; si!=se; ++si)
{
std::string str(si->begin() + si->find_last_of('/') + 1 , si->end() - 4) ;
strs.push_back(WXSTR_FROM_STR(str));
}
std::vector< GamepadPage* >::iterator i = m_padpages.begin(),
e = m_padpages.end();
for (; i != e; ++i)
{
(*i)->profile_cbox->Clear();
(*i)->profile_cbox->Append(strs);
}
}
AliAnalysisTaskEpRatio* AddTaskPHOSEpRatio (Bool_t kMC = kFALSE,
const char* name = "PHOSEpRatio",
const char* options = "",
UInt_t offlineTriggerMask = AliVEvent::kINT7 )
{
//Add a task AliAnalysisTaskEpRatio to the analysis train.
//Author: Boris Polishchuk.
AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
if (!mgr) {
::Error("AddTaskPHOSEpRatio", "No analysis manager to connect to");
return NULL;
}
if (!mgr->GetInputEventHandler()) {
::Error("AddTaskPHOSEpRatio", "This task requires an input event handler");
return NULL;
}
AliAnalysisTaskEpRatio* task = new AliAnalysisTaskEpRatio(Form("%sTask", name));
if(!kMC) task->SelectCollisionCandidates(offlineTriggerMask);
mgr->AddTask(task);
mgr->ConnectInput(task, 0, mgr->GetCommonInputContainer() );
TString cname(Form("%sCoutput1", name));
TString pname(Form("%s:%s", AliAnalysisManager::GetCommonFileName(), name));
AliAnalysisDataContainer *coutput1 = mgr->CreateContainer(cname.Data(), TList::Class(), AliAnalysisManager::kOutputContainer, pname.Data());
mgr->ConnectOutput(task, 1, coutput1);
return task;
}
BRect Settings::GetPosition(const char *name)
{
BString pname(name);
pname.Append(POSITION);
BRect pos = pref.FindRect(pname.String());
FitRectOnScreen(&pos);
return pos;
}
void Settings::SetPosition(const char *name, const BRect pos)
{
BString pname(name);
pname.Append(POSITION);
if (!pref.HasRect(pname.String()))
pref.AddRect(pname.String(), pos);
else
pref.ReplaceRect(pname.String(), pos);
}
BFont * Settings::GetFont(const char *name, fontspec family)
{
BString pname(name);
FFont f;
if (family == M_PLAIN_FONT) pname.Append(FONT);
else if (family == M_BOLD_FONT) pname.Append(BFONT);
else pname.Append(FFONT);
FindMessageFont(&pref, pname.String(), 0, &f);
return (new FFont(f));
}
void PluginWidget::setPluginTableRow(Plugin *p, int row)
{
QString pname(p->get_name());
ui.pluginTable->setItem(row, PluginWidget::NameField, new QTableWidgetItem(pname));
ui.pluginTable->item(row,0)->setToolTip(p->get_description());
ui.pluginTable->setItem(row, PluginWidget::VersionField, new QTableWidgetItem(p->get_version()));
ui.pluginTable->setItem(row, PluginWidget::AuthorField, new QTableWidgetItem(p->get_author()));
ui.pluginTable->setItem(row, PluginWidget::TypeField, new QTableWidgetItem(p->get_type()));
ui.pluginTable->setItem(row, PluginWidget::EngineField, new QTableWidgetItem(p->get_engine()));
}
char *aX_get_prog_res(const char *resname, const char* resclass)
{
XrmValue value;
char *str_type;
if(XrmGetResource(rDB, pname(resname), pclass(resclass),
&str_type, &value))
return (char *)value.addr;
else return NULL;
}
void Settings::SetFont(const char *name, const BFont *font, fontspec family)
{
BString pname(name);
FFont ff(font);
FFont dummy;
if (family == M_PLAIN_FONT) pname.Append(FONT);
else if (family == M_BOLD_FONT) pname.Append(BFONT);
else pname.Append(FFONT);
if (FindMessageFont(&pref, pname.String(), 0, &dummy) != B_OK)
AddMessageFont(&pref, pname.String(), &ff);
else
pref.ReplaceFlat(pname.String(), &ff);
}
void nuiObjectInspector::OnObjectSelection(const nuiEvent& rEvent)
{
nuiList* pList = (nuiList*)rEvent.mpUser;
nuiWidget* pW = pList->GetSelected();
nglString info(_T("no info"));
nglString name;
uint32 index = -1;
if (pW)
{
name = pW->GetProperty(_T("Object"));
index = pW->GetProperty(_T("Index")).GetCUInt();
}
mSlot.DisconnectAll();
// mSlot.Connect(pObject->Changed, nuiMakeDelegate(mpLabel, &nuiWidget::Invalidate));
// mSlot.Connect(pObject->Changed, nuiMakeDelegate(mpLabel->GetParent(), &nuiWidget::Invalidate));
if (index < 0)
return;
// build attributes list
std::map<nglString, nuiAttributeBase*> attributes;
nuiObject::GetAttributesOfClass(index, attributes);
uint32 i = 0;
std::map<nglString, nuiAttributeBase*>::const_iterator it_a = attributes.begin();
std::map<nglString, nuiAttributeBase*>::const_iterator end_a = attributes.end();
uint32 rows = mpAttributeGrid->GetNbRows();
if (rows)
mpAttributeGrid->RemoveRows(0, rows);
rows = attributes.size();
if (rows)
{
mpAttributeGrid->AddRows(0, rows);
}
while (it_a != end_a)
{
nglString pname(it_a->first);
//printf("\tattr: %s\n", pname.GetChars());
//nuiAttribBase Base = it_a->second;
//nuiAttributeEditor* pEditor = Base.GetEditor();
mpAttributeGrid->SetCell(0, i, new nuiLabel(pname + nglString(":")));
++it_a;
i++;
}
}
//**********************************************************************************************************************
vector<string> SetLogFileCommand::setParameters(){
try {
CommandParameter pappend("append", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pappend);
CommandParameter pname("name", "String", "", "", "", "", "","",false,true,true); parameters.push_back(pname);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "SetLogFileCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> DeUniqueSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pname);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "DeUniqueSeqsCommand", "setParameters");
exit(1);
}
}
/* iterative routine takes args as pbuf, pfile */
flagType fPFind (char *p, va_list ap)
{
//
// pArg is a pointer to an argument list. The first argument is a
// pointer to the file name. The second argument is a pointer to
// a buffer.
//
char *pa[2];
pa[1] = (char *)va_arg(ap, PCHAR);
pa[0] = (char *)va_arg(ap, PCHAR);
va_end(ap);
/* p == dir from env variable expansion or null
* pa[1] == file name
* pa[0] == buffer for getting p\pa[1] or pa[1] if p null
*/
strcpy ((char *)pa[0], p);
pathcat ((char *) pa[0], (char *) pa[1]);
{
HANDLE TmpHandle;
WIN32_FIND_DATA buffer;
TmpHandle = FindFirstFile((LPSTR)pa[0],&buffer);
if (TmpHandle == INVALID_HANDLE_VALUE) {
return FALSE;
}
FindClose(TmpHandle);
if ((buffer.dwFileAttributes & FILE_ATTRIBUTE_DIRECTORY)) {
return FALSE;
}
//struct stat sbuf;
//if (stat ((char *)pa[0], &sbuf) == -1)
// return FALSE;
//if ((sbuf.st_mode & S_IFREG) == 0)
// return FALSE;
}
pname ((char *) pa[0]);
return TRUE;
}
void pass3(struct dinode *ip)
{
struct direct dbuf[NDIR];
long doff;
struct direct *dp;
register i, j;
int k;
daddr_t d;
ino_t kno;
if((ip->di_mode&IFMT) != IFDIR)
return;
l4tol(iaddr, ip->di_addr, NADDR);
doff = 0;
for(i=0;; i++) {
if(doff >= ip->di_size)
break;
d = bmap(i);
if(d == 0)
break;
bread(d, (char *)dbuf, sizeof(dbuf));
for(j=0; j<NDIR; j++) {
if(doff >= ip->di_size)
break;
doff += sizeof(struct direct);
dp = dbuf+j;
kno = dp->d_ino;
if(kno == 0)
continue;
if(aflg==0 && dotname(dp))
continue;
if(ilist[0] == 0)
goto pr;
for(k=0; ilist[k] != 0; k++)
if(ilist[k] == kno)
goto pr;
continue;
pr:
printf("%u ", kno);
pname(ino, 0);
printf("/%.14s", dp->d_name);
if (lookup(kno, 0))
printf("/.");
printf("\n");
}
}
}
void pname(ino_t i, int lev)
{
register struct htab *hp;
if (i==ROOTINO)
return;
if ((hp = lookup(i, 0)) == 0) {
printf("???");
return;
}
if (lev > 10) {
printf("...");
return;
}
pname(hp->h_pino, ++lev);
printf("/%.14s", hp->h_name);
}
//**********************************************************************************************************************
vector<string> SetCurrentCommand::setParameters(){
try {
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pflow);
CommandParameter pfile("file", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pfile);
CommandParameter pbiom("biom", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pbiom);
CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pphylip);
CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcolumn);
CommandParameter psummary("summary", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psummary);
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pname);
CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pgroup);
CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(plist);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptaxonomy);
CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pconstaxonomy);
CommandParameter pcontigsreport("contigsreport", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcontigsreport);
CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pqfile);
CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prabund);
CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psabund);
CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pdesign);
CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(porder);
CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptree);
CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pshared);
CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pordergroup);
CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcount);
CommandParameter pcurrent("current", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcurrent);
CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prelabund);
CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psff);
CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(poligos);
CommandParameter pclear("clear", "String", "", "", "", "", "","",false,false); parameters.push_back(pclear);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "SetCurrentCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> SeqSummaryCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pcount);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "SeqSummaryCommand", "setParameters");
exit(1);
}
}
MyListView::MyListView(const char *name, const char *fname, BListItem (* New (Preference *r)), bool drag) :
PListView(name, B_SINGLE_SELECTION_LIST), maxWidth(32), listLimit(0), doDrags(drag)
{
MyItem *item;
BString pname("application/x-vnd.CI-BeCalc");
pname.Append(fname);
pref = new Preference((char *)pname.String());
if (pref->Load() == B_OK) {
int32 cnt = 0;
MyItem::count = 0;
pref->FindInt32(COUNT, &cnt);
for (int32 i = 0; i<cnt; i++) {
item = (MyItem *)New(pref);
AddItem(item);
}
}
pref->MakeEmpty(); // clear items
}
//**********************************************************************************************************************
vector<string> DeconvoluteCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-name",false,true,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","count",false,false,true); parameters.push_back(pcount);
CommandParameter pformat("format", "Multiple", "count-name", "name", "", "", "","",false,false, true); parameters.push_back(pformat);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "DeconvoluteCommand", "setParameters");
exit(1);
}
}