void remap(SNP **s1, int nums1, SNP **s2, int nums2)
{
SNP *cupt1, *cupt2 ;
SNP tcupt, *cupt ;
int i, k ;
for (i=0; i<nums2; ++i) {
cupt2 = s2[i] ;
k = snpindex(s1, nums1, cupt2 -> ID) ;
if (k<0) {
printf("%20s not found\n") ;
cupt2 -> ignore = YES ;
continue ;
}
cupt1 = s1[k] ;
fixaa(cupt1, cupt2) ;
if (cupt1 -> alleles[1] == 'X') {
cupt1 -> alleles[1] = cxx(cupt1 -> alleles, cupt2 -> alleles) ;
}
tcupt = *cupt2 ;
*cupt2 = *cupt1 ;
cupt = &tcupt ;
cupt2 -> chrom = cupt -> chrom ;
cupt2 -> genpos = cupt -> genpos ;
cupt2 -> physpos = cupt -> physpos ;
cupt2 -> alleles[0] = cupt -> alleles[0] ;
cupt2 -> alleles[1] = cupt -> alleles[1] ;
}
freesnpindex() ;
}
// do the actual cleanup
void CompileRequest::Process(IManager* manager)
{
wxString cmd;
wxString errMsg;
wxStringMap_t om;
BuildSettingsConfig* bsc(manager ? manager->GetBuildSettingsConfigManager() : BuildSettingsConfigST::Get());
BuildManager* bm(manager ? manager->GetBuildManager() : BuildManagerST::Get());
clCxxWorkspace* w(manager ? manager->GetWorkspace() : clCxxWorkspaceST::Get());
EnvironmentConfig* env(manager ? manager->GetEnv() : EnvironmentConfig::Instance());
ProjectPtr proj = w->FindProjectByName(m_info.GetProject(), errMsg);
if(!proj) {
AppendLine(_("Cant find project: ") + m_info.GetProject());
return;
}
wxString pname(proj->GetName());
// BuilderPtr builder = bm->GetBuilder(wxT("GNU makefile for g++/gcc"));
BuilderPtr builder = bm->GetSelectedBuilder();
if(m_fileName.IsEmpty() == false) {
// we got a complie request of a single file
cmd = m_preprocessOnly ?
builder->GetPreprocessFileCmd(m_info.GetProject(), m_info.GetConfiguration(), m_fileName, errMsg) :
builder->GetSingleFileCmd(m_info.GetProject(), m_info.GetConfiguration(), m_fileName);
} else if(m_info.GetProjectOnly()) {
switch(m_info.GetKind()) {
case QueueCommand::kRebuild:
cmd = builder->GetPORebuildCommand(m_info.GetProject(), m_info.GetConfiguration());
break;
default:
case QueueCommand::kBuild:
cmd = builder->GetPOBuildCommand(m_info.GetProject(), m_info.GetConfiguration());
break;
}
} else {
cmd = builder->GetBuildCommand(m_info.GetProject(), m_info.GetConfiguration());
}
// Notify plugins that a compile process is going to start
clBuildEvent event(wxEVT_BUILD_STARTING);
event.SetProjectName(pname);
event.SetConfigurationName(m_info.GetConfiguration());
if(EventNotifier::Get()->ProcessEvent(event)) {
// the build is being handled by some plugin, no need to build it
// using the standard way
return;
}
// Send the EVENT_STARTED : even if this event is sent, next event will
// be post, so no way to be sure the the build process has not started
SendStartMsg();
// if we require to run the makefile generation command only, replace the 'cmd' with the
// generation command line
BuildConfigPtr bldConf = w->GetProjBuildConf(m_info.GetProject(), m_info.GetConfiguration());
if(m_premakeOnly && bldConf) {
BuildConfigPtr bldConf = w->GetProjBuildConf(m_info.GetProject(), m_info.GetConfiguration());
if(bldConf) {
cmd = bldConf->GetMakeGenerationCommand();
}
}
if(bldConf) {
wxString cmpType = bldConf->GetCompilerType();
CompilerPtr cmp = bsc->GetCompiler(cmpType);
if(cmp) {
// Add the 'bin' folder of the compiler to the PATH environment variable
wxString scxx = cmp->GetTool("CXX");
scxx.Trim().Trim(false);
scxx.StartsWith("\"", &scxx);
scxx.EndsWith("\"", &scxx);
// Strip the double quotes
wxFileName cxx(scxx);
wxString pathvar;
pathvar << cxx.GetPath() << clPATH_SEPARATOR;
// If we have an additional path, add it as well
if(!cmp->GetPathVariable().IsEmpty()) {
pathvar << cmp->GetPathVariable() << clPATH_SEPARATOR;
}
pathvar << "$PATH";
om["PATH"] = pathvar;
}
}
if(cmd.IsEmpty()) {
// if we got an error string, use it
if(errMsg.IsEmpty() == false) {
AppendLine(errMsg);
} else {
AppendLine(_("Command line is empty. Build aborted."));
}
return;
}
WrapInShell(cmd);
DirSaver ds;
DoSetWorkingDirectory(proj, false, m_fileName.IsEmpty() == false);
// expand the variables of the command
cmd = ExpandAllVariables(cmd, w, m_info.GetProject(), m_info.GetConfiguration(), m_fileName);
// print the build command
AppendLine(cmd + wxT("\n"));
if(m_info.GetProjectOnly() || m_fileName.IsEmpty() == false) {
// set working directory
DoSetWorkingDirectory(proj, false, m_fileName.IsEmpty() == false);
}
// print the prefix message of the build start. This is important since the parser relies
// on this message
if(m_info.GetProjectOnly() || m_fileName.IsEmpty() == false) {
wxString configName(m_info.GetConfiguration());
// also, send another message to the main frame, indicating which project is being built
// and what configuration
wxString text;
text << wxGetTranslation(BUILD_PROJECT_PREFIX) << m_info.GetProject() << wxT(" - ") << configName << wxT(" ]");
if(m_fileName.IsEmpty()) {
text << wxT("----------\n");
} else if(m_preprocessOnly) {
text << wxT(" (Preprocess Single File)----------\n");
} else {
text << wxT(" (Single File Build)----------\n");
}
AppendLine(text);
}
EnvSetter envir(env, &om, proj->GetName());
m_proc = CreateAsyncProcess(this, cmd);
if(!m_proc) {
wxString message;
message << _("Failed to start build process, command: ") << cmd << _(", process terminated with exit code: 0");
AppendLine(message);
return;
}
}
