static BYTE getspbVRch(void) {
BYTE ret = 0;
if (getControlValue('spvl', 0)) {
ret++;
}
if (getControlValue('spvr', 0)) {
ret += 2;
}
return(ret);
}
Knob::Knob(const parameters::ParameterInfo& inParamInfo,
juce::AudioProcessor* inProcessor)
: Control(inParamInfo, inProcessor)
, juce::Slider(juce::Slider::RotaryHorizontalVerticalDrag, juce::Slider::TextBoxBelow)
{
setRange(0., 1., .005);
setValue(double(getControlValue()), juce::dontSendNotification);
setDoubleClickReturnValue(true, getNormalizedDefaultValue());
}
double Knob::getValueFromText(const juce::String& inText)
{
float val = 0.f;
if (getControlValueFromText(inText, val))
{
return double(val);
}
return double(getControlValue());
}
void control( void )
{
motorval val;
val = getControlValue();
Motor_rotate( &(robot.leftMotor) , val.leftmotor);
Motor_rotate( &(robot.rightMotor) , val.rightmotor);
Motor_rotate( &(robot.tailMotor) , val.tailmotor);
}
Combo::Combo(const parameters::ParameterInfo& inParamInfo,
juce::AudioProcessor* inProcessor)
: Control(inParamInfo, inProcessor)
{
const int numValues = static_cast<int>(getPlainValue(1.f)) + 1;
for (int i = 0; i < numValues; ++i)
{
addItem(getControlValueText(getNormalizedValue(float(i))), i + 1);
}
setJustificationType(juce::Justification::centred);
setSelectedItemIndex(static_cast<int>(getPlainValue(getControlValue())),
juce::dontSendNotification);
addListener(this);
}
static BYTE getsnd86int(void) {
switch (getControlValue('86in', 0))
{
case 1:
return(0x00);
case 2:
return(0x04);
case 4:
return(0x08);
}
return(0x0c);
}
//-----change
static BYTE getsnd26int(OSType board) {
switch (getControlValue(board, 0))
{
case 1:
return(0x00);
case 2:
return(0x80);
case 4:
return(0x40);
}
return(0xc0);
}
int main (int argc, char *argv[]) {
//HARDY WEINBERG EQUILIBRIUM QUALITY CONTROL
//Get the data
Datacube datacube;
datacube.loadData(argv[1]);
datacube.setVariablesMeaning(argv[6]);
int countsCol = datacube.values.at(0).size() - 1;//The column with the counts
//Set the threshold
float threshold;
threshold = atof(argv[2]);
//Set the target variables index if the test will only be applied on controls
bool onlyOnControls = false;
int targetVarIndex = countsCol - 1;
int CONTROL_VAL;
if(argv[3][0] == '1')
{
onlyOnControls = true;
CONTROL_VAL = getControlValue(&datacube,targetVarIndex);
}
bool keep[countsCol];
for(int i=0; i<datacube.values.at(0).size(); ++i)
{
//initialize the values of the vectors
keep[i] = true;
}
//initialize the counters
int minorHom=0, majorHom=0, h1count=0, h2count=0, heterozygous=0;
//Check which variables pass the HWE QC
double pValue;
for(int column=0;column<countsCol;column++)
{
//Only if the variable is a SNP
if(datacube.getVariableType(column).compare("SNP")==0)
{
h1count = 0;h2count = 0; heterozygous = 0;
for(int row=0;row<datacube.values.size();row++)
{
//chech if only controls should be used
if(!onlyOnControls || (onlyOnControls && datacube.values.at(row).at(targetVarIndex) == CONTROL_VAL))
{
switch(datacube.values.at(row).at(column))
{
//count the minor alleles
case HOMOZYGOUS_1:
h1count += datacube.values.at(row).at(countsCol);
break;
//count the heterozygous alleles
case HETEROZYGOUS:
heterozygous += datacube.values.at(row).at(countsCol);
break;
//count the major alleles
case HOMOZYGOUS_2:
h2count += datacube.values.at(row).at(countsCol);
}
}
}
//Set the minor and major alleles
if(h1count<h2count)
{
minorHom = h1count;
majorHom = h2count;
}
else
{
minorHom = h2count;
majorHom = h1count;
}
//If no alleles were counted (e.g. all missing, no controls)
if(h1count == 0 && h2count==0 && heterozygous==0)
{
keep[column] = false;
}
else
{
//calculate the HWE pValue
pValue = SNPHWE(heterozygous,minorHom,majorHom);
//Check if the SNP will be kept
if(pValue < threshold )
keep[column] = false;
}
}
}
//Remove the variables that did not pass the HWE QC
datacube.removeVariables(keep);
//output the data cube
datacube.writeToFile(argv[4]);
//Output the XML contents describing the algorithm
ofstream outpXML;
outpXML.open(argv[5]);
outpXML << "<log>" << endl;
outpXML << "<QualityControl algorithm_name=\"Hardy Weinberg Equilibrium Test\" algorithmParamsSetting=\"threshold=" << argv[2];
outpXML << " only_on_controls=" << argv[3] << "\"/>" << endl;
outpXML << "</log>";
outpXML.close();
}
static pascal OSStatus cfWinproc(EventHandlerCallRef myHandler, EventRef event, void* userData) {
OSStatus err = eventNotHandledErr;
HICommand cmd;
BYTE defaultmix[5] = {64, 64, 64, 64, 64};
BYTE b;
if (GetEventClass(event)==kEventClassCommand && GetEventKind(event)==kEventCommandProcess ) {
GetEventParameter(event, kEventParamDirectObject, typeHICommand, NULL, sizeof(HICommand), NULL, &cmd);
switch (cmd.commandID)
{
case 'vDEF':
initMixer(defaultmix);
break;
case '26io':
setjmper(&snd26, (getMenuValue == 1)?0x10:0x00, 0x10);
break;
case '26in':
setjmper(&snd26, getsnd26int(cmd.commandID), 0xc0);
break;
case '26rm':
setjmper(&snd26, getMenuValue, 0x07);
break;
case '26DF':
snd26 = 0xd1;
set26s(snd26, '26io', '26in', '26rm');
break;
case '86io':
setjmper(&snd86, (getMenuValue == 0)?0x01:0x00, 0x01);
break;
case '86it':
setjmper(&snd86, (getControlValue(cmd.commandID, 0))?0x10:0x00, 0x10);
break;
case '86in':
setjmper(&snd86, getsnd86int(), 0x0c);
break;
case '86id':
setjmper(&snd86, (~getMenuValue & 7) << 5, 0xe0);
break;
case '86rm':
setjmper(&snd86, (getControlValue(cmd.commandID, 0))?0x02:0x00, 0x02);
break;
case '86DF':
snd86 = 0x7f;
set86s();
break;
case 'spio':
setjmper(&spb, (getMenuValue == 1)?0x10:0x00, 0x10);
break;
case 'spin':
setjmper(&spb, getsnd26int(cmd.commandID), 0xc0);
break;
case 'sprm':
setjmper(&spb, getMenuValue, 0x07);
break;
case 'spvl':
case 'spvr':
b = getspbVRch();
if ((spbvrc ^ b) & 3) {
spbvrc = b;
}
break;
case 'spDF':
spb = 0xd1;
spbvrc = 0;
setSPB();
break;
case kHICommandOK:
changeSoundOpt();
endLoop(soundWin);
err=noErr;
break;
case kHICommandCancel:
revertTemporal();
endLoop(soundWin);
err=noErr;
break;
case JOYPAD_UP:
case JOYPAD_DOWN:
case JOYPAD_LEFT:
case JOYPAD_RIGHT:
case JOYPAD_ABUTTON:
case JOYPAD_BBUTTON:
err=setupJoyConfig(cmd.commandID);
break;
default:
break;
}
}
(void)myHandler;
(void)userData;
return err;
}
static void changeSoundOpt(void) {
SINT32 val;
UInt8 update;
int renewal;
short i,j;
renewal = 0;
for (j=0;j<5;j++) {
val = getControlValue('vMix', j);
if (val != *cfg[j]) {
*cfg[j] = val;
renewal = 1;
}
}
if (renewal) {
sysmng_update(SYS_UPDATECFG);
}
opngen_setvol(np2cfg.vol_fm);
psggen_setvol(np2cfg.vol_ssg);
rhythm_setvol(np2cfg.vol_rhythm);
rhythm_update(&g_rhythm);
adpcm_setvol(np2cfg.vol_adpcm);
adpcm_update(&g_adpcm);
pcm86gen_setvol(np2cfg.vol_pcm);
pcm86gen_update();
renewal = 0;
for (i=0;i<6;i++) {
val = getControlValue('vMix',i+10);
if (val != np2cfg.vol14[i]) {
np2cfg.vol14[i] = val;
renewal = 1;
}
}
if (renewal) {
sysmng_update(SYS_UPDATECFG);
tms3631_setvol(np2cfg.vol14);
}
if (np2cfg.snd26opt != snd26) {
np2cfg.snd26opt = snd26;
sysmng_update(SYS_UPDATECFG);
}
if (np2cfg.snd86opt != snd86) {
np2cfg.snd86opt = snd86;
sysmng_update(SYS_UPDATECFG);
}
update = 0;
if (np2cfg.spbopt != spb) {
np2cfg.spbopt = spb;
update |= SYS_UPDATECFG;
}
if (np2cfg.spb_vrc != spbvrc) {
np2cfg.spb_vrc = spbvrc;
update |= SYS_UPDATECFG;
}
val = getControlValue('splv', 0);
if (np2cfg.spb_vrl != val) {
np2cfg.spb_vrl = val;
update |= SYS_UPDATECFG;
}
opngen_setVR(np2cfg.spb_vrc, np2cfg.spb_vrl);
val = getControlValue('sprv', 0);
if (np2cfg.spb_x != val) {
np2cfg.spb_x = val;
update |= SYS_UPDATECFG;
}
sysmng_update(update);
changeJoyPadSetup();
}
