MooseEnumBase::MooseEnumBase(std::string names, bool allow_out_of_range) :
_out_of_range_index(allow_out_of_range ? INVALID_ID + 1 : 0)
{
if (names.find(',') != std::string::npos)
{
mooseDeprecated("Please use a space to separate options in a MooseEnum, commas are deprecated\nMooseEnum initialized with names: \"" << names << '\"');
fillNames(names, ",");
}
else
fillNames(names);
}
std::vector<std::string> ColorGradientPreparation::names() const
{
std::vector<std::string> result;
fillNames(result);
return result;
}
NameManager::NameManager() {
setLoggingName("NameManager");
initialize();
profaneNames = new Vector<String>(55, 5); //based on the original number of banned words
developerNames = new BannedNameSet();
reservedNames = new BannedNameSet();
fictionNames = new BannedNameSet();
fillNames();
setLogging(false);
}
void PeerData::updateNameDelayed(
const QString &newName,
const QString &newNameOrPhone,
const QString &newUsername) {
if (name == newName) {
if (isUser()) {
if (asUser()->nameOrPhone == newNameOrPhone
&& asUser()->username == newUsername) {
return;
}
} else if (isChannel()) {
if (asChannel()->username == newUsername) {
return;
}
} else if (isChat()) {
return;
}
}
++nameVersion;
name = newName;
nameText.setText(st::msgNameStyle, name, Ui::NameTextOptions());
refreshEmptyUserpic();
Notify::PeerUpdate update(this);
update.flags |= UpdateFlag::NameChanged;
update.oldNameFirstChars = nameFirstChars();
if (isUser()) {
if (asUser()->username != newUsername) {
asUser()->username = newUsername;
update.flags |= UpdateFlag::UsernameChanged;
}
asUser()->setNameOrPhone(newNameOrPhone);
} else if (isChannel()) {
if (asChannel()->username != newUsername) {
asChannel()->username = newUsername;
if (newUsername.isEmpty()) {
asChannel()->removeFlags(
MTPDchannel::Flag::f_username);
} else {
asChannel()->addFlags(MTPDchannel::Flag::f_username);
}
update.flags |= UpdateFlag::UsernameChanged;
}
}
fillNames();
Notify::PeerUpdated().notify(update, true);
}
void TestDataSet::createCountTable() {
fillGroup();
fillNames();
ct = new CountTable();
for (map<string, string>::iterator itNameMap = nameMap.begin(); itNameMap !=nameMap.end(); itNameMap++) {
string firstCol = itNameMap->first;
string secondCol = itNameMap->second;
vector<string> names;
util.splitAtChar(secondCol, names, ',');
//set to 0
map<string, int> groupCounts;
int total = 0;
vector<string> Groups = gMap->getNamesOfGroups();
ct->setNamesOfGroups(Groups);
for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
//get counts for each of the users groups
for (int i = 0; i < names.size(); i++) {
string group = gMap->getGroup(names[i]);
map<string, int>::iterator it = groupCounts.find(group);
//if not found, then this sequence is not from a group we care about
if (it != groupCounts.end()) {
it->second++;
total++;
}
}
if (total != 0) {
vector<int> abunds;
for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) { abunds.push_back(it->second); }
ct->push_back(firstCol, abunds);
}
}
delete gMap; gMap = NULL;
nameMap.clear();
}
int ibis::selectClause::parse(const char *cl) {
int ierr = 0;
if (cl != 0 && *cl != 0) {
clear();
LOGGER(ibis::gVerbose > 5)
<< "selectClause::parse cleared existing content before parsing \""
<< cl << "\"";
if (clause_.c_str() != cl)
clause_ = cl;
std::istringstream iss(clause_);
ibis::util::logger lg;
selectLexer lx(&iss, &(lg()));
selectParser parser(*this);
lexer = &lx;
#if DEBUG+0 > 2
parser.set_debug_level(DEBUG-1);
#elif _DEBUG+0 > 2
parser.set_debug_level(_DEBUG-1);
#endif
parser.set_debug_stream(lg());
ierr = parser.parse();
lexer = 0;
if (ierr == 0) {
fillNames();
}
else {
clear();
LOGGER(ibis::gVerbose > 0)
<< "Warning -- selectClause::parse failed to parse string \""
<< cl << "\"";
#ifdef FASTBIT_HALT_ON_PARSER_ERROR
throw "selectClause failed to parse the incoming string"
IBIS_FILE_LINE;
#endif
}
}
return ierr;
} // ibis::selectClause::parse
void menuUp1(uint8_t event)
{
FRESULT fr ;
struct fileControl *fc = &FileControl ;
static uint8_t mounted = 0 ;
static uint32_t state ;
static uint32_t firmwareAddress ;
uint32_t i ;
uint32_t width ;
if (UpdateItem == UPDATE_TYPE_BOOTLOADER ) // Bootloader
{
TITLE( "UPDATE BOOT" ) ;
}
else
{
#ifdef PCBX9D
if (UpdateItem == UPDATE_TYPE_SPORT_INT )
{
TITLE( "UPDATE Int. XJT" ) ;
}
else
{
TITLE( "UPDATE Ext. SPort" ) ;
}
#endif
#ifdef PCBSKY
#ifndef REVX
if (UpdateItem == UPDATE_TYPE_COPROCESSOR )
{
TITLE( "UPDATE COPROC" ) ;
}
else
{
TITLE( "UPDATE SPort" ) ;
}
#else
if (UpdateItem == UPDATE_TYPE_SPORT_EXT )
{
TITLE( "UPDATE SPort" ) ;
}
#endif
#endif
}
switch(event)
{
case EVT_ENTRY:
state = UPDATE_NO_FILES ;
if ( mounted == 0 )
{
#if defined(PCBTARANIS)
fr = f_mount(0, &g_FATFS_Obj) ;
#else
fr = f_mount(0, &g_FATFS) ;
#endif
#ifdef PCBX9D
unlockFlash() ;
#endif
}
else
{
fr = FR_OK ;
}
if ( fr == FR_OK)
{
mounted = 1 ;
}
if ( mounted )
{
fr = f_chdir( (TCHAR *)"\\firmware" ) ;
if ( fr == FR_OK )
{
state = UPDATE_NO_FILES ;
fc->index = 0 ;
fr = f_opendir( &Dj, (TCHAR *) "." ) ;
if ( fr == FR_OK )
{
if ( (UpdateItem > 1 ) )
{
fc->ext[0] = 'F' ;
fc->ext[1] = 'R' ;
fc->ext[2] = 'K' ;
}
else
{
fc->ext[0] = 'B' ;
fc->ext[1] = 'I' ;
fc->ext[2] = 'N' ;
}
fc->ext[3] = 0 ;
fc->index = 0 ;
fc->nameCount = fillNames( 0, fc ) ;
fc->hpos = 0 ;
fc->vpos = 0 ;
if ( fc->nameCount )
{
state = UPDATE_FILE_LIST ;
}
}
}
}
break ;
case EVT_KEY_FIRST(KEY_EXIT):
if ( state < UPDATE_ACTION )
{
chainMenu(menuUpdate) ;
killEvents(event) ;
}
break ;
}
switch ( state )
{
case UPDATE_NO_FILES :
lcd_puts_Pleft( 4*FH, "\005No Files" ) ;
lcd_outdez( 21*FW, 4*FH, mounted ) ;
break ;
case UPDATE_FILE_LIST :
SportVerValid = 0 ;
if ( fileList( event, &FileControl ) == 1 )
{
state = UPDATE_CONFIRM ;
}
break ;
case UPDATE_CONFIRM :
if ( (UpdateItem > UPDATE_TYPE_BOOTLOADER ) )
{
#ifdef PCBX9D
if ( (UpdateItem == UPDATE_TYPE_SPORT_INT ) )
{
lcd_puts_Pleft( 2*FH, "Flash Int. XJT from" ) ;
}
else
{
lcd_puts_Pleft( 2*FH, "Flash Ext.SP from" ) ;
}
SportVerValid = 0 ;
#else
#ifndef REVX
if ( (UpdateItem == UPDATE_TYPE_COPROCESSOR ) )
{
lcd_puts_Pleft( 2*FH, "Flash Co-Proc. from" ) ;
}
else
{
lcd_puts_Pleft( 2*FH, "Flash SPort from" ) ;
}
CoProcReady = 0 ;
#else
lcd_puts_Pleft( 2*FH, "Flash SPort from" ) ;
#endif
#endif
}
else
{
lcd_puts_Pleft( 2*FH, "Flash Bootloader from" ) ;
}
cpystr( cpystr( (uint8_t *)FlashFilename, (uint8_t *)"\\firmware\\" ), (uint8_t *)Filenames[fc->vpos] ) ;
#if defined(PCBTARANIS)
lcd_putsnAtt( 0, 4*FH, Filenames[fc->vpos], DISPLAY_CHAR_WIDTH, 0 ) ;
#else
lcd_putsnAtt0( 0, 4*FH, Filenames[fc->vpos], DISPLAY_CHAR_WIDTH, 0 ) ;
#endif
if ( event == EVT_KEY_LONG(KEY_MENU) )
{
state = UPDATE_SELECTED ;
}
if ( event == EVT_KEY_LONG(KEY_EXIT) )
{
state = UPDATE_FILE_LIST ; // Canceled
}
break ;
case UPDATE_SELECTED :
f_open( &FlashFile, FlashFilename, FA_READ ) ;
f_read( &FlashFile, (BYTE *)FileData, 1024, &BlockCount ) ;
i = 1 ;
if (UpdateItem == UPDATE_TYPE_BOOTLOADER ) // Bootloader
{
i = validateFile( (uint32_t *) FileData ) ;
}
if ( i == 0 )
{
state = UPDATE_INVALID ;
}
else
{
if (UpdateItem == UPDATE_TYPE_BOOTLOADER ) // Bootloader
{
#ifdef PCBX9D
firmwareAddress = 0x08000000 ;
#endif
#ifdef PCBSKY
firmwareAddress = 0x00400000 ;
#endif
}
#ifdef PCBSKY
#ifndef REVX
else if (UpdateItem == UPDATE_TYPE_COPROCESSOR ) // Bootloader
{
firmwareAddress = 0x00000080 ;
if ( check_ready() == 0 )
{
CoProcReady = 1 ;
}
}
#endif
#endif
else
{
// SPort update
SportState = SPORT_START ;
FirmwareSize = FileSize[fc->vpos] ;
BlockInUse = 0 ;
f_read( &FlashFile, (BYTE *)ExtraFileData, 1024, &XblockCount ) ;
}
BytesFlashed = 0 ;
BlockOffset = 0 ;
ByteEnd = 1024 ;
state = UPDATE_ACTION ;
}
break ;
case UPDATE_INVALID :
lcd_puts_Pleft( 2*FH, "Invalid File" ) ;
lcd_puts_Pleft( 4*FH, "Press EXIT" ) ;
if ( event == EVT_KEY_FIRST(KEY_EXIT) )
{
state = UPDATE_FILE_LIST ; // Canceled
killEvents(event) ;
}
break ;
case UPDATE_ACTION :
// Do the flashing
lcd_puts_Pleft( 3*FH, "Flashing" ) ;
if (UpdateItem == UPDATE_TYPE_BOOTLOADER ) // Bootloader
{
width = ByteEnd >> 9 ;
if ( BytesFlashed < ByteEnd )
{
program( (uint32_t *)firmwareAddress, &((uint32_t *)FileData)[BlockOffset] ) ; // size is 256 bytes
BlockOffset += 64 ; // 32-bit words (256 bytes)
firmwareAddress += 256 ;
BytesFlashed += 256 ;
}
else
{
if ( ByteEnd >= 32768 )
{
state = UPDATE_COMPLETE ;
}
else
{
f_read( &FlashFile, (BYTE *)FileData, 1024, &BlockCount ) ;
ByteEnd += 1024 ;
BlockOffset = 0 ;
}
}
}
#ifdef PCBSKY
#ifndef REVX
else if (UpdateItem == UPDATE_TYPE_COPROCESSOR ) // CoProcessor
uint32_t fileList(uint8_t event, struct fileControl *fc )
{
uint32_t limit ;
uint32_t result = 0 ;
uint8_t maxhsize ;
uint32_t i ;
limit = 6 ;
if ( fc->nameCount < limit )
{
limit = fc->nameCount ;
}
maxhsize = 0 ;
for ( i = 0 ; i < limit ; i += 1 )
{
uint32_t x ;
uint32_t len ;
len = x = strlen( Filenames[i] ) ;
if ( x > maxhsize )
{
maxhsize = x ;
}
if ( x > DISPLAY_CHAR_WIDTH )
{
if ( ( fc->hpos + DISPLAY_CHAR_WIDTH ) > x )
{
x = x - DISPLAY_CHAR_WIDTH ;
}
else
{
x = fc->hpos ;
}
len = DISPLAY_CHAR_WIDTH ;
}
else
{
x = 0 ;
}
lcd_putsn_P( 0, 16+FH*i, &Filenames[i][x], len ) ;
}
#if !defined(PCBTARANIS)
if ( event == 0 )
{
extern int32_t Rotary_diff ;
if ( Rotary_diff > 0 )
{
event = EVT_KEY_FIRST(KEY_DOWN) ;
}
else if ( Rotary_diff < 0 )
{
event = EVT_KEY_FIRST(KEY_UP) ;
}
Rotary_diff = 0 ;
}
#endif
if ( ( event == EVT_KEY_REPT(KEY_DOWN) ) || event == EVT_KEY_FIRST(KEY_DOWN) )
{
if ( fc->vpos < limit-1 )
{
fc->vpos += 1 ;
}
else
{
if ( fc->nameCount > limit )
{
fc->index += 1 ;
fc->nameCount = fillNames( fc->index, fc ) ;
}
}
}
if ( ( event == EVT_KEY_REPT(KEY_UP)) || ( event == EVT_KEY_FIRST(KEY_UP) ) )
{
if ( fc->vpos > 0 )
{
fc->vpos -= 1 ;
}
else
{
if ( fc->index )
{
fc->index -= 1 ;
fc->nameCount = fillNames( fc->index, fc ) ;
}
}
}
if ( ( event == EVT_KEY_REPT(MKEY_RIGHT)) || ( event == EVT_KEY_FIRST(MKEY_RIGHT) ) )
{
if ( fc->hpos + DISPLAY_CHAR_WIDTH < maxhsize ) fc->hpos += 1 ;
}
if ( ( event == EVT_KEY_REPT(MKEY_LEFT)) || ( event == EVT_KEY_FIRST(MKEY_LEFT) ) )
{
if ( fc->hpos ) fc->hpos -= 1 ;
}
if ( ( event == EVT_KEY_LONG(KEY_MENU) ) || ( event == EVT_KEY_BREAK(BTN_RE) ) )
{
// Select file to flash
killEvents(event);
result = 1 ;
}
if ( ( event == EVT_KEY_FIRST(KEY_EXIT) ) || ( event == EVT_KEY_LONG(BTN_RE) ) )
{
// Select file to flash
result = 2 ;
}
if ( event == EVT_KEY_BREAK(KEY_MENU) )
{
// Tag file
result = 3 ;
}
#if defined(PCBTARANIS)
lcd_filled_rect( 0, 2*FH+FH*fc->vpos, DISPLAY_CHAR_WIDTH*FW, 8, 0xFF, 0 ) ;
#else
lcd_char_inverse( 0, 2*FH+FH*fc->vpos, DISPLAY_CHAR_WIDTH*FW, 0 ) ;
#endif
return result ;
}
int main()
{
uint8_t index = 0;
uint8_t maxhsize = DISPLAY_CHAR_WIDTH;
FRESULT fr;
uint32_t state = ST_START;
uint32_t nameCount = 0;
uint32_t vpos = 0;
uint32_t hpos = 0;
#if defined(PCBTARANIS)
wdt_reset();
RCC->AHB1ENR |= RCC_AHB1ENR_GPIOAEN; // Enable portA clock
#endif
pwrInit();
#if defined(PCBSKY9X)
MATRIX->CCFG_SYSIO |= 0x000000F0L; // Disable syspins, enable B4,5,6,7
#endif
#if defined(PCBSKY9X)
init_SDcard();
PIOC->PIO_PER = PIO_PC25; // Enable bit C25 (USB-detect)
start_timer0();
#endif
lcdInit();
#if defined(PCBSKY9X)
extern uint8_t OptrexDisplay;
OptrexDisplay = 1;
#endif
lcd_clear();
lcd_putsLeft(0, BOOTLOADER_TITLE);
lcd_invert_line(0);
lcdRefresh();
#if defined(PCBSKY9X)
OptrexDisplay = 0;
lcdRefresh();
#endif
#if defined(PCBTARANIS)
keysInit();
I2C_EE_Init();
init_hw_timer();
#endif
__enable_irq();
init10msTimer();
#if defined(PCBSKY9X)
EblockAddress = -1;
init_spi();
#endif
#if defined(PCBSKY9X)
LockBits = readLockBits();
if (LockBits) {
clearLockBits();
}
#endif
#if defined(PCBTARANIS)
// SD card detect pin
sdInit();
usbInit();
usbStart();
#endif
for (;;) {
wdt_reset();
if (Tenms) {
if (EE_timer) {
if (--EE_timer == 0) {
#if defined(PCBSKY9X)
writeBlock();
#endif
}
}
Tenms = 0;
lcd_clear();
lcd_putsLeft(0, BOOTLOADER_TITLE);
lcd_invert_line(0);
uint8_t event = getEvent();
if (state != ST_USB) {
if (usbPlugged()) {
state = ST_USB;
if (!unlocked) {
unlocked = 1;
unlockFlash();
}
usbPluggedIn();
}
}
if (state == ST_START) {
lcd_putsLeft(2*FH, "\010Write Firmware");
lcd_putsLeft(3*FH, "\010Restore EEPROM");
lcd_putsLeft(4*FH, "\010Exit");
lcd_invert_line(2+vpos);
lcd_putsLeft(7*FH, INDENT "Or plug in a USB cable for mass storage");
if (event == EVT_KEY_FIRST(BOOT_KEY_DOWN)) {
vpos == 2 ? vpos = 0 : vpos = vpos+1;
}
else if (event == EVT_KEY_FIRST(BOOT_KEY_UP)) {
vpos == 0 ? vpos = 2 : vpos = vpos-1;
}
else if (event == EVT_KEY_BREAK(BOOT_KEY_MENU)) {
switch (vpos) {
case 0:
state = ST_FLASH_MENU;
break;
case 1:
state = ST_RESTORE_MENU;
break;
default:
state = ST_REBOOT;
}
}
}
if (state == ST_USB) {
lcd_putsLeft(4*FH, "\026USB Connected");
if (usbPlugged() == 0) {
vpos = 0;
if (unlocked) {
lockFlash();
unlocked = 0;
}
state = ST_START;
}
#if defined(PCBSKY9X)
usbMassStorage();
#endif
}
if (state == ST_FLASH_MENU || state == ST_RESTORE_MENU) {
sdInit();
memoryType = (state == ST_RESTORE_MENU ? MEM_EEPROM : MEM_FLASH);
state = ST_DIR_CHECK;
}
else if (state == ST_DIR_CHECK) {
fr = f_chdir(getBinaryPath());
if (fr == FR_OK) {
state = ST_OPEN_DIR;
}
else {
lcd_putsLeft(2*FH, INDENT "Directory is missing!");
if (event == EVT_KEY_BREAK(BOOT_KEY_EXIT) || event == EVT_KEY_BREAK(BOOT_KEY_MENU)) {
vpos = 0;
state = ST_START;
}
}
}
if (state == ST_OPEN_DIR) {
index = 0;
fr = f_opendir(&Dj, ".");
if (fr == FR_OK) {
state = ST_FILE_LIST;
nameCount = fillNames(0);
hpos = 0;
vpos = 0;
}
}
if (state == ST_FILE_LIST) {
uint32_t limit = 6;
if (nameCount < limit) {
limit = nameCount;
}
maxhsize = 0;
for (uint32_t i=0; i<limit; i++) {
uint32_t x;
x = strlen(Filenames[i]);
if (x > maxhsize) {
maxhsize = x;
}
if (x > DISPLAY_CHAR_WIDTH) {
if (hpos + DISPLAY_CHAR_WIDTH > x) {
x = x - DISPLAY_CHAR_WIDTH;
}
else {
x = hpos;
}
}
else {
x = 0;
}
lcd_putsnAtt(INDENT_WIDTH, 16 + FH * i, &Filenames[i][x], DISPLAY_CHAR_WIDTH, 0);
}
if (event == EVT_KEY_REPT(BOOT_KEY_DOWN) || event == EVT_KEY_FIRST(BOOT_KEY_DOWN)) {
if (vpos < limit - 1) {
vpos += 1;
}
else {
if (nameCount > limit) {
index += 1;
nameCount = fillNames(index);
}
}
}
else if (event == EVT_KEY_REPT(BOOT_KEY_UP) || event == EVT_KEY_FIRST(BOOT_KEY_UP)) {
if (vpos > 0) {
vpos -= 1;
}
else {
if (index) {
index -= 1;
nameCount = fillNames(index);
}
}
}
#if !defined(PCBTARANIS)
else if (event == EVT_KEY_REPT(BOOT_KEY_RIGHT) || event == EVT_KEY_FIRST(BOOT_KEY_RIGHT)) {
if (hpos + DISPLAY_CHAR_WIDTH < maxhsize) {
hpos += 1;
}
}
else if (event == EVT_KEY_REPT(BOOT_KEY_LEFT) || event == EVT_KEY_FIRST(BOOT_KEY_LEFT)) {
if (hpos) {
hpos -= 1;
}
}
#endif
else if (event == EVT_KEY_BREAK(BOOT_KEY_MENU)) {
// Select file to flash
state = ST_FLASH_CHECK;
Valid = 0;
}
else if (event == EVT_KEY_FIRST(BOOT_KEY_EXIT)) {
state = ST_START;
vpos = 0;
}
lcd_invert_line(2 + vpos);
}
else if (state == ST_FLASH_CHECK) {
int result = menuFlashFile(vpos, event);
FirmwareSize = FileSize[vpos] - BOOTLOADER_SIZE;
if (result == 0) {
// canceled
state = ST_FILE_LIST;
}
else if (result == 1) {
// confirmed
firmwareAddress = FIRMWARE_ADDRESS + BOOTLOADER_SIZE;
firmwareWritten = 0;
eepromAddress = 0;
eepromWritten = 0;
state = ST_FLASHING;
}
}
else if (state == ST_FLASHING) {
// commit to flashing
lcd_putsLeft(4*FH, "\032Writing...");
if (!unlocked && (memoryType == MEM_FLASH)) {
unlocked = 1;
unlockFlash();
}
int progress;
if (memoryType == MEM_FLASH) {
writeFlashBlock();
firmwareWritten += sizeof(Block_buffer);
progress = (200*firmwareWritten) / FirmwareSize;
}
else {
writeEepromBlock();
eepromWritten += sizeof(Block_buffer);
progress = (200*eepromWritten) / EESIZE;
}
lcd_rect( 3, 6*FH+4, 204, 7);
lcd_hline(5, 6*FH+6, progress, FORCE);
lcd_hline(5, 6*FH+7, progress, FORCE);
lcd_hline(5, 6*FH+8, progress, FORCE);
fr = f_read(&FlashFile, (BYTE *)Block_buffer, sizeof(Block_buffer), &BlockCount);
if (BlockCount == 0) {
state = ST_FLASH_DONE; // EOF
}
if (firmwareWritten >= FLASHSIZE - BOOTLOADER_SIZE) {
state = ST_FLASH_DONE; // Backstop
}
if (eepromWritten >= EESIZE) {
state = ST_FLASH_DONE; // Backstop
}
}
if (state == ST_FLASH_DONE) {
if (unlocked) {
lockFlash();
unlocked = 0;
}
lcd_putsLeft(4*FH, "\024Writing Complete");
if (event == EVT_KEY_FIRST(BOOT_KEY_EXIT) || event == EVT_KEY_BREAK(BOOT_KEY_MENU)) {
state = ST_START;
vpos = 0;
}
}
if (event == EVT_KEY_LONG(BOOT_KEY_EXIT)) {
state = ST_REBOOT;
}
lcdRefresh();
if (PowerUpDelay < 20) { // 200 mS
PowerUpDelay += 1;
}
else {
sdPoll10ms();
}
}
if (pwrCheck() == e_power_off && state != ST_FLASHING && state != ST_USB) {
pwrOff();
for (;;) {
// Wait for power to go off
}
}
if (state == ST_REBOOT) {
if ((~readKeys() & 0x7E) == 0) {
NVIC_SystemReset();
}
}
}
return 0;
}
int main()
{
uint8_t index = 0;
uint8_t maxhsize = DISPLAY_CHAR_WIDTH;
FRESULT fr;
uint32_t state = ST_START;
uint32_t nameCount = 0;
uint32_t vpos = 0;
uint32_t hpos = 0;
#if defined(PCBTARANIS)
wdt_reset();
RCC_AHB1PeriphClockCmd(PWR_RCC_AHB1Periph | KEYS_RCC_AHB1Periph | LCD_RCC_AHB1Periph | BACKLIGHT_RCC_AHB1Periph | I2C_RCC_AHB1Periph | SD_RCC_AHB1Periph, ENABLE);
RCC_APB1PeriphClockCmd(LCD_RCC_APB1Periph | BACKLIGHT_RCC_APB1Periph | INTERRUPT_5MS_APB1Periph | I2C_RCC_APB1Periph | SD_RCC_APB1Periph, ENABLE);
RCC_APB2PeriphClockCmd(BACKLIGHT_RCC_APB2Periph, ENABLE);
#endif
pwrInit();
delaysInit(); //needed for lcdInit()
lcdInit();
backlightInit();
lcd_clear();
lcd_putsn(0, 0, (const char *)bootloaderVersion, 0); // trick to avoid bootloaderVersion to be optimized out ...
lcd_putsLeft(0, BOOTLOADER_TITLE);
lcd_invert_line(0);
lcdRefresh();
keysInit();
i2cInit();
__enable_irq();
init10msTimer();
#if defined(PCBTARANIS)
// SD card detect pin
sdInit();
usbInit();
#endif
for (;;) {
wdt_reset();
if (Tenms) {
Tenms = 0;
lcdRefreshWait();
lcd_clear();
lcd_putsLeft(0, BOOTLOADER_TITLE);
lcd_invert_line(0);
uint8_t event = getEvent();
if (state != ST_USB) {
if (usbPlugged()) {
state = ST_USB;
if (!unlocked) {
unlocked = 1;
unlockFlash();
}
usbPluggedIn();
}
}
if (state == ST_START) {
lcd_putsLeft(2*FH, "\010Write Firmware");
lcd_putsLeft(3*FH, "\010Restore EEPROM");
lcd_putsLeft(4*FH, "\010Exit");
lcd_invert_line(2+vpos);
lcd_putsLeft(7*FH, INDENT "Or plug in a USB cable for mass storage");
if (event == EVT_KEY_FIRST(BOOT_KEY_DOWN)) {
vpos == 2 ? vpos = 0 : vpos = vpos+1;
}
else if (event == EVT_KEY_FIRST(BOOT_KEY_UP)) {
vpos == 0 ? vpos = 2 : vpos = vpos-1;
}
else if (event == EVT_KEY_BREAK(BOOT_KEY_MENU)) {
switch (vpos) {
case 0:
state = ST_FLASH_MENU;
break;
case 1:
state = ST_RESTORE_MENU;
break;
default:
state = ST_REBOOT;
}
}
}
if (state == ST_USB) {
lcd_putsLeft(4*FH, "\026USB Connected");
if (usbPlugged() == 0) {
vpos = 0;
if (unlocked) {
lockFlash();
unlocked = 0;
}
state = ST_START;
}
#if defined(PCBSKY9X)
usbMassStorage();
#endif
}
if (state == ST_FLASH_MENU || state == ST_RESTORE_MENU) {
sdInit();
memoryType = (state == ST_RESTORE_MENU ? MEM_EEPROM : MEM_FLASH);
state = ST_DIR_CHECK;
}
else if (state == ST_DIR_CHECK) {
fr = f_chdir(getBinaryPath());
if (fr == FR_OK) {
state = ST_OPEN_DIR;
}
else {
lcd_putsLeft(2*FH, INDENT "Directory is missing!");
if (event == EVT_KEY_BREAK(BOOT_KEY_EXIT) || event == EVT_KEY_BREAK(BOOT_KEY_MENU)) {
vpos = 0;
state = ST_START;
}
}
}
if (state == ST_OPEN_DIR) {
index = 0;
fr = f_opendir(&Dj, ".");
if (fr == FR_OK) {
state = ST_FILE_LIST;
nameCount = fillNames(0);
hpos = 0;
vpos = 0;
}
}
if (state == ST_FILE_LIST) {
uint32_t limit = 6;
if (nameCount < limit) {
limit = nameCount;
}
maxhsize = 0;
for (uint32_t i=0; i<limit; i++) {
uint32_t x;
x = strlen(Filenames[i]);
if (x > maxhsize) {
maxhsize = x;
}
if (x > DISPLAY_CHAR_WIDTH) {
if (hpos + DISPLAY_CHAR_WIDTH > x) {
x = x - DISPLAY_CHAR_WIDTH;
}
else {
x = hpos;
}
}
else {
x = 0;
}
lcd_putsnAtt(INDENT_WIDTH, 16 + FH * i, &Filenames[i][x], DISPLAY_CHAR_WIDTH, 0);
}
if (event == EVT_KEY_REPT(BOOT_KEY_DOWN) || event == EVT_KEY_FIRST(BOOT_KEY_DOWN)) {
if (vpos < limit - 1) {
vpos += 1;
}
else {
if (nameCount > limit) {
index += 1;
nameCount = fillNames(index);
}
}
}
else if (event == EVT_KEY_REPT(BOOT_KEY_UP) || event == EVT_KEY_FIRST(BOOT_KEY_UP)) {
if (vpos > 0) {
vpos -= 1;
}
else {
if (index) {
index -= 1;
nameCount = fillNames(index);
}
}
}
#if !defined(PCBTARANIS)
else if (event == EVT_KEY_REPT(BOOT_KEY_RIGHT) || event == EVT_KEY_FIRST(BOOT_KEY_RIGHT)) {
if (hpos + DISPLAY_CHAR_WIDTH < maxhsize) {
hpos += 1;
}
}
else if (event == EVT_KEY_REPT(BOOT_KEY_LEFT) || event == EVT_KEY_FIRST(BOOT_KEY_LEFT)) {
if (hpos) {
hpos -= 1;
}
}
#endif
else if (event == EVT_KEY_BREAK(BOOT_KEY_MENU)) {
// Select file to flash
state = ST_FLASH_CHECK;
Valid = 0;
}
else if (event == EVT_KEY_FIRST(BOOT_KEY_EXIT)) {
state = ST_START;
vpos = 0;
}
lcd_invert_line(2 + vpos);
}
else if (state == ST_FLASH_CHECK) {
int result = menuFlashFile(vpos, event);
FirmwareSize = FileSize[vpos] - BOOTLOADER_SIZE;
if (result == 0) {
// canceled
state = ST_FILE_LIST;
}
else if (result == 1) {
// confirmed
firmwareAddress = FIRMWARE_ADDRESS + BOOTLOADER_SIZE;
firmwareWritten = 0;
eepromAddress = 0;
eepromWritten = 0;
state = ST_FLASHING;
}
}
else if (state == ST_FLASHING) {
// commit to flashing
lcd_putsLeft(4*FH, "\032Writing...");
if (!unlocked && (memoryType == MEM_FLASH)) {
unlocked = 1;
unlockFlash();
}
int progress;
if (memoryType == MEM_FLASH) {
writeFlashBlock();
firmwareWritten += sizeof(Block_buffer);
progress = (200*firmwareWritten) / FirmwareSize;
}
else {
writeEepromBlock();
eepromWritten += sizeof(Block_buffer);
progress = (200*eepromWritten) / EESIZE;
}
lcd_rect( 3, 6*FH+4, 204, 7);
lcd_hline(5, 6*FH+6, progress, FORCE);
lcd_hline(5, 6*FH+7, progress, FORCE);
lcd_hline(5, 6*FH+8, progress, FORCE);
fr = f_read(&FlashFile, (BYTE *)Block_buffer, sizeof(Block_buffer), &BlockCount);
if (BlockCount == 0) {
state = ST_FLASH_DONE; // EOF
}
if (firmwareWritten >= FLASHSIZE - BOOTLOADER_SIZE) {
state = ST_FLASH_DONE; // Backstop
}
if (eepromWritten >= EESIZE) {
state = ST_FLASH_DONE; // Backstop
}
}
if (state == ST_FLASH_DONE) {
if (unlocked) {
lockFlash();
unlocked = 0;
}
lcd_putsLeft(4*FH, "\024Writing Complete");
if (event == EVT_KEY_FIRST(BOOT_KEY_EXIT) || event == EVT_KEY_BREAK(BOOT_KEY_MENU)) {
state = ST_START;
vpos = 0;
}
}
if (event == EVT_KEY_LONG(BOOT_KEY_EXIT)) {
state = ST_REBOOT;
}
lcdRefresh();
if (PowerUpDelay < 20) { // 200 mS
PowerUpDelay += 1;
}
else {
sdPoll10ms();
}
}
if (state != ST_FLASHING && state != ST_USB) {
#if defined(REV9E)
if (pwrPressed()) {
#else
if (pwrCheck() == e_power_off) {
#endif
lcdOff(); // this drains LCD caps
pwrOff();
for (;;) {
// Wait for power to go off
}
}
}
if (state == ST_REBOOT) {
if (readKeys() == 0) {
lcd_clear();
lcdRefresh();
lcdRefreshWait();
RCC->CSR |= RCC_CSR_RMVF; //clear the reset flags in RCC clock control & status register
NVIC_SystemReset();
}
}
}
return 0;
}
Sorter::Sorter(std::vector<PersonIntrinsic *> & toCopy){
fillNames(); //fills name of categories
//used to process all records into their intrinsic score
for (int counter = 0; counter < toCopy.size(); counter++){
//gets the next object
PersonIntrinsic * temp = toCopy.at(counter);
//checks to see if it faculty
if(temp->getRole() == "Faculty"){
/*
from this point on the basic structure is the same
gets the category and then checks to see if it is
positive, negative or neutral then adds to appropriate value
hindsight makes realize there is a more efficient way to do this
*/
int powerVar = temp->getPower();
if(powerVar == 0)
staffValues[1]++;
else if (powerVar > 0)
staffValues[0]++;
else if (powerVar < 0)
staffValues[2]++;
int independenceVar = temp->getIndepedence();
if(independenceVar == 0)
staffValues[4]++;
else if (independenceVar > 0)
staffValues[3]++;
else if (independenceVar < 0)
staffValues[5]++;
int curiosityVar = temp->getCuriosity();
if(curiosityVar == 0)
staffValues[7]++;
else if (curiosityVar > 0)
staffValues[6]++;
else if (curiosityVar < 0)
staffValues[8]++;
int acceptanceVar = temp->getAcceptance();
if(acceptanceVar == 0)
staffValues[10]++;
else if (acceptanceVar > 0)
staffValues[9]++;
else if (acceptanceVar < 0)
staffValues[11]++;
int orderVar = temp->getOrder();
if(orderVar == 0)
staffValues[13]++;
else if (orderVar > 0)
staffValues[12]++;
else if (orderVar < 0)
staffValues[14]++;
int savingVar = temp->getSaving();
if(savingVar == 0)
staffValues[16]++;
else if (savingVar > 0)
staffValues[15]++;
else if (savingVar < 0)
staffValues[17]++;
int honorVar = temp->getHonor();
if(honorVar == 0)
staffValues[19]++;
else if (honorVar > 0)
staffValues[18]++;
else if (honorVar < 0)
staffValues[20]++;
int idealismVar = temp->getIdealism();
if(idealismVar == 0)
staffValues[22]++;
else if (idealismVar > 0)
staffValues[21]++;
else if (idealismVar < 0)
staffValues[23]++;
int socialContactVar = temp->getSocialContact();
if(socialContactVar == 0)
staffValues[25]++;
else if (socialContactVar > 0)
staffValues[24]++;
else if (socialContactVar < 0)
staffValues[26]++;
int familyVar = temp->getFamily();
if(familyVar == 0)
staffValues[28]++;
else if (familyVar > 0)
staffValues[27]++;
else if (familyVar < 0)
staffValues[29]++;
int statusVar = temp->getStatus();
if(statusVar == 0)
staffValues[31]++;
else if (statusVar > 0)
staffValues[30]++;
else if (statusVar < 0)
staffValues[32]++;
int vengeanceVar = temp->getVengeance();
if(vengeanceVar == 0)
staffValues[34]++;
else if (vengeanceVar > 0)
staffValues[33]++;
else if (vengeanceVar < 0)
staffValues[35]++;
int eatingVar = temp->getEating();
if(eatingVar == 0)
staffValues[37]++;
else if (eatingVar > 0)
staffValues[36]++;
else if (eatingVar < 0)
staffValues[38]++;
int physicalActivityVar = temp->getPhysicalActivity();
if(physicalActivityVar == 0)
staffValues[40]++;
else if (physicalActivityVar > 0)
staffValues[39]++;
else if (physicalActivityVar < 0)
staffValues[41]++;
int tranquilityVar = temp->getTranquility();
if(tranquilityVar == 0)
staffValues[43]++;
else if (tranquilityVar > 0)
staffValues[42]++;
else if (tranquilityVar < 0)
staffValues[44]++;
}
//checks to see if the role is a student
else if (temp->getRole() == "Student"){
/*
from this point on the basic structure is the same
gets the category and then checks to see if it is
positive, negative or neutral then adds to appropriate value
hindsight makes realize there is a more efficient way to do this
*/
int powerVar = temp->getPower();
if(powerVar == 0)
studentValues[1]++;
else if (powerVar > 0)
studentValues[0]++;
else if (powerVar < 0)
studentValues[2]++;
int independenceVar = temp->getIndepedence();
if(independenceVar == 0)
studentValues[4]++;
else if (independenceVar > 0)
studentValues[3]++;
else if (independenceVar < 0)
studentValues[5]++;
int curiosityVar = temp->getCuriosity();
if(curiosityVar == 0)
studentValues[7]++;
else if (curiosityVar > 0)
studentValues[6]++;
else if (curiosityVar < 0)
studentValues[8]++;
int acceptanceVar = temp->getAcceptance();
if(acceptanceVar == 0)
studentValues[10]++;
else if (acceptanceVar > 0)
studentValues[9]++;
else if (acceptanceVar < 0)
studentValues[11]++;
int orderVar = temp->getOrder();
if(orderVar == 0)
studentValues[13]++;
else if (orderVar > 0)
studentValues[12]++;
else if (orderVar < 0)
studentValues[14]++;
int savingVar = temp->getSaving();
if(savingVar == 0)
studentValues[16]++;
else if (savingVar > 0)
studentValues[15]++;
else if (savingVar < 0)
studentValues[17]++;
int honorVar = temp->getHonor();
if(honorVar == 0)
studentValues[19]++;
else if (honorVar > 0)
studentValues[18]++;
else if (honorVar < 0)
studentValues[20]++;
int idealismVar = temp->getIdealism();
if(idealismVar == 0)
studentValues[22]++;
else if (idealismVar > 0)
studentValues[21]++;
else if (idealismVar < 0)
studentValues[23]++;
int socialContactVar = temp->getSocialContact();
if(socialContactVar == 0)
studentValues[25]++;
else if (socialContactVar > 0)
studentValues[24]++;
else if (socialContactVar < 0)
studentValues[26]++;
int familyVar = temp->getFamily();
if(familyVar == 0)
studentValues[28]++;
else if (familyVar > 0)
studentValues[27]++;
else if (familyVar < 0)
studentValues[29]++;
int statusVar = temp->getStatus();
if(statusVar == 0)
studentValues[31]++;
else if (statusVar > 0)
studentValues[30]++;
else if (statusVar < 0)
studentValues[32]++;
int vengeanceVar = temp->getVengeance();
if(vengeanceVar == 0)
studentValues[34]++;
else if (vengeanceVar > 0)
studentValues[33]++;
else if (vengeanceVar < 0)
studentValues[35]++;
int eatingVar = temp->getEating();
if(eatingVar == 0)
studentValues[37]++;
else if (eatingVar > 0)
studentValues[36]++;
else if (eatingVar < 0)
studentValues[38]++;
int physicalActivityVar = temp->getPhysicalActivity();
if(physicalActivityVar == 0)
studentValues[40]++;
else if (physicalActivityVar > 0)
studentValues[39]++;
else if (physicalActivityVar < 0)
studentValues[41]++;
int tranquilityVar = temp->getTranquility();
if(tranquilityVar == 0)
studentValues[43]++;
else if (tranquilityVar > 0)
studentValues[42]++;
else if (tranquilityVar < 0)
studentValues[44]++;
}
//checks to see if the role set to neither
else if (temp->getRole() == "Neither"){
/*
from this point on the basic structure is the same
gets the category and then checks to see if it is
positive, negative or neutral then adds to appropriate value
hindsight makes realize there is a more efficient way to do this
*/
int powerVar = temp->getPower();
if(powerVar == 0)
neitherValues[1]++;
else if (powerVar > 0)
neitherValues[0]++;
else if (powerVar < 0)
neitherValues[2]++;
int independenceVar = temp->getIndepedence();
if(independenceVar == 0)
neitherValues[4]++;
else if (independenceVar > 0)
neitherValues[3]++;
else if (independenceVar < 0)
neitherValues[5]++;
int curiosityVar = temp->getCuriosity();
if(curiosityVar == 0)
neitherValues[7]++;
else if (curiosityVar > 0)
neitherValues[6]++;
else if (curiosityVar < 0)
neitherValues[8]++;
int acceptanceVar = temp->getAcceptance();
if(acceptanceVar == 0)
neitherValues[10]++;
else if (acceptanceVar > 0)
neitherValues[9]++;
else if (acceptanceVar < 0)
neitherValues[11]++;
int orderVar = temp->getOrder();
if(orderVar == 0)
neitherValues[13]++;
else if (orderVar > 0)
neitherValues[12]++;
else if (orderVar < 0)
neitherValues[14]++;
int savingVar = temp->getSaving();
if(savingVar == 0)
neitherValues[16]++;
else if (savingVar > 0)
neitherValues[15]++;
else if (savingVar < 0)
neitherValues[17]++;
int honorVar = temp->getHonor();
if(honorVar == 0)
neitherValues[19]++;
else if (honorVar > 0)
neitherValues[18]++;
else if (honorVar < 0)
neitherValues[20]++;
int idealismVar = temp->getIdealism();
if(idealismVar == 0)
neitherValues[22]++;
else if (idealismVar > 0)
neitherValues[21]++;
else if (idealismVar < 0)
neitherValues[23]++;
int socialContactVar = temp->getSocialContact();
if(socialContactVar == 0)
neitherValues[25]++;
else if (socialContactVar > 0)
neitherValues[24]++;
else if (socialContactVar < 0)
neitherValues[26]++;
int familyVar = temp->getFamily();
if(familyVar == 0)
neitherValues[28]++;
else if (familyVar > 0)
neitherValues[27]++;
else if (familyVar < 0)
neitherValues[29]++;
int statusVar = temp->getStatus();
if(statusVar == 0)
neitherValues[31]++;
else if (statusVar > 0)
neitherValues[30]++;
else if (statusVar < 0)
neitherValues[32]++;
int vengeanceVar = temp->getVengeance();
if(vengeanceVar == 0)
neitherValues[34]++;
else if (vengeanceVar > 0)
neitherValues[33]++;
else if (vengeanceVar < 0)
neitherValues[35]++;
int eatingVar = temp->getEating();
if(eatingVar == 0)
neitherValues[37]++;
else if (eatingVar > 0)
neitherValues[36]++;
else if (eatingVar < 0)
neitherValues[38]++;
int physicalActivityVar = temp->getPhysicalActivity();
if(physicalActivityVar == 0)
neitherValues[40]++;
else if (physicalActivityVar > 0)
neitherValues[39]++;
else if (physicalActivityVar < 0)
neitherValues[41]++;
int tranquilityVar = temp->getTranquility();
if(tranquilityVar == 0)
neitherValues[43]++;
else if (tranquilityVar > 0)
neitherValues[42]++;
else if (tranquilityVar < 0)
neitherValues[44]++;
}
//all others will be caught here
else{
/*
from this point on the basic structure is the same
gets the category and then checks to see if it is
positive, negative or neutral then adds to appropriate value
hindsight makes realize there is a more efficient way to do this
*/
int powerVar = temp->getPower();
if(powerVar == 0)
otherValues[1]++;
else if (powerVar > 0)
otherValues[0]++;
else if (powerVar < 0)
otherValues[2]++;
int independenceVar = temp->getIndepedence();
if(independenceVar == 0)
otherValues[4]++;
else if (independenceVar > 0)
otherValues[3]++;
else if (independenceVar < 0)
otherValues[5]++;
int curiosityVar = temp->getCuriosity();
if(curiosityVar == 0)
otherValues[7]++;
else if (curiosityVar > 0)
otherValues[6]++;
else if (curiosityVar < 0)
otherValues[8]++;
int acceptanceVar = temp->getAcceptance();
if(acceptanceVar == 0)
otherValues[10]++;
else if (acceptanceVar > 0)
otherValues[9]++;
else if (acceptanceVar < 0)
otherValues[11]++;
int orderVar = temp->getOrder();
if(orderVar == 0)
otherValues[13]++;
else if (orderVar > 0)
otherValues[12]++;
else if (orderVar < 0)
otherValues[14]++;
int savingVar = temp->getSaving();
if(savingVar == 0)
otherValues[16]++;
else if (savingVar > 0)
otherValues[15]++;
else if (savingVar < 0)
otherValues[17]++;
int honorVar = temp->getHonor();
if(honorVar == 0)
otherValues[19]++;
else if (honorVar > 0)
otherValues[18]++;
else if (honorVar < 0)
otherValues[20]++;
int idealismVar = temp->getIdealism();
if(idealismVar == 0)
otherValues[22]++;
else if (idealismVar > 0)
otherValues[21]++;
else if (idealismVar < 0)
otherValues[23]++;
int socialContactVar = temp->getSocialContact();
if(socialContactVar == 0)
otherValues[25]++;
else if (socialContactVar > 0)
otherValues[24]++;
else if (socialContactVar < 0)
otherValues[26]++;
int familyVar = temp->getFamily();
if(familyVar == 0)
otherValues[28]++;
else if (familyVar > 0)
otherValues[27]++;
else if (familyVar < 0)
otherValues[29]++;
int statusVar = temp->getStatus();
if(statusVar == 0)
otherValues[31]++;
else if (statusVar > 0)
otherValues[30]++;
else if (statusVar < 0)
otherValues[32]++;
int vengeanceVar = temp->getVengeance();
if(vengeanceVar == 0)
otherValues[34]++;
else if (vengeanceVar > 0)
otherValues[33]++;
else if (vengeanceVar < 0)
otherValues[35]++;
int eatingVar = temp->getEating();
if(eatingVar == 0)
otherValues[37]++;
else if (eatingVar > 0)
otherValues[36]++;
else if (eatingVar < 0)
otherValues[38]++;
int physicalActivityVar = temp->getPhysicalActivity();
if(physicalActivityVar == 0)
otherValues[40]++;
else if (physicalActivityVar > 0)
otherValues[39]++;
else if (physicalActivityVar < 0)
otherValues[41]++;
int tranquilityVar = temp->getTranquility();
if(tranquilityVar == 0)
otherValues[43]++;
else if (tranquilityVar > 0)
otherValues[42]++;
else if (tranquilityVar < 0)
otherValues[44]++;
}
}
//this adds the name of the group and its value to a map, allowing it to be autosorted from high to low
for (int counter= 0; counter < 45; counter++){
student.insert(std::pair<int, std::string>(studentValues[counter], namesOfValues[counter]));
staff.insert(std::pair<int, std::string>(staffValues[counter], namesOfValues[counter]));
neither.insert(std::pair<int, std::string>(neitherValues[counter], namesOfValues[counter]));
other.insert(std::pair<int, std::string>(otherValues[counter], namesOfValues[counter]));
}
}
Sorter::Sorter(){
fillNames();
}
int RemoveGroupsCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get groups you want to remove
if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); }
if (groupfile != "") {
groupMap = new GroupMap(groupfile);
groupMap->readMap();
//make sure groups are valid
//takes care of user setting groupNames that are invalid or setting groups=all
vector<string> namesGroups = groupMap->getNamesOfGroups();
vector<string> checkedGroups;
for (int i = 0; i < Groups.size(); i++) {
if (m->inUsersGroups(Groups[i], namesGroups)) { checkedGroups.push_back(Groups[i]); }
else { m->mothurOut("[WARNING]: " + Groups[i] + " is not a valid group in your groupfile, ignoring.\n"); }
}
if (checkedGroups.size() == 0) { m->mothurOut("[ERROR]: no valid groups, aborting.\n"); delete groupMap; return 0; }
else {
Groups = checkedGroups;
m->setGroups(Groups);
}
//fill names with names of sequences that are from the groups we want to remove
fillNames();
delete groupMap;
}else if (countfile != ""){
if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
}
CountTable ct;
ct.readTable(countfile, true, false);
if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
vector<string> gNamesOfGroups = ct.getNamesOfGroups();
SharedUtil util;
util.setGroups(Groups, gNamesOfGroups);
vector<string> namesOfSeqs = ct.getNamesOfSeqs();
sort(Groups.begin(), Groups.end());
for (int i = 0; i < namesOfSeqs.size(); i++) {
vector<string> thisSeqsGroups = ct.getGroups(namesOfSeqs[i]);
if (m->isSubset(Groups, thisSeqsGroups)) { //you only have seqs from these groups so remove you
names.insert(namesOfSeqs[i]);
}
}
}
if (m->control_pressed) { return 0; }
//read through the correct file and output lines you want to keep
if (namefile != "") { readName(); }
if (fastafile != "") { readFasta(); }
if (groupfile != "") { readGroup(); }
if (countfile != "") { readCount(); }
if (listfile != "") { readList(); }
if (taxfile != "") { readTax(); }
if (sharedfile != "") { readShared(); }
if (designfile != "") { readDesign(); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (outputNames.size() != 0) {
m->mothurOutEndLine();
m->mothurOut("Output File names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
//set fasta file as new current fastafile
string current = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
}
itTypes = outputTypes.find("name");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
}
itTypes = outputTypes.find("list");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
}
itTypes = outputTypes.find("taxonomy");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
}
itTypes = outputTypes.find("shared");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
}
itTypes = outputTypes.find("design");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setDesignFile(current); }
}
itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
}
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "execute");
exit(1);
}
}