void DMTC1(unsigned long word)
{ //05 (05)
sprintf(dis_op, "dmtc1\t%s, %s", gpr_rn[getRT(word)], fpr_rn[getFD(word)]);
}
void CTC1(unsigned long word)
{ //06 (06)
sprintf(dis_op, "ctc1\t%s, %s", gpr_rn[getRT(word)], fpr_rn[getFD(word)]);
}
void CFC1(unsigned long word)
{ //02 (02)
sprintf(dis_op, "cfc1\t%s, %s", gpr_rn[getRT(word)], fpr_rn[getFD(word)]);
}
void MTC1(unsigned long word)
{ //04 (04)
sprintf(dis_op, "mtc1\t%s, %s", gpr_rn[getRT(word)], fpr_rn[getFD(word)]);
}
void DMFC1(unsigned long word)
{ //01 (01)
sprintf(dis_op, "dmfc1\t%s, %s", gpr_rn[getRT(word)], fpr_rn[getFD(word)]);
}
void MFC1(unsigned long word)
{ //00 (00)
sprintf(dis_op, "mfc1\t%s, %s", gpr_rn[getRT(word)], fpr_rn[getFD(word)]);
}
int main (void)
{
//定义状态返回值
uchar ret;
uchar adCnt;
uchar iCnt;
//初始化发送地址
for (adCnt = 0; adCnt < TX_ADR_WIDTH; adCnt ++)
txAddr[adCnt] = TX_ADDRESS[adCnt];
//初始化打印终端
termialInit();
//开启硬件接收中断
ret = uartRxISR();
if (!ret)
printf ("Error: enable Rx ISR error!\n");
//spi模块初始化
spiInit();
//输出logo
logoPrint();
while (1)
{
//进入命令模式(默认进入)
if (mode == CMD_MODE)
{
//输出命令提示信息
printCmdRe();
//获取命令
getCommand();
}
//进入正常模式
else if (mode == NOMAL_MODE)
{
printf ("Enter NOMAL_MODE\n");
//输出模式选择选项
printRTRe();
//等待接收选择的模式
getRT();
}
//进入到数据发送模式
else if (mode == TX_MODE)
{
//发送缓冲区中的数据
if (txCnt != 0)
{
printf ("sendOne\n");
nrfSend(txAddr, txBuf);
txCnt = 0;
for (iCnt = 0; iCnt < TX_PLOAD_WIDTH; iCnt ++)
txBuf[iCnt] = '\0';
}
}
//进入到数据接收模式
else if (mode == RX_MODE)
{
//printf ("Enter RX_MODE\n");
//接收数据并放入到缓冲区rxBuf中
nrfRecv(txAddr, rxBuf);
//将rxBuf中的数据通过串口发送出去
if (rxBuf[0] != '\0')
{
printf ("%s", rxBuf);
for (iCnt = 0; iCnt < TX_PLOAD_WIDTH; iCnt++)
rxBuf[iCnt] = '\0';
}
}
else
printf ("ERROR: MODE SELECT ERROR!!!\n");
}
return 0;
}
void
InteractionEnergyVrna::
computeES( const Accessibility & acc, InteractionEnergyVrna::EsMatrix & esToFill )
{
// prepare container
esToFill.resize( acc.getSequence().size(), acc.getSequence().size() );
// sequence length
const int seqLength = (int)acc.getSequence().size();
const E_type RT = getRT();
// VRNA compatible data structures
char * sequence = (char *) vrna_alloc(sizeof(char) * (seqLength + 1));
char * structureConstraint = (char *) vrna_alloc(sizeof(char) * (seqLength + 1));
for (int i=0; i<seqLength; i++) {
// copy sequence
sequence[i] = acc.getSequence().asString().at(i);
// copy accessibility constraint if present
structureConstraint[i] = acc.getAccConstraint().getVrnaDotBracket(i);
}
sequence[seqLength] = structureConstraint[seqLength] = '\0';
// prepare folding data
vrna_md_t curModel;
vrna_md_copy( &curModel, &foldModel );
// set maximal base pair span
curModel.max_bp_span = acc.getAccConstraint().getMaxBpSpan();
if (curModel.max_bp_span >= (int)acc.getSequence().size()) {
curModel.max_bp_span = -1;
}
// TODO check if VRNA_OPTION_WINDOW reasonable to speedup
vrna_fold_compound_t * foldData = vrna_fold_compound( sequence, &foldModel, VRNA_OPTION_PF);
// Adding hard constraints from pseudo dot-bracket
unsigned int constraint_options = VRNA_CONSTRAINT_DB_DEFAULT;
// enforce constraints
constraint_options |= VRNA_CONSTRAINT_DB_ENFORCE_BP;
vrna_constraints_add( foldData, (const char *)structureConstraint, constraint_options);
// compute correct partition function scaling via mfe
FLT_OR_DBL min_free_energy = vrna_mfe( foldData, NULL );
vrna_exp_params_rescale( foldData, &min_free_energy);
// compute partition functions
const float ensembleE = vrna_pf( foldData, NULL );
if (foldData->exp_matrices == NULL) {
throw std::runtime_error("AccessibilityVrna::computeES() : partition functions after computation not available");
}
if (foldData->exp_matrices->qm == NULL) {
throw std::runtime_error("AccessibilityVrna::computeES() : partition functions Qm after computation not available");
}
// copy ensemble energies of multi loop parts = ES values
FLT_OR_DBL qm_val = 0.0;
const int minLoopSubseqLength = foldModel.min_loop_size + 2;
for (int i=0; i<seqLength; i++) {
for (int j=i; j<seqLength; j++) {
// check if too short to enable a base pair
if (j-i+1 < minLoopSubseqLength) {
// make unfavorable
esToFill(i,j) = E_INF;
} else {
// get Qm value
// indexing via iindx starts with 1 instead of 0
qm_val = foldData->exp_matrices->qm[foldData->iindx[i+1]-j+1];
if ( E_equal(qm_val, 0.) ) {
esToFill(i,j) = E_INF;
} else {
// ES energy = -RT*log( Qm )
esToFill(i,j) = (E_type)( - RT*( std::log(qm_val)
+((FLT_OR_DBL)(j-i+1))*std::log(foldData->exp_params->pf_scale)));
}
}
}
}
// garbage collection
vrna_fold_compound_free(foldData);
free(structureConstraint);
free(sequence);
}
/* Very hackish way to get arguments for function calls. It'll work for now */
void mips_EvalWord(unsigned int * words, int pos)
{
unsigned int word = flip32(words[pos]), CalcAddr;
int i, imm;
for(i=0;i<SpecialOpCount;i++){
if((word & SpecialOps[i].mask) == SpecialOps[i].Op){
if(!(word & 0xFC000000)) //R type ops
regs[getRD(word)] = SpecialOps[i].Value;
else
regs[getRT(word)] = SpecialOps[i].Value;
return;
}
}
switch((word >> 26) & 0x3F)
{
case MIPS_OP_JAL:
{
/* delay slot */
mips_EvalWord( words, pos+1);
/* report function */
mips_ReportFunc( getTARGET(word) );
/* clear registers */
clearregs:
regs[1] = 0;
regs[2] = 0;
regs[3] = 0;
regs[4] = 0;
regs[5] = 0;
regs[6] = 0;
regs[7] = 0;
regs[8] = 0;
regs[9] = 0;
regs[10] = 0;
regs[11] = 0;
regs[12] = 0;
regs[13] = 0;
regs[14] = 0;
regs[15] = 0;
regs[24] = 0;
regs[25] = 0;
regs[26] = 0;
regs[27] = 0;
break;
}
case MIPS_OP_ADDIU:
imm = getIMM(word);
if(imm & 0x8000){
imm |= 0xFFFF0000;
}
regs[getRT(word)] = regs[getRS(word)] + imm;
if(getRT(word) == getRS(word) && getRT(word) == MIPS_REG_SP){
stack_pos += (signed short)imm;
}
break;
case MIPS_OP_LUI:
regs[getRT(word)] = getIMM(word)<<16;
break;
case MIPS_OP_ORI:
regs[getRT(word)] = regs[getRS(word)] | getIMM(word);
break;
case MIPS_OP_SW:
if(getRS(word) == MIPS_REG_SP){
stack[stack_pos+getIMM(word)] = regs[getRT(word)];
}
break;
case MIPS_OP_LW:
imm = getIMM(word);
if(imm & 0x8000){
imm |= 0xFFFF0000;
}
CalcAddr = imm + regs[getRS(word)];
if(getRS(word) == MIPS_REG_SP){
regs[getRT(word)] = stack[stack_pos+imm];
break;
}
for(i=0; i<mipsRAMSetCount; i++){
if(CalcAddr > mipsRAM[i].Addr && mipsRAM[i].Size + mipsRAM[i].Addr > CalcAddr){
regs[getRT(word)] = Read32(mipsRAM[i].Data, CalcAddr -mipsRAM[i].Addr );
break;
}
}
break;
case MIPS_OP_TYPE_R:
{
switch (word & 0x3F)
{
case MIPS_ROP_SLL:
regs[getRD(word)] = regs[getRT(word)] << getSA(word);
break;
case MIPS_ROP_SRA:
regs[getRD(word)] = regs[getRT(word)] >> getSA(word);
break;
case MIPS_ROP_ADDU:
regs[getRD(word)] = regs[getRT(word)] + regs[getRS(word)];
break;
case MIPS_ROP_JR:
if(getRS(word) == mips_ra){
goto clearregs;
}
break;
}
}
break;
}
}
