/**
@SYMTestCaseID PDS-STORE-UT-4055
@SYMTestCaseDesc Test for DEF141471 - STORE, new stream performance tests.
PREQ2505 Insturmentation of PDS.
RMemWriteStream & RMemReadStream performance tests.
@SYMTestPriority High
@SYMTestActions Test for DEF141471 - STORE, new stream performance tests.
@SYMTestExpectedResults Test must not fail
@SYMDEF DEF141471
*/
void MemStreamTestL()
{
HBufC8* buf = HBufC8::NewLC(KBufSize);
TPtr8 bufPtr = buf->Des();
//RMemWriteStream::Open()
RMemWriteStream strm1;
TUint32 fc = User::FastCounter();
strm1.Open(const_cast <TUint8*> (bufPtr.Ptr()), KBufSize);
TUint32 openFc = CalcTickDiff(fc, User::FastCounter());
PrintFcDiffAsUs(_L("### RMemWriteStream::Open(), Time=%d us\r\n"), openFc);
strm1.Close();
//RMemWriteStream::RMemWriteStream(TAny*,...)
fc = User::FastCounter();
RMemWriteStream strm2(const_cast <TUint8*> (bufPtr.Ptr()), KBufSize);
TUint32 constrFc = CalcTickDiff(fc, User::FastCounter());
PrintFcDiffAsUs(_L("### RMemWriteStream::RMemWriteStream(TAny*,...), Time=%d us\r\n"), constrFc);
CleanupClosePushL(strm2);
DoStreamWriteTestL(strm2);
CleanupStack::PopAndDestroy(&strm2);
//RMemReadStream::Open()
RMemReadStream strm3;
fc = User::FastCounter();
strm3.Open(bufPtr.Ptr(), KBufSize);
openFc = CalcTickDiff(fc, User::FastCounter());
PrintFcDiffAsUs(_L("### RMemReadStream::Open(), Time=%d us\r\n"), openFc);
strm3.Close();
//RMemReadStream::RMemReadStream(TAny*,...)
fc = User::FastCounter();
RMemReadStream strm4(bufPtr.Ptr(), KBufSize);
constrFc = CalcTickDiff(fc, User::FastCounter());
PrintFcDiffAsUs(_L("### RMemReadStream::RMemReadStream(TAny*,...), Time=%d us\r\n"), openFc);
CleanupClosePushL(strm4);
DoStreamReadTestL(strm4);
CleanupStack::PopAndDestroy(&strm4);
CleanupStack::PopAndDestroy(buf);
}
Alignment * interactive_domain_extraction ( Constraint_list *CL)
{
int LEN=0;
int START=1;
int SCALE=2;
int GOPP=3;
int iteration=0;
char *choice;
int a,b, c;
int index;
char *s;
char last_start[100];
char out_format[100];
Alignment *RESULT=NULL;
Alignment *PREVIOUS=NULL;
Alignment *C=NULL;
Alignment *EA=NULL;
int **parameters;
choice=(char*)vcalloc ( 100, sizeof (char));
parameters=declare_int (10000, 4);
parameters[0][START]=(CL->moca)->moca_start;
parameters[0][LEN]= (CL->moca)->moca_len;
parameters[0][SCALE]=(CL->moca)->moca_scale;
parameters[0][GOPP]=CL->gop;
iteration=0;
sprintf ( last_start, "%d", (CL->moca)->moca_start);
sprintf ( out_format, "mocca_aln");
print_moca_interactive_choices ();
while ( !strm4 (choice, "Q","X", "q", "x" ))
{
c=choice[0];
if (c=='b' || c=='B')
{
iteration-=atoi(choice+1)+1;
if (iteration<0)iteration=1;
}
else
{
iteration++;
parameters[iteration][START]=parameters[iteration-1][START];
parameters[iteration][LEN]=parameters[iteration-1][LEN];
parameters[iteration][SCALE]=parameters[iteration-1][SCALE];
parameters[iteration][GOPP]=parameters[iteration-1][GOPP];
if ( c=='>')parameters[iteration][LEN]=atoi(choice+1);
else if ( c=='|')
{
sprintf ( last_start, "%s", choice);
parameters[iteration][START]=0;
s=strrchr(choice, ':');
if (s==NULL)
{
parameters[iteration][START]=atoi(choice+1);
}
else
{
s[0]='\0';
if((index=name_is_in_list (choice+1,(CL->S)->name,(CL->S)->nseq,100))==-1)
{
fprintf ( stderr, "\n\tERROR: %s NOT in Sequence Set",choice+1);
continue;
}
for ( a=0; a< index; a++)
{
parameters[iteration][START]+=(CL->S)->len[a]+1;
}
parameters[iteration][START]+=atoi(s+1)-1;
}
}
else if ( c=='C'||c=='c')parameters[iteration][SCALE]=atoi(choice+1);
else if ( c=='G'||c=='g')
{
parameters[iteration][GOPP]=atoi(choice+1);
CL->gop=parameters[iteration][GOPP];
}
else if ( c=='F'||c=='f')
{
sprintf ( out_format, "%s", choice+1);
}
else if ( c=='S'||c=='s')
{
if (choice[1]=='\0')sprintf ( choice, "default.domain_aln.%d", iteration);
output_format_aln (out_format,RESULT,EA=fast_coffee_evaluate_output(RESULT, CL),choice+1);
fprintf (stderr, "\tOutput file [%15s] in [%10s] format\n",choice+1,out_format);
free_aln (EA);
}
else if (c=='\0')
{
if ( parameters[iteration][SCALE]>0)
{
fprintf ( stderr, "\nWARNING: THRESHOLD RESET to 0");
parameters[iteration][SCALE]=0;
}
(CL->moca)->moca_scale=parameters[iteration][SCALE];
CL->gop=parameters[iteration][GOPP];
C=extract_domain_with_coordinates (C,parameters[iteration][START],parameters[iteration][LEN],CL);
if ( C==NULL)
{
fprintf ( stderr, "\nERROR: ILLEGAL COORDINATES! SEQUENCE BOUNDARY CROSSED\n");
for ( b=1,a=0; a< (CL->S)->nseq-1; a++)
{
fprintf ( stderr, "\n\t%15s=> Abs:[%d %d] Rel:[0 %d]", (CL->S)->name[a],b, b+(CL->S)->len[a]-1,(CL->S)->len[a]);
b+=(CL->S)->len[a];
}
fprintf ( stderr, "\n");
}
else if (parameters[iteration][START]==0 && parameters[iteration][LEN]==0)
{
fprintf ( stderr, "\n\tEnter the following parameters:\n\n\t\tSTART value: |x [Return]\n\t\tLENgth value: >y [Return]\n\t\ttype [Return]\n\n");
fprintf ( stderr, "\n\n\tSTART is measured on the total length of the concatenated sequences\n\tx and y are positive integers\n\n");
}
else if ( C->nseq==0)
{
fprintf ( stderr, "\nNO MATCH FOUND: LOWER THE SCALE (C)\n");
}
else
{
RESULT=copy_aln ( C, RESULT);
unpack_seq_aln (RESULT, CL);
RESULT->output_res_num=1;
output_format_aln (out_format,RESULT,EA=fast_coffee_evaluate_output(RESULT, CL),"stdout");
free_aln(EA);
PREVIOUS=copy_aln ( RESULT, PREVIOUS);
free_aln (C);
print_moca_interactive_choices ();
}
}
fprintf ( stderr, "\t[ITERATION %3d][START=%s][LEN=%3d][GOPP=%3d][SCALE=%4d]\t",iteration,last_start,parameters[iteration][LEN],parameters[iteration][GOPP],parameters[iteration][SCALE]);
a=0;
fprintf ( stderr, "Your Choice: ");
while ( (c=fgetc(stdin))!='\n')choice[a++]=c;
choice[a]=0;
}
}
if (!RESULT)myexit(EXIT_SUCCESS);
if ( RESULT)RESULT->output_res_num=0;
return RESULT;
}
