void DIALOG_DRC_CONTROL::OnStartdrcClick( wxCommandEvent& event )
{
wxString reportName, msg;
bool make_report = m_CreateRptCtrl->IsChecked();
if( make_report ) // Create a rpt file
{
reportName = m_RptFilenameCtrl->GetValue();
if( reportName.IsEmpty() )
{
wxCommandEvent dummy;
OnButtonBrowseRptFileClick( dummy );
}
if( !reportName.IsEmpty() )
reportName = makeValidFileNameReport();
}
SetDrcParmeters();
m_tester->m_doZonesTest = m_cbReportTracksToZonesErrors->GetValue();
m_tester->m_rptFilename = reportName;
m_tester->m_doCreateRptFile = make_report;
m_tester->m_refillZones = m_cbRefillZones->GetValue();
m_tester->m_drcInLegacyRoutingMode = false;
m_tester->m_reportAllTrackErrors = m_cbReportAllTrackErrors->GetValue();
m_tester->m_testFootprints = m_cbTestFootprints->GetValue();
DelDRCMarkers();
wxBeginBusyCursor();
wxWindowDisabler disabler;
// run all the tests, with no UI at this time.
m_Messages->Clear();
wxSafeYield(); // Allows time slice to refresh the Messages
m_brdEditor->GetBoard()->m_Status_Pcb = 0; // Force full connectivity and ratsnest calculations
m_tester->RunTests(m_Messages);
m_Notebook->ChangeSelection( 0 ); // display the "Problems/Markers" tab
// Generate the report
if( !reportName.IsEmpty() )
{
if( writeReport( reportName ) )
{
msg.Printf( _( "Report file \"%s\" created" ), GetChars( reportName ) );
wxMessageDialog popupWindow( this, msg, _( "Disk File Report Completed" ) );
popupWindow.ShowModal();
}
else
{
msg.Printf( _( "Unable to create report file \"%s\"" ), GetChars( reportName ) );
DisplayError( this, msg );
}
}
wxEndBusyCursor();
RedrawDrawPanel();
}
void DIALOG_DRC_CONTROL::OnListUnconnectedClick( wxCommandEvent& event )
{
wxString reportName;
bool make_report = m_CreateRptCtrl->IsChecked();
if( make_report ) // Create a file rpt
{
reportName = m_RptFilenameCtrl->GetValue();
if( reportName.IsEmpty() )
{
wxCommandEvent junk;
OnButtonBrowseRptFileClick( junk );
}
if( !reportName.IsEmpty() )
reportName = makeValidFileNameReport();
}
SetDrcParmeters();
m_tester->SetSettings( true, // Pad to pad DRC test enabled
true, // unconnected pads DRC test enabled
true, // DRC test for zones enabled
true, // DRC test for keepout areas enabled
reportName, make_report );
DelDRCMarkers();
wxBeginBusyCursor();
m_Messages->Clear();
m_tester->ListUnconnectedPads();
m_Notebook->ChangeSelection( 1 ); // display the 2nd tab "Unconnected..."
// Generate the report
if( !reportName.IsEmpty() )
{
if( writeReport( reportName ) )
{
wxString msg;
msg.Printf( _( "Report file \"%s\" created" ), GetChars( reportName ) );
wxString caption( _( "Disk File Report Completed" ) );
wxMessageDialog popupWindow( this, msg, caption );
popupWindow.ShowModal();
}
else
DisplayError( this, wxString::Format( _( "Unable to create report file '%s' "),
GetChars( reportName ) ) );
}
UpdateDisplayedCounts();
wxEndBusyCursor();
/* there is currently nothing visible on the DrawPanel for unconnected pads
* RedrawDrawPanel();
*/
}
void DIALOG_DRC_CONTROL::OnStartdrcClick( wxCommandEvent& event )
{
wxString reportName;
bool make_report = m_CreateRptCtrl->IsChecked();
if( make_report ) // Create a rpt file
{
reportName = m_RptFilenameCtrl->GetValue();
if( reportName.IsEmpty() )
{
wxCommandEvent dummy;
OnButtonBrowseRptFileClick( dummy );
}
if( !reportName.IsEmpty() )
reportName = makeValidFileNameReport();
}
SetDrcParmeters();
m_tester->SetSettings( true, // Pad to pad DRC test enabled
true, // unconnected pads DRC test enabled
true, // DRC test for zones enabled
true, // DRC test for keepout areas enabled
m_cbCourtyardOverlap->GetValue(),
m_cbCourtyardMissing->GetValue(),
reportName, make_report );
DelDRCMarkers();
wxBeginBusyCursor();
// run all the tests, with no UI at this time.
m_Messages->Clear();
wxSafeYield(); // Allows time slice to refresh the m_Messages window
m_brdEditor->GetBoard()->m_Status_Pcb = 0; // Force full connectivity and ratsnest recalculations
m_tester->RunTests(m_Messages);
m_Notebook->ChangeSelection( 0 ); // display the 1at tab "...Markers ..."
// Generate the report
if( !reportName.IsEmpty() )
{
if( writeReport( reportName ) )
{
wxString msg;
msg.Printf( _( "Report file \"%s\" created" ), GetChars( reportName ) );
wxString caption( _( "Disk File Report Completed" ) );
wxMessageDialog popupWindow( this, msg, caption );
popupWindow.ShowModal();
}
else
DisplayError( this, wxString::Format( _( "Unable to create report file \"%s\" "),
GetChars( reportName ) ) );
}
wxEndBusyCursor();
RedrawDrawPanel();
}
/* main filter function */
int main_filter(int argc, char *argv[]){
char *output, *subfam, *out, *outReport;
unsigned long long int *cnt;
struct hash *hashRmsk = newHash(0);
struct hash *hashRep = newHash(0);
struct hash *hashFam = newHash(0);
struct hash *hashCla = newHash(0);
int optSam = 0, optthreshold = 1;
char *optoutput = NULL, *optname = NULL, *optclass = NULL, *optfamily = NULL;
unsigned int optreadlist = 0, optQual = 10, optisize = 500, optExt = 150;
int filterField = 0, c, optDup = 0, optNorm = 0, optaddChr = 0, optDis =0, optTreat = 0;
float optCov = 0.0001;
time_t start_time, end_time;
start_time = time(NULL);
while ((c = getopt(argc, argv, "SQ:g:N:n:c:t:f:rRTDCE:I:o:h?")) >= 0) {
switch (c) {
case 'S': optSam = 1; break;
case 'Q': optQual = (unsigned int)strtol(optarg, 0, 0); break;
case 'g': optCov = atof(optarg); break;
case 'N': optNorm = (unsigned int)strtol(optarg, 0, 0); break;
case 't': optthreshold = (unsigned int)strtol(optarg, 0, 0); break;
case 'r': optreadlist = 1; break;
case 'R': optDup = 1; break;
case 'T': optTreat = 1; break;
case 'D': optDis = 1; break;
case 'C': optaddChr = 1; break;
case 'n': optname = strdup(optarg); break;
case 'c': optclass = strdup(optarg); break;
case 'f': optfamily = strdup(optarg); break;
case 'E': optExt = (unsigned int)strtol(optarg, 0, 0); break;
case 'I': optisize = (unsigned int)strtol(optarg, 0, 0); break;
case 'o': optoutput = strdup(optarg); break;
case 'h':
case '?': return filter_usage(); break;
default: return 1;
}
}
if (optind + 4 > argc)
return filter_usage();
char *chr_size_file = argv[optind];
char *rep_size_file = argv[optind+1];
char *rmsk_file = argv[optind+2];
char *sam_file = argv[optind+3];
if ( (optname && optclass) || (optname && optfamily) || (optclass && optfamily) || (optname && optclass && optfamily))
errAbort("Please specify only one filter, either -n, -c or -f.");
int nindex = 0;
if (optNorm == 0){
nindex = 7;
} else if (optNorm == 1){
nindex = 8;
} else if (optNorm == 2) {
nindex = 6;
} else if (optNorm == 3) {
nindex = 4;
} else{
errAbort("Wrong normalization method specified");
}
subfam = cloneString("ALL");
if (optname) {
optclass = NULL;
optfamily = NULL;
subfam = cloneString(optname);
filterField = 10;
}else if (optclass) {
optname = NULL;
optfamily = NULL;
subfam = cloneString(optclass);
filterField = 11;
} else if (optfamily) {
optname = NULL;
optclass= NULL;
subfam = cloneString(optfamily);
filterField = 12;
}
if (sameString(subfam, "ALL")){
fprintf(stderr, "* You didn't specify any filter, will output all repeats\n");
filterField = 0;
}
if(optoutput) {
output = optoutput;
} else {
output = cloneString(get_filename_without_ext(basename(sam_file)));
}
struct hash *chrHash = hashNameIntFile(chr_size_file);
struct hash *repHash = hashNameIntFile(rep_size_file);
fprintf(stderr, "* Start to parse the rmsk file\n");
rmsk2binKeeperHash(rmsk_file, chrHash, repHash, &hashRmsk, &hashRep, &hashFam, &hashCla, filterField, subfam);
//sam file
fprintf(stderr, "* Start to parse the SAM/BAM file\n");
//if (optPair){
// cnt = PEsamFile2nodupRepbedFile(sam_file, chrHash, hashRmsk, hashRep, hashFam, hashCla, optSam, optQual, 1, optDup, optaddChr, optisize);
//} else {
// cnt = samFile2nodupRepbedFile(sam_file, chrHash, hashRmsk, hashRep, hashFam, hashCla, optSam, optQual, 1, optDup, optaddChr);
//}
cnt = samFile2nodupRepbedFileNew(sam_file, chrHash, hashRmsk, hashRep, hashFam, hashCla, optSam, optQual, 1, optDup, optaddChr, optDis, optisize, optExt, optCov, optTreat, NULL, NULL, 0);
fprintf(stderr, "* Preparing the output file\n");
if (asprintf(&out, "%s_%s.iteres.loci", output, subfam) < 0)
errAbort("Preparing output wrong");
if (asprintf(&outReport, "%s_%s.iteres.reportloci", output, subfam) < 0)
errAbort("Preparing output wrong");
writeFilterOut(hashRmsk, out, optreadlist, optthreshold, subfam, cnt[nindex]);
//write report file
fprintf(stderr, "* Preparing report file\n");
writeReport(outReport, cnt, optQual, subfam);
hashFree(&chrHash);
hashFree(&repHash);
hashFree(&hashRmsk);
hashFree(&hashRep);
hashFree(&hashFam);
hashFree(&hashCla);
free(out);
free(outReport);
end_time = time(NULL);
fprintf(stderr, "* Done, time used %.0f seconds.\n", difftime(end_time, start_time));
return 0;
}
/*-------------------------------------------------------------------------
Run n copies of the test.
Return value is 0 on success.
-------------------------------------------------------------------------*/
int /* */
run_n_nodes(
char *exe, /* */
int loops) /* */
{
char *childArgs[7] = {NULL, NULL, "nhosts", "nloops", "childnum", "nextadr.possibly.internet.address:maybeWithPortNumber", NULL};
int* procs = NULL;
int* result = NULL;
int i;
childArgs[0] = exe;
childArgs[1] = results.driver;
if ((procs = (int *) malloc(results.n_hosts * sizeof(int))) == NULL)
abortTest(logFile, 3, "Unable to allocate process handle storage.\n", NULL);
if((result = (int *) malloc(results.n_hosts * sizeof(int))) == NULL)
abortTest(logFile, 3, "Unable to allocate result storage.\n", NULL);
/* Start tests */
for (i=0; i < results.n_hosts; i++) {
sprintf(childArgs[2], "%d", results.n_hosts);
sprintf(childArgs[3], "%d", loops);
sprintf(childArgs[4], "%d", i);
#if LOOPBACK_ADDRESS
sprintf(childArgs[5], "%d.0.0.0", ((i+1) % results.n_hosts) + 1);
#elif INTERNET_ADDRESS
sprintf(childArgs[5], "207.82.188.88:%d", ((i+1) % results.n_hosts) + PORT_OFFSET);
#else
Warning: Must choose one of the above defines.
#endif
printf("Launching %s %s %s %s %s %s\n",
childArgs[0],
childArgs[1],
childArgs[2],
childArgs[3],
childArgs[4],
childArgs[5]);
procs[i] = _spawnv(_P_NOWAIT, exe, childArgs);
if(procs[i] == -1) {
sprintf(buf, "Unable to start process %d: %s\n", i, strerror(errno));
abortTest(logFile, 4, buf, NULL);
}
}
/* Wait for tests to finish */
for (i=0; i < results.n_hosts; i++) {
_cwait(&(result[i]), procs[i], 0);
printf("Node %d returned %d\n", i, result[i]);
}
/* Get test results */
{
FILE* fp;
char fname[256];
sprintf(fname, LOGNAME, 0);
if ((fp = fopen(fname, "r")) != NULL) {
readReport(fp, &results);
} else
fprintf(logFile, "Can't read client %d's logfile %s\n", 0, fname);
}
writeReport(logFile, &results);
return 0;
}
/*-------------------------------------------------------------------------
This is called by the dptab_handlePacket when a new variable arrives or
an old one is deleted.
Note the time of the callback in the result block.
-------------------------------------------------------------------------*/
int dp_PASCAL
table_cb(
dptab_t *dptab, /* table owner */
dptab_table_t *table, /* table */
playerHdl_t src, /* */
playerHdl_t dest, /* */
char *subkey, /* key of variable */
int subkeylen, /* number of bytes in subkey */
void *buf, /* pointer to variable */
size_t sent,
size_t total,
int seconds_left,
void *context, /* whatever we gave it */
dp_result_t err) /* operation completed upon variable */
{
clock_t now = eclock();
printf("Node %d: table_cb: type:%d src h:%x dest h:%x table:%s key:%s\n",
results.thisHost, err, src, dest, key2a(table->key, table->keylen),
key2a2(subkey, subkeylen));
if (err == dp_RES_CREATED || err == dp_RES_CHANGED) {
/*printf("table_cb: CREATED/CHANGED: src h:%x dest h:%x table:%s key:%s\n",
src, dest, key2a(table->key, table->keylen),
key2a2(subkey, subkeylen));*/
if ((dest == PLAYER_ME) && (sent == total)) {
/* Got a variable */
switch (subkey[0]) {
case SUBKEY_SINGLE_SMALL:
if(table->key[0] == 2) {
results.gotSingleSmallTime = now;
results.singleSmallTime = ((float)now - results.sentSingleSmallTime) / ECLOCKS_PER_SEC;
/* Move this statement to right after last measurement taken */
writeReport(logFile, &results);
}
break;
case SUBKEY_SINGLE_LARGE:
results.gotSingleLargeTime = now;
break;
case SUBKEY_MULTIPLE_SMALL:
results.gotMultipleSmallTime = now;
break;
default:
;
}
printf("Node %d: Got variable from h:%x; table %s, subkey %s; len %d\n",
results.thisHost,
src,
key2a(table->key, table->keylen),
key2a2(subkey, subkeylen),
total);
}
} else if (err == dp_RES_CLOSED) {
/*printf("table_cb: Deleted: src h:%x dest h:%x\n", src, dest);*/
if (dest == PLAYER_ME) {
switch (subkey[0]) {
case SUBKEY_SINGLE_SMALL:
results.gotDeleteTime = now;
results.deleteTime = ((float)now - results.sentDeleteTime) / ECLOCKS_PER_SEC;
break;
default:
;
}
printf("Node %d: Got delete variable from h:%x; table %s, subkey %s\n",
results.thisHost,
src,
key2a(table->key, table->keylen),
key2a2(subkey, subkeylen));
}
}
(void) dptab;
(void) buf;
(void) seconds_left;
(void) context;
return TRUE;
}
