UIDownloaderExtensionPack::UIDownloaderExtensionPack()
{
/* Prepare instance: */
if (!m_spInstance)
m_spInstance = this;
/* Prepare source/target: */
QString strExtPackUnderscoredName(QString(GUI_ExtPackName).replace(' ', '_'));
QString strTemplateSourcePath("http://download.virtualbox.org/virtualbox/%1/");
QString strTemplateSourceName(QString("%1-%2.vbox-extpack").arg(strExtPackUnderscoredName));
QString strSourcePath(strTemplateSourcePath.arg(vboxGlobal().vboxVersionStringNormalized()));
QString strSourceName(strTemplateSourceName.arg(vboxGlobal().vboxVersionStringNormalized()));
QString strSource(strSourcePath + strSourceName);
QString strTargetPath(vboxGlobal().homeFolder());
QString strTargetName(strSourceName);
QString strTarget(QDir(strTargetPath).absoluteFilePath(strTargetName));
/* Set source/target: */
setSource(strSource);
setTarget(strTarget);
}
//
// =======================================================================================================================
// Map_ImportFile Timo 09/01/99:: called by CXYWnd::Paste & Map_ImportFile if Map_ImportFile ( prefab ), the buffer
// may contain brushes in old format ( conversion needed )
// =======================================================================================================================
//
void Map_ImportBuffer(char *buf, bool renameEntities) {
entity_t *ent;
brush_t *b = NULL;
CPtrArray ptrs;
Select_Deselect();
Undo_Start("import buffer");
g_qeglobals.d_parsed_brushes = 0;
if (buf) {
CMapStringToString mapStr;
StartTokenParsing(buf);
g_qeglobals.d_num_entities = 0;
//
// Timo will be used in Entity_Parse to detect if a conversion between brush
// formats is needed
//
g_qeglobals.bNeedConvert = false;
g_qeglobals.bOldBrushes = false;
g_qeglobals.bPrimitBrushes = false;
g_qeglobals.mapVersion = 1.0;
if (GetToken(true)) {
if (stricmp(token, "Version") == 0) {
GetToken(false);
g_qeglobals.mapVersion = atof(token);
common->Printf("Map version: %1.2f\n", g_qeglobals.mapVersion);
} else {
UngetToken();
}
}
idDict RemappedNames; // since I can't use "map <string, string>"... sigh. So much for STL...
while (1) {
//
// use the selected brushes list as it's handy ent = Entity_Parse (false,
// &selected_brushes);
//
ent = Entity_Parse(false, &active_brushes);
if (!ent) {
break;
}
// end entity for undo
Undo_EndEntity(ent);
// end brushes for undo
for (b = ent->brushes.onext; b && b != &ent->brushes; b = b->onext) {
Undo_EndBrush(b);
}
if (!strcmp(ValueForKey(ent, "classname"), "worldspawn")) {
// world brushes need to be added to the current world entity
b = ent->brushes.onext;
while (b && b != &ent->brushes) {
brush_t *bNext = b->onext;
Entity_UnlinkBrush(b);
Entity_LinkBrush(world_entity, b);
ptrs.Add(b);
b = bNext;
}
}
else {
// the following bit remaps conflicting target/targetname key/value pairs
CString str = ValueForKey(ent, "target");
CString strKey;
CString strTarget("");
if (str.GetLength() > 0) {
if (FindEntity("target", str.GetBuffer(0))) {
if (!mapStr.Lookup(str, strKey)) {
idStr key;
UniqueTargetName(key);
strKey = key;
mapStr.SetAt(str, strKey);
}
strTarget = strKey;
SetKeyValue(ent, "target", strTarget.GetBuffer(0));
}
}
/*
* str = ValueForKey(ent, "name"); if (str.GetLength() > 0) { if
* (FindEntity("name", str.GetBuffer(0))) { if (!mapStr.Lookup(str, strKey)) {
* UniqueTargetName(strKey); mapStr.SetAt(str, strKey); } Entity_SetName(ent,
* strKey.GetBuffer(0)); } }
*/
CString cstrNameOld = ValueForKey(ent, "name");
Entity_Name(ent, renameEntities);
CString cstrNameNew = ValueForKey(ent, "name");
if (cstrNameOld != cstrNameNew)
{
RemappedNames.Set(cstrNameOld, cstrNameNew);
}
//
// if (strTarget.GetLength() > 0) SetKeyValue(ent, "target",
// strTarget.GetBuffer(0));
// add the entity to the end of the entity list
//
ent->next = &entities;
ent->prev = entities.prev;
entities.prev->next = ent;
entities.prev = ent;
g_qeglobals.d_num_entities++;
for (b = ent->brushes.onext; b != &ent->brushes; b = b->onext) {
ptrs.Add(b);
}
}
}
// now iterate through the remapped names, and see if there are any target-connections that need remaking...
//
// (I could probably write this in half the size with STL, but WTF, work with what we have...)
//
int iNumKeyVals = RemappedNames.GetNumKeyVals();
for (int iKeyVal=0; iKeyVal < iNumKeyVals; iKeyVal++)
{
const idKeyValue *pKeyVal = RemappedNames.GetKeyVal( iKeyVal );
LPCSTR psOldName = pKeyVal->GetKey().c_str();
LPCSTR psNewName = pKeyVal->GetValue().c_str();
entity_t *pEntOld = FindEntity("name", psOldName); // original ent we cloned from
entity_t *pEntNew = FindEntity("name", psNewName); // cloned ent
if (pEntOld && pEntNew)
{
CString cstrTargetNameOld = ValueForKey(pEntOld, "target");
if (!cstrTargetNameOld.IsEmpty())
{
// ok, this ent was targeted at another ent, so it's clone needs updating to point to
// the clone of that target, so...
//
entity_t *pEntOldTarget = FindEntity("name", cstrTargetNameOld);
if ( pEntOldTarget )
{
LPCSTR psNewTargetName = RemappedNames.GetString( cstrTargetNameOld );
if (psNewTargetName && psNewTargetName[0])
{
SetKeyValue(pEntNew, "target", psNewTargetName);
}
}
}
}
}
}
//
// ::ShowWindow(g_qeglobals.d_hwndEntity, FALSE);
// ::LockWindowUpdate(g_qeglobals.d_hwndEntity);
//
g_bScreenUpdates = false;
for (int i = 0; i < ptrs.GetSize(); i++) {
Brush_Build(reinterpret_cast < brush_t * > (ptrs[i]), true, false);
Select_Brush(reinterpret_cast < brush_t * > (ptrs[i]), true, false);
}
// ::LockWindowUpdate(NULL);
g_bScreenUpdates = true;
ptrs.RemoveAll();
//
// reset the "need conversion" flag conversion to the good format done in
// Map_BuildBrushData
//
g_qeglobals.bNeedConvert = false;
Sys_UpdateWindows(W_ALL);
// Sys_MarkMapModified();
mapModified = 1;
Undo_End();
}
void HHRImpl::populateResultVector() {
char line[500];
int counter = 0;
string inFilename(inputFileLocation);
inFilename += "/";
inFilename += rootName;
inFilename += "/";
inFilename += "/query.hhr";
//cout << inFilename << endl;
FILE* inputFile = fopen((char*) inFilename.c_str(), "r");
if (inputFile == NULL) {
cout << "input file: " << inFilename << " can't open" << endl;
}
HHRResult result;
while (fgets(line, 500, inputFile) != NULL) {
if (strstr(line, ">") != NULL && !result.isFirstStateReached()) {
//set first block information
char proteinName[7];
char* pos1 = strstr(line, ">");
sscanf(pos1 + 1, "%s", proteinName);
string proteinNameStr(proteinName);
result.setProteinName(proteinNameStr);
while (strstr(line, "Probab=") == NULL) {
fgets(line, 500, inputFile); //skip long name
}
//get probab, E-value, Score, Aligned_cols, Identities, Similarity, Sum_probs
pos1 = strstr(line, "=");
float probab;
sscanf(pos1 + 1, "%f", &probab);
result.setProbab(probab);
char* pos2 = strstr(pos1 + 1, "=");
float eValue;
sscanf(pos2 + 1, "%f", &eValue);
result.setExpect(eValue);
char* pos3 = strstr(pos2 + 1, "=");
float score;
sscanf(pos3 + 1, "%f", &score);
result.setScore(score);
char* pos4 = strstr(pos3 + 1, "=");
int alignedCols;
sscanf(pos4 + 1, "%d", &alignedCols);
result.setAlignedCols(alignedCols);
char* pos5 = strstr(pos4 + 1, "=");
float identities;
sscanf(pos5 + 1, "%f", &identities);
result.setIdentities(identities);
result.setFirstStateReached(true);
}
if ((strstr(line, "Q ref|") != NULL)
&& !result.isSecondStateReached()) {
//set second block information
//get the query
int queryStart;
char query[100];
int queryEnd;
sscanf(line + 17, "%d %s %d", &queryStart, query, &queryEnd);
result.setQueryStart(queryStart);
string strQuery(query);
result.setQuery(strQuery);
result.setQueryEnd(queryEnd);
//get the Q Consensus
fgets(line, 200, inputFile);
int QConsensusStart;
char QConsensus[100];
int QConsensusEnd;
sscanf(line + 17, "%d %s %d", &QConsensusStart, QConsensus,
&QConsensusEnd);
string strQConsensus(QConsensus);
result.setQueryConsensus(strQConsensus);
//get alignment
fgets(line, 200, inputFile);
char alignment[100];
sscanf(line + 17, "%s", alignment);
string strAlignment(alignment);
result.setAlignment(strAlignment);
//get the T Consensus
fgets(line, 200, inputFile);
int targetStart;
char targetConsensus[100];
int targetEnd;
sscanf(line + 17, "%d %s %d", &targetStart, targetConsensus,
&targetEnd);
result.setTargetStart(targetStart);
string strTargetConsensus(targetConsensus);
result.setTargetConsensus(strTargetConsensus);
result.setTargetEnd(targetEnd);
//get the Target
fgets(line, 200, inputFile);
char target[100];
sscanf(line + 17, "%d %s %d", &targetStart, target, &targetEnd);
string strTarget(target);
result.setTarget(strTarget);
//get the TPred
fgets(line, 200, inputFile);
char tPred[100];
sscanf(line + 17, "%s", tPred);
string strTPred(tPred);
result.setTargetSsPred(strTPred);
//get the TConf
fgets(line, 200, inputFile);
char tConf[100];
sscanf(line + 17, "%s", tConf);
string strTConf(tConf);
result.setConfidence(strTConf);
result.setSecondStateReached(true);
}
if ((strstr(line, "Q ref|") != NULL) && result.isSecondStateReached()) {
//update second block information, so in this case
//quert, alignment and target should be long string
//the queryEnd and targetEnd should also be updated
//get the query
int queryStart;
char query[100];
int queryEnd;
sscanf(line + 17, "%d %s %d", &queryStart, query, &queryEnd);
string additionalQuery(query);
string newQuery = result.getQuery();
newQuery += additionalQuery;
result.setQuery(newQuery);
result.setQueryEnd(queryEnd);
//get the Q Consensus
fgets(line, 200, inputFile);
int QConsensusStart;
char QConsensus[100];
int QConsensusEnd;
sscanf(line + 17, "%d %s %d", &QConsensusStart, QConsensus,
&QConsensusEnd);
string additionalQConsensus(QConsensus);
string newQConsesus = result.getQueryConsensus();
newQConsesus += additionalQConsensus;
result.setQueryConsensus(newQConsesus);
//get alignment
fgets(line, 200, inputFile);
char alignment[100];
sscanf(line + 17, "%s", alignment);
string additionalAlignment(alignment);
string newAlignment = result.getAlignment();
newAlignment += additionalAlignment;
result.setAlignment(newAlignment);
//get the T Consensus
fgets(line, 200, inputFile);
int targetStart;
char targetConsensus[100];
int targetEnd;
sscanf(line + 17, "%d %s %d", &targetStart, targetConsensus,
&targetEnd);
string additionalTargetConsensus(targetConsensus);
string newTargetConsensus = result.getTargetConsensus();
newTargetConsensus += additionalTargetConsensus;
result.setTargetConsensus(newTargetConsensus);
result.setTargetEnd(targetEnd);
//get the Target
fgets(line, 200, inputFile);
char target[100];
sscanf(line + 17, "%d %s %d", &targetStart, target, &targetEnd);
string additionalTarget(target);
string newTarget = result.getTarget();
newTarget += additionalTarget;
result.setTarget(newTarget);
//get the TPred
fgets(line, 200, inputFile);
char tPred[100];
sscanf(line + 17, "%s", tPred);
string additionalTPred(tPred);
string newTPred = result.getTargetSsPred();
newTPred += additionalTPred;
result.setTargetSsPred(newTPred);
//get the TConf
fgets(line, 200, inputFile);
char tConf[100];
sscanf(line + 17, "%s", tConf);
string additionalTConf(tConf);
string newTConf = result.getConfidence();
newTConf += additionalTConf;
result.setConfidence(newTConf);
}
if ((strstr(line, ">") != NULL) && result.isFirstStateReached()) {
//first push the result to the vector
hhrResultVector.push_back(result);
//then update the information set the first state flag
//set first block information
char proteinName[7];
char* pos1 = strstr(line, ">");
sscanf(pos1 + 1, "%s", proteinName);
string proteinNameStr(proteinName);
result.setProteinName(proteinNameStr);
while (strstr(line, "Probab=") == NULL) {
fgets(line, 500, inputFile); //skip long name
}
//get probab, E-value, Score, Aligned_cols, Identities, Similarity, Sum_probs
pos1 = strstr(line, "=");
float probab;
sscanf(pos1 + 1, "%f", &probab);
result.setProbab(probab);
char* pos2 = strstr(pos1 + 1, "=");
float eValue;
sscanf(pos2 + 1, "%f", &eValue);
result.setExpect(eValue);
char* pos3 = strstr(pos2 + 1, "=");
float score;
sscanf(pos3 + 1, "%f", &score);
result.setScore(score);
char* pos4 = strstr(pos3 + 1, "=");
int alignedCols;
sscanf(pos4 + 1, "%d", &alignedCols);
result.setAlignedCols(alignedCols);
char* pos5 = strstr(pos4 + 1, "=");
float identities;
sscanf(pos5 + 1, "%f", &identities);
result.setIdentities(identities);
result.setFirstStateReached(true);
result.setSecondStateReached(false);
}
}
hhrResultVector.push_back(result);
fclose(inputFile);
}
void HHRNR2Json::convert() {
char line[500];
int counter = 0;
string inFilename(inputFileLocation);
inFilename += inputFilename;
FILE* inputFile = fopen((char*) inFilename.c_str(), "r");
if (inputFile == NULL) {
cout << "input file: " << inFilename << " can't open" << endl;
}
HHRNRResult result;
while (fgets(line, 200, inputFile) != NULL) {
if (strstr(line, ">") != NULL) {
counter++;
char proteinName[7];
char* pos1 = strstr(line, ">");
sscanf(pos1 + 1, "%s", proteinName);
string proteinNameStr(proteinName);
result.setProteinName(proteinNameStr);
while (strstr(line, "Probab=") == NULL) {
fgets(line, 500, inputFile); //skip long name
}
//get probab, E-value, Score, Aligned_cols, Identities, Similarity, Sum_probs
pos1 = strstr(line, "=");
float probab;
sscanf(pos1 + 1, "%f", &probab);
result.setProbab(probab);
char* pos2 = strstr(pos1 + 1, "=");
float eValue;
sscanf(pos2 + 1, "%f", &eValue);
result.setExpect(eValue);
char* pos3 = strstr(pos2 + 1, "=");
float score;
sscanf(pos3 + 1, "%f", &score);
result.setScore(score);
char* pos4 = strstr(pos3 + 1, "=");
int alignedCols;
sscanf(pos4 + 1, "%d", &alignedCols);
result.setAlignedCols(alignedCols);
char* pos5 = strstr(pos4 + 1, "=");
float identities;
sscanf(pos5 + 1, "%f", &identities);
result.setIdentities(identities);
char* pos6 = strstr(pos5 + 1, "=");
float similarity;
sscanf(pos6 + 1, "%f", &similarity);
result.setSimilarities(similarity);
char* pos7 = strstr(pos6 + 1, "=");
float sumProbs;
sscanf(pos7 + 1, "%f", &sumProbs);
result.setSumProbs(sumProbs);
fgets(line, 200, inputFile); //blank
//get the query
fgets(line, 200, inputFile);
char query_ss_pred[100];
sscanf(line + 17, "%s", query_ss_pred);
string strQuery_ss_pred(query_ss_pred);
result.setQuerySsPred(strQuery_ss_pred);
fgets(line, 200, inputFile);
int queryStart;
char query[100];
int queryEnd;
sscanf(line + 17, "%d %s %d", &queryStart, query, &queryEnd);
result.setQueryStart(queryStart);
string strQuery(query);
result.setQuery(strQuery);
result.setQueryEnd(queryEnd);
//get the Q Consensus
fgets(line, 200, inputFile);
int QConsensusStart;
char QConsensus[100];
int QConsensusEnd;
sscanf(line + 17, "%d %s %d", &QConsensusStart, QConsensus,
&QConsensusEnd);
string strQConsensus(QConsensus);
result.setQueryConsensus(strQConsensus);
//get alignment
fgets(line, 200, inputFile);
char alignment[100];
sscanf(line + 17, "%s", alignment);
string strAlignment(alignment);
result.setAlignment(strAlignment);
//get the T Consensus
fgets(line, 200, inputFile);
int targetStart;
char targetConsensus[100];
int targetEnd;
sscanf(line + 17, "%d %s %d", &targetStart, targetConsensus,
&targetEnd);
result.setTargetStart(targetStart);
string strTargetConsensus(targetConsensus);
result.setTargetConsensus(strTargetConsensus);
result.setTargetEnd(targetEnd);
//get the Target
fgets(line, 200, inputFile);
char target[100];
sscanf(line + 17, "%d %s %d", &targetStart, target, &targetEnd);
string strTarget(target);
result.setTarget(strTarget);
//get the TDssp
fgets(line, 200, inputFile);
char tDssp[100];
sscanf(line + 17, "%s", tDssp);
string strTDssp(tDssp);
result.setTargetSsDssp(strTDssp);
//get the TPred
fgets(line, 200, inputFile);
char tPred[100];
sscanf(line + 17, "%s", tPred);
string strTPred(tPred);
result.setTargetSsPred(strTPred);
counter++;
HHRNRResultVector.push_back(result);
}
}
fclose(inputFile);
}
//
//================
//Map_ImportFile
// Timo 09/01/99 : called by CXYWnd::Paste & Map_ImportFile
// if Map_ImportFile ( prefab ), the buffer may contain brushes in old format ( conversion needed )
//================
//
void Map_ImportBuffer (char* buf)
{
entity_t* ent;
brush_t* b = NULL;
CPtrArray ptrs;
Select_Deselect();
Undo_Start("import buffer");
g_qeglobals.d_parsed_brushes = 0;
if (buf)
{
CMapStringToString mapStr;
StartTokenParsing (buf);
g_qeglobals.d_num_entities = 0;
// Timo
// will be used in Entity_Parse to detect if a conversion between brush formats is needed
g_qeglobals.bNeedConvert = false;
g_qeglobals.bOldBrushes = false;
g_qeglobals.bPrimitBrushes = false;
while (1)
{
// use the selected brushes list as it's handy
//ent = Entity_Parse (false, &selected_brushes);
ent = Entity_Parse (false, &active_brushes);
if (!ent)
break;
//end entity for undo
Undo_EndEntity(ent);
//end brushes for undo
for(b = ent->brushes.onext; b && b != &ent->brushes; b = b->onext)
{
Undo_EndBrush(b);
}
if (!strcmp(ValueForKey (ent, "classname"), "worldspawn"))
{
// world brushes need to be added to the current world entity
b=ent->brushes.onext;
while (b && b != &ent->brushes)
{
brush_t* bNext = b->onext;
Entity_UnlinkBrush(b);
Entity_LinkBrush(world_entity, b);
ptrs.Add(b);
b = bNext;
}
}
else
{
// the following bit remaps conflicting target/targetname key/value pairs
CString str = ValueForKey(ent, "target");
CString strKey;
CString strTarget("");
if (str.GetLength() > 0)
{
if (FindEntity("target", str.GetBuffer(0)))
{
if (!mapStr.Lookup(str, strKey))
{
UniqueTargetName(strKey);
mapStr.SetAt(str, strKey);
}
strTarget = strKey;
SetKeyValue(ent, "target", strTarget.GetBuffer(0));
}
}
str = ValueForKey(ent, "targetname");
if (str.GetLength() > 0)
{
if (FindEntity("targetname", str.GetBuffer(0)))
{
if (!mapStr.Lookup(str, strKey))
{
UniqueTargetName(strKey);
mapStr.SetAt(str, strKey);
}
SetKeyValue(ent, "targetname", strKey.GetBuffer(0));
}
}
//if (strTarget.GetLength() > 0)
// SetKeyValue(ent, "target", strTarget.GetBuffer(0));
// add the entity to the end of the entity list
ent->next = &entities;
ent->prev = entities.prev;
entities.prev->next = ent;
entities.prev = ent;
g_qeglobals.d_num_entities++;
for (b=ent->brushes.onext ; b != &ent->brushes ; b=b->onext)
{
ptrs.Add(b);
}
}
}
}
//::ShowWindow(g_qeglobals.d_hwndEntity, FALSE);
//::LockWindowUpdate(g_qeglobals.d_hwndEntity);
g_bScreenUpdates = false;
for (int i = 0; i < ptrs.GetSize(); i++)
{
Brush_Build(reinterpret_cast<brush_t*>(ptrs[i]), true, false);
Select_Brush(reinterpret_cast<brush_t*>(ptrs[i]), true, false);
}
//::LockWindowUpdate(NULL);
g_bScreenUpdates = true;
ptrs.RemoveAll();
// reset the "need conversion" flag
// conversion to the good format done in Map_BuildBrushData
g_qeglobals.bNeedConvert=false;
Sys_UpdateWindows (W_ALL);
//Sys_MarkMapModified();
modified = true;
Undo_End();
}