void xmlWriter::removeBuild(int buildID){
QMap <QString,QString> tmpID;
QMap <QString,QString> tmpName;
QMap <QString,QString> tmpDesc;
QMap <QString,QString> tmpDir;
QMapIterator<QString, QString> i(buildUniqueID);
QMapIterator<QString, QString> j(buildName);
QMapIterator<QString, QString> k(buildDescription);
QMapIterator<QString, QString> l(buildDirectory);
int m = 0;
while (i.hasNext() && j.hasNext() && k.hasNext() && l.hasNext())
{
i.next(); j.next(); k.next(); l.next();
if(buildUniqueID.values().at(m).compare(QString::number(buildID))){
//if the build is not the same include the build
tmpID.insertMulti("buildUniqueID",buildUniqueID.values().at(m));
tmpName.insertMulti("buildName",buildName.values().at(m));
tmpDesc.insertMulti("buildDescription",buildDescription.values().at(m));
tmpDir.insertMulti("buildDirectory",buildDirectory.values().at(m));
}
m++;
}
//replace the current values
buildUniqueID = tmpID;
buildName = tmpName;
buildDescription = tmpDesc;
buildDirectory = tmpDir;
createXMLFile();
}
void getTransFromFile(FILE* infile, char *path)
{
FILE* outfile = NULL;
int start, end, tmNumber, count, seqLength;
char *line, *token;
struct dyString *proteinID = newDyString(24);
start = end = tmNumber = count = seqLength = 0;
while( ( line = readLine(infile) ) != NULL )
{ /*grab the protein ID after each <PRE> tag*/
while( (token = nextWord(&line)) != NULL )
{
if( sameString(token,"<PRE>#"))
{ /*create a new xml file*/
token = nextWord(&line);
dyStringAppend(proteinID, token);
token = lastWordInLine(line);
seqLength = atoi(token);
}
if( sameString(token,"predicted") )
{ /*grab the number of transmembrane helices*/
token = lastWordInLine(line);
tmNumber = atoi(token);
if(tmNumber > 0)
{
outfile = createXMLFile(proteinID->string, path);
populateXMLFile(outfile, tmNumber, proteinID->string, path);
}
}
if( sameString(token,"</PRE>") )
{ /*close the xml file*/
carefulClose(&outfile);
dyStringClear(proteinID);
count = 0;
}
if( sameString(token,"TMhelix") )
{
if( (token = nextWord(&line)) != NULL )
{ /*get the start*/
start = atoi(token);
if( (token = nextWord(&line)) != NULL )
end = atoi(token);
}
if( count == 0)
addCoordinatesToXMLFile(outfile, 1, start-1, "N-term", count);
count++;
addCoordinatesToXMLFile(outfile, start, end, "TM", count);
if( count == tmNumber && outfile != NULL )
{
addCoordinatesToXMLFile(outfile,end+1,seqLength,"C-term",count);
finishXMLFile(outfile, proteinID->string, seqLength);
}
}
} /*end inner while*/
} /*end outer while*/
freeMem(line);
freeDyString(&proteinID);
}
void xmlWriter::updateBuildDir(int buildID, QString newBuildDir){
int index = findBuildIndex(buildID);
if(index <= -1 || index >= buildUniqueID.values().size()){
return;
}
QString theBuildName = buildName.values().at(index);
QString buildDescr = buildDescription.values().at(index);
QString theBuildID = buildUniqueID.values().at(index);
RemoveBuildToBeUpdated(buildID);
buildUniqueID.insertMulti("buildUniqueID",theBuildID);
buildName.insertMulti("buildName",theBuildName);
buildDescription.insertMulti("buildDescription",buildDescr);
buildDirectory.insertMulti("buildDirectory",newBuildDir);
createXMLFile();
}
