/** Gets all Genomic Data. */
private ProfileDataSummary getGenomicData(
String cancerStudyId,
HashMap<String, GeneticProfile> defaultGeneticProfileSet,
SampleList defaultSampleSet,
String geneListStr,
ArrayList<SampleList> sampleList,
HttpServletRequest request,
HttpServletResponse response)
throws IOException, ServletException, DaoException {
// parse geneList, written in the OncoPrintSpec language (except for changes by XSS clean)
double zScore =
ZScoreUtil.getZScore(
new HashSet<String>(defaultGeneticProfileSet.keySet()),
new ArrayList<GeneticProfile>(defaultGeneticProfileSet.values()),
request);
double rppaScore = ZScoreUtil.getRPPAScore(request);
ParserOutput theOncoPrintSpecParserOutput =
OncoPrintSpecificationDriver.callOncoPrintSpecParserDriver(
geneListStr,
new HashSet<String>(defaultGeneticProfileSet.keySet()),
new ArrayList<GeneticProfile>(defaultGeneticProfileSet.values()),
zScore,
rppaScore);
ArrayList<String> geneList = new ArrayList<String>();
geneList.addAll(theOncoPrintSpecParserOutput.getTheOncoPrintSpecification().listOfGenes());
ArrayList<ProfileData> profileDataList = new ArrayList<ProfileData>();
Set<String> warningUnion = new HashSet<String>();
for (GeneticProfile profile : defaultGeneticProfileSet.values()) {
try {
GetProfileData remoteCall =
new GetProfileData(
profile, geneList, StringUtils.join(defaultSampleSet.getSampleList(), " "));
ProfileData pData = remoteCall.getProfileData();
warningUnion.addAll(remoteCall.getWarnings());
profileDataList.add(pData);
} catch (IllegalArgumentException e) {
e.getStackTrace();
}
}
ProfileMerger merger = new ProfileMerger(profileDataList);
ProfileData mergedProfile = merger.getMergedProfile();
ProfileDataSummary dataSummary =
new ProfileDataSummary(
mergedProfile,
theOncoPrintSpecParserOutput.getTheOncoPrintSpecification(),
zScore,
rppaScore);
return dataSummary;
}
void readValue(VRMLparser parser) throws IOException {
// no [] around data (SFImage is a "single" field)
StrTokenizer st = parser.istok;
ParserOutput pout = parser.pout;
values.clearData(); // clear default image
changed = true;
read1Value(parser); // width
if (readerror) {
pout.error(
"[SFImage] [Error] width (int) expected on parsing SFImage " + Node.atCurrLine(st));
return;
}
read1Value(parser); // height
if (readerror) {
pout.error(
"[SFImage] [Error] height (int) expected on parsing SFImage " + Node.atCurrLine(st));
return;
}
read1Value(parser); // no. of components
if (readerror) {
pout.error(
"[SFImage] [Error] no. of components (int) expected on parsing SFImage "
+ Node.atCurrLine(st));
return;
}
int[] vals = values.getData();
// System.out.println ("SFImage. width: " + vals[0] + ", height: " + vals[1]);
int numpixel = vals[0] * vals[1]; // read (width*height) pixels
for (int i = 0; i < numpixel; i++) {
read1Value(parser);
if (readerror) {
pout.error(
"[SFImage] [Error] could not read pixel no. "
+ i
+ " of SFImage (total "
+ numpixel
+ ")"
+ Node.atCurrLine(st));
return;
}
} // for
} // readValue