private Path holePathVonNeuemLaufwerk(ArrayList<Path> initial, ArrayList<Path> aktuell) {
ArrayList<Path> test, test1;
test = (ArrayList<Path>) aktuell.clone();
test1 = (ArrayList<Path>) initial.clone();
test.removeAll(test1);
return test.get(test.size() - 1);
}
/**
* Check if components required by specified products are available.
*
* @param products list of ProdOrderProductVO objects
* @params compAltComps collection of <component item code,HashSet of alternative component item
* codes>; filled by this method (and given back by reference)
* @return VOListResponse of ProdOrderComponentVO objects
*/
public final Response checkComponentsAvailability(
Connection conn,
Hashtable compAltComps,
ArrayList products,
UserSessionParameters userSessionPars,
HttpServletRequest request,
HttpServletResponse response,
HttpSession userSession,
ServletContext context) {
String serverLanguageId = ((JAIOUserSessionParameters) userSessionPars).getServerLanguageId();
try {
// retrieve internationalization settings (Resources object)...
ServerResourcesFactory factory =
(ServerResourcesFactory) context.getAttribute(Controller.RESOURCES_FACTORY);
Resources resources = factory.getResources(userSessionPars.getLanguageId());
if (products.size() == 0) {
return new VOListResponse(new ArrayList(), false, 0);
}
// fill in comps hashtable with the collection of required components...
ItemPK pk = null;
ProdOrderProductVO prodVO = null;
ArrayList components = null;
MaterialVO compVO = null;
Response res = null;
ProdOrderComponentVO componentVO = null;
Hashtable comps =
new Hashtable(); // collection of <component item code,ProdOrderComponentVO object>
for (int i = 0; i < products.size(); i++) {
// retrieve bill of materials for each product...
prodVO = (ProdOrderProductVO) products.get(i);
pk = new ItemPK(prodVO.getCompanyCodeSys01DOC23(), prodVO.getItemCodeItm01DOC23());
res =
bean.getBillOfMaterials(
conn, pk, userSessionPars, request, response, userSession, context);
if (res.isError()) {
return res;
}
// extract components only (leaf nodes)...
components =
getComponents(
(DefaultMutableTreeNode) ((TreeModel) ((VOResponse) res).getVo()).getRoot());
for (int j = 0; j < components.size(); j++) {
compVO = (MaterialVO) components.get(j);
componentVO = (ProdOrderComponentVO) comps.get(compVO.getItemCodeItm01ITM03());
if (componentVO == null) {
componentVO = new ProdOrderComponentVO();
comps.put(compVO.getItemCodeItm01ITM03(), componentVO);
componentVO.setAvailableQty(new BigDecimal(0));
componentVO.setCompanyCodeSys01DOC24(compVO.getCompanyCodeSys01ITM03());
componentVO.setDescriptionSYS10(compVO.getDescriptionSYS10());
componentVO.setDocNumberDOC24(prodVO.getDocNumberDOC23());
componentVO.setDocYearDOC24(prodVO.getDocYearDOC23());
componentVO.setItemCodeItm01DOC24(compVO.getItemCodeItm01ITM03());
componentVO.setMinSellingQtyUmCodeReg02ITM01(compVO.getMinSellingQtyUmCodeReg02ITM01());
componentVO.setQtyDOC24(new BigDecimal(0));
}
componentVO.setQtyDOC24(
componentVO.getQtyDOC24().add(compVO.getQtyITM03().multiply(prodVO.getQtyDOC23())));
}
}
// check components availability in the specified warehouse...
Enumeration en = comps.keys();
GridParams gridParams = new GridParams();
gridParams
.getOtherGridParams()
.put(ApplicationConsts.COMPANY_CODE_SYS01, prodVO.getCompanyCodeSys01DOC23());
gridParams
.getOtherGridParams()
.put(ApplicationConsts.WAREHOUSE_CODE, prodVO.getWarehouseCodeWar01DOC22());
gridParams.getOtherGridParams().put(ApplicationConsts.LOAD_ALL, Boolean.TRUE);
ItemAvailabilityVO availVO = null;
BigDecimal availability, altAvailability, delta;
String itemCode = null;
ArrayList list, availList;
AltComponentVO altVO = null;
ArrayList alternativeComps = new ArrayList();
ArrayList compsToRemove = new ArrayList();
ProdOrderComponentVO altComponentVO = null;
HashSet altCodes = null; // list of alternative component item codes...
BigDecimal altQty = null;
while (en.hasMoreElements()) {
itemCode = en.nextElement().toString();
componentVO = (ProdOrderComponentVO) comps.get(itemCode);
gridParams
.getOtherGridParams()
.put(
ApplicationConsts.ITEM_PK, new ItemPK(prodVO.getCompanyCodeSys01DOC23(), itemCode));
res =
avail.executeCommand(
gridParams, userSessionPars, request, response, userSession, context);
if (res.isError()) return res;
availList = ((VOListResponse) res).getRows();
componentVO.setAvailabilities(availList);
availability = new BigDecimal(0);
for (int i = 0; i < availList.size(); i++) {
availVO = (ItemAvailabilityVO) availList.get(i);
availability = availability.add(availVO.getAvailableQtyWAR03());
}
componentVO.setAvailableQty(availability);
if (componentVO.getQtyDOC24().doubleValue() > componentVO.getAvailableQty().doubleValue()) {
// check if there exist some alternative component...
res =
altComps.executeCommand(
gridParams, userSessionPars, request, response, userSession, context);
if (res.isError()) return res;
list = ((VOListResponse) res).getRows();
for (int i = 0; i < list.size(); i++) {
altVO = (AltComponentVO) list.get(i);
gridParams
.getOtherGridParams()
.put(
ApplicationConsts.ITEM_PK,
new ItemPK(prodVO.getCompanyCodeSys01DOC23(), altVO.getItemCodeItm01ITM04()));
res =
avail.executeCommand(
gridParams, userSessionPars, request, response, userSession, context);
if (res.isError()) return res;
availList = ((VOListResponse) res).getRows();
altAvailability = new BigDecimal(0);
for (int j = 0; j < availList.size(); j++) {
availVO = (ItemAvailabilityVO) availList.get(j);
altAvailability = altAvailability.add(availVO.getAvailableQtyWAR03());
}
if (altAvailability.doubleValue() > 0) {
altComponentVO = new ProdOrderComponentVO();
altComponentVO.setAvailabilities(availList);
altComponentVO.setAvailableQty(altAvailability);
altComponentVO.setCompanyCodeSys01DOC24(altVO.getCompanyCodeSys01ITM04());
altComponentVO.setDescriptionSYS10(altVO.getDescriptionSYS10());
altComponentVO.setDocNumberDOC24(prodVO.getDocNumberDOC23());
altComponentVO.setDocYearDOC24(prodVO.getDocYearDOC23());
altComponentVO.setItemCodeItm01DOC24(altVO.getItemCodeItm01ITM04());
altComponentVO.setMinSellingQtyUmCodeReg02ITM01(
altVO.getMinSellingQtyUmCodeReg02ITM01());
altQty =
conv.convertQty(
altVO.getMinSellingQtyUmCodeReg02ITM01(),
componentVO.getMinSellingQtyUmCodeReg02ITM01(),
altAvailability,
userSessionPars,
request,
response,
userSession,
context);
if (componentVO.getQtyDOC24().subtract(availability).doubleValue()
> altQty.doubleValue()) {
delta = altQty;
altComponentVO.setQtyDOC24(altAvailability);
} else {
delta = componentVO.getQtyDOC24();
altComponentVO.setQtyDOC24(
conv.convertQty(
componentVO.getMinSellingQtyUmCodeReg02ITM01(),
altVO.getMinSellingQtyUmCodeReg02ITM01(),
delta,
userSessionPars,
request,
response,
userSession,
context));
}
componentVO.setQtyDOC24(componentVO.getQtyDOC24().subtract(delta));
alternativeComps.add(altComponentVO);
altCodes = (HashSet) compAltComps.get(itemCode);
if (altCodes == null) {
altCodes = new HashSet();
compAltComps.put(itemCode, altCodes);
}
altCodes.add(altVO.getItemCodeItm01ITM04());
if (componentVO.getQtyDOC24().doubleValue() == 0) {
compsToRemove.add(componentVO);
break;
}
if (componentVO.getQtyDOC24().subtract(availability).doubleValue() == 0) break;
}
}
}
}
list = new ArrayList(comps.values());
list.addAll(alternativeComps);
list.removeAll(compsToRemove);
return new VOListResponse(list, false, list.size());
} catch (Throwable ex) {
Logger.error(
userSessionPars.getUsername(),
this.getClass().getName(),
"checkComponentsAvailability",
"Error while retrieving components availability for the specified production order",
ex);
return new ErrorResponse(ex.getMessage());
}
}
public void CrawlRT(String RTPage) throws IOException {
ArrayList<String> t = new ArrayList<String>();
String crawlData;
String crawlData2;
String crawlData3;
FileReader freader = new FileReader("Crawl.txt");
BufferedReader br = new BufferedReader(freader);
FileReader freader2 = new FileReader("Tocrawl.txt");
BufferedReader br2 = new BufferedReader(freader2);
FileWriter fwriter2 = new FileWriter("Tocrawl.txt", true);
BufferedWriter bw2 = new BufferedWriter(fwriter2);
FileWriter fwriter = new FileWriter("Crawl.txt", true);
BufferedWriter bw = new BufferedWriter(fwriter);
/*while(null != (crawlData2 = br.readLine()))
{
if(crawlData2 !=null)
Crawl.add(crawlData2);
}
t = collectLinks(RTPage);
Iterator<String> e3= t.iterator();
while(e3.hasNext())
{
String ee = e3.next();
if(!Crawl.contains(ee))
{
bw2.write(ee+"\r\n");
}
}
br.close();
br2.close();
bw.close();
bw2.close();*/
if (null == (crawlData = br.readLine()))
// if(true)
{
// initial iteration
bw.write(RTPage + "\r\n");
Crawl.add(RTPage);
t = collectLinks(RTPage);
ToCrawl.addAll(t);
} else {
// collect data from files and load to array lists
while (null != (crawlData2 = br.readLine())) {
if (crawlData2 != null) Crawl.add(crawlData2);
}
while (null != (crawlData3 = br2.readLine())) {
if (crawlData3 != null) ToCrawl.add(crawlData3);
}
}
System.out.println("Crawlled");
// Number of movies to be crawled
for (int i = 0; i < 1000; i++) {
if (ToCrawl.size() > 0) {
Crawl.removeAll(Collections.singleton(null));
ToCrawl.removeAll(Collections.singleton(null));
String c = ToCrawl.get(0);
if (Crawl.contains(c)) ToCrawl.remove(c);
else {
// collect links and collect data from a particular link
Crawl.add(c);
t = collectLinks(c);
CollectData(c);
ToCrawl.remove(c);
Iterator<String> e3 = t.iterator();
while (e3.hasNext()) {
String ee = e3.next();
if (!ToCrawl.contains(ee)) {
if (!Crawl.contains(ee)) {
ToCrawl.add(ee);
}
}
}
bw.write(c + "\r\n");
}
}
}
System.out.println("To Be Crawlled");
Iterator<String> e2 = ToCrawl.iterator();
while (e2.hasNext()) {
// write to file the movies still to be crawled.
bw2.write(e2.next() + "\r\n");
}
prop.setProperty("Id", Integer.toString(n));
prop.store(new FileOutputStream("config.properties"), null);
br.close();
br2.close();
bw.close();
bw2.close();
}
public static void main(String args[]) {
double totalTime;
double startTime = System.currentTimeMillis();
parseArguments(args);
// preprocess input files to find the chromosomal boundaries in terms of line number
/*
* All files should be sorted in chromosomal order
*/
System.out.println("Preprocessing input files to find chromosome boundaries...");
System.out.println("\tExons file..");
ArrayList<Integer> exonFileChrBoundaries = getChromosomalBoundaries(exonFileName, 0);
System.out.println("\tExpression file..");
ArrayList<Integer> exprFileChrBoundaries = getChromosomalBoundaries(expressionFileName, 2);
System.out.println("\tMapped reads file..");
ArrayList<Integer> readsFileChrBoundaries = getChromosomalBoundaries(mappedReadsFileName, 2);
try {
BufferedReader inputExons = new BufferedReader(new FileReader(exonFileName));
BufferedReader inputExpr = new BufferedReader(new FileReader(expressionFileName));
BufferedReader inputSAMData = new BufferedReader(new FileReader(mappedReadsFileName));
for (int chromosome : chromosomes) {
int arrayPosition = chromosome - chromosomes.get(0) + 1;
System.out.println("Chromosome " + chromosome);
System.out.println("Reading exons file....");
int numberOfLines =
exonFileChrBoundaries.get(arrayPosition) - exonFileChrBoundaries.get(arrayPosition - 1);
double currentTime = System.currentTimeMillis();
Exons = Exon.readExon(inputExons, chromosome, numberOfLines);
double totalExonReadTime = (System.currentTimeMillis() - currentTime) / 1000F;
Exon.sortExons(Exons);
System.out.println("Reading expression file....");
numberOfLines =
exprFileChrBoundaries.get(arrayPosition) - exprFileChrBoundaries.get(arrayPosition - 1);
ArrayList<Expression> Expressions = new ArrayList<Expression>();
currentTime = System.currentTimeMillis();
Expressions = Expression.readExon(inputExpr, chromosome, numberOfLines);
double totalExprReadTime = (System.currentTimeMillis() - currentTime) / 1000F;
int numberOfExpr = Expressions.size();
System.out.println("Calculating FPKMs....");
currentTime = System.currentTimeMillis();
Exon.getFPKM(Expressions, Exons);
double totalFPKMCalcTime = (System.currentTimeMillis() - currentTime) / 1000F;
Expressions.removeAll(Expressions); // explicitly deleting to free up memory
System.out.println("Reading mapped reads SAM file....");
numberOfLines =
readsFileChrBoundaries.get(arrayPosition)
- readsFileChrBoundaries.get(arrayPosition - 1);
ArrayList<MappedReads> mappedReads = new ArrayList<MappedReads>();
currentTime = System.currentTimeMillis();
mappedReads = MappedReads.readMappedReads(inputSAMData, chromosome, numberOfLines);
double totalReadsReadTime = (System.currentTimeMillis() - currentTime) / 1000F;
MappedReads.sort(mappedReads);
int numberOfReads = mappedReads.size();
System.out.println("Reading reference genome file....");
String referenceFileName = referenceDirectory + "/chr" + chromosome + ".fa";
currentTime = System.currentTimeMillis();
RandomAccessFile inputReference = new RandomAccessFile(referenceFileName, "r");
for (Exon e : Exons) {
e.getReferenceSequence(inputReference);
}
double totalRefCalcTime = (System.currentTimeMillis() - currentTime) / 1000F;
System.out.println("Calculating SNPs....");
currentTime = System.currentTimeMillis();
Exon.getSNPs(Exons, mappedReads);
double totalSNPsCalcTime = (System.currentTimeMillis() - currentTime) / 1000F;
mappedReads.removeAll(mappedReads);
System.out.println("Calculating States....");
currentTime = System.currentTimeMillis();
HiddenMarkovModel.getStates(Exons);
double totalStateCalcTime = (System.currentTimeMillis() - currentTime) / 1000F;
// Print output
if (outputFileName.equals("")) {
// print to stdout
for (Exon e : Exons) System.out.println(e);
} else {
Writer output = new BufferedWriter(new FileWriter(outputFileName));
for (Exon e : Exons) output.write(e + "\n");
output.close();
}
// prints the timing metrics to std out
if (printTimingMetrics) {
double endTime = System.currentTimeMillis();
totalTime = (endTime - startTime) / 1000F;
System.out.println("Total Time: " + totalTime);
System.out.println(
"Time for reading exons file : " + totalExonReadTime + ", " + Exons.size());
System.out.println(
"Time for reading expression file : " + totalExprReadTime + ", " + numberOfExpr);
System.out.println(
"Time for reading mapped reads file: " + totalReadsReadTime + ", " + numberOfReads);
System.out.println("Time for getting reference seq : " + totalRefCalcTime);
System.out.println("Time for calculating FPKM : " + totalFPKMCalcTime);
System.out.println("Time for calculating Num of SNPs : " + totalSNPsCalcTime);
System.out.println("Time for calculating States : " + totalStateCalcTime);
}
}
} catch (Exception e) {
System.err.println("Exception: " + e.getMessage());
e.printStackTrace();
}
}