public DictionaryEntry lookup(byte utfBytes[], int hashCode, int charLength) {
int res = Arrays.binarySearch(hashCodes, hashCode);
if (res < 0) {
return null;
}
DictionaryEntry entry = entries[res];
if (Arrays.equals(entry.entryBytes, utfBytes)) {
return entry;
}
int pos = res - 1;
while ((pos >= 0) && (hashCodes[pos] == hashCode)) {
entry = entries[pos];
if (Arrays.equals(entry.entryBytes, utfBytes)) {
return entry;
}
--pos;
}
pos = res + 1;
while ((pos < entries.length) && (hashCodes[pos] == hashCode)) {
entry = entries[pos];
if (Arrays.equals(entry.entryBytes, utfBytes)) {
return entry;
}
++pos;
}
return UNKNOWN;
}
/**
* Copy from the copy method in StructUtil. Did not want to drag that code in. maybe this actually
* should go to struct.
*
* @param from
* @param to
* @param excludes
* @return
* @throws Exception
*/
public static <T extends struct> T xcopy(struct from, T to, String... excludes) throws Exception {
Arrays.sort(excludes);
for (Field f : from.fields()) {
if (Arrays.binarySearch(excludes, f.getName()) >= 0) continue;
Object o = f.get(from);
if (o == null) continue;
Field tof = to.getField(f.getName());
if (tof != null)
try {
tof.set(to, Converter.cnv(tof.getGenericType(), o));
} catch (Exception e) {
System.out.println(
"Failed to convert "
+ f.getName()
+ " from "
+ from.getClass()
+ " to "
+ to.getClass()
+ " value "
+ o
+ " exception "
+ e);
}
}
return to;
}
/**
* Returns an int to int hash map with old row numbers mapped to new row numbers, which defines a
* sorted order for this column
*
* @param validRows row numbers from which the sorted order is retrieved.
*/
public VIntIntHashMap getNewOrder(int[] validRows) {
Object[] sortedValues = getValuesInRange(validRows[0], validRows[validRows.length - 1]);
Object[] rawValues = getValues(validRows);
// will hold the new order, the returned value.
int[] newOrder = new int[validRows.length];
// a flag array. occupiedIndices[j] == true mean that the row number
// stored at validRows[j] was already mapped to a value in tempMap
boolean[] ocuupiedIndices = new boolean[validRows.length];
// for each valid row validRows[i]
for (int i = 0; i < validRows.length; i++) {
// finding the index of its mapped Object in values
int newRow = Arrays.binarySearch(sortedValues, rawValues[i]);
// because binarySearch can return the same index for items that are identical
// checking for this option too.
if (ocuupiedIndices[newRow]) {
// if newRow index was already used - finding an alternative index
newRow = getNewRow(rawValues[i], sortedValues, newRow, ocuupiedIndices);
// marking the associated flag as true
}
ocuupiedIndices[newRow] = true;
newOrder[newRow] = validRows[i];
} // end of for
return VHashService.getMappedOrder(validRows, newOrder);
}
/**
* Binary search of a key in a list. If there are several hits the last one is returned.
*
* @param a array to search into
* @param e key to search for
* @return index of the found hit or where the key ought to be inserted
*/
private int sortedLastIndexOf(final int[] a, final int e) {
int i = Arrays.binarySearch(a, 0, rows, e);
if (i >= 0) {
while (++i < rows && a[i] == e) ;
return i - 1;
}
return i;
}
public final int readCharacter(final char[] allowed) throws IOException {
// if we restrict to a limited set and the current character
// is not in the set, then try again.
char c;
Arrays.sort(allowed); // always need to sort before binarySearch
while (Arrays.binarySearch(allowed, c = (char) readVirtualKey()) < 0) ;
return c;
}
/**
* Inserts a new record.
*
* @param pre record PRE
* @param id record ID
* @param c number of inserted records
*/
public void insert(final int pre, final int id, final int c) {
if (rows == 0 && pre == id && id == baseid + 1) {
// no mapping and we append at the end => nothing to do
baseid += c;
return;
}
int pos = 0;
int inc = c;
int oid = pre;
if (rows > 0) {
pos = Arrays.binarySearch(pres, 0, rows, pre);
if (pos < 0) {
pos = -pos - 1;
if (pos != 0) {
// check if inserting into an existing id interval
final int prev = pos - 1;
final int prevcnt = nids[prev] - fids[prev] + 1;
final int prevpre = pres[prev];
if (pre < prevpre + prevcnt) {
// split the id interval
final int split = pre - prevpre;
final int fid = fids[prev] + split;
// add a new next interval
add(pos, pre, fid, nids[prev], incs[prev], oids[prev]);
// shrink the previous interval
nids[prev] = fid - 1;
incs[prev] -= prevcnt - split;
oid = oids[prev];
inc += incs[prev];
} else {
oid = pre - incs[prev];
inc += incs[prev];
}
}
} else if (pos > 0) {
oid = oids[pos];
inc += incs[pos - 1];
}
increment(pos, c);
}
// add the new interval
add(pos, pre, id, id + c - 1, inc, oid);
}
/** {@inheritDoc} */
public boolean retainAll(int[] array) {
boolean changed = false;
Arrays.sort(array);
int[] values = _values;
byte[] states = _states;
for (int i = values.length; i-- > 0; ) {
if (states[i] == FULL && (Arrays.binarySearch(array, values[i]) < 0)) {
removeAt(i);
changed = true;
}
}
return changed;
}
public boolean retainAll(final int[] array) {
boolean changed = false;
Arrays.sort(array);
final int[] set = this._set;
final byte[] states = this._states;
int i = set.length;
while (i-- > 0) {
if (states[i] == 1 && Arrays.binarySearch(array, set[i]) < 0) {
this.remove(set[i]);
changed = true;
}
}
return changed;
}
/** {@inheritDoc} */
public boolean retainAll(long[] array) {
boolean changed = false;
Arrays.sort(array);
long[] set = _set;
byte[] states = _states;
for (int i = set.length; i-- > 0; ) {
if (states[i] == FULL && (Arrays.binarySearch(array, set[i]) < 0)) {
removeAt(i);
changed = true;
}
}
return changed;
}
/** {@inheritDoc} */
@Override
public boolean retainAll(char[] array) {
boolean changed = false;
Arrays.sort(array);
TCharOffheapArray values = _values;
TByteOffheapArray states = _states;
for (int i = capacity(); i-- > 0; ) {
if (states.get(i) == FULL && (Arrays.binarySearch(array, values.get(i)) < 0)) {
removeAt(i);
changed = true;
}
}
return changed;
}
/**
* Gets a list of all the devices found on the bus matching the specified set of product IDs. Any
* device with a product ID equal to one of the products listed in <i>productIDs[]</i> will be
* returned. You can search for devices by product name using {@link #productNameToID( String[]
* productName ) productNameToID()}, like so:
*
* <pre>USBDevice[] devices = deviceManager.getDeviceByProductID(
* deviceManager.productNameToID( new String[] { "USB-AO16-16A", "USB-AO16-16" } ) );</pre>
*
* @param productIDs an array containing one or more product IDs to search for.
* @return An array of all the devices found. If no devices were found matching the specified set
* of product IDs, the array will be empty (i.e. contain zero items).
* @throws IllegalArgumentException
*/
public USBDevice[] getDeviceByProductID(int[] productIDs) {
if (productIDs == null || productIDs.length < 1)
throw new IllegalArgumentException("Invalid product ID array");
for (int index = 0; index < productIDs.length; index++) {
if (productIDs[index] < MIN_PRODUCT_ID || productIDs[index] > MAX_PRODUCT_ID)
throw new IllegalArgumentException("Invalid product ID: " + productIDs[index]);
} // for( int index ...
int[] sortedProductIDs = productIDs.clone();
Arrays.sort(sortedProductIDs);
Vector<USBDevice> devices = new Vector<USBDevice>();
for (int index = 0; index < deviceList.size(); index++) {
final int productID = deviceList.get(index).getProductID();
if (Arrays.binarySearch(sortedProductIDs, productID) >= 0) devices.add(deviceList.get(index));
} // for( int index ...
return devices.toArray(new USBDevice[0]);
} // getDeviceByProductID()
/**
* /* return the address of the function that address is in
*
* @param vma
* @return
*/
public Symbol getSymbol(final long vma) {
if (this.symbols == null) {
return null;
}
// @@@ If this works, move it to a single instance in this class.
final SymbolComparator symbol_comparator = new SymbolComparator();
int ndx = Arrays.binarySearch(this.symbols, vma, symbol_comparator);
if (ndx > 0) {
return this.symbols[ndx];
}
if (ndx == -1) {
return null;
}
ndx = -ndx - 1;
return this.symbols[ndx - 1];
}
/** Copy the doc files for the current ClassDoc if necessary. */
private void copyDocFiles() {
PackageDoc containingPackage = annotationTypeDoc.containingPackage();
if ((configuration.packages == null
|| Arrays.binarySearch(configuration.packages, containingPackage) < 0)
&& !containingPackagesSeen.contains(containingPackage.name())) {
// Only copy doc files dir if the containing package is not
// documented AND if we have not documented a class from the same
// package already. Otherwise, we are making duplicate copies.
Util.copyDocFiles(
configuration,
Util.getPackageSourcePath(configuration, annotationTypeDoc.containingPackage())
+ DirectoryManager.getDirectoryPath(annotationTypeDoc.containingPackage())
+ File.separator,
DocletConstants.DOC_FILES_DIR_NAME,
true);
containingPackagesSeen.add(containingPackage.name());
}
}
public void solve() {
n = ni();
int m = ni();
int a[] = new int[n];
for (int i = 0; i < n; i++) a[i] = ni();
Arrays.sort(a);
for (int i = 0; i < m; i++) {
int t = ni();
int w = Arrays.binarySearch(a, t);
if (w < 0) {
w = (-w) - 1;
int min = Integer.MAX_VALUE;
if (is(w) && min > Math.abs(t - a[w])) min = Math.abs(t - a[w]);
if (is(w - 1) && min > Math.abs(t - a[w - 1])) min = Math.abs(t - a[w - 1]);
if (is(w + 1) && min > Math.abs(t - a[w + 1])) min = Math.abs(t - a[w + 1]);
pw.print(min + " ");
} else {
pw.print(0 + " ");
}
}
}
public final ClusNode getTree(int fold) {
int idx = Arrays.binarySearch(m_Folds, fold);
ClusNode node = m_Nodes[idx];
if (node.hasBestTest() && node.atBottomLevel()) {
OptXValSplit split = null;
int nb = getNbChildren();
for (int i = 0; i < nb; i++) {
OptXValSplit msplit = (OptXValSplit) getChild(i);
if (msplit.contains(fold)) {
split = msplit;
break;
}
}
int arity = node.updateArity();
for (int i = 0; i < arity; i++) {
OptXValNode subnode = (OptXValNode) split.getChild(i);
node.setChild(subnode.getTree(fold), i);
}
}
return node;
}
public static void main(String[] args) throws IOException {
BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
int T = parseInt(br.readLine());
int N = T;
int[] A = new int[T];
for (int t = 0; t < T; t++) {
StringTokenizer st = new StringTokenizer(br.readLine());
A[t] = parseInt(st.nextToken());
}
int[] fe = new int[N * N * N];
int cnt = 0;
for (int a = 0; a < T; a++)
for (int b = 0; b < T; b++) for (int c = 0; c < T; c++) fe[cnt++] = (A[a] + A[b]) * A[c];
Arrays.sort(fe);
System.out.println(Arrays.toString(fe));
int ret = 0;
for (int i = 0; i < N; i++)
for (int j = 0; j < N; j++)
for (int k = 0; k < N; k++) {
int abc = A[i] * A[j] + A[k];
int ai = Arrays.binarySearch(fe, abc);
if (ai >= 0) {
while (ai >= 0 && fe[ai] == abc) ai--;
ai++;
while (ai < N * N * N && fe[ai] == abc) {
ai++;
ret++;
}
}
System.out.println(abc + " " + ret);
}
System.out.println(ret);
br.close();
}
/**
* Loads options from a reader into this instance. Will read from the stream until it hits a
* section header, ie a '[' character, and resets the reader to point to this character.
*
* @param reader where to read from
* @throws IOException at an I/O problem
*/
public void load(BufferedReader reader) throws IOException {
while (reader.ready()) {
reader.mark(NAME_MAXLENGTH);
String line = reader.readLine().trim();
// Check for section header
if (line.length() > 0 && line.charAt(0) == HEADER_START) {
reader.reset();
return;
}
int delimIndex = -1;
// blank line
if (line.equals("")) {
this.addBlankLine();
}
// comment line
else if ((delimIndex = Arrays.binarySearch(this.commentDelimsSorted, line.charAt(0)))
>= 0) {
addComment(line.substring(1), this.commentDelimsSorted[delimIndex]);
}
// option line
else {
delimIndex = -1;
int delimNum = -1;
int lastSpaceIndex = -1;
for (int i = 0, l = line.length(); i < l && delimIndex < 0; i++) {
delimNum = Arrays.binarySearch(this.optionDelimsSorted, line.charAt(i));
if (delimNum >= 0) {
delimIndex = i;
} else {
boolean isSpace =
Arrays.binarySearch(this.OPTION_DELIMS_WHITESPACE, line.charAt(i)) >= 0;
if (!isSpace && lastSpaceIndex >= 0) {
break;
} else if (isSpace) {
lastSpaceIndex = i;
}
}
}
// delimiter at start of line
if (delimIndex == 0) {
// XXX what's a man got to do?
}
// no delimiter found
else if (delimIndex < 0) {
if (lastSpaceIndex < 0) {
this.set(line, "");
} else {
this.set(line.substring(0, lastSpaceIndex), line.substring(lastSpaceIndex + 1));
}
}
// delimiter found
else {
this.set(
line.substring(0, delimIndex),
line.substring(delimIndex + 1),
line.charAt(delimIndex));
}
}
}
}
/**
* Reads CEL files. <code>readCel</code> reads the intensity signals from the tumor sample and the
* normal sample. The copy number at a particular locus is calculated using the ratio of the tumor
* intensity at that locus and the correspoding normal intensity times 2.
*
* @param normalCelFileName Affymetrix CEL file of the paired normal sample
* @param tumorCelFileName Affymetrix CEL file of the tumor sample
* @param cdfFileName Affymetrix library file (CDF file) for the platform on which the samples are
* generated
*/
private void readCel(String normalCelFileName, String tumorCelFileName, String cdfFileName) {
FusionCELData celNormal;
FusionCELData celTumor;
FusionCDFData cdf;
celNormal = new FusionCELData();
celNormal.setFileName(normalCelFileName);
if (celNormal.read() == false) {
System.out.println("Failed to read the CEL file.");
return;
}
celTumor = new FusionCELData();
celTumor.setFileName(tumorCelFileName);
if (celTumor.read() == false) {
System.out.println("Failed to read the CEL file.");
return;
}
cdf = new FusionCDFData();
cdf.setFileName(cdfFileName);
if (cdf.read() == false) {
System.out.println("Failed to read the CDF file.");
return;
}
int nsets = cdf.getHeader().getNumProbeSets();
ProbeSetIntensityData[] probeSetDataNormal = new ProbeSetIntensityData[nsets];
ProbeSetIntensityData[] probeSetDataTumor = new ProbeSetIntensityData[nsets];
// SNP array structure:
// 1. Each probeset contains several groups (the number of groups varies among different
// probeset)
// 2. Each group contains several cells (the number of cells also varies among different
// groups)
for (int iset = 0; iset < nsets; iset++) {
String probeSetName = cdf.getProbeSetName(iset); // get the probeset name
FusionCDFProbeSetInformation set = new FusionCDFProbeSetInformation();
cdf.getProbeSetInformation(iset, set);
int ngroups = set.getNumGroups();
int numPmANormal = 0; // Pm : perfect match
int numPmBNormal = 0;
int numPmATumor = 0;
int numPmBTumor = 0;
int numMmANormal = 0; // Mm: Mis-Match
int numMmBNormal = 0;
int numMmATumor = 0;
int numMmBTumor = 0;
probeSetDataNormal[iset] = new ProbeSetIntensityData();
probeSetDataTumor[iset] = new ProbeSetIntensityData();
probeSetDataNormal[iset].probeSetType = set.getProbeSetType();
probeSetDataTumor[iset].probeSetType = set.getProbeSetType();
probeSetDataNormal[iset].probeSetID = cdf.getProbeSetName(iset) + "";
probeSetDataTumor[iset].probeSetID = cdf.getProbeSetName(iset) + "";
for (int igroup = 0; igroup < ngroups; igroup++) {
FusionCDFProbeGroupInformation group = new FusionCDFProbeGroupInformation();
set.getGroup(igroup, group);
int ncells = group.getNumCells();
for (int icell = 0; icell < ncells; icell++) {
FusionCDFProbeInformation probe = new FusionCDFProbeInformation();
group.getCell(icell, probe);
try {
char pBase = probe.getPBase();
char tBase = probe.getTBase();
// only If the match is perfect, the intensity of this cell
// contributes
if ((((pBase + tBase) == 213) || ((pBase + tBase) == 202))) {
// Perfect match is the match that with pBase:tBase = a:t or c:g
if ((igroup % 2) == 0) {
if (!celNormal.isOutlier(probe.getX(), probe.getY())) {
probeSetDataNormal[iset].pmA +=
celNormal.getIntensity(probe.getX(), probe.getY());
numPmANormal++;
}
if (!celTumor.isOutlier(probe.getX(), probe.getY())) {
probeSetDataTumor[iset].pmA += celTumor.getIntensity(probe.getX(), probe.getY());
numPmATumor++;
}
} else {
if (!celNormal.isOutlier(probe.getX(), probe.getY())) {
probeSetDataNormal[iset].pmB +=
celNormal.getIntensity(probe.getX(), probe.getY());
numPmBNormal++;
}
if (!celTumor.isOutlier(probe.getX(), probe.getY())) {
probeSetDataTumor[iset].pmB += celTumor.getIntensity(probe.getX(), probe.getY());
numPmBTumor++;
}
}
}
} catch (Exception e) {
}
}
}
// using the average of intensity of the perfect match cells as the intensity for certain
// probeset
if (numPmANormal != 0) {
probeSetDataNormal[iset].pmA = probeSetDataNormal[iset].pmA / numPmANormal;
}
if (numPmBNormal != 0) {
probeSetDataNormal[iset].pmB = probeSetDataNormal[iset].pmB / numPmBNormal;
}
if (numPmATumor != 0) {
probeSetDataTumor[iset].pmA = probeSetDataTumor[iset].pmA / numPmATumor;
}
if (numPmBTumor != 0) {
probeSetDataTumor[iset].pmB = probeSetDataTumor[iset].pmB / numPmBTumor;
}
}
try {
genotypeCalling(probeSetDataNormal); // to decide whether certain probe is AB type
} catch (Exception e) {
}
Arrays.sort(probeSetDataNormal);
Arrays.sort(probeSetDataTumor);
ArrayList<Integer> indexFoundList = new ArrayList<Integer>(probeSetDataNormal.length);
ArrayList<Integer> indexFoundListSNP = new ArrayList<Integer>(probeSetDataNormal.length);
for (int i = 0; i < numAnnotatedProbeSet; i++) {
int indexFound =
Arrays.binarySearch(probeSetDataNormal, new ProbeSetIntensityData(probeSetID[i]));
if (indexFound >= 0) {
isGenotypeAB[i] = probeSetDataNormal[indexFound].isGenotypeAB;
probeSetType[i] = probeSetDataNormal[indexFound].probeSetType;
copyNumber[i] =
2
* (probeSetDataTumor[indexFound].pmA + probeSetDataTumor[indexFound].pmB)
/ (probeSetDataNormal[indexFound].pmA + probeSetDataNormal[indexFound].pmB);
intensityNormal[i] =
probeSetDataNormal[indexFound].pmA + probeSetDataNormal[indexFound].pmB;
intensityTumor[i] = probeSetDataTumor[indexFound].pmA + probeSetDataTumor[indexFound].pmB;
// For 250k affymetrix chip, all the probes are SNP probes
if (probeSetType[i] == FusionGeneChipProbeSetType.GenotypingProbeSetType) {
alleleA[i] = probeSetDataTumor[indexFound].pmA / probeSetDataNormal[indexFound].pmA;
alleleB[i] = probeSetDataTumor[indexFound].pmB / probeSetDataNormal[indexFound].pmB;
if (alleleA[i] > 1E-10
&& alleleA[i] <= 30
&& alleleB[i] >= 1E-10
&& alleleB[i] <= 30
&& copyNumber[i] > 1E-10
&& copyNumber[i] <= 30) {
isOutlier[i] = false;
indexFoundList.add(i);
indexFoundListSNP.add(i);
}
}
// For SNP6.0, there are half SNP probes and half CN probes
if (probeSetType[i] == FusionGeneChipProbeSetType.CopyNumberProbeSetType) {
if (copyNumber[i] > 1E-10 && copyNumber[i] <= 30) {
isOutlier[i] = false;
indexFoundList.add(i);
}
}
}
}
/* Median filtering on the intensity data before calculating the copy numbers*/
// Filters f1 = new Filters(intensityNormal);
// f1.medianFilter(3);
// Filters f2 = new Filters(intensityTumor);
// f2.medianFilter(3);
// for (int j = 0; j < indexFoundList.size(); j ++) {
// int i = indexFoundList.get(j);
// copyNumber[i] = intensityTumor[i] / intensityNormal[i] * 2;
// if (!(copyNumber[i] > 1E-10 && copyNumber[i] <=30)) {
// copyNumber[i] = 2.0;
// isOutlier[i] = true;
// }
// }
globalNormalization(indexFoundList, indexFoundListSNP);
}
/**
* @param args
* @throws IOException
*/
public static void main(String[] args) throws IOException {
if (args.length == 1) {
Configuration.parseConfigurationFile(args[0]);
} else {
Configuration.parseConfigurationFile(
"/scratch/weale/data/config/enwiki/CreateTitleWordMapping.xml");
}
System.out.println("Creating File: link-" + Configuration.stemming);
System.out.println("Initializing Valid ID List.");
String vidFileName =
Configuration.baseDir
+ "/"
+ Configuration.binaryDir
+ "/"
+ Configuration.type
+ "/"
+ Configuration.date
+ "/"
+ Configuration.type
+ "-"
+ Configuration.date
+ "-"
+ Configuration.graph
+ ".vid";
IDVertexTranslation vid = null;
try {
ObjectInputStream oos = new ObjectInputStream(new FileInputStream(vidFileName));
vid = (IDVertexTranslation) oos.readObject();
oos.close();
} catch (Exception e) {
System.err.println("Problem with file:" + vidFileName);
e.printStackTrace();
System.exit(1);
}
System.out.println("Initializing Redirect List.");
IDIDRedirect rdl = null;
String rdlFileName =
Configuration.baseDir
+ "/"
+ Configuration.binaryDir
+ "/"
+ Configuration.type
+ "/"
+ Configuration.date
+ "/"
+ Configuration.type
+ "-"
+ Configuration.date
+ "-"
+ Configuration.graph
+ ".rdr";
try {
ObjectInputStream oos = new ObjectInputStream(new FileInputStream(rdlFileName));
rdl = (IDIDRedirect) oos.readObject();
oos.close();
} // end: try{}
catch (Exception e) {
System.err.println("Problem with file:" + rdlFileName);
e.printStackTrace();
System.exit(1);
}
String csvFile =
Configuration.baseDir
+ "/"
+ Configuration.sourceDir
+ "/"
+ Configuration.type
+ "/"
+ Configuration.date
+ "/"
+ "anchor.csv";
System.out.println("Opening .csv File");
Scanner in = new Scanner(new FileReader(csvFile));
// Set stem flag
stem = Configuration.stemming.equals("t");
/* STEP 1
*
* Create the word set in order to know how many terms
* are in our initial file.
*/
System.out.println("Creating Term Array");
TreeSet<String> ts = new TreeSet<String>();
while (in.hasNext()) {
String s = in.nextLine();
int lastComma = s.lastIndexOf(',');
int secondLastComma = s.substring(0, lastComma - 1).lastIndexOf(',');
String term = s.substring(1, secondLastComma - 1);
term = term.toLowerCase();
int count = Integer.parseInt(s.substring(lastComma + 1));
int id = Integer.parseInt(s.substring(secondLastComma + 1, lastComma));
// Check for valid ID
int vertex = -1;
if (vid.isValidWikiID(id)) {
vertex = vid.getVertex(id);
} else if (rdl.isRedirectID(id)) {
vertex = vid.getVertex(rdl.redirectIDToValidID(id));
}
// Valid ID. Add term.
if (vertex >= 0) {
if (stem) {
ts.add(PorterStemmerTokenizerFactory.stem(term));
} else {
ts.add(term);
}
}
} // end: while(in)
in.close();
System.out.println(ts.size());
/* STEP 2
*
* Create the TermToVertexCount array of the appropriate size
* and initialize objects.
*
* We use arrays for space efficiency -- these can get large.
*/
int valid = 0;
TermToVertexCount[] terms = new TermToVertexCount[ts.size()];
Iterator<String> set = ts.iterator();
int i = 0;
while (set.hasNext()) {
terms[i] = new TermToVertexCount(set.next());
i++;
} // end: while(set)
Arrays.sort(terms, new TermToVertexCountComparator());
ts = null; // Free Up Memory (?)
in = new Scanner(new FileReader(csvFile));
while (in.hasNext()) {
String s = in.nextLine();
int lastComma = s.lastIndexOf(',');
int secondLastComma = s.substring(0, lastComma - 1).lastIndexOf(',');
String term = s.substring(1, secondLastComma - 1);
term = term.toLowerCase();
int count = Integer.parseInt(s.substring(lastComma + 1));
int id = Integer.parseInt(s.substring(secondLastComma + 1, lastComma));
// Check for valid ID
int vertex = -1;
if (vid.isValidWikiID(id)) {
vertex = vid.getVertex(id);
} else if (rdl.isRedirectID(id)) {
vertex = vid.getVertex(rdl.redirectIDToValidID(id));
}
// Valid ID. Add term.
if (vertex >= 0) {
valid++;
if (stem) {
term = PorterStemmerTokenizerFactory.stem(term);
}
int pos =
Arrays.binarySearch(
terms, new TermToVertexCount(term), new TermToVertexCountComparator());
if (pos >= 0) {
terms[pos].addVertex(vertex, count);
} else {
System.err.println("Invalid Term Found: " + term);
}
} // end: if(vertex)
} // end: while(in)
/* STEP 4
*
* Write objects to the .tvc file
*/
System.out.println("Writing Mappings To File");
TermToVertexMapping tvm = new TermToVertexMapping(terms);
ObjectOutputStream out =
new ObjectOutputStream(
new FileOutputStream(
Configuration.baseDir
+ "/"
+ Configuration.binaryDir
+ "/"
+ Configuration.type
+ "/"
+ Configuration.date
+ "/"
+ Configuration.type
+ "-"
+ Configuration.date
+ "-"
+ Configuration.graph
+ "-"
+ "link-"
+ Configuration.stemming
+ ".tvc"));
out.writeObject(tvm);
out.close();
terms = null; // Free Up Memory (?)
/* STEP 5
*
* Create the vertex set in order to know how many verticies
* are in our initial file.
*/
in = new Scanner(new FileReader(csvFile));
System.out.println("Creating Integer Array");
TreeSet<Integer> vertexSet = new TreeSet<Integer>();
while (in.hasNext()) {
String s = in.nextLine();
int lastComma = s.lastIndexOf(',');
int secondLastComma = s.substring(0, lastComma - 1).lastIndexOf(',');
String term = s.substring(1, secondLastComma - 1);
int count = Integer.parseInt(s.substring(lastComma + 1));
int id = Integer.parseInt(s.substring(secondLastComma + 1, lastComma));
// Check for valid ID
int vertex = -1;
if (vid.isValidWikiID(id)) {
vertex = vid.getVertex(id);
} else if (rdl.isRedirectID(id)) {
vertex = vid.getVertex(rdl.redirectIDToValidID(id));
}
// Valid ID. Add term.
if (vertex >= 0) {
vertexSet.add(vertex);
}
}
/* STEP 6
*
* Create the VertexToTermCount array of the appropriate size
* and initialize objects.
*
* We use arrays for space efficiency -- these can get large.
*/
VertexToTermCount[] verticies = new VertexToTermCount[vertexSet.size()];
Iterator<Integer> it = vertexSet.iterator();
i = 0;
while (it.hasNext()) {
verticies[i] = new VertexToTermCount(it.next());
i++;
} // end: while(set)
Arrays.sort(verticies, new VertexToTermCountComparator());
vertexSet = null; // Free Up Memory (?)
in.close();
/* STEP 7
*
* Add terms to our VertexToTermCount objects.
*/
System.out.println("Creating Term Mappings");
in = new Scanner(new FileReader(csvFile));
while (in.hasNext()) {
String s = in.nextLine();
int lastComma = s.lastIndexOf(',');
int secondLastComma = s.substring(0, lastComma - 1).lastIndexOf(',');
String term = s.substring(1, secondLastComma - 1);
term = term.toLowerCase();
int count = Integer.parseInt(s.substring(lastComma + 1));
int id = Integer.parseInt(s.substring(secondLastComma + 1, lastComma));
// Check for valid ID
int vertex = -1;
if (vid.isValidWikiID(id)) {
vertex = vid.getVertex(id);
} else if (rdl.isRedirectID(id)) {
vertex = vid.getVertex(rdl.redirectIDToValidID(id));
}
// Valid ID. Add term.
if (vertex >= 0) {
int pos =
Arrays.binarySearch(
verticies, new VertexToTermCount(vertex), new VertexToTermCountComparator());
if (pos >= 0) {
verticies[pos].addTerm(term, count);
} else {
System.err.println("Invalid vertex Found: " + vertex);
}
}
} // end: while(true)
in.close();
/* STEP 8
*
* Write objects to the .vtc file
*/
System.out.println("Writing Mappings to File");
VertexToTermMapping vwm = new VertexToTermMapping(verticies);
out =
new ObjectOutputStream(
new FileOutputStream(
Configuration.baseDir
+ "/"
+ Configuration.binaryDir
+ "/"
+ Configuration.type
+ "/"
+ Configuration.date
+ "/"
+ Configuration.type
+ "-"
+ Configuration.date
+ "-"
+ Configuration.graph
+ "-"
+ "link-"
+ Configuration.stemming
+ ".vtc"));
out.writeObject(vwm);
out.close();
verticies = null; // Free Up Memory (?)
} // end: main()
public final void setNode(int fold, ClusNode node) {
int idx = Arrays.binarySearch(m_Folds, fold);
m_Nodes[idx] = node;
}