public String toString() {
StringBuilder out = new StringBuilder();
Formatter formatter = new Formatter(out, Locale.US);
for (int topic = 0; topic < numTopics; topic++) {
formatter.format("Topic %d", topic);
for (TopicScores scores : diagnostics) {
formatter.format("\t%s=%.4f", scores.name, scores.scores[topic]);
}
formatter.format("\n");
for (int position = 0; position < topicTopWords[topic].length; position++) {
if (topicTopWords[topic][position] == null) {
break;
}
formatter.format(" %s", topicTopWords[topic][position]);
for (TopicScores scores : diagnostics) {
if (scores.wordScoresDefined) {
formatter.format("\t%s=%.4f", scores.name, scores.topicWordScores[topic][position]);
}
}
out.append("\n");
}
}
return out.toString();
}
private boolean filterTinv(
Grib2Record gr, FeatureCollectionConfig.GribIntvFilter intvFilter, Formatter f) {
int[] intv = tables.getForecastTimeIntervalOffset(gr);
if (intv == null) return false;
int haveLength = intv[1] - intv[0];
// HACK
if (haveLength == 0 && intvFilter.isZeroExcluded()) { // discard 0,0
if ((intv[0] == 0) && (intv[1] == 0)) {
f.format(" FILTER INTV [0, 0] %s%n", gr);
return true;
}
return false;
} else if (intvFilter.hasMap()) {
int discipline = gr.getIs().getDiscipline();
int category = gr.getPDS().getParameterCategory();
int number = gr.getPDS().getParameterNumber();
int id = (discipline << 16) + (category << 8) + number;
Integer needLength = intvFilter.getLengthById(id);
if (needLength != null && needLength != haveLength) {
f.format(" FILTER INTV [%d != %d] %s%n", haveLength, needLength, gr);
return true;
}
}
return false;
}
/**
* Returns a string describing a method declaration. It contains the access flags (public,
* private, static, etc), the return type, the method name, and the types of each of its
* arguments.
*/
public static String get_method_declaration(Method m) {
StringBuilder sb = new StringBuilder();
Formatter f = new Formatter(sb);
f.format("%s %s %s (", get_access_flags(m), m.getReturnType(), m.getName());
for (Type at : m.getArgumentTypes()) {
f.format("%s, ", at);
}
f.format(")");
return (sb.toString().replace(", )", ")"));
}
public TestFile writelns(Iterable<String> lines) {
Formatter formatter = new Formatter();
for (String line : lines) {
formatter.format("%s%n", line);
}
return write(formatter);
}
@Override
protected void printDocumentResults(Results results) {
printSeparator();
Formatter formatter = new Formatter(System.out, Locale.US);
formatter.format(" | Total: |");
results.printResults(formatter);
}
private void setExecutablePermissions(File gradleHome) {
if (isWindows()) {
return;
}
File gradleCommand = new File(gradleHome, "bin/gradle");
String errorMessage = null;
try {
ProcessBuilder pb = new ProcessBuilder("chmod", "755", gradleCommand.getCanonicalPath());
Process p = pb.start();
if (p.waitFor() == 0) {
System.out.println("Set executable permissions for: " + gradleCommand.getAbsolutePath());
} else {
BufferedReader is = new BufferedReader(new InputStreamReader(p.getInputStream()));
Formatter stdout = new Formatter();
String line;
while ((line = is.readLine()) != null) {
stdout.format("%s%n", line);
}
errorMessage = stdout.toString();
}
} catch (IOException e) {
errorMessage = e.getMessage();
} catch (InterruptedException e) {
errorMessage = e.getMessage();
}
if (errorMessage != null) {
System.out.println(
"Could not set executable permissions for: " + gradleCommand.getAbsolutePath());
System.out.println("Please do this manually if you want to use the Gradle UI.");
}
}
@Override
public void getDetailInfo(Formatter f) {
super.getDetailInfo(f);
if (runMatcher != null) f.format(" runMatcher=%s%n", runMatcher);
/* if (forecastMatcher != null)
f.format(" forecastMatcher=%s%n", forecastMatcher);
if (offsetMatcher != null)
f.format(" offsetMatcher=%s%n", offsetMatcher); */
}
private boolean createIndex(File indexFile, CollectionManager.Force ff, Formatter f)
throws IOException {
long start = System.currentTimeMillis();
ArrayList<String> filenames = new ArrayList<String>();
List<Group> groups = makeAggregatedGroups(filenames, ff, f);
createIndex(indexFile, groups, filenames, f);
long took = System.currentTimeMillis() - start;
f.format("That took %d msecs%n", took);
return true;
}
/**
* Constructor.
*
* @param ncfile the netccdf file
* @param typedDataVariables list of data variables; all record variables will be added to this
* list, except . You can remove extra
* @param obsTimeVName observation time variable name (required)
* @param nomTimeVName nominal time variable name (may be null)
* @throws IllegalArgumentException if ncfile has no unlimited dimension and recDimName is null.
*/
public RecordDatasetHelper(
NetcdfDataset ncfile,
String obsTimeVName,
String nomTimeVName,
List<VariableSimpleIF> typedDataVariables,
String recDimName,
Formatter errBuffer) {
this.ncfile = ncfile;
this.obsTimeVName = obsTimeVName;
this.nomTimeVName = nomTimeVName;
this.errs = errBuffer;
// check if we already have a structure vs if we have to add it.
if (this.ncfile.hasUnlimitedDimension()) {
this.ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);
this.recordVar = (StructureDS) this.ncfile.getRootGroup().findVariable("record");
this.obsDim = ncfile.getUnlimitedDimension();
} else {
if (recDimName == null)
throw new IllegalArgumentException(
"File <"
+ this.ncfile.getLocation()
+ "> has no unlimited dimension, specify psuedo record dimension with observationDimension global attribute.");
this.obsDim = this.ncfile.getRootGroup().findDimension(recDimName);
this.recordVar = new StructurePseudoDS(this.ncfile, null, "record", null, obsDim);
}
// create member variables
List<Variable> recordMembers = ncfile.getVariables();
for (Variable v : recordMembers) {
if (v == recordVar) continue;
if (v.isScalar()) continue;
if (v.getDimension(0) == this.obsDim) typedDataVariables.add(v);
}
// need the time units
Variable timeVar = ncfile.findVariable(obsTimeVName);
String timeUnitString =
ncfile.findAttValueIgnoreCase(timeVar, CDM.UNITS, "seconds since 1970-01-01");
try {
timeUnit = new DateUnit(timeUnitString);
} catch (Exception e) {
if (null != errs) errs.format("Error on string = %s == %s%n", timeUnitString, e.getMessage());
try {
timeUnit = new DateUnit("seconds since 1970-01-01");
} catch (Exception e1) {
// cant happen
}
}
}
/**
* Prints a usage message to the given stream.
*
* @param out The output stream to write to.
*/
public void printUsage(Appendable out) {
Formatter formatter = new Formatter(out);
Set<CommandLineOption> orderedOptions = new TreeSet<CommandLineOption>(new OptionComparator());
orderedOptions.addAll(optionsByString.values());
Map<String, String> lines = new LinkedHashMap<String, String>();
for (CommandLineOption option : orderedOptions) {
Set<String> orderedOptionStrings = new TreeSet<String>(new OptionStringComparator());
orderedOptionStrings.addAll(option.getOptions());
List<String> prefixedStrings = new ArrayList<String>();
for (String optionString : orderedOptionStrings) {
if (optionString.length() == 1) {
prefixedStrings.add("-" + optionString);
} else {
prefixedStrings.add("--" + optionString);
}
}
String key = join(prefixedStrings, ", ");
String value = option.getDescription();
if (value == null || value.length() == 0) {
value = "";
}
lines.put(key, value);
}
int max = 0;
for (String optionStr : lines.keySet()) {
max = Math.max(max, optionStr.length());
}
for (Map.Entry<String, String> entry : lines.entrySet()) {
if (entry.getValue().length() == 0) {
formatter.format("%s%n", entry.getKey());
} else {
formatter.format("%-" + max + "s %s%n", entry.getKey(), entry.getValue());
}
}
formatter.flush();
}
// single file
private Grib2CollectionBuilder(File file, Formatter f) throws IOException {
try {
// String spec = StringUtil2.substitute(file.getPath(), "\\", "/");
CollectionManager dcm = new DatasetCollectionSingleFile(file);
this.collections.add(dcm);
this.gc = new Grib2Collection(file.getName(), new File(dcm.getRoot()));
} catch (Exception e) {
ByteArrayOutputStream bos = new ByteArrayOutputStream(10000);
e.printStackTrace(new PrintStream(bos));
f.format("%s", bos.toString());
throw new IOException(e);
}
}
@Override
public String augmentSetup(String setup, String alias, Map<String, String> parameters)
throws Exception {
Formatter f = new Formatter();
f.format("%s", setup);
try {
f.format("\n#\n# Change disk layout to fit maven\n#\n\n");
f.format("-outputmask = ${@bsn}-${version;===S;${@version}}.jar\n");
f.format("src=src/main/java\n");
f.format("bin=target/classes\n");
f.format("testsrc=src/test/java\n");
f.format("testbin=target/test-classes\n");
f.format("target-dir=target\n");
return f.toString();
} finally {
f.close();
}
}
public void setLocationInfo(String latVName, String lonVName, String zcoordVName) {
this.latVName = latVName;
this.lonVName = lonVName;
this.zcoordVName = zcoordVName;
// check for meter conversion
if (zcoordVName != null) {
Variable v = ncfile.findVariable(zcoordVName);
zcoordUnits = ncfile.findAttValueIgnoreCase(v, CDM.UNITS, null);
if (zcoordUnits != null)
try {
altScaleFactor = getMetersConversionFactor(zcoordUnits);
} catch (Exception e) {
if (errs != null) errs.format("%s", e.getMessage());
}
}
}
// single file
private Grib2CollectionBuilder(MFile file, FeatureCollectionConfig.GribConfig config, Formatter f)
throws IOException {
this.isSingleFile = true;
try {
// String spec = StringUtil2.substitute(file.getPath(), "\\", "/");
CollectionManager dcm = new CollectionManagerSingleFile(file);
if (config != null) dcm.putAuxInfo(FeatureCollectionConfig.AUX_GRIB_CONFIG, config);
this.collections.add(dcm);
this.gc = new Grib2Collection(file.getName(), new File(dcm.getRoot()), config);
} catch (Exception e) {
ByteArrayOutputStream bos = new ByteArrayOutputStream(10000);
e.printStackTrace(new PrintStream(bos));
f.format("%s", bos.toString());
throw new IOException(e);
}
}
private String listSupportFiles(List<File> toDelete) throws Exception {
Formatter f = new Formatter();
try {
if (toDelete == null) {
toDelete = new ArrayList<File>();
}
int precount = toDelete.size();
File confFile = IO.getFile(platform.getConfigFile()).getCanonicalFile();
if (confFile.exists()) {
f.format(" * %s \t0 Config file%n", confFile);
toDelete.add(confFile);
}
String result = (toDelete.size() > precount) ? f.toString() : null;
return result;
} finally {
f.close();
}
}
public void saveFile() {
try {
cardFormatter = new Formatter(currentFile);
} catch (Exception e) {
System.out.print("That File doesn't exist");
}
cardFormatter.format("%s%n", currentPlayer.getName());
cardFormatter.format("%d%n", currentPlayer.getTotalCardsOwned());
cardFormatter.format("%d%n", currentPlayer.getNumberOfCardsInDeck());
cardFormatter.format("%d%n", currentPlayer.getWins());
cardFormatter.format("%d%n", currentPlayer.getLosses());
cardFormatter.format("%d%n", currentPlayer.getMoney());
Card[] deck = currentPlayer.getDeck();
for (int count = 0; count < deck.length; count++) {
cardFormatter.format("%d%n", deck[count].getCardIndex());
cardFormatter.format("%b%n", deck[count].getInDeck());
}
cardFormatter.close();
}
private String listFiles(final File cache, List<File> toDelete) throws Exception {
boolean stopServices = false;
if (toDelete == null) {
toDelete = new ArrayList<File>();
} else {
stopServices = true;
}
int count = 0;
Formatter f = new Formatter();
f.format(" - Cache:%n * %s%n", cache.getCanonicalPath());
f.format(" - Commands:%n");
for (CommandData cdata : getCommands(new File(cache, COMMANDS))) {
f.format(" * %s \t0 handle for \"%s\"%n", cdata.bin, cdata.name);
toDelete.add(new File(cdata.bin));
count++;
}
f.format(" - Services:%n");
for (ServiceData sdata : getServices(new File(cache, SERVICE))) {
if (sdata != null) {
f.format(" * %s \t0 service directory for \"%s\"%n", sdata.sdir, sdata.name);
toDelete.add(new File(sdata.sdir));
File initd = platform.getInitd(sdata);
if (initd != null && initd.exists()) {
f.format(" * %s \t0 init.d file for \"%s\"%n", initd.getCanonicalPath(), sdata.name);
toDelete.add(initd);
}
if (stopServices) {
Service s = getService(sdata);
try {
s.stop();
} catch (Exception e) {
}
}
count++;
}
}
f.format("%n");
String result = (count > 0) ? f.toString() : null;
f.close();
return result;
}
private static void test(Locale l, String fs, String exp, Object... args) {
Formatter f = new Formatter(new StringBuilder(), l);
f.format(fs, args);
ck(fs, exp, f.toString());
}
public String toXML() {
int[] tokensPerTopic = model.tokensPerTopic;
StringBuilder out = new StringBuilder();
Formatter formatter = new Formatter(out, Locale.US);
out.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
out.append("<model>\n");
for (int topic = 0; topic < numTopics; topic++) {
int[][] matrix = topicCodocumentMatrices[topic];
formatter.format("<topic id='%d'", topic);
for (TopicScores scores : diagnostics) {
formatter.format(" %s='%.4f'", scores.name, scores.scores[topic]);
}
out.append(">\n");
TreeSet<IDSorter> sortedWords = topicSortedWords.get(topic);
// How many words should we report? Some topics may have fewer than
// the default number of words with non-zero weight.
int limit = numTopWords;
if (sortedWords.size() < numTopWords) {
limit = sortedWords.size();
}
double cumulativeProbability = 0.0;
Iterator<IDSorter> iterator = sortedWords.iterator();
for (int position = 0; position < limit; position++) {
IDSorter info = iterator.next();
double probability = info.getWeight() / tokensPerTopic[topic];
cumulativeProbability += probability;
formatter.format(
"<word rank='%d' count='%.0f' prob='%.5f' cumulative='%.5f' docs='%d'",
position + 1,
info.getWeight(),
probability,
cumulativeProbability,
matrix[position][position]);
for (TopicScores scores : diagnostics) {
if (scores.wordScoresDefined) {
formatter.format(" %s='%.4f'", scores.name, scores.topicWordScores[topic][position]);
}
}
formatter.format(
">%s</word>\n",
topicTopWords[topic][position].replaceAll("&", "&").replaceAll("<", ">"));
}
out.append("</topic>\n");
}
out.append("</model>\n");
return out.toString();
}
// read all records in all files,
// divide into groups based on GDS hash
// each group has an arraylist of all records that belong to it.
// for each group, run rectlizer to derive the coordinates and variables
public List<Group> makeAggregatedGroups(
ArrayList<String> filenames, CollectionManager.Force force, Formatter f) throws IOException {
Map<Integer, Group> gdsMap = new HashMap<Integer, Group>();
f.format("GribCollection %s: makeAggregatedGroups%n", gc.getName());
int total = 0;
int fileno = 0;
for (CollectionManager dcm : collections) {
// dcm.scanIfNeeded(); // LOOK ??
f.format(" dcm= %s%n", dcm);
Map<Integer, Integer> gdsConvert = (Map<Integer, Integer>) dcm.getAuxInfo("gdsHash");
for (MFile mfile : dcm.getFiles()) {
// f.format("%3d: %s%n", fileno, mfile.getPath());
filenames.add(mfile.getPath());
Grib2Index index = new Grib2Index();
try {
if (!index.readIndex(
mfile.getPath(),
mfile.getLastModified(),
force)) { // heres where the index date is checked against the data file
index.makeIndex(mfile.getPath(), f);
f.format(
" Index written: %s == %d records %n",
mfile.getName() + Grib2Index.IDX_EXT, index.getRecords().size());
} else if (debug) {
f.format(
" Index read: %s == %d records %n",
mfile.getName() + Grib2Index.IDX_EXT, index.getRecords().size());
}
} catch (IOException ioe) {
f.format(
"GribCollectionBuilder: reading/Creating gbx9 index failed err=%s%n skipping %s%n",
ioe.getMessage(), mfile.getPath() + Grib2Index.IDX_EXT);
continue;
}
for (Grib2Record gr : index.getRecords()) {
gr.setFile(fileno); // each record tracks which file it belongs to
int gdsHash =
gr.getGDSsection().getGDS().hashCode(); // use GDS hash code to group records
if (gdsConvert != null
&& gdsConvert.get(gdsHash)
!= null) { // allow external config to muck with gdsHash. Why? because of error in
// encoding
gdsHash = (Integer) gdsConvert.get(gdsHash); // and we need exact hash matching
}
Group g = gdsMap.get(gdsHash);
if (g == null) {
g = new Group(gr.getGDSsection(), gdsHash);
gdsMap.put(gdsHash, g);
}
g.records.add(gr);
total++;
}
fileno++;
}
}
f.format(" total grib records= %d%n", total);
Grib2Rectilyser.Counter c = new Grib2Rectilyser.Counter();
List<Group> result = new ArrayList<Group>(gdsMap.values());
for (Group g : result) {
g.rect = new Grib2Rectilyser(g.records, g.gdsHash);
f.format(" GDS hash %d == ", g.gdsHash);
g.rect.make(f, c);
}
f.format(
" Rectilyser: nvars=%d records unique=%d total=%d dups=%d (%f) %n",
c.vars, c.recordsUnique, c.records, c.dups, ((float) c.dups) / c.records);
return result;
}
private void createIndex(
File indexFile, List<Group> groups, ArrayList<String> filenames, Formatter f)
throws IOException {
Grib2Record first = null; // take global metadata from here
if (indexFile.exists()) indexFile.delete(); // replace it
f.format(" createIndex for %s%n", indexFile.getPath());
RandomAccessFile raf = new RandomAccessFile(indexFile.getPath(), "rw");
raf.order(RandomAccessFile.BIG_ENDIAN);
try {
//// header message
raf.write(MAGIC_START.getBytes("UTF-8"));
raf.writeInt(version);
long lenPos = raf.getFilePointer();
raf.writeLong(0); // save space to write the length of the record section
long countBytes = 0;
int countRecords = 0;
for (Group g : groups) {
g.fileSet = new HashSet<Integer>();
for (Grib2Rectilyser.VariableBag vb : g.rect.getGribvars()) {
if (first == null) first = vb.first;
GribCollectionProto.VariableRecords vr = writeRecordsProto(vb, g.fileSet);
byte[] b = vr.toByteArray();
vb.pos = raf.getFilePointer();
vb.length = b.length;
raf.write(b);
countBytes += b.length;
countRecords += vb.recordMap.length;
}
}
long bytesPerRecord = countBytes / ((countRecords == 0) ? 1 : countRecords);
f.format(
" write RecordMaps: bytes = %d record = %d bytesPerRecord=%d%n",
countBytes, countRecords, bytesPerRecord);
if (first == null) {
logger.error("GribCollection {}: has no files\n{}", gc.getName(), f.toString());
throw new IllegalArgumentException("GribCollection " + gc.getName() + " has no files");
}
long pos = raf.getFilePointer();
raf.seek(lenPos);
raf.writeLong(countBytes);
raf.seek(pos); // back to the output.
GribCollectionProto.GribCollectionIndex.Builder indexBuilder =
GribCollectionProto.GribCollectionIndex.newBuilder();
indexBuilder.setName(gc.getName());
for (String fn : filenames) indexBuilder.addFiles(fn);
for (Group g : groups) indexBuilder.addGroups(writeGroupProto(g));
/* int count = 0;
for (DatasetCollectionManager dcm : collections) {
indexBuilder.addParams(makeParamProto(new Parameter("spec" + count, dcm.())));
count++;
} */
// what about just storing first ??
Grib2SectionIdentification ids = first.getId();
indexBuilder.setCenter(ids.getCenter_id());
indexBuilder.setSubcenter(ids.getSubcenter_id());
indexBuilder.setMaster(ids.getMaster_table_version());
indexBuilder.setLocal(ids.getLocal_table_version());
Grib2Pds pds = first.getPDS();
indexBuilder.setGenProcessType(pds.getGenProcessType());
indexBuilder.setGenProcessId(pds.getGenProcessId());
indexBuilder.setBackProcessId(pds.getBackProcessId());
GribCollectionProto.GribCollectionIndex index = indexBuilder.build();
byte[] b = index.toByteArray();
NcStream.writeVInt(raf, b.length); // message size
raf.write(b); // message - all in one gulp
f.format(" write GribCollectionIndex= %d bytes%n", b.length);
} finally {
f.format(" file size = %d bytes%n", raf.length());
raf.close();
if (raf != null) raf.close();
}
}
protected void printItemResults(int pageIndex, Results results) {
Formatter formatter = new Formatter(System.out, Locale.US);
formatter.format(" | %8d |", pageIndex + 1);
results.printResults(formatter);
}
public void printResults(Formatter formatter) {
zoneLevel.printResults(formatter);
lineLevel.printResults(formatter);
wordLevel.printResults(formatter);
formatter.format("%n");
}
public String what(String key, boolean oneliner) throws Exception {
byte[] sha;
Matcher m = SHA_P.matcher(key);
if (m.matches()) {
sha = Hex.toByteArray(key);
} else {
m = URL_P.matcher(key);
if (m.matches()) {
URL url = new URL(key);
sha = SHA1.digest(url.openStream()).digest();
} else {
File jarfile = new File(key);
if (!jarfile.exists()) {
reporter.error("File does not exist: %s", jarfile.getCanonicalPath());
}
sha = SHA1.digest(jarfile).digest();
}
}
reporter.trace("sha %s", Hex.toHexString(sha));
Revision revision = library.getRevision(sha);
if (revision == null) {
return null;
}
StringBuilder sb = new StringBuilder();
Formatter f = new Formatter(sb);
Justif justif = new Justif(120, 20, 70, 20, 75);
DateFormat dateFormat = DateFormat.getDateInstance();
try {
if (oneliner) {
f.format("%20s %s%n", Hex.toHexString(revision._id), createCoord(revision));
} else {
f.format("Artifact: %s%n", revision.artifactId);
if (revision.organization != null && revision.organization.name != null) {
f.format(" (%s)", revision.organization.name);
}
f.format("%n");
f.format("Coordinates\t0: %s%n", createCoord(revision));
f.format("Created\t0: %s%n", dateFormat.format(new Date(revision.created)));
f.format("Size\t0: %d%n", revision.size);
f.format("Sha\t0: %s%n", Hex.toHexString(revision._id));
f.format("URL\t0: %s%n", createJpmLink(revision));
f.format("%n");
f.format("%s%n", revision.description);
f.format("%n");
f.format("Dependencies\t0:%n");
boolean flag = false;
Iterable<RevisionRef> closure = library.getClosure(revision._id, true);
for (RevisionRef dep : closure) {
f.format(
" - %s \t2- %s \t3- %s%n",
dep.name, createCoord(dep), dateFormat.format(new Date(dep.created)));
flag = true;
}
if (!flag) {
f.format(" None%n");
}
f.format("%n");
}
f.flush();
justif.wrap(sb);
return sb.toString();
} finally {
f.close();
}
}
public void deinit(Appendable out, boolean force) throws Exception {
Settings settings = new Settings(platform.getConfigFile());
if (!force) {
Justif justify = new Justif(80, 40);
StringBuilder sb = new StringBuilder();
Formatter f = new Formatter(sb);
try {
String list = listFiles(platform.getGlobal());
if (list != null) {
f.format("In global default environment:%n");
f.format(list);
}
list = listFiles(platform.getLocal());
if (list != null) {
f.format("In local default environment:%n");
f.format(list);
}
if (settings.containsKey(JPM_CACHE_GLOBAL)) {
list = listFiles(IO.getFile(settings.get(JPM_CACHE_GLOBAL)));
if (list != null) {
f.format("In global configured environment:%n");
f.format(list);
}
}
if (settings.containsKey(JPM_CACHE_LOCAL)) {
list = listFiles(IO.getFile(settings.get(JPM_CACHE_LOCAL)));
if (list != null) {
f.format("In local configured environment:%n");
f.format(list);
}
}
list = listSupportFiles();
if (list != null) {
f.format("jpm support files:%n");
f.format(list);
}
f.format("%n%n");
f.format(
"All files listed above will be deleted if deinit is run with the force flag set"
+ " (\"jpm deinit -f\" or \"jpm deinit --force\"%n%n");
f.flush();
justify.wrap(sb);
out.append(sb.toString());
} finally {
f.close();
}
} else { // i.e. if(force)
int count = 0;
File[] caches = {platform.getGlobal(), platform.getLocal(), null, null};
if (settings.containsKey(JPM_CACHE_LOCAL)) {
caches[2] = IO.getFile(settings.get(JPM_CACHE_LOCAL));
}
if (settings.containsKey(JPM_CACHE_GLOBAL)) {
caches[3] = IO.getFile(settings.get(JPM_CACHE_GLOBAL));
}
ArrayList<File> toDelete = new ArrayList<File>();
for (File cache : caches) {
if (cache == null || !cache.exists()) {
continue;
}
listFiles(cache, toDelete);
if (toDelete.size() > count) {
count = toDelete.size();
if (!cache.canWrite()) {
reporter.error(PERMISSION_ERROR + " (" + cache + ")");
return;
}
toDelete.add(cache);
}
}
listSupportFiles(toDelete);
for (File f : toDelete) {
if (f.exists() && !f.canWrite()) {
reporter.error(PERMISSION_ERROR + " (" + f + ")");
}
}
if (reporter.getErrors().size() > 0) {
return;
}
for (File f : toDelete) {
if (f.exists()) {
IO.deleteWithException(f);
}
}
}
}
public void printResults(Formatter formatter) {
formatter.format(" %8d %8d %7.2f%% |", all, matched, getScore() * 100);
}
public void printSummary(Formatter formatter) {
formatter.format(" * all : %8d%n", all);
formatter.format(" * matched : %8d%n", matched);
formatter.format(" * score : %7.2f%%%n", getScore() * 100);
}
private static void test(String fs) {
Formatter f = new Formatter(new StringBuilder(), Locale.US);
f.format(fs, "fail");
ck(fs, "fail", f.toString());
}
public void addRecord() {
System.out.println("Adding record ... ");
f.format("%s%s%s%s", "Author: ", "Melvin ", "Kong ", "Cabatuan");
}
private void run(String[] argv) throws IOException {
int i, index;
BufferedReader fp = null, fp_restore = null;
String save_filename = null;
String restore_filename = null;
String data_filename = null;
for (i = 0; i < argv.length; i++) {
if (argv[i].charAt(0) != '-') break;
++i;
switch (argv[i - 1].charAt(1)) {
case 'l':
lower = Double.parseDouble(argv[i]);
break;
case 'u':
upper = Double.parseDouble(argv[i]);
break;
case 'y':
y_lower = Double.parseDouble(argv[i]);
++i;
y_upper = Double.parseDouble(argv[i]);
y_scaling = true;
break;
case 's':
save_filename = argv[i];
break;
case 'r':
restore_filename = argv[i];
break;
default:
System.err.println("unknown option");
exit_with_help();
}
}
if (!(upper > lower) || (y_scaling && !(y_upper > y_lower))) {
System.err.println("inconsistent lower/upper specification");
System.exit(1);
}
if (restore_filename != null && save_filename != null) {
System.err.println("cannot use -r and -s simultaneously");
System.exit(1);
}
if (argv.length != i + 1) exit_with_help();
data_filename = argv[i];
try {
fp = new BufferedReader(new FileReader(data_filename));
} catch (Exception e) {
System.err.println("can't open file " + data_filename);
System.exit(1);
}
/* assumption: min index of attributes is 1 */
/* pass 1: find out max index of attributes */
max_index = 0;
if (restore_filename != null) {
int idx, c;
try {
fp_restore = new BufferedReader(new FileReader(restore_filename));
} catch (Exception e) {
System.err.println("can't open file " + restore_filename);
System.exit(1);
}
if ((c = fp_restore.read()) == 'y') {
fp_restore.readLine();
fp_restore.readLine();
fp_restore.readLine();
}
fp_restore.readLine();
fp_restore.readLine();
String restore_line = null;
while ((restore_line = fp_restore.readLine()) != null) {
StringTokenizer st2 = new StringTokenizer(restore_line);
idx = Integer.parseInt(st2.nextToken());
max_index = Math.max(max_index, idx);
}
fp_restore = rewind(fp_restore, restore_filename);
}
while (readline(fp) != null) {
StringTokenizer st = new StringTokenizer(line, " \t\n\r\f:");
System.out.println(line);
st.nextToken();
while (st.hasMoreTokens()) {
index = Integer.parseInt(st.nextToken());
max_index = Math.max(max_index, index);
st.nextToken();
num_nonzeros++;
}
}
try {
feature_max = new double[(max_index + 1)];
feature_min = new double[(max_index + 1)];
} catch (OutOfMemoryError e) {
System.err.println("can't allocate enough memory");
System.exit(1);
}
for (i = 0; i <= max_index; i++) {
feature_max[i] = -Double.MAX_VALUE;
feature_min[i] = Double.MAX_VALUE;
}
fp = rewind(fp, data_filename);
/* pass 2: find out min/max value */
while (readline(fp) != null) {
int next_index = 1;
double target;
double value;
StringTokenizer st = new StringTokenizer(line, " \t\n\r\f:");
target = Double.parseDouble(st.nextToken());
y_max = Math.max(y_max, target);
y_min = Math.min(y_min, target);
while (st.hasMoreTokens()) {
index = Integer.parseInt(st.nextToken());
value = Double.parseDouble(st.nextToken());
for (i = next_index; i < index; i++) {
feature_max[i] = Math.max(feature_max[i], 0);
feature_min[i] = Math.min(feature_min[i], 0);
}
feature_max[index] = Math.max(feature_max[index], value);
feature_min[index] = Math.min(feature_min[index], value);
next_index = index + 1;
}
for (i = next_index; i <= max_index; i++) {
feature_max[i] = Math.max(feature_max[i], 0);
feature_min[i] = Math.min(feature_min[i], 0);
}
}
fp = rewind(fp, data_filename);
/* pass 2.5: save/restore feature_min/feature_max */
if (restore_filename != null) {
// fp_restore rewinded in finding max_index
int idx, c;
double fmin, fmax;
fp_restore.mark(2); // for reset
if ((c = fp_restore.read()) == 'y') {
fp_restore.readLine(); // pass the '\n' after 'y'
StringTokenizer st = new StringTokenizer(fp_restore.readLine());
y_lower = Double.parseDouble(st.nextToken());
y_upper = Double.parseDouble(st.nextToken());
st = new StringTokenizer(fp_restore.readLine());
y_min = Double.parseDouble(st.nextToken());
y_max = Double.parseDouble(st.nextToken());
y_scaling = true;
} else fp_restore.reset();
if (fp_restore.read() == 'x') {
fp_restore.readLine(); // pass the '\n' after 'x'
StringTokenizer st = new StringTokenizer(fp_restore.readLine());
lower = Double.parseDouble(st.nextToken());
upper = Double.parseDouble(st.nextToken());
String restore_line = null;
while ((restore_line = fp_restore.readLine()) != null) {
StringTokenizer st2 = new StringTokenizer(restore_line);
idx = Integer.parseInt(st2.nextToken());
fmin = Double.parseDouble(st2.nextToken());
fmax = Double.parseDouble(st2.nextToken());
if (idx <= max_index) {
feature_min[idx] = fmin;
feature_max[idx] = fmax;
}
}
}
fp_restore.close();
}
if (save_filename != null) {
Formatter formatter = new Formatter(new StringBuilder());
BufferedWriter fp_save = null;
try {
fp_save = new BufferedWriter(new FileWriter(save_filename));
} catch (IOException e) {
System.err.println("can't open file " + save_filename);
System.exit(1);
}
if (y_scaling) {
formatter.format("y\n");
formatter.format("%.16g %.16g\n", y_lower, y_upper);
formatter.format("%.16g %.16g\n", y_min, y_max);
}
formatter.format("x\n");
formatter.format("%.16g %.16g\n", lower, upper);
for (i = 1; i <= max_index; i++) {
if (feature_min[i] != feature_max[i])
formatter.format("%d %.16g %.16g\n", i, feature_min[i], feature_max[i]);
}
fp_save.write(formatter.toString());
fp_save.close();
}
/* pass 3: scale */
while (readline(fp) != null) {
int next_index = 1;
double target;
double value;
StringTokenizer st = new StringTokenizer(line, " \t\n\r\f:");
target = Double.parseDouble(st.nextToken());
output_target(target);
while (st.hasMoreElements()) {
index = Integer.parseInt(st.nextToken());
value = Double.parseDouble(st.nextToken());
for (i = next_index; i < index; i++) output(i, 0);
output(index, value);
next_index = index + 1;
}
for (i = next_index; i <= max_index; i++) output(i, 0);
System.out.print("\n");
}
if (new_num_nonzeros > num_nonzeros)
System.err.print(
"WARNING: original #nonzeros "
+ num_nonzeros
+ "\n"
+ " new #nonzeros "
+ new_num_nonzeros
+ "\n"
+ "Use -l 0 if many original feature values are zeros\n");
fp.close();
}