List of usage examples for java.io PrintWriter print
public void print(Object obj)
From source file:gov.nih.nci.caarray.application.translation.geosoft.GeoSoftFileWriterUtil.java
@SuppressWarnings("PMD.ExcessiveMethodLength") private static void writeSampleSection(Hybridization h, PrintWriter out) { final Set<Source> sources = new TreeSet<Source>(ENTITY_COMPARATOR); final Set<Sample> samples = new TreeSet<Sample>(ENTITY_COMPARATOR); final Set<Extract> extracts = new TreeSet<Extract>(ENTITY_COMPARATOR); final Set<LabeledExtract> labeledExtracts = new TreeSet<LabeledExtract>(ENTITY_COMPARATOR); GeoSoftFileWriterUtil.collectBioMaterials(h, sources, samples, extracts, labeledExtracts); out.print("^SAMPLE="); out.println(h.getName());/* w ww . j a va 2s . com*/ out.print("!Sample_title="); out.println(h.getName()); writeDescription(out, h, samples); writeData(h, out); writeSources(out, sources); writeOrganism(sources, samples, h.getExperiment(), out); final Set<ProtocolApplication> pas = new TreeSet<ProtocolApplication>(ENTITY_COMPARATOR); pas.addAll(h.getProtocolApplications()); collectAllProtocols(labeledExtracts, pas); collectAllProtocols(extracts, pas); collectAllProtocols(samples, pas); collectAllProtocols(sources, pas); writeProtocol(pas, "Sample_treatment_protocol", PREDICATE_TREATMENT, out); writeProtocol(pas, "Sample_growth_protocol", PREDICATE_GROWTH, out); writeProtocol(pas, "Sample_extract_protocol", PREDICATE_EXTRACT, out); writeProtocol(getAllProtocols(extracts), "Sample_label_protocol", PREDICATE_LABELING, out); writeProtocol(getAllProtocols(labeledExtracts), "Sample_hyb_protocol", PREDICATE_HYB, out); writeProtocol(h.getProtocolApplications(), "Sample_scan_protocol", PREDICATE_SCAN, out); writeProtocolsForData(h.getRawDataCollection(), "Sample_data_processing", out); for (final LabeledExtract labeledExtract : labeledExtracts) { out.print("!Sample_label="); out.println(labeledExtract.getLabel().getValue()); } writeProviders(sources, out); out.print("!Sample_platform_id="); out.println(h.getArray().getDesign().getGeoAccession()); final Set<String> uniqueEntries = new HashSet<String>(); for (final AbstractFactorValue fv : h.getFactorValues()) { writeCharacteristics(fv.getFactor().getName(), fv.getDisplayValue(), out, uniqueEntries); } writeCharacteristics(labeledExtracts, out, uniqueEntries); writeCharacteristics(extracts, out, uniqueEntries); writeCharacteristics(samples, out, uniqueEntries); writeCharacteristics(sources, out, uniqueEntries); writeMaterialTypes(extracts, labeledExtracts, out); }
From source file:it.greenvulcano.util.txt.TextUtils.java
/** * Writes a text String into a file/*w w w. ja v a 2 s .c o m*/ * * @param contentString * The String to be written into the file * @param file * The destination file * @param append * If true the data are appended to existent file * @throws IOException */ public static void writeFile(String contentString, File file, boolean append) throws IOException { PrintWriter out = null; try { out = new PrintWriter(new FileWriter(file, append)); out.print(contentString); out.flush(); } finally { if (out != null) { out.close(); } } }
From source file:mx.unam.ecologia.gye.coalescence.app.CreateSampleConfiguration.java
protected static final void writeSampleConfig(List leaves, String fname) { try {//from www . ja v a 2 s . co m FileOutputStream fout = new FileOutputStream(fname); PrintWriter pw = new PrintWriter(fout); HaplotypeFreqSet len1 = new HaplotypeFreqSet(new CompoundSequenceLengthComparator()); HaplotypeFreqSet len2 = new HaplotypeFreqSet(new CompoundSequenceLengthComparator()); HaplotypeFreqSet ident = new HaplotypeFreqSet(new CompoundSequenceIdentityComparator()); for (int i = 0; i < leaves.size(); i++) { UniParentalGene upgene = (UniParentalGene) leaves.get(i); CompoundSequence h = upgene.getCompoundSequence(); len1.add(h); ident.add(h); CompoundSequence cs = h.getCopy(); cs.setLocus(true); len2.add(cs); int numloc = h.getSequenceCount(); for (int n = 0; n < numloc; n++) { Sequence s = h.get(n); pw.print(s.toFullString()); pw.print(" "); } pw.println(); } //print length as locus pw.println(); pw.println("Haplotypes by Length (locus)"); pw.println(len2.toString()); pw.println("Haplotypes by Length (multilocus)"); pw.println(len1.toString()); pw.println("Haplotypes by Identity"); pw.println(ident.toFullString()); pw.println(); //System.out.println("TEST"); //ident.sort(new CSAncestryComparator()); //System.out.println(ident.toFullString()); //System.out.println(ident.findMostFrequent() + 1); pw.flush(); pw.close(); fout.close(); } catch (IOException ex) { CreateSampleConfiguration.log.error("writeSampleConfig()", ex); } }
From source file:com.adito.util.Utils.java
public static void printIndent(PrintWriter out, int indent) { out.print(indent(indent)); }
From source file:eu.pawelsz.apache.beam.coders.TupleCoderGenerator.java
private static void writeTupleCoderClass(PrintWriter w, int numFields) { final String tupleClass = "Tuple" + numFields; final String className = tupleClass + "Coder"; StringBuilder sb = new StringBuilder(); for (int i = 0; i < numFields; i++) { if (i > 0) { sb.append(", "); }//from ww w . j av a 2 s. co m sb.append(GEN_TYPE_PREFIX + i); } final String types = sb.toString(); final int maxIdx = numFields - 1; // head w.print(HEADER); // package and imports w.println("package " + PACKAGE + ';'); w.println(); w.println("import com.fasterxml.jackson.annotation.JsonCreator;"); w.println("import com.fasterxml.jackson.annotation.JsonProperty;"); w.println("import com.google.common.base.Preconditions;"); w.println("import org.apache.beam.sdk.coders.Coder;"); w.println("import org.apache.beam.sdk.coders.CoderException;"); w.println("import org.apache.beam.sdk.coders.StandardCoder;"); w.println("import org.apache.beam.sdk.util.PropertyNames;"); w.println("import org.apache.beam.sdk.util.common.ElementByteSizeObserver;"); w.println("import org.apache.flink.api.java.tuple." + tupleClass + ";"); w.println(""); w.println("import java.io.IOException;"); w.println("import java.io.InputStream;"); w.println("import java.io.OutputStream;"); w.println("import java.util.Arrays;"); w.println("import java.util.List;"); w.println(""); w.println("public class " + className + "<" + types + "> extends StandardCoder<" + tupleClass + "<" + types + ">> {"); w.println(); w.println(""); w.println(" public static <" + types + "> " + className + "<" + types + "> of("); for (int i = 0; i < numFields - 1; i++) { w.println(" Coder<" + GEN_TYPE_PREFIX + i + "> t" + i + ","); } w.println(" Coder<" + GEN_TYPE_PREFIX + maxIdx + "> t" + maxIdx + ") {"); w.print(" return new " + className + "<>("); for (int i = 0; i < numFields; i++) { if (i > 0) { w.print(", "); } w.print("t" + i); } w.println(");"); w.println(" }"); w.println(""); w.println(" @JsonCreator"); w.print(" public static " + className + "<"); for (int i = 0; i < numFields; i++) { if (i > 0) { w.print(", "); } w.print("?"); } w.println("> of("); w.println(" @JsonProperty(PropertyNames.COMPONENT_ENCODINGS)"); w.println(" List<Coder<?>> components) {"); w.println(" Preconditions.checkArgument(components.size() == " + numFields + ","); w.println(" \"Expecting " + numFields + " components, got\" + components.size());"); w.println(" return of("); for (int i = 0; i < numFields; i++) { if (i > 0) { w.println(","); } w.print(" components.get(" + i + ")"); } w.println(");"); w.println(" }"); w.println(""); w.println(" public static <" + types + "> List<Object> getInstanceComponents("); w.println(" " + tupleClass + "<" + types + "> exampleValue) {"); w.println(" return Arrays.asList("); for (int i = 0; i < numFields; i++) { if (i > 0) { w.println(","); } w.print(" exampleValue.f" + i); } w.println(");"); w.println(" }"); for (int i = 0; i < numFields; i++) { w.println(""); w.println(" public Coder<" + GEN_TYPE_PREFIX + i + "> getF" + i + "Coder() {"); w.println(" return t" + i + "Coder;"); w.println(" }"); } w.println(""); for (int i = 0; i < numFields; i++) { w.println(" private final Coder<" + GEN_TYPE_PREFIX + i + "> t" + i + "Coder;"); } w.println(""); w.println(" private " + className + "("); for (int i = 0; i < numFields; i++) { if (i > 0) { w.println(","); } w.print(" Coder<" + GEN_TYPE_PREFIX + i + "> t" + i + "Coder"); } w.println(") {"); for (int i = 0; i < numFields; i++) { w.println(" this.t" + i + "Coder = t" + i + "Coder;"); } w.println(" }"); w.println(""); w.println(" @Override"); w.println(" public void encode(" + tupleClass + "<" + types + "> tuple, OutputStream outputStream, Context context)"); w.println(" throws CoderException, IOException {"); w.println(" if (tuple == null) {"); w.println(" throw new CoderException(\"cannot encode a null " + tupleClass + "\");"); w.println(" }"); w.println(" Context nestedContext = context.nested();"); for (int i = 0; i < numFields; i++) { w.println(" t" + i + "Coder.encode(tuple.f" + i + ", outputStream, nestedContext);"); } w.println(" }"); w.println(""); w.println(" @Override"); w.println(" public " + tupleClass + "<" + types + "> decode(InputStream inputStream, Context context)"); w.println(" throws CoderException, IOException {"); w.println(" Context nestedContext = context.nested();"); for (int i = 0; i < numFields; i++) { w.println(" " + GEN_TYPE_PREFIX + i + " f" + i + " = t" + i + "Coder.decode(inputStream, nestedContext);"); } w.print(" return " + tupleClass + ".of("); for (int i = 0; i < numFields; i++) { if (i > 0) { w.print(", "); } w.print("f" + i); } w.println(");"); w.println(" }"); w.println(""); w.println(" @Override"); w.println(" public List<? extends Coder<?>> getCoderArguments() {"); w.print(" return Arrays.asList("); for (int i = 0; i < numFields; i++) { if (i > 0) { w.print(", "); } w.print("t" + i + "Coder"); } w.print(");"); w.println(" }"); w.println(""); w.println(" @Override"); w.println(" public void verifyDeterministic() throws NonDeterministicException {"); for (int i = 0; i < numFields; i++) { w.println(" verifyDeterministic(\"Coder of T" + i + " must be deterministic\", t" + i + "Coder);"); } w.println(" }"); w.println(""); w.println(" @Override"); w.println(" public boolean consistentWithEquals() {"); w.print(" return"); for (int i = 0; i < numFields; i++) { if (i > 0) { w.print("\n &&"); } w.print(" t" + i + "Coder.consistentWithEquals()"); } w.println(";"); w.println(" }"); w.println(""); w.println(" @Override"); w.println(" public Object structuralValue(" + tupleClass + "<" + types + "> tuple) throws Exception {"); w.println(" if (consistentWithEquals()) {"); w.println(" return tuple;"); w.println(" } else {"); w.println(" return " + tupleClass + ".of("); for (int i = 0; i < numFields; i++) { if (i > 0) { w.println(","); } w.print(" t" + i + "Coder.structuralValue(tuple.f" + i + ")"); } w.println(");"); w.println(" }"); w.println(" }"); w.println(""); w.println(" @Override"); w.println(" public boolean isRegisterByteSizeObserverCheap(" + tupleClass + "<" + types + "> tuple, Context context) {"); w.print(" return"); for (int i = 0; i < numFields; i++) { if (i > 0) { w.print("\n &&"); } w.print(" t" + i + "Coder.isRegisterByteSizeObserverCheap(tuple.f" + i + ", context.nested())"); } w.println(";"); w.println(" }"); w.println(""); w.println(" @Override"); w.println(" public void registerByteSizeObserver(" + tupleClass + "<" + types + "> tuple,"); w.println(" ElementByteSizeObserver observer,"); w.println(" Context context) throws Exception {"); w.println(" if (tuple == null) {"); w.println(" throw new CoderException(\"cannot encode a null " + tupleClass + " \");"); w.println(" }"); w.println(" Context nestedContext = context.nested();"); for (int i = 0; i < numFields; i++) { w.println(" t" + i + "Coder.registerByteSizeObserver(tuple.f" + i + ", observer, nestedContext);"); } w.println(" }"); w.println("}"); }
From source file:it.greenvulcano.util.txt.TextUtils.java
/** * Writes a text String into a file//from ww w.j av a2 s . co m * * @param contentString * The String to be written into the file * @param filename * The name of the file * @param append * If true the data are appended to existent file * @throws IOException */ public static void writeFile(String contentString, String filename, boolean append) throws IOException { PrintWriter out = null; try { filename = adjustPath(filename); out = new PrintWriter(new FileWriter(filename, append)); out.print(contentString); out.flush(); } finally { if (out != null) { out.close(); } } }
From source file:Executable.LinkImputeR.java
private static void writeSumHeader(PrintWriter sum, boolean partial) { sum.print("Name\tSamples\tPositions\tAccuracy\tCorrelation\tFilters\tAdditional"); if (partial) { sum.print("\tPartials (Accuracy)\tPartials (Correlation)"); }//from w w w. j ava 2s.c om sum.println(); }
From source file:contract_net.main.java
public static void writeToTxt(List<AuctionResult> auctionResults, DispatchAgent da) { PrintWriter writer = null; try {// w w w . j a v a 2s . c om // generate a unique name for each experiment String logFileName = new SimpleDateFormat("yyyyMMddHHmmss'.txt'").format(new Date()); String logNumberFileName = da + "_" + logFileName; writer = new PrintWriter(new BufferedWriter(new FileWriter(logNumberFileName))); for (AuctionResult auctionResult : auctionResults) { // auction result data are tab delimited, so we can read them as columns writer.print(da.toString()); writer.print("\t"); writer.print(auctionResult.hashCode()); writer.print("\t"); writer.print(auctionResult.getAuction()); writer.print("\t"); writer.print(auctionResult.getWinner()); writer.print("\t"); writer.print(auctionResult.getBestProposal()); writer.print("\t"); writer.print(auctionResult.getBestProposal().getTimeCostProposal()); writer.print("\t"); writer.print(auctionResult.getBestProposal() .getDistanceCostProposal(auctionResult.getBestProposal().getTimeCostProposal())); writer.print("\t"); writer.print(auctionResult.getAuctionDuration()); writer.print("\t"); writer.print(auctionResult.getRealTimeTruckToPickup()); writer.print("\t"); writer.print(auctionResult.getRealTimePickupToDelivery()); writer.print("\t"); writer.print(auctionResult.getRealTimeTruckToPickupToDelivery()); writer.print("\t"); writer.print(auctionResult.getPickupTardiness(auctionResult.getBestProposal(), auctionResult.getRealTimeTruckToPickup())); writer.print("\t"); writer.print(auctionResult.getDeliveryTardiness(auctionResult.getBestProposal(), auctionResult.getRealTimePickupToDelivery())); writer.print("\t"); writer.print(auctionResult.getPickupDeliveryTardiness(auctionResult.getBestProposal(), auctionResult.getRealTimeTruckToPickupToDelivery())); writer.print("\t"); writer.print(auctionResult.getRealTimeCFPDelivery()); writer.print("\t"); //TODO maybe leave away this one writer.print(auctionResult.getRejectedProposals()); // new line for new auction writer.println(); } } catch (IOException e) { e.printStackTrace(); } finally { if (writer != null) { writer.close(); } } }
From source file:edu.ucsd.ccdb.cil.xml2json.XML2JsonUtil.java
public void outputStringToFile(File f, String json) throws Exception { FileOutputStream fout = new FileOutputStream(f); PrintWriter pw = new PrintWriter(fout); pw.print(json); pw.close();//from w w w .j a va2s. co m }
From source file:com.atlassian.clover.reporters.console.ConsoleReporter.java
static void printMetricsSummary(PrintWriter out, String title, ClassMetrics metrics, ConsoleReporterConfig cfg) {/* w ww . ja va 2 s . com*/ out.println(title); out.println("Coverage:-"); final String methodSummary = infoSummaryString(metrics.getNumCoveredMethods(), metrics.getNumMethods(), metrics.getPcCoveredMethods()); final String stmtSummary = infoSummaryString(metrics.getNumCoveredStatements(), metrics.getNumStatements(), metrics.getPcCoveredStatements()); final String branchSummary = infoSummaryString(metrics.getNumCoveredBranches(), metrics.getNumBranches(), metrics.getPcCoveredBranches()); final String totalSummary = Color.make(Formatting.getPercentStr(metrics.getPcCoveredElements())).b() .toString(); out.print(" Methods: " + methodSummary); printPcBar(out, methodSummary, metrics.getPcCoveredMethods()); out.print(" Statements: " + stmtSummary); printPcBar(out, stmtSummary, metrics.getPcCoveredStatements()); out.print(" Branches: " + branchSummary); printPcBar(out, branchSummary, metrics.getPcCoveredBranches()); out.print(" Total: " + totalSummary); printPcBar(out, totalSummary, metrics.getPcCoveredElements()); out.println("Complexity:-"); out.println(" Avg Method: " + Formatting.format3d(metrics.getAvgMethodComplexity())); out.println(" Density: " + Formatting.format3d(metrics.getComplexityDensity())); out.println(" Total: " + metrics.getComplexity()); if ((cfg != null) && (cfg.isShowUnitTests())) { out.println("Tests:-"); out.println(" Available: " + metrics.getNumTests()); out.println(" Executed: " + metrics.getNumTestsRun()); out.println(" Passed: " + metrics.getNumTestPasses()); out.println(" Failed: " + metrics.getNumTestFailures()); out.println(" Errors: " + metrics.getNumTestErrors()); } }