List of usage examples for java.io BufferedReader BufferedReader
public BufferedReader(Reader in)
From source file:com.wxpay.ClientCustomSSL.java
public final static void main(String[] args) throws Exception { KeyStore keyStore = KeyStore.getInstance("PKCS12"); FileInputStream instream = new FileInputStream(new File("E:/apiclient_cert1.p12")); try {//from w w w .j ava2 s . com keyStore.load(instream, "1269885501".toCharArray()); } finally { instream.close(); } // Trust own CA and all self-signed certs SSLContext sslcontext = SSLContexts.custom().loadKeyMaterial(keyStore, "1269885501".toCharArray()).build(); // Allow TLSv1 protocol only SSLConnectionSocketFactory sslsf = new SSLConnectionSocketFactory(sslcontext, new String[] { "TLSv1" }, null, SSLConnectionSocketFactory.BROWSER_COMPATIBLE_HOSTNAME_VERIFIER); CloseableHttpClient httpclient = HttpClients.custom().setSSLSocketFactory(sslsf).build(); try { HttpGet httpget = new HttpGet("https://api.mch.weixin.qq.com/secapi/pay/refund"); System.out.println("executing request" + httpget.getRequestLine()); CloseableHttpResponse response = httpclient.execute(httpget); try { HttpEntity entity = response.getEntity(); System.out.println("----------------------------------------"); System.out.println(response.getStatusLine()); if (entity != null) { System.out.println("Response content length: " + entity.getContentLength()); BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(entity.getContent())); String text; while ((text = bufferedReader.readLine()) != null) { System.out.println(text); } } EntityUtils.consume(entity); } finally { response.close(); } } finally { httpclient.close(); } }
From source file:org.gzk.image.junit.ClientCustomSSL.java
public final static void main(String[] args) throws Exception { KeyStore keyStore = KeyStore.getInstance("PKCS12"); FileInputStream instream = new FileInputStream(new File("D:/apiclient_cert.p12")); try {/* www . j a va 2 s . c o m*/ keyStore.load(instream, "1374938902".toCharArray()); } finally { instream.close(); } // Trust own CA and all self-signed certs SSLContext sslcontext = SSLContexts.custom().loadKeyMaterial(keyStore, "1374938902".toCharArray()).build(); // Allow TLSv1 protocol only SSLConnectionSocketFactory sslsf = new SSLConnectionSocketFactory(sslcontext, new String[] { "TLSv1" }, null, SSLConnectionSocketFactory.BROWSER_COMPATIBLE_HOSTNAME_VERIFIER); CloseableHttpClient httpclient = HttpClients.custom().setSSLSocketFactory(sslsf).build(); try { HttpGet httpget = new HttpGet("https://api.mch.weixin.qq.com/secapi/pay/refund"); System.out.println("executing request" + httpget.getRequestLine()); CloseableHttpResponse response = httpclient.execute(httpget); try { HttpEntity entity = response.getEntity(); System.out.println("----------------------------------------"); System.out.println(response.getStatusLine()); if (entity != null) { System.out.println("Response content length: " + entity.getContentLength()); BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(entity.getContent())); String text; while ((text = bufferedReader.readLine()) != null) { System.out.println(text); } } EntityUtils.consume(entity); } finally { response.close(); } } finally { httpclient.close(); } }
From source file:com.magicbeans.banjiuwan.util.ClientCustomSSL.java
public final static void main(String[] args) throws Exception { KeyStore keyStore = KeyStore.getInstance("PKCS12"); FileInputStream instream = new FileInputStream(new File("D:/10016225.p12")); try {/*from www . j av a 2s . com*/ keyStore.load(instream, "10016225".toCharArray()); } finally { instream.close(); } // Trust own CA and all self-signed certs SSLContext sslcontext = SSLContexts.custom().loadKeyMaterial(keyStore, "10016225".toCharArray()).build(); // Allow TLSv1 protocol only SSLConnectionSocketFactory sslsf = new SSLConnectionSocketFactory(sslcontext, new String[] { "TLSv1" }, null, SSLConnectionSocketFactory.BROWSER_COMPATIBLE_HOSTNAME_VERIFIER); CloseableHttpClient httpclient = HttpClients.custom().setSSLSocketFactory(sslsf).build(); try { HttpGet httpget = new HttpGet("https://api.mch.weixin.qq.com/secapi/pay/refund"); System.out.println("executing request" + httpget.getRequestLine()); CloseableHttpResponse response = httpclient.execute(httpget); try { HttpEntity entity = response.getEntity(); System.out.println("----------------------------------------"); System.out.println(response.getStatusLine()); if (entity != null) { System.out.println("Response content length: " + entity.getContentLength()); BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(entity.getContent())); String text; while ((text = bufferedReader.readLine()) != null) { System.out.println(text); } } EntityUtils.consume(entity); } finally { response.close(); } } finally { httpclient.close(); } }
From source file:ProxyTunnelDemo.java
public static void main(String[] args) throws Exception { ProxyClient proxyclient = new ProxyClient(); // set the host the proxy should create a connection to //// w w w .j a v a 2 s . c o m // Note: By default port 80 will be used. Some proxies only allow conections // to ports 443 and 8443. This is because the HTTP CONNECT method was intented // to be used for tunneling HTTPS. proxyclient.getHostConfiguration().setHost("www.yahoo.com"); // set the proxy host and port proxyclient.getHostConfiguration().setProxy("10.0.1.1", 3128); // set the proxy credentials, only necessary for authenticating proxies proxyclient.getState().setProxyCredentials(new AuthScope("10.0.1.1", 3128, null), new UsernamePasswordCredentials("proxy", "proxy")); // create the socket ProxyClient.ConnectResponse response = proxyclient.connect(); if (response.getSocket() != null) { Socket socket = response.getSocket(); try { // go ahead and do an HTTP GET using the socket Writer out = new OutputStreamWriter(socket.getOutputStream(), "ISO-8859-1"); out.write("GET http://www.yahoo.com/ HTTP/1.1\r\n"); out.write("Host: www.yahoo.com\r\n"); out.write("Agent: whatever\r\n"); out.write("\r\n"); out.flush(); BufferedReader in = new BufferedReader( new InputStreamReader(socket.getInputStream(), "ISO-8859-1")); String line = null; while ((line = in.readLine()) != null) { System.out.println(line); } } finally { // be sure to close the socket when we're done socket.close(); } } else { // the proxy connect was not successful, check connect method for reasons why System.out.println("Connect failed: " + response.getConnectMethod().getStatusLine()); System.out.println(response.getConnectMethod().getResponseBodyAsString()); } }
From source file:com.era7.bioinfo.annotation.AutomaticQualityControl.java
public static void main(String[] args) { if (args.length != 4) { System.out.println("This program expects four parameters: \n" + "1. Gene annotation XML filename \n" + "2. Reference protein set (.fasta)\n" + "3. Output TXT filename\n" + "4. Initial Blast XML results filename (the one used at the very beginning of the semiautomatic annotation process)\n"); } else {//from www.j av a2 s.c o m BufferedWriter outBuff = null; try { File inFile = new File(args[0]); File fastaFile = new File(args[1]); File outFile = new File(args[2]); File blastFile = new File(args[3]); //Primero cargo todos los datos del archivo xml del blast BufferedReader buffReader = new BufferedReader(new FileReader(blastFile)); StringBuilder stBuilder = new StringBuilder(); String line = null; while ((line = buffReader.readLine()) != null) { stBuilder.append(line); } buffReader.close(); System.out.println("Creating blastoutput..."); BlastOutput blastOutput = new BlastOutput(stBuilder.toString()); System.out.println("BlastOutput created! :)"); stBuilder.delete(0, stBuilder.length()); HashMap<String, String> blastProteinsMap = new HashMap<String, String>(); ArrayList<Iteration> iterations = blastOutput.getBlastOutputIterations(); for (Iteration iteration : iterations) { blastProteinsMap.put(iteration.getQueryDef().split("\\|")[1].trim(), iteration.toString()); } //freeing some memory blastOutput = null; //------------------------------------------------------------------------ //Initializing writer for output file outBuff = new BufferedWriter(new FileWriter(outFile)); //reading gene annotation xml file..... buffReader = new BufferedReader(new FileReader(inFile)); stBuilder = new StringBuilder(); line = null; while ((line = buffReader.readLine()) != null) { stBuilder.append(line); } buffReader.close(); XMLElement genesXML = new XMLElement(stBuilder.toString()); //freeing some memory I don't need anymore stBuilder.delete(0, stBuilder.length()); //reading file with the reference proteins set ArrayList<String> proteinsReferenceSet = new ArrayList<String>(); buffReader = new BufferedReader(new FileReader(fastaFile)); while ((line = buffReader.readLine()) != null) { if (line.charAt(0) == '>') { proteinsReferenceSet.add(line.split("\\|")[1]); } } buffReader.close(); Element pGenes = genesXML.asJDomElement().getChild(PredictedGenes.TAG_NAME); List<Element> contigs = pGenes.getChildren(ContigXML.TAG_NAME); System.out.println("There are " + contigs.size() + " contigs to be checked... "); outBuff.write("There are " + contigs.size() + " contigs to be checked... \n"); outBuff.write("Proteins reference set: \n"); for (String st : proteinsReferenceSet) { outBuff.write(st + ","); } outBuff.write("\n"); for (Element elem : contigs) { ContigXML contig = new ContigXML(elem); //escribo el id del contig en el que estoy outBuff.write("Checking contig: " + contig.getId() + "\n"); outBuff.flush(); List<XMLElement> geneList = contig.getChildrenWith(PredictedGene.TAG_NAME); System.out.println("geneList.size() = " + geneList.size()); int numeroDeGenesParaAnalizar = geneList.size() / FACTOR; if (numeroDeGenesParaAnalizar == 0) { numeroDeGenesParaAnalizar++; } ArrayList<Integer> indicesUtilizados = new ArrayList<Integer>(); outBuff.write("\nThe contig has " + geneList.size() + " predicted genes, let's analyze: " + numeroDeGenesParaAnalizar + "\n"); for (int j = 0; j < numeroDeGenesParaAnalizar; j++) { int geneIndex; boolean geneIsDismissed = false; do { geneIsDismissed = false; geneIndex = (int) Math.round(Math.floor(Math.random() * geneList.size())); PredictedGene tempGene = new PredictedGene(geneList.get(geneIndex).asJDomElement()); if (tempGene.getStatus().equals(PredictedGene.STATUS_DISMISSED)) { geneIsDismissed = true; } } while (indicesUtilizados.contains(new Integer(geneIndex)) && geneIsDismissed); indicesUtilizados.add(geneIndex); System.out.println("geneIndex = " + geneIndex); //Ahora hay que sacar el gen correspondiente al indice y hacer el control de calidad PredictedGene gene = new PredictedGene(geneList.get(geneIndex).asJDomElement()); outBuff.write("\nAnalyzing gene with id: " + gene.getId() + " , annotation uniprot id: " + gene.getAnnotationUniprotId() + "\n"); outBuff.write("eValue: " + gene.getEvalue() + "\n"); //--------------PETICION POST HTTP BLAST---------------------- PostMethod post = new PostMethod(BLAST_URL); post.addParameter("program", "blastx"); post.addParameter("sequence", gene.getSequence()); post.addParameter("database", "uniprotkb"); post.addParameter("email", "ppareja@era7.com"); post.addParameter("exp", "1e-10"); post.addParameter("stype", "dna"); // execute the POST HttpClient client = new HttpClient(); int status = client.executeMethod(post); System.out.println("status post = " + status); InputStream inStream = post.getResponseBodyAsStream(); String fileName = "jobid.txt"; FileOutputStream outStream = new FileOutputStream(new File(fileName)); byte[] buffer = new byte[1024]; int len; while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //Once the file is created I just have to read one line in order to extract the job id buffReader = new BufferedReader(new FileReader(new File(fileName))); String jobId = buffReader.readLine(); buffReader.close(); System.out.println("jobId = " + jobId); //--------------HTTP CHECK JOB STATUS REQUEST---------------------- GetMethod get = new GetMethod(CHECK_JOB_STATUS_URL + jobId); String jobStatus = ""; do { try { Thread.sleep(1000);//sleep for 1000 ms } catch (InterruptedException ie) { //If this thread was intrrupted by nother thread } status = client.executeMethod(get); //System.out.println("status get = " + status); inStream = get.getResponseBodyAsStream(); fileName = "jobStatus.txt"; outStream = new FileOutputStream(new File(fileName)); while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //Once the file is created I just have to read one line in order to extract the job id buffReader = new BufferedReader(new FileReader(new File(fileName))); jobStatus = buffReader.readLine(); //System.out.println("jobStatus = " + jobStatus); buffReader.close(); } while (!jobStatus.equals(FINISHED_JOB_STATUS)); //Once I'm here the blast should've already finished //--------------JOB RESULTS HTTP REQUEST---------------------- get = new GetMethod(JOB_RESULT_URL + jobId + "/out"); status = client.executeMethod(get); System.out.println("status get = " + status); inStream = get.getResponseBodyAsStream(); fileName = "jobResults.txt"; outStream = new FileOutputStream(new File(fileName)); while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //--------parsing the blast results file----- TreeSet<GeneEValuePair> featuresBlast = new TreeSet<GeneEValuePair>(); buffReader = new BufferedReader(new FileReader(new File(fileName))); while ((line = buffReader.readLine()) != null) { if (line.length() > 3) { String prefix = line.substring(0, 3); if (prefix.equals("TR:") || prefix.equals("SP:")) { String[] columns = line.split(" "); String id = columns[1]; //System.out.println("id = " + id); String e = ""; String[] arraySt = line.split("\\.\\.\\."); if (arraySt.length > 1) { arraySt = arraySt[1].trim().split(" "); int contador = 0; for (int k = 0; k < arraySt.length && contador <= 2; k++) { String string = arraySt[k]; if (!string.equals("")) { contador++; if (contador == 2) { e = string; } } } } else { //Number before e- String[] arr = arraySt[0].split("e-")[0].split(" "); String numeroAntesE = arr[arr.length - 1]; String numeroDespuesE = arraySt[0].split("e-")[1].split(" ")[0]; e = numeroAntesE + "e-" + numeroDespuesE; } double eValue = Double.parseDouble(e); //System.out.println("eValue = " + eValue); GeneEValuePair g = new GeneEValuePair(id, eValue); featuresBlast.add(g); } } } GeneEValuePair currentGeneEValuePair = new GeneEValuePair(gene.getAnnotationUniprotId(), gene.getEvalue()); System.out.println("currentGeneEValuePair.id = " + currentGeneEValuePair.id); System.out.println("currentGeneEValuePair.eValue = " + currentGeneEValuePair.eValue); boolean blastContainsGene = false; for (GeneEValuePair geneEValuePair : featuresBlast) { if (geneEValuePair.id.equals(currentGeneEValuePair.id)) { blastContainsGene = true; //le pongo la e que tiene en el wu-blast para poder comparar currentGeneEValuePair.eValue = geneEValuePair.eValue; break; } } if (blastContainsGene) { outBuff.write("The protein was found in the WU-BLAST result.. \n"); //Una vez que se que esta en el blast tengo que ver que sea la mejor GeneEValuePair first = featuresBlast.first(); outBuff.write("Protein with best eValue according to the WU-BLAST result: " + first.id + " , " + first.eValue + "\n"); if (first.id.equals(currentGeneEValuePair.id)) { outBuff.write("Proteins with best eValue match up \n"); } else { if (first.eValue == currentGeneEValuePair.eValue) { outBuff.write( "The one with best eValue is not the same protein but has the same eValue \n"); } else if (first.eValue > currentGeneEValuePair.eValue) { outBuff.write( "The one with best eValue is not the same protein but has a worse eValue :) \n"); } else { outBuff.write( "The best protein from BLAST has an eValue smaller than ours, checking if it's part of the reference set...\n"); //System.exit(-1); if (proteinsReferenceSet.contains(first.id)) { //The protein is in the reference set and that shouldn't happen outBuff.write( "The protein was found on the reference set, checking if it belongs to the same contig...\n"); String iterationSt = blastProteinsMap.get(gene.getAnnotationUniprotId()); if (iterationSt != null) { outBuff.write( "The protein was found in the BLAST used at the beginning of the annotation process.\n"); Iteration iteration = new Iteration(iterationSt); ArrayList<Hit> hits = iteration.getIterationHits(); boolean contigFound = false; Hit errorHit = null; for (Hit hit : hits) { if (hit.getHitDef().indexOf(contig.getId()) >= 0) { contigFound = true; errorHit = hit; break; } } if (contigFound) { outBuff.write( "ERROR: A hit from the same contig was find in the Blast file: \n" + errorHit.toString() + "\n"); } else { outBuff.write("There is no hit with the same contig! :)\n"); } } else { outBuff.write( "The protein is NOT in the BLAST used at the beginning of the annotation process.\n"); } } else { //The protein was not found on the reference set so everything's ok outBuff.write( "The protein was not found on the reference, everything's ok :)\n"); } } } } else { outBuff.write("The protein was NOT found on the WU-BLAST !! :( \n"); //System.exit(-1); } } } } catch (Exception ex) { ex.printStackTrace(); } finally { try { //closing outputfile outBuff.close(); } catch (IOException ex) { Logger.getLogger(AutomaticQualityControl.class.getName()).log(Level.SEVERE, null, ex); } } } }
From source file:com.adobe.aem.demo.Analytics.java
public static void main(String[] args) { String hostname = null;// w w w . j a va2 s . c om String url = null; String eventfile = null; // Command line options for this tool Options options = new Options(); options.addOption("h", true, "Hostname"); options.addOption("u", true, "Url"); options.addOption("f", true, "Event data file"); CommandLineParser parser = new BasicParser(); try { CommandLine cmd = parser.parse(options, args); if (cmd.hasOption("u")) { url = cmd.getOptionValue("u"); } if (cmd.hasOption("f")) { eventfile = cmd.getOptionValue("f"); } if (cmd.hasOption("h")) { hostname = cmd.getOptionValue("h"); } if (eventfile == null || hostname == null || url == null) { System.out.println("Command line parameters: -h hostname -u url -f path_to_XML_file"); System.exit(-1); } } catch (ParseException ex) { logger.error(ex.getMessage()); } URLConnection urlConn = null; DataOutputStream printout = null; BufferedReader input = null; String u = "http://" + hostname + "/" + url; String tmp = null; try { URL myurl = new URL(u); urlConn = myurl.openConnection(); urlConn.setDoInput(true); urlConn.setDoOutput(true); urlConn.setUseCaches(false); urlConn.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); printout = new DataOutputStream(urlConn.getOutputStream()); String xml = readFile(eventfile, StandardCharsets.UTF_8); printout.writeBytes(xml); printout.flush(); printout.close(); input = new BufferedReader(new InputStreamReader(urlConn.getInputStream())); logger.debug(xml); while (null != ((tmp = input.readLine()))) { logger.debug(tmp); } printout.close(); input.close(); } catch (Exception ex) { logger.error(ex.getMessage()); } }
From source file:gentracklets.GenTracklets.java
public static void main(String[] args) throws OrekitException { // load the data files File data = new File("/home/zittersteijn/Documents/java/libraries/orekit-data.zip"); DataProvidersManager DM = DataProvidersManager.getInstance(); ZipJarCrawler crawler = new ZipJarCrawler(data); DM.clearProviders();/* www . j a v a2 s .c o m*/ DM.addProvider(crawler); // Read in TLE elements File tleFile = new File("/home/zittersteijn/Documents/TLEs/ASTRA20151207.tle"); FileReader TLEfr; Vector<TLE> tles = new Vector<>(); tles.setSize(30); try { // read and save TLEs to a vector TLEfr = new FileReader("/home/zittersteijn/Documents/TLEs/ASTRA20151207.tle"); BufferedReader readTLE = new BufferedReader(TLEfr); Scanner s = new Scanner(tleFile); String line1, line2; TLE2 tle = new TLE2(); int nrOfObj = 4; for (int ii = 1; ii < nrOfObj + 1; ii++) { System.out.println(ii); line1 = s.nextLine(); line2 = s.nextLine(); if (TLE.isFormatOK(line1, line2)) { tles.setElementAt(new TLE(line1, line2), ii); System.out.println(tles.get(ii).toString()); } else { System.out.println("format problem"); } } readTLE.close(); // define a groundstation Frame inertialFrame = FramesFactory.getEME2000(); TimeScale utc = TimeScalesFactory.getUTC(); double longitude = FastMath.toRadians(7.465); double latitude = FastMath.toRadians(46.87); double altitude = 950.; GeodeticPoint station = new GeodeticPoint(latitude, longitude, altitude); Frame earthFrame = FramesFactory.getITRF(IERSConventions.IERS_2010, true); BodyShape earth = new OneAxisEllipsoid(Constants.WGS84_EARTH_EQUATORIAL_RADIUS, Constants.WGS84_EARTH_FLATTENING, earthFrame); TopocentricFrame staF = new TopocentricFrame(earth, station, "station"); Vector<Orbit> eles = new Vector<>(); eles.setSize(tles.size()); for (int ii = 1; ii < nrOfObj + 1; ii++) { double a = FastMath.pow(Constants.WGS84_EARTH_MU / FastMath.pow(tles.get(ii).getMeanMotion(), 2), (1.0 / 3)); // convert them to orbits Orbit kep = new KeplerianOrbit(a, tles.get(ii).getE(), tles.get(ii).getI(), tles.get(ii).getPerigeeArgument(), tles.get(ii).getRaan(), tles.get(ii).getMeanAnomaly(), PositionAngle.MEAN, inertialFrame, tles.get(ii).getDate(), Constants.WGS84_EARTH_MU); eles.setElementAt(kep, ii); // set up propagators KeplerianPropagator kepler = new KeplerianPropagator(eles.get(ii)); System.out.println("a: " + a); // Initial state definition double mass = 1000.0; SpacecraftState initialState = new SpacecraftState(kep, mass); // Adaptive step integrator // with a minimum step of 0.001 and a maximum step of 1000 double minStep = 0.001; double maxstep = 1000.0; double positionTolerance = 10.0; OrbitType propagationType = OrbitType.KEPLERIAN; double[][] tolerances = NumericalPropagator.tolerances(positionTolerance, kep, propagationType); AdaptiveStepsizeIntegrator integrator = new DormandPrince853Integrator(minStep, maxstep, tolerances[0], tolerances[1]); NumericalPropagator propagator = new NumericalPropagator(integrator); propagator.setOrbitType(propagationType); // set up and add force models double AMR = 0.4; double crossSection = mass * AMR; double Cd = 0.01; double Cr = 0.5; double Co = 0.8; NormalizedSphericalHarmonicsProvider provider = GravityFieldFactory.getNormalizedProvider(4, 4); ForceModel holmesFeatherstone = new HolmesFeatherstoneAttractionModel( FramesFactory.getITRF(IERSConventions.IERS_2010, true), provider); SphericalSpacecraft ssc = new SphericalSpacecraft(crossSection, Cd, Cr, Co); PVCoordinatesProvider sun = CelestialBodyFactory.getSun(); SolarRadiationPressure srp = new SolarRadiationPressure(sun, Constants.WGS84_EARTH_EQUATORIAL_RADIUS, ssc); propagator.addForceModel(srp); propagator.addForceModel(holmesFeatherstone); propagator.setInitialState(initialState); // propagate the orbits with steps size and tracklet lenght at several epochs (tracklets) Vector<AbsoluteDate> startDates = new Vector<>(); startDates.setSize(3); startDates.setElementAt(new AbsoluteDate(2015, 12, 8, 20, 00, 00, utc), 0); startDates.setElementAt(new AbsoluteDate(2015, 12, 9, 21, 00, 00, utc), 1); startDates.setElementAt(new AbsoluteDate(2015, 12, 10, 22, 00, 00, utc), 2); double tstep = 30; int l = 7; for (int tt = 0; tt < startDates.size(); tt++) { // set up output file String app = "S_" + tles.get(ii).getSatelliteNumber() + "_" + startDates.get(tt) + ".txt"; // FileWriter trackletsOutKep = new FileWriter("/home/zittersteijn/Documents/tracklets/simulated/keplerian/ASTRA/dt1h/AMR040/" + app); // FileWriter trackletsOutPer = new FileWriter("/home/zittersteijn/Documents/tracklets/simulated/perturbed/ASTRA/dt1h/AMR040/" + app); // BufferedWriter trackletsKepBW = new BufferedWriter(trackletsOutKep); // BufferedWriter trackletsPerBW = new BufferedWriter(trackletsOutPer); // with formatted output File file1 = new File( "/home/zittersteijn/Documents/tracklets/simulated/keplerian/ASTRA/dt1d/AMR040/" + app); File file2 = new File( "/home/zittersteijn/Documents/tracklets/simulated/perturbed/ASTRA/dt1d/AMR040/" + app); file1.createNewFile(); file2.createNewFile(); Formatter fmt1 = new Formatter(file1); Formatter fmt2 = new Formatter(file2); for (int kk = 0; kk < l; kk++) { AbsoluteDate propDate = startDates.get(tt).shiftedBy(tstep * kk); SpacecraftState currentStateKep = kepler.propagate(propDate); SpacecraftState currentStatePer = propagator.propagate(propDate); System.out.println(currentStateKep.getPVCoordinates().getPosition() + "\t" + currentStateKep.getDate()); // convert to RADEC coordinates double[] radecKep = conversions.geo2radec(currentStateKep.getPVCoordinates(), staF, inertialFrame, propDate); double[] radecPer = conversions.geo2radec(currentStatePer.getPVCoordinates(), staF, inertialFrame, propDate); // write the tracklets to seperate files with the RA, DEC, epoch and fence given // System.out.println(tles.get(kk).getSatelliteNumber() + "\t" + radec[0] / (2 * FastMath.PI) * 180 + "\t" + currentState.getDate()); AbsoluteDate year = new AbsoluteDate(YEAR, utc); fmt1.format("%.12f %.12f %.12f %d%n", radecKep[0], radecKep[2], (currentStateKep.getDate().durationFrom(year) / (24 * 3600)), (tt + 1)); fmt2.format("%.12f %.12f %.12f %d%n", radecPer[0], radecPer[2], (currentStateKep.getDate().durationFrom(year) / (24 * 3600)), (tt + 1)); } fmt1.flush(); fmt1.close(); fmt2.flush(); fmt2.close(); } } } catch (FileNotFoundException ex) { Logger.getLogger(GenTracklets.class.getName()).log(Level.SEVERE, null, ex); } catch (IOException iox) { Logger.getLogger(GenTracklets.class.getName()).log(Level.SEVERE, null, iox); } }
From source file:keepassj.cli.KeepassjCli.java
/** * @param args the command line arguments * @throws org.apache.commons.cli.ParseException * @throws java.io.IOException/*ww w . ja v a2 s. c o m*/ */ public static void main(String[] args) throws ParseException, IOException { Options options = KeepassjCli.getOptions(); CommandLineParser parser = new DefaultParser(); CommandLine cmd = parser.parse(options, args); if (!KeepassjCli.validateOptions(cmd)) { HelpFormatter help = new HelpFormatter(); help.printHelp("Usage: java -jar KeepassjCli -f dbfile [options]", options); } else { String password; if (cmd.hasOption('p')) { password = cmd.getOptionValue('p'); } else { Console console = System.console(); char[] hiddenString = console.readPassword("Enter password for %s\n", cmd.getOptionValue('f')); password = String.valueOf(hiddenString); } KeepassjCli instance = new KeepassjCli(cmd.getOptionValue('f'), password, cmd.getOptionValue('k')); System.out.println("Description:" + instance.db.getDescription()); PwGroup rootGroup = instance.db.getRootGroup(); System.out.println(String.valueOf(rootGroup.GetEntriesCount(true)) + " entries"); if (cmd.hasOption('l')) { instance.printEntries(rootGroup.GetEntries(true), false); } else if (cmd.hasOption('s')) { PwObjectList<PwEntry> results = instance.search(cmd.getOptionValue('s')); System.out.println("Found " + results.getUCount() + " results for:" + cmd.getOptionValue('s')); instance.printEntries(results, false); } else if (cmd.hasOption('i')) { System.out.println("Entering interactive mode."); BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(System.in)); String input = null; PwObjectList<PwEntry> results = null; while (!"\\q".equals(input)) { if (results != null) { System.out.println("Would you like to view a specific entry? y/n"); input = bufferedReader.readLine(); if ("y".equalsIgnoreCase(input)) { System.out.print("Enter the title number:"); input = bufferedReader.readLine(); instance.printCompleteEntry(results.GetAt(Integer.parseInt(input) - 1)); // Since humans start counting at 1 } results = null; System.out.println(); } else { System.out.print("Enter something to search for (or \\q to quit):"); input = bufferedReader.readLine(); if (!"\\q".equalsIgnoreCase(input)) { results = instance.search(input); instance.printEntries(results, true); } } } } // Close before exit instance.db.Close(); } }
From source file:edu.msu.cme.rdp.probematch.cli.PrimerMatch.java
public static void main(String[] args) throws Exception { PrintStream out = new PrintStream(System.out); int maxDist = Integer.MAX_VALUE; try {//from ww w . ja v a 2 s . com CommandLine line = new PosixParser().parse(options, args); if (line.hasOption("outFile")) { out = new PrintStream(new File(line.getOptionValue("outFile"))); } if (line.hasOption("maxDist")) { maxDist = Integer.valueOf(line.getOptionValue("maxDist")); } args = line.getArgs(); if (args.length != 2) { throw new Exception("Unexpected number of command line arguments"); } } catch (Exception e) { System.err.println("Error: " + e.getMessage()); new HelpFormatter().printHelp("PrimerMatch <primer_list | primer_file> <seq_file>", options); return; } List<PatternBitMask64> primers = new ArrayList(); if (new File(args[0]).exists()) { File primerFile = new File(args[0]); SequenceFormat seqformat = SeqUtils.guessFileFormat(primerFile); if (seqformat.equals(SequenceFormat.FASTA)) { SequenceReader reader = new SequenceReader(primerFile); Sequence seq; while ((seq = reader.readNextSequence()) != null) { primers.add(new PatternBitMask64(seq.getSeqString(), true, seq.getSeqName())); } reader.close(); } else { BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line; while ((line = reader.readLine()) != null) { line = line.trim(); if (!line.equals("")) { primers.add(new PatternBitMask64(line, true)); } } reader.close(); } } else { for (String primer : args[0].split(",")) { primers.add(new PatternBitMask64(primer, true)); } } SeqReader seqReader = new SequenceReader(new File(args[1])); Sequence seq; String primerRegion; out.println("#seqname\tdesc\tprimer_index\tprimer_name\tposition\tmismatches\tseq_primer_region"); while ((seq = seqReader.readNextSequence()) != null) { for (int index = 0; index < primers.size(); index++) { PatternBitMask64 primer = primers.get(index); BitVector64Result results = BitVector64.process(seq.getSeqString().toCharArray(), primer, maxDist); for (BitVector64Match result : results.getResults()) { primerRegion = seq.getSeqString().substring( Math.max(0, result.getPosition() - primer.getPatternLength()), result.getPosition()); if (result.getPosition() < primer.getPatternLength()) { for (int pad = result.getPosition(); pad < primer.getPatternLength(); pad++) { primerRegion = "x" + primerRegion; } } out.println(seq.getSeqName() + "\t" + seq.getDesc() + "\t" + (index + 1) + "\t" + primer.getPrimerName() + "\t" + result.getPosition() + "\t" + result.getScore() + "\t" + primerRegion); } } } out.close(); seqReader.close(); }
From source file:clientpaxos.ClientPaxos.java
/** * @param args the command line arguments *//*from www. j a v a 2s . c om*/ public static void main(String[] args) throws IOException, InterruptedException, Exception { // TODO code application logic here String host = ""; int port = 0; try (BufferedReader br = new BufferedReader(new FileReader("ipserver.txt"))) { StringBuilder sb = new StringBuilder(); String line = br.readLine(); if (line != null) { host = line; line = br.readLine(); if (line != null) { port = Integer.parseInt(line); } } } scanner = new Scanner(System.in); //System.out.print("Input server IP hostname : "); //host = scan.nextLine(); //System.out.print("Input server Port : "); //port = scan.nextInt(); //scan.nextLine(); tcpSocket = new Socket(host, port); System.out.println("Connected"); Thread t = new Thread(new StringGetter()); t.start(); while (true) { sleep(100); if (!voteInput) { System.out.print("COMMAND : "); } //send msg to server String msg = scanner.next(); //if ((day && isAlive == 1) || (!day && role.equals("werewolf") && isAlive == 1)) { ParseCommand(msg); //} } }