List of usage examples for java.io DataInputStream readUTF
public final String readUTF() throws IOException
readUTF method of DataInput. From source file:MiGA.StatsSelection.java
public void getPerfectSSRs(String[] organisms, int length, boolean flag) throws FileNotFoundException, SQLException, ClassNotFoundException, IOException { for (int i = 0; i < organisms.length; i++) { // 18/11/2013 added starting here String filetype = ""; String filepro = ""; if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else//from w ww . j a v a 2s .c o m indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } //List<String> files = getFiles(organisms[i], minlen, flag); // 18/11/2013 added ending here countmono.set(i, 0); countdi.set(i, 0); counttri.set(i, 0); counttetra.set(i, 0); countpenta.set(i, 0); counthexa.set(i, 0); countmonore.set(i, 0); countdire.set(i, 0); counttrire.set(i, 0); counttetrare.set(i, 0); countpentare.set(i, 0); counthexare.set(i, 0); Amono.set(i, 0); Adi.set(i, 0); Atri.set(i, 0); Atetra.set(i, 0); Apenta.set(i, 0); Ahexa.set(i, 0); Tmono.set(i, 0); Tdi.set(i, 0); Ttri.set(i, 0); Ttetra.set(i, 0); Tpenta.set(i, 0); Thexa.set(i, 0); Gmono.set(i, 0); Gdi.set(i, 0); Gtri.set(i, 0); Gtetra.set(i, 0); Gpenta.set(i, 0); Ghexa.set(i, 0); Cmono.set(i, 0); Cdi.set(i, 0); Ctri.set(i, 0); Ctetra.set(i, 0); Cpenta.set(i, 0); Chexa.set(i, 0); while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); //for (int j = 0; j < files.size(); j++) { List<File> exis = new ArrayList<File>(); exis.add(new File(files + "_" + length + "_monoPerfect.temp")); exis.add(new File(files + "_" + length + "_diPerfect.temp")); exis.add(new File(files + "_" + length + "_triPerfect.temp")); exis.add(new File(files + "_" + length + "_tetraPerfect.temp")); exis.add(new File(files + "_" + length + "_pentaPerfect.temp")); exis.add(new File(files + "_" + length + "_hexaPerfect.temp")); int num = 0; for (int temp = 0; temp < exis.size(); temp++) { if (exis.get(temp).exists()) { num++; } } if (num != exis.size()) { DataInputStream in = new DataInputStream(new BufferedInputStream(new FileInputStream(files))); // DataOutputStream outmono = new DataOutputStream(new BufferedOutputStream( new FileOutputStream(files + "_" + length + "_monoPerfect.temp"))); DataOutputStream outdi = new DataOutputStream(new BufferedOutputStream( new FileOutputStream(files + "_" + length + "_diPerfect.temp"))); DataOutputStream outtri = new DataOutputStream(new BufferedOutputStream( new FileOutputStream(files + "_" + length + "_triPerfect.temp"))); DataOutputStream outtetra = new DataOutputStream(new BufferedOutputStream( new FileOutputStream(files + "_" + length + "_tetraPerfect.temp"))); DataOutputStream outpenta = new DataOutputStream(new BufferedOutputStream( new FileOutputStream(files + "_" + length + "_pentaPerfect.temp"))); DataOutputStream outhexa = new DataOutputStream(new BufferedOutputStream( new FileOutputStream(files + "_" + length + "_hexaPerfect.temp"))); boolean eof = false; while (!eof) { try { int len = in.readInt(); int line = in.readInt(); for (int k = 0; k < len; k++) { SSR.add(in.readUTF()); int end = in.readInt(); repeats.add(in.readInt()); EndOfSsr.add(end + (line - 1) * 20000); } for (int c = 0; c < SSR.size(); c++) { if (!SSR.get(c).contains("N")) { if (repeats.get(c) * SSR.get(c).length() >= length) { if (SSR.get(c).length() == 1) { countmono.set(i, countmono.get(i) + 1); countmonore.set(i, countmonore.get(i) + repeats.get(c)); if (SSR.get(c).contains("A")) { Amono.set(i, Amono.get(i) + repeats.get(c)); } if (SSR.get(c).contains("T")) { Tmono.set(i, Tmono.get(i) + repeats.get(c)); } if (SSR.get(c).contains("G")) { Gmono.set(i, Gmono.get(i) + repeats.get(c)); } if (SSR.get(c).contains("C")) { Cmono.set(i, Cmono.get(i) + repeats.get(c)); } outmono.writeUTF(SSR.get(c)); outmono.writeInt(repeats.get(c)); outmono.writeInt(EndOfSsr.get(c)); } else if (SSR.get(c).length() == 2) { countdi.set(i, countdi.get(i) + 1); countdire.set(i, countdire.get(i) + repeats.get(c)); if (SSR.get(c).contains("A")) { Adi.set(i, Adi.get(i) + repeats.get(c)); } if (SSR.get(c).contains("T")) { Tdi.set(i, Tdi.get(i) + repeats.get(c)); } if (SSR.get(c).contains("G")) { Gdi.set(i, Gdi.get(i) + repeats.get(c)); } if (SSR.get(c).contains("C")) { Cdi.set(i, Cdi.get(i) + repeats.get(c)); } outdi.writeUTF(SSR.get(c)); outdi.writeInt(repeats.get(c)); outdi.writeInt(EndOfSsr.get(c)); } else if (SSR.get(c).length() == 3) { counttri.set(i, counttri.get(i) + 1); counttrire.set(i, counttrire.get(i) + repeats.get(c)); if (SSR.get(c).contains("A")) { Atri.set(i, Atri.get(i) + repeats.get(c) * StringUtils.countMatches(SSR.get(c), "A")); } if (SSR.get(c).contains("T")) { Ttri.set(i, Ttri.get(i) + repeats.get(c) * StringUtils.countMatches(SSR.get(c), "T")); } if (SSR.get(c).contains("G")) { Gtri.set(i, Gtri.get(i) + repeats.get(c) * StringUtils.countMatches(SSR.get(c), "G")); } if (SSR.get(c).contains("C")) { Ctri.set(i, Ctri.get(i) + repeats.get(c) * StringUtils.countMatches(SSR.get(c), "C")); } outtri.writeUTF(SSR.get(c)); outtri.writeInt(repeats.get(c)); outtri.writeInt(EndOfSsr.get(c)); } else if (SSR.get(c).length() == 4) { counttetra.set(i, counttetra.get(i) + 1); counttetrare.set(i, counttetrare.get(i) + repeats.get(c)); if (SSR.get(c).contains("A")) { Atetra.set(i, Atetra.get(i) + repeats.get(c) * StringUtils.countMatches(SSR.get(c), "A")); } if (SSR.get(c).contains("T")) { Ttetra.set(i, Ttetra.get(i) + repeats.get(c) * StringUtils.countMatches(SSR.get(c), "T")); } if (SSR.get(c).contains("G")) { Gtetra.set(i, Gtetra.get(i) + repeats.get(c) * StringUtils.countMatches(SSR.get(c), "G")); } if (SSR.get(c).contains("C")) { Ctetra.set(i, Ctetra.get(i) + repeats.get(c) * StringUtils.countMatches(SSR.get(c), "C")); } outtetra.writeUTF(SSR.get(c)); outtetra.writeInt(repeats.get(c)); outtetra.writeInt(EndOfSsr.get(c)); } else if (SSR.get(c).length() == 5) { countpenta.set(i, countpenta.get(i) + 1); countpentare.set(i, countpentare.get(i) + repeats.get(c)); if (SSR.get(c).contains("A")) { Apenta.set(i, Apenta.get(i) + repeats.get(c) * StringUtils.countMatches(SSR.get(c), "A")); } if (SSR.get(c).contains("T")) { Tpenta.set(i, Tpenta.get(i) + repeats.get(c) * StringUtils.countMatches(SSR.get(c), "T")); } if (SSR.get(c).contains("G")) { Gpenta.set(i, Gpenta.get(i) + repeats.get(c) * StringUtils.countMatches(SSR.get(c), "G")); } if (SSR.get(c).contains("C")) { Cpenta.set(i, Cpenta.get(i) + repeats.get(c) * StringUtils.countMatches(SSR.get(c), "C")); } outpenta.writeUTF(SSR.get(c)); outpenta.writeInt(repeats.get(c)); outpenta.writeInt(EndOfSsr.get(c)); } else if (SSR.get(c).length() == 6) { counthexa.set(i, counthexa.get(i) + 1); counthexare.set(i, counthexare.get(i) + repeats.get(c)); if (SSR.get(c).contains("A")) { Ahexa.set(i, Ahexa.get(i) + repeats.get(c) * StringUtils.countMatches(SSR.get(c), "A")); } if (SSR.get(c).contains("T")) { Thexa.set(i, Thexa.get(i) + repeats.get(c) * StringUtils.countMatches(SSR.get(c), "T")); } if (SSR.get(c).contains("G")) { Ghexa.set(i, Ghexa.get(i) + repeats.get(c) * StringUtils.countMatches(SSR.get(c), "G")); } if (SSR.get(c).contains("C")) { Chexa.set(i, Chexa.get(i) + repeats.get(c) * StringUtils.countMatches(SSR.get(c), "C")); } outhexa.writeUTF(SSR.get(c)); outhexa.writeInt(repeats.get(c)); outhexa.writeInt(EndOfSsr.get(c)); } } } } SSR = new ArrayList<String>(); repeats = new ArrayList<Integer>(); EndOfSsr = new ArrayList<Integer>(); } catch (EOFException e) { eof = true; } } outmono.close(); outdi.close(); outtri.close(); outtetra.close(); outpenta.close(); outhexa.close(); // in.close(); DataOutputStream save = new DataOutputStream(new BufferedOutputStream( new FileOutputStream(files.substring(0, files.lastIndexOf('/')) + "/perf_stats"))); save.writeInt(countmono.get(i)); save.writeInt(countdi.get(i)); save.writeInt(counttri.get(i)); save.writeInt(counttetra.get(i)); save.writeInt(countpenta.get(i)); save.writeInt(counthexa.get(i)); save.writeInt(countmonore.get(i)); save.writeInt(countdire.get(i)); save.writeInt(counttrire.get(i)); save.writeInt(counttetrare.get(i)); save.writeInt(countpentare.get(i)); save.writeInt(counthexare.get(i)); save.writeInt(Amono.get(i)); save.writeInt(Tmono.get(i)); save.writeInt(Gmono.get(i)); save.writeInt(Cmono.get(i)); save.writeInt(Adi.get(i)); save.writeInt(Tdi.get(i)); save.writeInt(Gdi.get(i)); save.writeInt(Cdi.get(i)); save.writeInt(Atri.get(i)); save.writeInt(Ttri.get(i)); save.writeInt(Gtri.get(i)); save.writeInt(Ctri.get(i)); save.writeInt(Atetra.get(i)); save.writeInt(Ttetra.get(i)); save.writeInt(Gtetra.get(i)); save.writeInt(Ctetra.get(i)); save.writeInt(Apenta.get(i)); save.writeInt(Tpenta.get(i)); save.writeInt(Gpenta.get(i)); save.writeInt(Cpenta.get(i)); save.writeInt(Ahexa.get(i)); save.writeInt(Thexa.get(i)); save.writeInt(Ghexa.get(i)); save.writeInt(Chexa.get(i)); save.close(); } else { DataInputStream save = new DataInputStream(new BufferedInputStream( new FileInputStream(files.substring(0, files.lastIndexOf('/')) + "/perf_stats"))); countmono.set(i, save.readInt()); countdi.set(i, save.readInt()); counttri.set(i, save.readInt()); counttetra.set(i, save.readInt()); countpenta.set(i, save.readInt()); counthexa.set(i, save.readInt()); countmonore.set(i, save.readInt()); countdire.set(i, save.readInt()); counttrire.set(i, save.readInt()); counttetrare.set(i, save.readInt()); countpentare.set(i, save.readInt()); counthexare.set(i, save.readInt()); Amono.set(i, save.readInt()); Tmono.set(i, save.readInt()); Gmono.set(i, save.readInt()); Cmono.set(i, save.readInt()); Adi.set(i, save.readInt()); Tdi.set(i, save.readInt()); Gdi.set(i, save.readInt()); Cdi.set(i, save.readInt()); Atri.set(i, save.readInt()); Ttri.set(i, save.readInt()); Gtri.set(i, save.readInt()); Ctri.set(i, save.readInt()); Atetra.set(i, save.readInt()); Ttetra.set(i, save.readInt()); Gtetra.set(i, save.readInt()); Ctetra.set(i, save.readInt()); Apenta.set(i, save.readInt()); Tpenta.set(i, save.readInt()); Gpenta.set(i, save.readInt()); Cpenta.set(i, save.readInt()); Ahexa.set(i, save.readInt()); Thexa.set(i, save.readInt()); Ghexa.set(i, save.readInt()); Chexa.set(i, save.readInt()); save.close(); } } } }
From source file:MiGA.StatsSelection.java
public void getImPerfectSSRs(String[] organisms, int length, boolean flag, int gap) throws SQLException, ClassNotFoundException, FileNotFoundException, IOException { for (int i = 0; i < organisms.length; i++) { countmono.set(i, 0);//from www.j a v a 2s .c o m countdi.set(i, 0); counttri.set(i, 0); counttetra.set(i, 0); countpenta.set(i, 0); counthexa.set(i, 0); countmonore.set(i, 0); countdire.set(i, 0); counttrire.set(i, 0); counttetrare.set(i, 0); countpentare.set(i, 0); counthexare.set(i, 0); Amono.set(i, 0); Adi.set(i, 0); Atri.set(i, 0); Atetra.set(i, 0); Apenta.set(i, 0); Ahexa.set(i, 0); Tmono.set(i, 0); Tdi.set(i, 0); Ttri.set(i, 0); Ttetra.set(i, 0); Tpenta.set(i, 0); Thexa.set(i, 0); Gmono.set(i, 0); Gdi.set(i, 0); Gtri.set(i, 0); Gtetra.set(i, 0); Gpenta.set(i, 0); Ghexa.set(i, 0); Cmono.set(i, 0); Cdi.set(i, 0); Ctri.set(i, 0); Ctetra.set(i, 0); Cpenta.set(i, 0); Chexa.set(i, 0); boolean found = false; String buffer = new String(); int seekstart = 0; int seekend = 0; List<String> ssrs = new ArrayList<String>(); // 18/11/2013 added starting here String filetype = ""; String filepro = ""; if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } //List<String> files = getFiles(organisms[i], minlen, flag); // 18/11/2013 added ending here while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); List<File> exis = new ArrayList<File>(); exis.add(new File(files + "_" + length + "_" + gap + "_monoImPerfect.temp")); exis.add(new File(files + "_" + length + "_" + gap + "_diImPerfect.temp")); exis.add(new File(files + "_" + length + "_" + gap + "_triImPerfect.temp")); exis.add(new File(files + "_" + length + "_" + gap + "_tetraImPerfect.temp")); exis.add(new File(files + "_" + length + "_" + gap + "_pentaImPerfect.temp")); exis.add(new File(files + "_" + length + "_" + gap + "_hexaImPerfect.temp")); int num = 0; for (int temp = 0; temp < exis.size(); temp++) { if (exis.get(temp).exists()) { num++; } } if (num != exis.size()) { DataInputStream in = new DataInputStream(new BufferedInputStream(new FileInputStream(files))); DataOutputStream outmono = new DataOutputStream(new BufferedOutputStream( new FileOutputStream(files + "_" + length + "_" + gap + "_monoImPerfect.temp"))); DataOutputStream outdi = new DataOutputStream(new BufferedOutputStream( new FileOutputStream(files + "_" + length + "_" + gap + "_diImPerfect.temp"))); DataOutputStream outtri = new DataOutputStream(new BufferedOutputStream( new FileOutputStream(files + "_" + length + "_" + gap + "_triImPerfect.temp"))); DataOutputStream outtetra = new DataOutputStream(new BufferedOutputStream( new FileOutputStream(files + "_" + length + "_" + gap + "_tetraImPerfect.temp"))); DataOutputStream outpenta = new DataOutputStream(new BufferedOutputStream( new FileOutputStream(files + "_" + length + "_" + gap + "_pentaImPerfect.temp"))); DataOutputStream outhexa = new DataOutputStream(new BufferedOutputStream( new FileOutputStream(files + "_" + length + "_" + gap + "_hexaImPerfect.temp"))); boolean eof = false; while (!eof) { try { SSR = new ArrayList<String>(); repeats = new ArrayList<Integer>(); EndOfSsr = new ArrayList<Integer>(); start = new ArrayList<Integer>(); int len = in.readInt(); int line = in.readInt(); //try{ for (int k = 0; k < len; k++) { String temp = in.readUTF(); //THIS //if(!temp.contains("N")){ SSR.add(temp); EndOfSsr.add(in.readInt()); repeats.add(in.readInt()); start.add(EndOfSsr.get(k) - (SSR.get(k).length() * repeats.get(k))); /*}else{ int junk = in.readInt(); junk = in.readInt(); k--; len--; }*/ } /*} catch(IndexOutOfBoundsException e){ System.out.println(SSR.size()); System.out.println(EndOfSsr.size()); System.out.println(repeats.size()); System.out.println(start.size()); }*/ List<String> SSRlen = new ArrayList<String>(); List<Integer> Endlen = new ArrayList<Integer>(); List<Integer> repslen = new ArrayList<Integer>(); List<Integer> startlen = new ArrayList<Integer>(); for (int k = 0; k < SSR.size(); k++) { if (SSR.get(k).length() * repeats.get(k) >= length) { SSRlen.add(SSR.get(k)); Endlen.add(EndOfSsr.get(k)); repslen.add(repeats.get(k)); startlen.add(start.get(k)); } } List<Integer> sortedstart = new ArrayList<Integer>(); List<Integer> sortedend = new ArrayList<Integer>(); for (int t = 0; t < startlen.size(); t++) { sortedstart.add(startlen.get(t)); sortedend.add(Endlen.get(t)); } Collections.sort(sortedstart); Collections.sort(sortedend); //List<String> tofile = new ArrayList<String>(); for (int k = 0; k < sortedstart.size() - 1; k++) { found = false; ssrs.clear(); ssrs = new ArrayList<String>(); if (sortedstart.get(k + 1) - sortedend.get(k) <= gap && sortedstart.get(k + 1) - sortedend.get(k) >= 0) { seekstart = sortedstart.get(k); while (k < sortedstart.size() - 1 && sortedstart.get(k + 1) - sortedend.get(k) <= gap && sortedstart.get(k + 1) - sortedend.get(k) >= 0) { for (int c = 0; c < startlen.size(); c++) { if (sortedstart.get(k) == startlen.get(c)) { ssrs.add(SSRlen.get(c)); } if (sortedstart.get(k + 1) == startlen.get(c)) { ssrs.add(SSRlen.get(c)); seekend = Endlen.get(c); found = true; } } k++; } k--; } boolean check = checkallsame(ssrs); if (found && check) { BufferedReader stdin = null; if (flag) { String[] temp = files.split("/"); boolean type = CheckForKaryotype(organisms[i]); String newdir = ""; if (type) { newdir = temp[0] + "/" + temp[1] + "/chrom-" + temp[3].substring(0, temp[3].lastIndexOf('.')) + "-slices.txt"; } else { newdir = temp[0] + "/" + temp[1] + "/slice-" + temp[3].substring(0, temp[3].lastIndexOf('.')) + ".txt"; } stdin = new BufferedReader(new FileReader(newdir)); } else { //files.add("local/" + organism + "/data/" + temp + ".ssr"); String[] temp = files.split("data/"); String newdir = temp[0] + "/" + temp[1].substring(0, temp[1].lastIndexOf('.')) + ".txt"; stdin = new BufferedReader(new FileReader(newdir)); } buffer = ""; for (int c = 0; c < line; c++) { buffer = stdin.readLine(); } //System.out.println(buffer.length() + "\t" + seekstart + "\t" + seekend); int real_end = ((Integer) (line - 1) * 20000) + seekend; int real_start = ((Integer) (line - 1) * 20000) + seekstart; //tofile.add("SSR: "+buffer.substring(seekstart, seekend) + "start-end: "+ real_start + "-" +real_end ); if (ssrs.get(1).length() == 1) { countmono.set(i, countmono.get(i) + 1); countmonore.set(i, countmonore.get(i) + real_end - real_start); outmono.writeUTF(buffer.substring(seekstart + 1, seekend + 1)); if (buffer.substring(seekstart + 1, seekend + 1).contains("A") || buffer.substring(seekstart + 1, seekend + 1).contains("a")) { Amono.set(i, Amono.get(i) + StringUtils.countMatches( buffer.substring(seekstart + 1, seekend + 1), "A") + StringUtils.countMatches( buffer.substring(seekstart + 1, seekend + 1), "a")); } if (buffer.substring(seekstart + 1, seekend + 1).contains("T") || buffer.substring(seekstart + 1, seekend + 1).contains("t")) { Tmono.set(i, Tmono.get(i) + StringUtils.countMatches( buffer.substring(seekstart + 1, seekend + 1), "T") + StringUtils.countMatches( buffer.substring(seekstart + 1, seekend + 1), "t")); } if (buffer.substring(seekstart + 1, seekend + 1).contains("G") || buffer.substring(seekstart + 1, seekend + 1).contains("g")) { Gmono.set(i, Gmono.get(i) + StringUtils.countMatches( buffer.substring(seekstart + 1, seekend + 1), "G") + StringUtils.countMatches( buffer.substring(seekstart + 1, seekend + 1), "g")); } if (buffer.substring(seekstart + 1, seekend + 1).contains("C") || buffer.substring(seekstart + 1, seekend + 1).contains("c")) { Cmono.set(i, Cmono.get(i) + StringUtils.countMatches( buffer.substring(seekstart + 1, seekend + 1), "C") + StringUtils.countMatches( buffer.substring(seekstart + 1, seekend + 1), "c")); } outmono.writeInt(real_start + 1); outmono.writeInt(real_end + 1); } else if (ssrs.get(1).length() == 2) { countdi.set(i, countdi.get(i) + 1); countdire.set(i, countdire.get(i) + real_end - real_start); if (buffer.substring(seekstart, seekend).contains("A") || buffer.substring(seekstart, seekend).contains("a")) { Adi.set(i, Adi.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "A") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "a")); } if (buffer.substring(seekstart, seekend).contains("T") || buffer.substring(seekstart, seekend).contains("t")) { Tdi.set(i, Tdi.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "T") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "t")); } if (buffer.substring(seekstart, seekend).contains("G") || buffer.substring(seekstart, seekend).contains("g")) { Gdi.set(i, Gdi.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "G") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "g")); } if (buffer.substring(seekstart, seekend).contains("C") || buffer.substring(seekstart, seekend).contains("c")) { Cdi.set(i, Cdi.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "C") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "c")); } outdi.writeUTF(buffer.substring(seekstart, seekend)); outdi.writeInt(real_start); outdi.writeInt(real_end); } else if (ssrs.get(1).length() == 3) { counttri.set(i, counttri.get(i) + 1); counttrire.set(i, counttrire.get(i) + real_end - real_start); if (buffer.substring(seekstart, seekend).contains("A") || buffer.substring(seekstart, seekend).contains("a")) { Atri.set(i, Atri.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "A") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "a")); } if (buffer.substring(seekstart, seekend).contains("T") || buffer.substring(seekstart, seekend).contains("t")) { Ttri.set(i, Ttri.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "T") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "t")); } if (buffer.substring(seekstart, seekend).contains("G") || buffer.substring(seekstart, seekend).contains("g")) { Gtri.set(i, Gtri.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "G") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "g")); } if (buffer.substring(seekstart, seekend).contains("C") || buffer.substring(seekstart, seekend).contains("c")) { Ctri.set(i, Ctri.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "C") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "c")); } outtri.writeUTF(buffer.substring(seekstart, seekend)); outtri.writeInt(real_start); outtri.writeInt(real_end); } else if (ssrs.get(1).length() == 4) { counttetra.set(i, counttetra.get(i) + 1); counttetrare.set(i, counttetrare.get(i) + real_end - real_start); if (buffer.substring(seekstart, seekend).contains("A") || buffer.substring(seekstart, seekend).contains("a")) { Atetra.set(i, Atetra.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "A") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "a")); } if (buffer.substring(seekstart, seekend).contains("T") || buffer.substring(seekstart, seekend).contains("t")) { Ttetra.set(i, Ttetra.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "T") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "t")); } if (buffer.substring(seekstart, seekend).contains("G") || buffer.substring(seekstart, seekend).contains("g")) { Gtetra.set(i, Gtetra.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "G") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "g")); } if (buffer.substring(seekstart, seekend).contains("C") || buffer.substring(seekstart, seekend).contains("c")) { Ctetra.set(i, Ctetra.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "C") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "c")); } outtetra.writeUTF(buffer.substring(seekstart, seekend)); outtetra.writeInt(real_start); outtetra.writeInt(real_end); } else if (ssrs.get(1).length() == 5) { countpenta.set(i, countpenta.get(i) + 1); countpentare.set(i, countpentare.get(i) + real_end - real_start); if (buffer.substring(seekstart, seekend).contains("A") || buffer.substring(seekstart, seekend).contains("a")) { Apenta.set(i, Apenta.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "A") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "a")); } if (buffer.substring(seekstart, seekend).contains("T") || buffer.substring(seekstart, seekend).contains("t")) { Tpenta.set(i, Tpenta.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "T") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "t")); } if (buffer.substring(seekstart, seekend).contains("G") || buffer.substring(seekstart, seekend).contains("g")) { Gpenta.set(i, Gpenta.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "G") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "g")); } if (buffer.substring(seekstart, seekend).contains("C") || buffer.substring(seekstart, seekend).contains("c")) { Cpenta.set(i, Cpenta.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "C") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "c")); } outpenta.writeUTF(buffer.substring(seekstart, seekend)); outpenta.writeInt(real_start); outpenta.writeInt(real_end); } else if (ssrs.get(1).length() == 6) { counthexa.set(i, counthexa.get(i) + 1); counthexare.set(i, counthexare.get(i) + real_end - real_start); if (buffer.substring(seekstart, seekend).contains("A") || buffer.substring(seekstart, seekend).contains("a")) { Ahexa.set(i, Ahexa.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "A") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "a")); } if (buffer.substring(seekstart, seekend).contains("T") || buffer.substring(seekstart, seekend).contains("t")) { Thexa.set(i, Thexa.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "T") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "t")); } if (buffer.substring(seekstart, seekend).contains("G") || buffer.substring(seekstart, seekend).contains("g")) { Ghexa.set(i, Ghexa.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "G") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "g")); } if (buffer.substring(seekstart, seekend).contains("C") || buffer.substring(seekstart, seekend).contains("c")) { Chexa.set(i, Chexa.get(i) + StringUtils.countMatches( buffer.substring(seekstart, seekend), "C") + StringUtils.countMatches( buffer.substring(seekstart, seekend), "c")); } outhexa.writeUTF(buffer.substring(seekstart, seekend)); outhexa.writeInt(real_start); outhexa.writeInt(real_end); } //out.println("SSR: " + buffer.substring(seekstart, seekend) + " start-end: " + real_start + "-" + real_end); stdin.close(); } } } catch (EOFException e) { eof = true; } } in.close(); outmono.close(); outdi.close(); outtri.close(); outtetra.close(); outpenta.close(); outhexa.close(); DataOutputStream save = new DataOutputStream(new BufferedOutputStream( new FileOutputStream(files.substring(0, files.lastIndexOf('/')) + "/imperf_stats"))); save.writeInt(countmono.get(i)); save.writeInt(countdi.get(i)); save.writeInt(counttri.get(i)); save.writeInt(counttetra.get(i)); save.writeInt(countpenta.get(i)); save.writeInt(counthexa.get(i)); save.writeInt(countmonore.get(i)); save.writeInt(countdire.get(i)); save.writeInt(counttrire.get(i)); save.writeInt(counttetrare.get(i)); save.writeInt(countpentare.get(i)); save.writeInt(counthexare.get(i)); save.writeInt(Amono.get(i)); save.writeInt(Tmono.get(i)); save.writeInt(Gmono.get(i)); save.writeInt(Cmono.get(i)); save.writeInt(Adi.get(i)); save.writeInt(Tdi.get(i)); save.writeInt(Gdi.get(i)); save.writeInt(Cdi.get(i)); save.writeInt(Atri.get(i)); save.writeInt(Ttri.get(i)); save.writeInt(Gtri.get(i)); save.writeInt(Ctri.get(i)); save.writeInt(Atetra.get(i)); save.writeInt(Ttetra.get(i)); save.writeInt(Gtetra.get(i)); save.writeInt(Ctetra.get(i)); save.writeInt(Apenta.get(i)); save.writeInt(Tpenta.get(i)); save.writeInt(Gpenta.get(i)); save.writeInt(Cpenta.get(i)); save.writeInt(Ahexa.get(i)); save.writeInt(Thexa.get(i)); save.writeInt(Ghexa.get(i)); save.writeInt(Chexa.get(i)); save.close(); } else { DataInputStream save = new DataInputStream(new BufferedInputStream( new FileInputStream(files.substring(0, files.lastIndexOf('/')) + "/imperf_stats"))); countmono.set(i, save.readInt()); countdi.set(i, save.readInt()); counttri.set(i, save.readInt()); counttetra.set(i, save.readInt()); countpenta.set(i, save.readInt()); counthexa.set(i, save.readInt()); countmonore.set(i, save.readInt()); countdire.set(i, save.readInt()); counttrire.set(i, save.readInt()); counttetrare.set(i, save.readInt()); countpentare.set(i, save.readInt()); counthexare.set(i, save.readInt()); Amono.set(i, save.readInt()); Tmono.set(i, save.readInt()); Gmono.set(i, save.readInt()); Cmono.set(i, save.readInt()); Adi.set(i, save.readInt()); Tdi.set(i, save.readInt()); Gdi.set(i, save.readInt()); Cdi.set(i, save.readInt()); Atri.set(i, save.readInt()); Ttri.set(i, save.readInt()); Gtri.set(i, save.readInt()); Ctri.set(i, save.readInt()); Atetra.set(i, save.readInt()); Ttetra.set(i, save.readInt()); Gtetra.set(i, save.readInt()); Ctetra.set(i, save.readInt()); Apenta.set(i, save.readInt()); Tpenta.set(i, save.readInt()); Gpenta.set(i, save.readInt()); Cpenta.set(i, save.readInt()); Ahexa.set(i, save.readInt()); Thexa.set(i, save.readInt()); Ghexa.set(i, save.readInt()); Chexa.set(i, save.readInt()); save.close(); } } } }
From source file:com.codename1.impl.android.AndroidImplementation.java
/** * Gets the service properties. Will read properties from file so that * they are available even if CN1 is not initialized. * @param a/*from w w w . j av a 2s . c o m*/ * @return */ public static Map<String, String> getServiceProperties(Context a) { if (serviceProperties == null) { InputStream i = null; try { serviceProperties = new HashMap<String, String>(); i = a.openFileInput("CN1$AndroidServiceProperties"); if (i == null) { return serviceProperties; } DataInputStream is = new DataInputStream(i); int count = is.readInt(); for (int idx = 0; idx < count; idx++) { String key = is.readUTF(); String value = is.readUTF(); serviceProperties.put(key, value); } } catch (IOException ex) { Logger.getLogger(AndroidImplementation.class.getName()).log(Level.SEVERE, null, ex); } finally { try { if (i != null) i.close(); } catch (Throwable ex) { Logger.getLogger(AndroidImplementation.class.getName()).log(Level.SEVERE, null, ex); } } } return serviceProperties; }
From source file:com.codename1.impl.android.AndroidImplementation.java
public static void firePendingPushes(final PushCallback c, final Context a) { try {//from w ww.j a v a 2 s . c o m if (c != null) { InputStream i = a.openFileInput("CN1$AndroidPendingNotifications"); if (i == null) { return; } DataInputStream is = new DataInputStream(i); int count = is.readByte(); for (int iter = 0; iter < count; iter++) { boolean hasType = is.readBoolean(); String actualType = null; if (hasType) { actualType = is.readUTF(); } final String t; final String b; final String category; final String image; if ("99".equals(actualType)) { // This was a rich push Map<String, String> vals = splitQuery(is.readUTF()); t = vals.get("type"); b = vals.get("body"); category = vals.get("category"); image = vals.get("image"); } else { t = actualType; b = is.readUTF(); category = null; image = null; } long s = is.readLong(); Display.getInstance().callSerially(new Runnable() { @Override public void run() { Display.getInstance().setProperty("pendingPush", "true"); Display.getInstance().setProperty("pushType", t); initPushContent(b, image, t, category, a); if (t != null && ("3".equals(t) || "6".equals(t))) { String[] a = b.split(";"); c.push(a[0]); c.push(a[1]); } else if (t != null && ("101".equals(t))) { c.push(b.substring(b.indexOf(" ") + 1)); } else { c.push(b); } Display.getInstance().setProperty("pendingPush", null); } }); } a.deleteFile("CN1$AndroidPendingNotifications"); } } catch (IOException err) { } }
From source file:com.codename1.impl.android.AndroidImplementation.java
public static String[] getPendingPush(String type, Context a) { InputStream i = null;//w w w . ja v a2 s .c o m try { i = a.openFileInput("CN1$AndroidPendingNotifications"); if (i == null) { return null; } DataInputStream is = new DataInputStream(i); int count = is.readByte(); Vector v = new Vector<String>(); for (int iter = 0; iter < count; iter++) { boolean hasType = is.readBoolean(); String actualType = null; if (hasType) { actualType = is.readUTF(); } final String t; final String b; if ("99".equals(actualType)) { // This was a rich push Map<String, String> vals = splitQuery(is.readUTF()); t = vals.get("type"); b = vals.get("body"); //category = vals.get("category"); //image = vals.get("image"); } else { t = actualType; b = is.readUTF(); //category = null; //image = null; } long s = is.readLong(); if (t != null && ("3".equals(t) || "6".equals(t))) { String[] m = b.split(";"); v.add(m[0]); } else if (t != null && "4".equals(t)) { String[] m = b.split(";"); v.add(m[1]); } else if (t != null && "2".equals(t)) { continue; } else if (t != null && "101".equals(t)) { v.add(b.substring(b.indexOf(" ") + 1)); } else { v.add(b); } } String[] retVal = new String[v.size()]; for (int j = 0; j < retVal.length; j++) { retVal[j] = (String) v.get(j); } return retVal; } catch (Exception ex) { ex.printStackTrace(); } finally { try { if (i != null) { i.close(); } } catch (IOException ex) { } } return null; }