List of usage examples for java.io DataOutputStream writeUTF
public final void writeUTF(String str) throws IOException
From source file:carnero.cgeo.original.libs.Base.java
public boolean runExternalMap(int application, Activity activity, Resources res, Warning warning, GoogleAnalyticsTracker tracker, Cache cache, Waypoint waypoint, Double latitude, Double longitude) { if (cache == null && waypoint == null && latitude == null && longitude == null) { return false; }//from ww w . j a va2 s . c o m if (application == mapAppLocus) { // locus try { final Intent intentTest = new Intent(Intent.ACTION_VIEW); intentTest.setData(Uri.parse("menion.points:x")); if (isIntentAvailable(activity, intentTest) == true) { final ArrayList<Waypoint> waypoints = new ArrayList<Waypoint>(); // get only waypoints with coordinates if (cache != null && cache.waypoints != null && cache.waypoints.isEmpty() == false) { for (Waypoint wp : cache.waypoints) { if (wp.latitude != null && wp.longitude != null) { waypoints.add(wp); } } } final ByteArrayOutputStream baos = new ByteArrayOutputStream(); final DataOutputStream dos = new DataOutputStream(baos); dos.writeInt(1); // not used if (cache != null) { if (waypoints == null || waypoints.isEmpty() == true) { dos.writeInt(1); // cache only } else { dos.writeInt((1 + waypoints.size())); // cache and waypoints } } else { dos.writeInt(1); // one waypoint } int icon = -1; if (cache != null) { icon = getIcon(true, cache.type, cache.own, cache.found, cache.disabled || cache.archived); } else if (waypoint != null) { icon = getIcon(false, waypoint.type, false, false, false); } else { icon = getIcon(false, "waypoint", false, false, false); } if (icon > 0) { // load icon Bitmap bitmap = BitmapFactory.decodeResource(res, icon); ByteArrayOutputStream baos2 = new ByteArrayOutputStream(); bitmap.compress(Bitmap.CompressFormat.PNG, 100, baos2); byte[] image = baos2.toByteArray(); dos.writeInt(image.length); dos.write(image); } else { // no icon dos.writeInt(0); // no image } // name if (cache != null && cache.name != null && cache.name.length() > 0) { dos.writeUTF(cache.name); } else if (waypoint != null && waypoint.name != null && waypoint.name.length() > 0) { dos.writeUTF(waypoint.name); } else { dos.writeUTF(""); } // description if (cache != null && cache.geocode != null && cache.geocode.length() > 0) { dos.writeUTF(cache.geocode.toUpperCase()); } else if (waypoint != null && waypoint.lookup != null && waypoint.lookup.length() > 0) { dos.writeUTF(waypoint.lookup.toUpperCase()); } else { dos.writeUTF(""); } // additional data :: keyword, button title, package, activity, data name, data content if (cache != null && cache.geocode != null && cache.geocode.length() > 0) { dos.writeUTF("intent;c:geo;carnero.cgeo;carnero.cgeo.cgeodetail;geocode;" + cache.geocode); } else if (waypoint != null && waypoint.id != null && waypoint.id > 0) { dos.writeUTF("intent;c:geo;carnero.cgeo;carnero.cgeo.cgeowaypoint;id;" + waypoint.id); } else { dos.writeUTF(""); } if (cache != null && cache.latitude != null && cache.longitude != null) { dos.writeDouble(cache.latitude); // latitude dos.writeDouble(cache.longitude); // longitude } else if (waypoint != null && waypoint.latitude != null && waypoint.longitude != null) { dos.writeDouble(waypoint.latitude); // latitude dos.writeDouble(waypoint.longitude); // longitude } else { dos.writeDouble(latitude); // latitude dos.writeDouble(longitude); // longitude } // cache waypoints if (waypoints != null && waypoints.isEmpty() == false) { for (Waypoint wp : waypoints) { if (wp == null || wp.latitude == null || wp.longitude == null) { continue; } final int wpIcon = getIcon(false, wp.type, false, false, false); if (wpIcon > 0) { // load icon Bitmap bitmap = BitmapFactory.decodeResource(res, wpIcon); ByteArrayOutputStream baos2 = new ByteArrayOutputStream(); bitmap.compress(Bitmap.CompressFormat.PNG, 100, baos2); byte[] image = baos2.toByteArray(); dos.writeInt(image.length); dos.write(image); } else { // no icon dos.writeInt(0); // no image } // name if (wp.lookup != null && wp.lookup.length() > 0) { dos.writeUTF(wp.lookup.toUpperCase()); } else { dos.writeUTF(""); } // description if (wp.name != null && wp.name.length() > 0) { dos.writeUTF(wp.name); } else { dos.writeUTF(""); } // additional data :: keyword, button title, package, activity, data name, data content if (wp.id != null && wp.id > 0) { dos.writeUTF("intent;c:geo;carnero.cgeo;carnero.cgeo.cgeowaypoint;id;" + wp.id); } else { dos.writeUTF(""); } dos.writeDouble(wp.latitude); // latitude dos.writeDouble(wp.longitude); // longitude } } final Intent intent = new Intent(); intent.setAction(Intent.ACTION_VIEW); intent.setData(Uri.parse("menion.points:data")); intent.putExtra("data", baos.toByteArray()); activity.startActivity(intent); sendAnal(activity, tracker, "/external/locus"); return true; } } catch (Exception e) { // nothing } } if (application == mapAppRmaps) { // rmaps try { final Intent intent = new Intent("com.robert.maps.action.SHOW_POINTS"); if (isIntentAvailable(activity, intent) == true) { final ArrayList<String> locations = new ArrayList<String>(); if (cache != null && cache.latitude != null && cache.longitude != null) { locations.add(String.format((Locale) null, "%.6f", cache.latitude) + "," + String.format((Locale) null, "%.6f", cache.longitude) + ";" + cache.geocode + ";" + cache.name); } else if (waypoint != null && waypoint.latitude != null && waypoint.longitude != null) { locations.add(String.format((Locale) null, "%.6f", waypoint.latitude) + "," + String.format((Locale) null, "%.6f", waypoint.longitude) + ";" + waypoint.lookup + ";" + waypoint.name); } intent.putStringArrayListExtra("locations", locations); activity.startActivity(intent); sendAnal(activity, tracker, "/external/rmaps"); return true; } } catch (Exception e) { // nothing } } if (application == mapAppAny) { // fallback try { if (cache != null && cache.latitude != null && cache.longitude != null) { activity.startActivity(new Intent(Intent.ACTION_VIEW, Uri.parse("geo:" + cache.latitude + "," + cache.longitude))); // INFO: q parameter works with Google Maps, but breaks cooperation with all other apps } else if (waypoint != null && waypoint.latitude != null && waypoint.longitude != null) { activity.startActivity(new Intent(Intent.ACTION_VIEW, Uri.parse("geo:" + waypoint.latitude + "," + waypoint.longitude))); // INFO: q parameter works with Google Maps, but breaks cooperation with all other apps } sendAnal(activity, tracker, "/external/native/maps"); return true; } catch (Exception e) { // nothing } } Log.i(Settings.tag, "cgBase.runExternalMap: No maps application available."); if (warning != null && res != null) { warning.showToast(res.getString(R.string.err_application_no)); } return false; }
From source file:carnero.cgeo.cgBase.java
public boolean runExternalMap(int application, Activity activity, Resources res, cgWarning warning, GoogleAnalyticsTracker tracker, cgCache cache, cgWaypoint waypoint, Double latitude, Double longitude) { if (cache == null && waypoint == null && latitude == null && longitude == null) { return false; }/*w w w. java 2 s. c o m*/ if (application == mapAppLocus) { // locus try { final Intent intentTest = new Intent(Intent.ACTION_VIEW); intentTest.setData(Uri.parse("menion.points:x")); if (isIntentAvailable(activity, intentTest) == true) { final ArrayList<cgWaypoint> waypoints = new ArrayList<cgWaypoint>(); // get only waypoints with coordinates if (cache != null && cache.waypoints != null && cache.waypoints.isEmpty() == false) { for (cgWaypoint wp : cache.waypoints) { if (wp.latitude != null && wp.longitude != null) { waypoints.add(wp); } } } final ByteArrayOutputStream baos = new ByteArrayOutputStream(); final DataOutputStream dos = new DataOutputStream(baos); dos.writeInt(1); // not used if (cache != null) { if (waypoints == null || waypoints.isEmpty() == true) { dos.writeInt(1); // cache only } else { dos.writeInt((1 + waypoints.size())); // cache and waypoints } } else { dos.writeInt(1); // one waypoint } int icon = -1; if (cache != null) { icon = getIcon(true, cache.type, cache.own, cache.found, cache.disabled || cache.archived); } else if (waypoint != null) { icon = getIcon(false, waypoint.type, false, false, false); } else { icon = getIcon(false, "waypoint", false, false, false); } if (icon > 0) { // load icon Bitmap bitmap = BitmapFactory.decodeResource(res, icon); ByteArrayOutputStream baos2 = new ByteArrayOutputStream(); bitmap.compress(Bitmap.CompressFormat.PNG, 100, baos2); byte[] image = baos2.toByteArray(); dos.writeInt(image.length); dos.write(image); } else { // no icon dos.writeInt(0); // no image } // name if (cache != null && cache.name != null && cache.name.length() > 0) { dos.writeUTF(cache.name); } else if (waypoint != null && waypoint.name != null && waypoint.name.length() > 0) { dos.writeUTF(waypoint.name); } else { dos.writeUTF(""); } // description if (cache != null && cache.geocode != null && cache.geocode.length() > 0) { dos.writeUTF(cache.geocode.toUpperCase()); } else if (waypoint != null && waypoint.lookup != null && waypoint.lookup.length() > 0) { dos.writeUTF(waypoint.lookup.toUpperCase()); } else { dos.writeUTF(""); } // additional data :: keyword, button title, package, activity, data name, data content if (cache != null && cache.geocode != null && cache.geocode.length() > 0) { dos.writeUTF("intent;c:geo;carnero.cgeo;carnero.cgeo.cgeodetail;geocode;" + cache.geocode); } else if (waypoint != null && waypoint.id != null && waypoint.id > 0) { dos.writeUTF("intent;c:geo;carnero.cgeo;carnero.cgeo.cgeowaypoint;id;" + waypoint.id); } else { dos.writeUTF(""); } if (cache != null && cache.latitude != null && cache.longitude != null) { dos.writeDouble(cache.latitude); // latitude dos.writeDouble(cache.longitude); // longitude } else if (waypoint != null && waypoint.latitude != null && waypoint.longitude != null) { dos.writeDouble(waypoint.latitude); // latitude dos.writeDouble(waypoint.longitude); // longitude } else { dos.writeDouble(latitude); // latitude dos.writeDouble(longitude); // longitude } // cache waypoints if (waypoints != null && waypoints.isEmpty() == false) { for (cgWaypoint wp : waypoints) { if (wp == null || wp.latitude == null || wp.longitude == null) { continue; } final int wpIcon = getIcon(false, wp.type, false, false, false); if (wpIcon > 0) { // load icon Bitmap bitmap = BitmapFactory.decodeResource(res, wpIcon); ByteArrayOutputStream baos2 = new ByteArrayOutputStream(); bitmap.compress(Bitmap.CompressFormat.PNG, 100, baos2); byte[] image = baos2.toByteArray(); dos.writeInt(image.length); dos.write(image); } else { // no icon dos.writeInt(0); // no image } // name if (wp.lookup != null && wp.lookup.length() > 0) { dos.writeUTF(wp.lookup.toUpperCase()); } else { dos.writeUTF(""); } // description if (wp.name != null && wp.name.length() > 0) { dos.writeUTF(wp.name); } else { dos.writeUTF(""); } // additional data :: keyword, button title, package, activity, data name, data content if (wp.id != null && wp.id > 0) { dos.writeUTF("intent;c:geo;carnero.cgeo;carnero.cgeo.cgeowaypoint;id;" + wp.id); } else { dos.writeUTF(""); } dos.writeDouble(wp.latitude); // latitude dos.writeDouble(wp.longitude); // longitude } } final Intent intent = new Intent(); intent.setAction(Intent.ACTION_VIEW); intent.setData(Uri.parse("menion.points:data")); intent.putExtra("data", baos.toByteArray()); activity.startActivity(intent); sendAnal(activity, tracker, "/external/locus"); return true; } } catch (Exception e) { // nothing } } if (application == mapAppRmaps) { // rmaps try { final Intent intent = new Intent("com.robert.maps.action.SHOW_POINTS"); if (isIntentAvailable(activity, intent) == true) { final ArrayList<String> locations = new ArrayList<String>(); if (cache != null && cache.latitude != null && cache.longitude != null) { locations.add(String.format((Locale) null, "%.6f", cache.latitude) + "," + String.format((Locale) null, "%.6f", cache.longitude) + ";" + cache.geocode + ";" + cache.name); } else if (waypoint != null && waypoint.latitude != null && waypoint.longitude != null) { locations.add(String.format((Locale) null, "%.6f", waypoint.latitude) + "," + String.format((Locale) null, "%.6f", waypoint.longitude) + ";" + waypoint.lookup + ";" + waypoint.name); } intent.putStringArrayListExtra("locations", locations); activity.startActivity(intent); sendAnal(activity, tracker, "/external/rmaps"); return true; } } catch (Exception e) { // nothing } } if (application == mapAppAny) { // fallback try { if (cache != null && cache.latitude != null && cache.longitude != null) { activity.startActivity(new Intent(Intent.ACTION_VIEW, Uri.parse("geo:" + cache.latitude + "," + cache.longitude))); // INFO: q parameter works with Google Maps, but breaks cooperation with all other apps } else if (waypoint != null && waypoint.latitude != null && waypoint.longitude != null) { activity.startActivity(new Intent(Intent.ACTION_VIEW, Uri.parse("geo:" + waypoint.latitude + "," + waypoint.longitude))); // INFO: q parameter works with Google Maps, but breaks cooperation with all other apps } sendAnal(activity, tracker, "/external/native/maps"); return true; } catch (Exception e) { // nothing } } Log.i(cgSettings.tag, "cgBase.runExternalMap: No maps application available."); if (warning != null && res != null) { warning.showToast(res.getString(R.string.err_application_no)); } return false; }
From source file:com.codename1.impl.android.AndroidImplementation.java
public static void writeServiceProperties(Context a) { if (servicePropertiesDirty()) { Map<String, String> out = getServiceProperties(a); for (String key : servicePropertyKeys) { String val = Display.getInstance().getProperty(key, null); if (val != null) { out.put(key, val); }/* www . jav a2 s. c om*/ if ("true".equals(Display.getInstance().getProperty(key + "#delete", null))) { out.remove(key); } } OutputStream os = null; try { os = a.openFileOutput("CN1$AndroidServiceProperties", 0); if (os == null) { System.out.println("Failed to save service properties null output stream"); return; } DataOutputStream dos = new DataOutputStream(os); dos.writeInt(out.size()); for (String key : out.keySet()) { dos.writeUTF(key); dos.writeUTF((String) out.get(key)); } serviceProperties = null; } catch (FileNotFoundException ex) { System.out.println( "Service properties file not found. This is normal for the first run. On subsequent runs, the file should exist."); } catch (IOException ex) { Logger.getLogger(AndroidImplementation.class.getName()).log(Level.SEVERE, null, ex); } finally { try { if (os != null) os.close(); } catch (Throwable ex) { Logger.getLogger(AndroidImplementation.class.getName()).log(Level.SEVERE, null, ex); } } } }
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 w w . j av a 2 s. co 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:com.codename1.impl.android.AndroidImplementation.java
public static void appendNotification(String type, String body, String image, String category, Context a) { try {/* ww w. jav a2s . co m*/ String[] fileList = a.fileList(); byte[] data = null; for (int iter = 0; iter < fileList.length; iter++) { if (fileList[iter].equals("CN1$AndroidPendingNotifications")) { InputStream is = a.openFileInput("CN1$AndroidPendingNotifications"); if (is != null) { data = readInputStream(is); sCleanup(a); break; } } } DataOutputStream os = new DataOutputStream(a.openFileOutput("CN1$AndroidPendingNotifications", 0)); if (data != null) { data[0]++; os.write(data); } else { os.writeByte(1); } String bodyType = type; if (image != null || category != null) { type = "99"; } if (type != null) { os.writeBoolean(true); os.writeUTF(type); } else { os.writeBoolean(false); } if ("99".equals(type)) { String msg = "body=" + java.net.URLEncoder.encode(body, "UTF-8") + "&type=" + java.net.URLEncoder.encode(bodyType, "UTF-8"); if (category != null) { msg += "&category=" + java.net.URLEncoder.encode(category, "UTF-8"); } if (image != null) { image += "&image=" + java.net.URLEncoder.encode(image, "UTF-8"); } os.writeUTF(msg); } else { os.writeUTF(body); } os.writeLong(System.currentTimeMillis()); } catch (IOException err) { err.printStackTrace(); } }
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 w w w .j a va2 s. 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(); } } } }