Example usage for java.util HashSet size

List of usage examples for java.util HashSet size

  1. HOME
  2. Java
  3. java
  4. java.util.*
  5. HashSet
  6. size

Introduction

In this page you can find the example usage for java.util HashSet size.

Prototype

public int size()

Source Link

Document

Returns the number of elements in this set (its cardinality).

Usage

From source file:org.runnerup.export.SyncManager.java

public void loadWorkouts(final HashSet<WorkoutRef> pendingWorkouts, final Callback callback) {
    int cnt = pendingWorkouts.size();
    mSpinner.setTitle("Downloading workouts (" + cnt + ")");
    mSpinner.show();/*from  w  w w. ja va 2s  . co m*/
    new AsyncTask<String, String, Synchronizer.Status>() {

        @Override
        protected void onProgressUpdate(String... values) {
            mSpinner.setMessage("Loading " + values[0] + " from " + values[1]);
        }

        @Override
        protected Synchronizer.Status doInBackground(String... params0) {
            for (WorkoutRef ref : pendingWorkouts) {
                publishProgress(ref.workoutName, ref.synchronizer);
                Synchronizer synchronizer = synchronizers.get(ref.synchronizer);
                File f = WorkoutSerializer.getFile(mContext, ref.workoutName);
                File w = f;
                if (f.exists()) {
                    w = WorkoutSerializer.getFile(mContext, ref.workoutName + ".tmp");
                }
                try {
                    synchronizer.downloadWorkout(w, ref.workoutKey);
                    if (w != f) {
                        if (compareFiles(w, f) != true) {
                            Log.e(getClass().getName(), "overwriting " + f.getPath() + " with " + w.getPath());
                            // TODO dialog
                            f.delete();
                            w.renameTo(f);
                        } else {
                            Log.e(getClass().getName(), "file identical...deleting temporary " + w.getPath());
                            w.delete();
                        }
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                    w.delete();
                }
            }
            return Synchronizer.Status.OK;
        }

        @Override
        protected void onPostExecute(Synchronizer.Status result) {
            mSpinner.dismiss();
            if (callback != null) {
                callback.run(null, Synchronizer.Status.OK);
            }
        }
    }.execute("string");
}

From source file:nl.hnogames.domoticz.Preference.Preference.java

private void setPreferences() {
    final android.preference.SwitchPreference MultiServerPreference = (android.preference.SwitchPreference) findPreference(
            "enableMultiServers");
    android.preference.Preference ServerSettings = findPreference("server_settings");
    android.preference.Preference PermissionsSettings = findPreference("permissionssettings");
    android.preference.Preference NotificationLogged = findPreference("notification_show_logs");
    android.preference.Preference fetchServerConfig = findPreference("server_force_fetch_config");
    android.preference.Preference resetApplication = findPreference("reset_settings");
    android.preference.ListPreference displayLanguage = (ListPreference) findPreference("displayLanguage");
    final android.preference.Preference registrationId = findPreference("notification_registration_id");
    android.preference.Preference GeoSettings = findPreference("geo_settings");
    android.preference.SwitchPreference WearPreference = (android.preference.SwitchPreference) findPreference(
            "enableWearItems");
    android.preference.Preference NFCPreference = findPreference("nfc_settings");
    android.preference.Preference QRCodePreference = findPreference("qrcode_settings");
    android.preference.Preference SpeechPreference = findPreference("speech_settings");
    android.preference.SwitchPreference EnableNFCPreference = (android.preference.SwitchPreference) findPreference(
            "enableNFC");
    android.preference.SwitchPreference EnableQRCodePreference = (android.preference.SwitchPreference) findPreference(
            "enableQRCode");
    android.preference.SwitchPreference EnableSpeechPreference = (android.preference.SwitchPreference) findPreference(
            "enableSpeech");
    android.preference.SwitchPreference EnableTalkBackPreference = (android.preference.SwitchPreference) findPreference(
            "talkBack");
    MultiSelectListPreference drawerItems = (MultiSelectListPreference) findPreference("enable_menu_items");
    @SuppressWarnings("SpellCheckingInspection")
    android.preference.SwitchPreference AlwaysOnPreference = (android.preference.SwitchPreference) findPreference(
            "alwayson");
    @SuppressWarnings("SpellCheckingInspection")
    android.preference.PreferenceScreen preferenceScreen = (android.preference.PreferenceScreen) findPreference(
            "settingsscreen");
    android.preference.PreferenceCategory premiumCategory = (android.preference.PreferenceCategory) findPreference(
            "premium_category");
    android.preference.Preference premiumPreference = findPreference("premium_settings");
    NotificationsMultiSelectListPreference notificationsMultiSelectListPreference = (NotificationsMultiSelectListPreference) findPreference(
            "suppressNotifications");
    NotificationsMultiSelectListPreference alarmMultiSelectListPreference = (NotificationsMultiSelectListPreference) findPreference(
            "alarmNotifications");
    android.preference.SwitchPreference ThemePreference = (android.preference.SwitchPreference) findPreference(
            "darkTheme");
    android.preference.Preference FingerPrintSettingsPreference = findPreference("SecuritySettings");
    android.preference.SwitchPreference FingerPrintPreference = (android.preference.SwitchPreference) findPreference(
            "enableSecurity");

    if (!BuildConfig.DEBUG) {
        PreferenceCategory oAndroidAutoCategory = (android.preference.PreferenceCategory) findPreference(
                "androidautocategory");
        PreferenceScreen oNotificationScreen = (android.preference.PreferenceScreen) findPreference(
                "notificationscreen");
        oNotificationScreen.removePreference(oAndroidAutoCategory);
    }//from   w w w. j  ava 2  s  .c  o  m

    List<String> notifications = mSharedPrefs.getReceivedNotifications();
    if (notifications == null || notifications.size() <= 0) {
        notificationsMultiSelectListPreference.setEnabled(false);
        alarmMultiSelectListPreference.setEnabled(false);
    } else {
        notificationsMultiSelectListPreference.setEnabled(true);
        alarmMultiSelectListPreference.setEnabled(true);
    }

    PermissionsSettings
            .setOnPreferenceClickListener(new android.preference.Preference.OnPreferenceClickListener() {
                @Override
                public boolean onPreferenceClick(android.preference.Preference preference) {
                    permissionHelper.openSettingsScreen();
                    return true;
                }
            });

    drawerItems.setOnPreferenceChangeListener(new android.preference.Preference.OnPreferenceChangeListener() {
        @Override
        public boolean onPreferenceChange(android.preference.Preference preference, Object newValue) {
            try {
                final HashSet selectedDrawerItems = (HashSet) newValue;
                if (selectedDrawerItems.size() < 1) {
                    showSnackbar(mContext.getString(R.string.error_atLeastOneItemInDrawer));
                    return false;
                }
            } catch (Exception ex) {
                ex.printStackTrace();
                return false;
            }
            return true;
        }
    });

    ThemePreference
            .setOnPreferenceChangeListener(new android.preference.Preference.OnPreferenceChangeListener() {
                @Override
                public boolean onPreferenceChange(android.preference.Preference preference, Object newValue) {
                    if (BuildConfig.LITE_VERSION || !mSharedPrefs.isAPKValidated()) {
                        showPremiumSnackbar(getString(R.string.category_theme));
                        return false;
                    } else {
                        ((SettingsActivity) getActivity()).reloadSettings();
                        return true;
                    }
                }
            });

    MultiServerPreference
            .setOnPreferenceChangeListener(new android.preference.Preference.OnPreferenceChangeListener() {
                @Override
                public boolean onPreferenceChange(android.preference.Preference preference, Object newValue) {
                    if (BuildConfig.LITE_VERSION || !mSharedPrefs.isAPKValidated()) {
                        showPremiumSnackbar(getString(R.string.multi_server));
                        return false;
                    }
                    return true;
                }
            });

    ServerSettings.setOnPreferenceClickListener(new android.preference.Preference.OnPreferenceClickListener() {
        @Override
        public boolean onPreferenceClick(android.preference.Preference preference) {
            if (!MultiServerPreference.isChecked()) {
                Intent intent = new Intent(mContext, ServerSettingsActivity.class);
                startActivity(intent);
            } else {
                Intent intent = new Intent(mContext, ServerListSettingsActivity.class);
                startActivity(intent);
            }
            return true;
        }
    });

    FingerPrintSettingsPreference
            .setOnPreferenceClickListener(new android.preference.Preference.OnPreferenceClickListener() {
                @Override
                public boolean onPreferenceClick(android.preference.Preference preference) {
                    mContext.startActivity(new Intent(Settings.ACTION_SECURITY_SETTINGS));
                    return true;
                }
            });

    fetchServerConfig
            .setOnPreferenceClickListener(new android.preference.Preference.OnPreferenceClickListener() {
                @Override
                public boolean onPreferenceClick(android.preference.Preference preference) {
                    UsefulBits.getServerConfigForActiveServer(mContext, true, new ConfigReceiver() {
                        @Override
                        public void onReceiveConfig(ConfigInfo settings) {
                            showSnackbar(mContext.getString(R.string.fetched_server_config_success));
                        }

                        @Override
                        public void onError(Exception error) {
                            showSnackbar(mContext.getString(R.string.fetched_server_config_failed));
                        }
                    }, null);
                    return true;
                }
            });

    displayLanguage
            .setOnPreferenceChangeListener(new android.preference.Preference.OnPreferenceChangeListener() {
                @Override
                public boolean onPreferenceChange(android.preference.Preference preference, Object newValue) {
                    showRestartMessage();
                    return true;
                }
            });

    registrationId.setOnPreferenceClickListener(new android.preference.Preference.OnPreferenceClickListener() {
        @Override
        public boolean onPreferenceClick(android.preference.Preference preference) {
            if (Build.VERSION.SDK_INT >= Build.VERSION_CODES.M) {
                if (!PermissionsUtil.canAccessDeviceState(mContext)) {
                    permissionHelper.request(PermissionsUtil.INITIAL_DEVICE_PERMS);
                } else {
                    pushGCMRegistrationIds();
                }
            } else {
                pushGCMRegistrationIds();
            }
            return true;
        }
    });

    GeoSettings.setOnPreferenceClickListener(new android.preference.Preference.OnPreferenceClickListener() {
        @Override
        public boolean onPreferenceClick(android.preference.Preference preference) {
            if (BuildConfig.LITE_VERSION || !mSharedPrefs.isAPKValidated()) {
                showPremiumSnackbar(getString(R.string.geofence));
                return false;
            } else {
                Intent intent = new Intent(mContext, GeoSettingsActivity.class);
                startActivity(intent);
                return true;
            }
        }
    });

    EnableNFCPreference
            .setOnPreferenceChangeListener(new android.preference.Preference.OnPreferenceChangeListener() {
                @Override
                public boolean onPreferenceChange(android.preference.Preference preference, Object newValue) {
                    if (BuildConfig.LITE_VERSION || !mSharedPrefs.isAPKValidated()) {
                        showPremiumSnackbar(getString(R.string.category_nfc));
                        return false;
                    }

                    if (NfcAdapter.getDefaultAdapter(mContext) == null) {
                        showSnackbar(mContext.getString(R.string.nfc_not_supported));
                        return false;
                    }
                    return true;
                }
            });

    EnableQRCodePreference
            .setOnPreferenceChangeListener(new android.preference.Preference.OnPreferenceChangeListener() {
                @Override
                public boolean onPreferenceChange(android.preference.Preference preference, Object newValue) {
                    if (BuildConfig.LITE_VERSION || !mSharedPrefs.isAPKValidated()) {
                        showPremiumSnackbar(getString(R.string.category_QRCode));
                        return false;
                    }

                    return true;
                }
            });

    EnableSpeechPreference
            .setOnPreferenceChangeListener(new android.preference.Preference.OnPreferenceChangeListener() {
                @Override
                public boolean onPreferenceChange(android.preference.Preference preference, Object newValue) {
                    if (BuildConfig.LITE_VERSION || !mSharedPrefs.isAPKValidated()) {
                        showPremiumSnackbar(getString(R.string.category_Speech));
                        return false;
                    }
                    return true;
                }
            });

    EnableTalkBackPreference
            .setOnPreferenceChangeListener(new android.preference.Preference.OnPreferenceChangeListener() {
                @Override
                public boolean onPreferenceChange(android.preference.Preference preference, Object newValue) {
                    if (BuildConfig.LITE_VERSION || !mSharedPrefs.isAPKValidated()) {
                        showPremiumSnackbar(getString(R.string.category_talk_back));
                        return false;
                    }
                    return true;
                }
            });

    NFCPreference.setOnPreferenceClickListener(new android.preference.Preference.OnPreferenceClickListener() {
        @Override
        public boolean onPreferenceClick(android.preference.Preference preference) {
            if (BuildConfig.LITE_VERSION || !mSharedPrefs.isAPKValidated()) {
                showPremiumSnackbar(getString(R.string.category_nfc));
                return false;
            } else {
                Intent intent = new Intent(mContext, NFCSettingsActivity.class);
                startActivity(intent);
                return true;
            }
        }
    });

    QRCodePreference
            .setOnPreferenceClickListener(new android.preference.Preference.OnPreferenceClickListener() {
                @Override
                public boolean onPreferenceClick(android.preference.Preference preference) {
                    if (BuildConfig.LITE_VERSION || !mSharedPrefs.isAPKValidated()) {
                        showPremiumSnackbar(getString(R.string.category_QRCode));
                        return false;
                    } else {
                        Intent intent = new Intent(mContext, QRCodeSettingsActivity.class);
                        startActivity(intent);
                        return true;
                    }
                }
            });

    SpeechPreference
            .setOnPreferenceClickListener(new android.preference.Preference.OnPreferenceClickListener() {
                @Override
                public boolean onPreferenceClick(android.preference.Preference preference) {
                    if (BuildConfig.LITE_VERSION || !mSharedPrefs.isAPKValidated()) {
                        showPremiumSnackbar(getString(R.string.category_Speech));
                        return false;
                    } else {
                        Intent intent = new Intent(mContext, SpeechSettingsActivity.class);
                        startActivity(intent);
                        return true;
                    }
                }
            });

    WearPreference
            .setOnPreferenceChangeListener(new android.preference.Preference.OnPreferenceChangeListener() {
                @Override
                public boolean onPreferenceChange(android.preference.Preference preference, Object newValue) {
                    if (BuildConfig.LITE_VERSION || !mSharedPrefs.isAPKValidated()) {
                        showPremiumSnackbar(getString(R.string.category_wear));
                        return false;
                    }
                    return true;
                }
            });

    AlwaysOnPreference
            .setOnPreferenceChangeListener(new android.preference.Preference.OnPreferenceChangeListener() {
                @Override
                public boolean onPreferenceChange(android.preference.Preference preference, Object newValue) {
                    if (BuildConfig.LITE_VERSION || !mSharedPrefs.isAPKValidated()) {
                        showPremiumSnackbar(getString(R.string.always_on_title));
                        return false;
                    }
                    return true;
                }
            });

    NotificationLogged
            .setOnPreferenceClickListener(new android.preference.Preference.OnPreferenceClickListener() {
                @Override
                public boolean onPreferenceClick(android.preference.Preference preference) {
                    //show dialog
                    List<String> logs = mSharedPrefs.getLoggedNotifications();
                    if (logs != null && logs.size() > 0) {
                        Collections.reverse(logs);
                        new MaterialDialog.Builder(mContext)
                                .title(mContext.getString(R.string.notification_show_title))
                                .items((CharSequence[]) logs.toArray(new String[0])).show();
                    } else
                        UsefulBits.showSimpleToast(mContext, getString(R.string.notification_show_nothing),
                                Toast.LENGTH_LONG);
                    return true;
                }
            });

    //noinspection PointlessBooleanExpression
    if (!BuildConfig.LITE_VERSION) {
        preferenceScreen.removePreference(premiumCategory);
    } else {
        premiumPreference
                .setOnPreferenceClickListener(new android.preference.Preference.OnPreferenceClickListener() {
                    @Override
                    public boolean onPreferenceClick(android.preference.Preference preference) {
                        String packageID = mContext.getPackageName() + ".premium";
                        try {
                            startActivity(new Intent(Intent.ACTION_VIEW,
                                    Uri.parse("market://details?id=" + packageID)));
                        } catch (android.content.ActivityNotFoundException ignored) {
                            startActivity(new Intent(Intent.ACTION_VIEW,
                                    Uri.parse("https://play.google.com/store/apps/details?id=" + packageID)));
                        }

                        return true;
                    }
                });
    }

    resetApplication
            .setOnPreferenceClickListener(new android.preference.Preference.OnPreferenceClickListener() {
                @Override
                public boolean onPreferenceClick(android.preference.Preference preference) {
                    if (Build.VERSION.SDK_INT >= Build.VERSION_CODES.KITKAT) {
                        new MaterialDialog.Builder(mContext).title(R.string.category_Reset)
                                .content(R.string.are_you_sure).positiveText(R.string.ok)
                                .negativeText(R.string.cancel)
                                .onPositive(new MaterialDialog.SingleButtonCallback() {
                                    @SuppressLint("NewApi")
                                    @Override
                                    public void onClick(@NonNull MaterialDialog dialog,
                                            @NonNull DialogAction which) {
                                        ((ActivityManager) mContext.getSystemService(Context.ACTIVITY_SERVICE))
                                                .clearApplicationUserData();
                                    }
                                }).show();
                    } else {
                        startActivityForResult(new Intent(android.provider.Settings.ACTION_SETTINGS), 0);
                    }
                    return true;
                }
            });

    FingerPrintPreference
            .setOnPreferenceChangeListener(new android.preference.Preference.OnPreferenceChangeListener() {
                @SuppressLint("NewApi")
                @Override
                public boolean onPreferenceChange(android.preference.Preference preference, Object o) {
                    if (mSharedPrefs.isStartupSecurityEnabled())
                        return true;
                    if (BuildConfig.LITE_VERSION || !mSharedPrefs.isAPKValidated()) {
                        showPremiumSnackbar(getString(R.string.category_startup_security));
                        return false;
                    } else {
                        if (Build.VERSION.SDK_INT < Build.VERSION_CODES.M) {
                            UsefulBits.showSimpleToast(mContext, getString(R.string.fingerprint_not_supported),
                                    Toast.LENGTH_LONG);
                            return false;
                        }
                        if (!PermissionsUtil.canAccessFingerprint(mContext)) {
                            permissionHelper.request(PermissionsUtil.INITIAL_FINGERPRINT_PERMS);
                        } else {
                            FingerprintManager fingerprintManager = (FingerprintManager) mContext
                                    .getSystemService(Context.FINGERPRINT_SERVICE);
                            if (ActivityCompat.checkSelfPermission(mContext,
                                    Manifest.permission.USE_FINGERPRINT) != PackageManager.PERMISSION_GRANTED) {
                                return false;
                            }
                            if (Build.VERSION.SDK_INT >= Build.VERSION_CODES.M) {
                                if (!fingerprintManager.isHardwareDetected()) {
                                    return false;
                                } else if (!fingerprintManager.hasEnrolledFingerprints()) {
                                    UsefulBits.showSimpleToast(mContext,
                                            getString(R.string.fingerprint_not_setup_in_android),
                                            Toast.LENGTH_LONG);
                                    return false;
                                } else {
                                    new MaterialDialog.Builder(mContext)
                                            .title(R.string.category_startup_security)
                                            .content(R.string.fingerprint_sure).positiveText(R.string.ok)
                                            .negativeText(R.string.cancel)
                                            .onPositive(new MaterialDialog.SingleButtonCallback() {
                                                @Override
                                                public void onClick(@NonNull MaterialDialog dialog,
                                                        @NonNull DialogAction which) {
                                                    mSharedPrefs.setStartupSecurityEnabled(true);
                                                    ((SettingsActivity) getActivity()).reloadSettings();
                                                }
                                            }).show();

                                    return false;
                                }
                            }
                        }
                    }
                    return false;
                }
            });
}

From source file:net.unicon.sakora.impl.csv.CsvCommonHandlerService.java

protected int setCurrentAcademicSessions(String[] sessions) {
    HashSet<String> currentAcademicSessionEids;
    if (sessions != null) {
        currentAcademicSessionEids = new HashSet<String>(sessions.length);
        for (int i = 0; i < sessions.length; i++) {
            currentAcademicSessionEids.add(sessions[i]);
        }/*from   w  w  w  . j a  v  a  2s .  com*/
    } else {
        currentAcademicSessionEids = new HashSet<String>(0);
    }
    if (currentAcademicSessionEids.isEmpty()) {
        log.warn(
                "SakoraCSV has no current academic sessions, this is typically not a valid state, please check your sessions.csv file");
    }
    setCurrentSyncVar(CURRENT_SESSION_EIDS, currentAcademicSessionEids);
    return currentAcademicSessionEids.size();
}

From source file:it.iit.genomics.cru.structures.bridges.uniprot.UniprotkbUtils.java

/**
 *
 * @param genes/*from  w  ww.jav  a 2 s .  c  o m*/
 * @return
 * @throws BridgesRemoteAccessException
 */
public MapOfMap<String, MoleculeEntry> getUniprotEntriesFromGenes(Collection<String> genes)
        throws BridgesRemoteAccessException {
    String tool = UNIPROT_TOOL;

    MapOfMap<String, MoleculeEntry> gene2uniprots = new MapOfMap<>(genes);

    HashSet<String> genes2get = new HashSet<>();

    try {
        for (String gene : genes) {
            if (cache.containsKey(gene.toUpperCase())) {
                gene2uniprots.addAll(gene, cache.get(gene.toUpperCase()));
            } else {
                genes2get.add(gene);

                // if size == limit, do query
                if (genes2get.size() == maxQueries) {
                    String location = UNIPROT_SERVER + tool + "/?" + "query=keyword:181+AND+organism:"
                            + URLEncoder.encode("\"" + taxid + "\"", "UTF-8") + "+AND+(gene:"
                            + URLEncoder.encode(StringUtils.join(genes2get, " OR gene:"), "UTF-8") + ")";

                    Collection<MoleculeEntry> uniprotEntries = getUniprotEntriesXML(location);

                    for (MoleculeEntry entry : uniprotEntries) {
                        String geneName = entry.getGeneName();

                        // Only use the first one. Using synomyms may cause
                        // ambiguity.
                        if (geneName != null && gene2uniprots.containsKey(geneName)) {
                            gene2uniprots.add(geneName, entry);
                        }
                    }

                    genes2get.clear();
                }

            }
        }

        if (genes2get.isEmpty()) {
            return gene2uniprots;
        }

        String location = UNIPROT_SERVER + tool + "/?" + "query=keyword:181+AND+organism:"
                + URLEncoder.encode("\"" + taxid + "\"", "UTF-8") + "+AND+(gene:"
                + URLEncoder.encode(StringUtils.join(genes2get, " OR gene:"), "UTF-8") + ")";

        Collection<MoleculeEntry> uniprotEntries = getUniprotEntriesXML(location);

        for (MoleculeEntry entry : uniprotEntries) {
            String geneName = entry.getGeneName();

            // Only use the first one. Using synomyms may cause ambiguity.
            if (geneName != null && gene2uniprots.containsKey(geneName)) {
                gene2uniprots.add(geneName, entry);
            }
        }

    } catch (UnsupportedEncodingException e) {
        logger.error("cannot get proteins for " + StringUtils.join(genes, ", "), e);
    }

    return gene2uniprots;
}

From source file:it.iit.genomics.cru.structures.bridges.uniprot.UniprotkbUtils.java

/**
 *
 * @param xrefs/*w  ww . ja  v  a2  s .c  o m*/
 * @param filterTaxid
 * @return
 * @throws BridgesRemoteAccessException
 */
public HashMap<String, MoleculeEntry> getUniprotEntriesFromUniprotAccessions(Collection<String> xrefs,
        boolean filterTaxid) throws BridgesRemoteAccessException {
    String tool = UNIPROT_TOOL;

    // remove xrefs that are not uniprotAcs
    Collection<String> uniprotAcs = getUniprotAcs(xrefs);

    HashMap<String, MoleculeEntry> results = new HashMap<>();

    HashSet<String> ref2get = new HashSet<>();

    try {
        for (String ref : uniprotAcs) {
            if (cache.containsKey(ref.toUpperCase())) {
                results.put(ref, cache.get(ref.toUpperCase()).iterator().next());
            } else {
                ref2get.add(ref);

                // if size == limit, do query
                if (ref2get.size() == maxQueries) {
                    String location = UNIPROT_SERVER + tool + "/?" + "query=(accession:"
                            + URLEncoder.encode(StringUtils.join(ref2get, " OR accession:") + "", "UTF-8")
                            + ")";
                    if (filterTaxid) {
                        location += "+AND+keyword:181+AND+organism:"
                                + URLEncoder.encode("\"" + taxid + "\"", "UTF-8");
                    }

                    Collection<MoleculeEntry> uniprotEntries = getUniprotEntriesXML(location);

                    for (MoleculeEntry entry : uniprotEntries) {
                        results.put(entry.getUniprotAc(), entry);
                    }
                    ref2get.clear();
                }
            }
        }

        if (ref2get.isEmpty()) {
            return results;
        }

        String location = UNIPROT_SERVER + tool + "/?" + "query=(accession:"
                + URLEncoder.encode(StringUtils.join(ref2get, " OR accession:") + "", "UTF-8") + ")";
        if (filterTaxid) {
            location += "+AND+keyword:181+AND+organism:" + URLEncoder.encode("\"" + taxid + "\"", "UTF-8");
        }
        Collection<MoleculeEntry> uniprotEntries = getUniprotEntriesXML(location);

        for (MoleculeEntry entry : uniprotEntries) {
            results.put(entry.getUniprotAc(), entry);
        }

    } catch (UnsupportedEncodingException e) {
        logger.error("cannot get proteins for " + StringUtils.join(xrefs, ", "), e);
    }

    return results;
}

From source file:org.lockss.config.TdbTitle.java

/**
 * Return the complete list of unique ISSNs for this title.
 * //www. j  a  v a  2 s. co  m
 * @return an array of unique ISSNs for this title
 */
public String[] getIssns() {
    HashSet<String> issns = new HashSet<String>();
    String issn = getPrintIssn();
    if (issn != null)
        issns.add(issn);
    issn = getEissn();
    if (issn != null)
        issns.add(issn);
    issn = getIssnL();
    if (issn != null)
        issns.add(issn);
    return issns.toArray(new String[issns.size()]);
}

From source file:de.dfki.km.perspecting.obie.experiments.RelevanceRatingExperiment.java

@Test
public void analyseMeanRatings() throws Exception {

    String[] paths = new String[] {
            // "/home/adrian/Dokumente/diss/scoobie/results/dbpedia_en2/relevance_wikipedia_combined.csv"};
            // "/home/adrian/Dokumente/diss/scoobie/results/dbpedia_en2/relevance_gutenberg_combined.csv"};
            "/home/adrian/Dokumente/diss/scoobie/results/dbpedia_en2/relevance_wikinews_combined.csv" };
    // "/home/adrian/Dokumente/diss/scoobie/results/bbc_wildlife/relevance_bbc_nature_combined.csv"};
    // "/home/adrian/Dokumente/diss/scoobie/results/bbc_music/relevance_bbc_music_combined.csv"
    // };/* ww w  .  j  a  v  a  2 s  .co  m*/
    for (String path : paths) {
        System.out.println(path);
        BufferedReader r = new BufferedReader(new FileReader(path));

        TObjectDoubleHashMap<String> map = new TObjectDoubleHashMap<String>();
        final HashSet<String> docs = new HashSet<String>();

        int i = 0;
        for (String line = r.readLine(); line != null; line = r.readLine()) {
            String[] row = line.split("\t");
            double rel = Double.parseDouble(row[2].replace(",", "."));
            map.adjustOrPutValue(row[1], rel, rel);
            docs.add(row[0]);

            // if (i < 9) {
            // System.out.println((i++) + ": " + row[1]);
            // }
        }

        map.transformValues(new TDoubleFunction() {

            @Override
            public double execute(double value) {
                return value / docs.size();
            }
        });

        map.forEachEntry(new TObjectDoubleProcedure<String>() {

            @Override
            public boolean execute(String a, double b) {
                a = a.replaceAll("\\[", "").replaceAll("\\]", "");
                a = a.replace("0", "AuthorityBasedRating");
                a = a.replace("1", "HubBasedRating");
                a = a.replace("2", "PageRankBasedRating");
                a = a.replace("3", "DegreeBasedRating");
                a = a.replace("4", "CapacityBasedRating");
                a = a.replace("5", "RandomRating");
                a = a.replace("6", "PositionBasedRating");
                a = a.replace("7", "TermFrequencyBasedRating");
                a = a.replace("8", "InverseDocumentFrequencyBasedRating");
                System.out.println(String.format(Locale.US, "%s\t%1.3f", a, b));
                return true;
            }
        });

        System.out.println("-------------------------------------------------------");
    }

}

From source file:com.clustercontrol.jobmanagement.factory.ModifyJob.java

public Long replaceJobunit(List<JobInfo> oldList, List<JobInfo> newList, String userId)
        throws JobInvalid, JobMasterNotFound, EntityExistsException, HinemosUnknown, JobMasterDuplicate,
        InvalidSetting, InvalidRole {/*from   w  w  w  .jav  a  2s. c om*/
    //?ID?
    String jobunitId = newList.get(0).getJobunitId();

    // 
    long start = HinemosTime.currentTimeMillis();

    HashSet<JobInfo> delJobs = new HashSet<JobInfo>(oldList);
    HashSet<JobInfo> newJobs = new HashSet<JobInfo>(newList);
    delJobs.removeAll(newJobs);

    long timeJobToDelete = HinemosTime.currentTimeMillis();
    m_log.info("Find jobs to delete " + (timeJobToDelete - start) + "ms");

    HashSet<JobInfo> addJobs = newJobs;
    addJobs.removeAll(new HashSet<JobInfo>(oldList));

    long timeJobToAdd = HinemosTime.currentTimeMillis();
    m_log.info("Find jobs to add " + (timeJobToAdd - timeJobToDelete) + "ms");
    m_log.info("oldList=" + oldList.size() + ", newList=" + newList.size() + ", delJobs=" + delJobs.size()
            + ", addJobs=" + addJobs.size());

    JpaTransactionManager jtm = new JpaTransactionManager();
    for (JobInfo delJob : delJobs) {
        JobMstEntity entity = QueryUtil.getJobMstPK(delJob.getJobunitId(), delJob.getId());
        deleteJob(entity);
    }

    jtm.flush();

    long timestamp = HinemosTime.currentTimeMillis();

    // ????????
    for (JobInfo addJob : addJobs) {
        int type = addJob.getType();
        if (type == JobConstant.TYPE_JOBUNIT) {
            String jobId = addJob.getId();
            String parentJobId = addJob.getParentId();
            if (jobunitId.equals(jobId)) {
                parentJobId = CreateJobSession.TOP_JOB_ID;
            }
            createJobMasterData(addJob, jobunitId, parentJobId, userId, timestamp);
            addJobs.remove(addJob);
            break;
        }
    }
    for (JobInfo addJob : addJobs) {
        String jobId = addJob.getId();
        String parentJobId = addJob.getParentId();
        if (jobunitId.equals(jobId)) {
            parentJobId = CreateJobSession.TOP_JOB_ID;
        }
        createJobMasterData(addJob, jobunitId, parentJobId, userId, timestamp);
    }

    // ??
    String jobId = newList.get(0).getId();
    JobMstEntity entity = QueryUtil.getJobMstPK(jobunitId, jobId);
    entity.setUpdateDate(timestamp);
    m_log.info("Left tasks in replaceJobunit " + (HinemosTime.currentTimeMillis() - timeJobToAdd) + "ms");

    // ??
    return timestamp;
}

From source file:com.tamingtext.tagrecommender.TestStackOverflowTagger.java

public void execute() {
    PrintStream out = null;/*w  ww. j  av a2s. co  m*/

    try {
        OpenObjectIntHashMap<String> tagCounts = new OpenObjectIntHashMap<String>();
        OpenObjectIntHashMap<String> tagCorrect = new OpenObjectIntHashMap<String>();
        loadTags(tagCounts);

        StackOverflowStream stream = new StackOverflowStream();
        stream.open(inputFile.getAbsolutePath());

        out = new PrintStream(new FileOutputStream(outputFile));

        int correctTagCount = 0;
        int postCount = 0;

        HashSet<String> postTags = new HashSet<String>();
        float postPctCorrect;

        int totalSingleCorrect = 0;
        int totalHalfCorrect = 0;

        for (StackOverflowPost post : stream) {
            correctTagCount = 0;
            postCount++;

            postTags.clear();
            postTags.addAll(post.getTags());
            for (String tag : post.getTags()) {
                if (tagCounts.containsKey(tag)) {
                    tagCounts.adjustOrPutValue(tag, 1, 1);
                }
            }

            ScoreTag[] tags = client.getTags(post.getTitle() + "\n" + post.getBody(), maxTags);

            for (ScoreTag tag : tags) {
                if (postTags.contains(tag.getTag())) {
                    correctTagCount += 1;
                    tagCorrect.adjustOrPutValue(tag.getTag(), 1, 1);
                }
            }

            if (correctTagCount > 0) {
                totalSingleCorrect += 1;
            }

            postPctCorrect = correctTagCount / (float) postTags.size();
            if (postPctCorrect >= 0.50f) {
                totalHalfCorrect += 1;
            }

            if ((postCount % 100) == 0) {
                dumpStats(System.err, postCount, totalSingleCorrect, totalHalfCorrect);
            }

        }

        dumpStats(System.err, postCount, totalSingleCorrect, totalHalfCorrect);
        dumpStats(out, postCount, totalSingleCorrect, totalHalfCorrect);
        dumpTags(out, tagCounts, tagCorrect);
    } catch (Exception ex) {
        throw (RuntimeException) new RuntimeException().initCause(ex);
    } finally {
        if (out != null) {
            out.close();
        }
    }
}

From source file:it.iit.genomics.cru.igb.bundles.mi.business.MIResult.java

public float getScore() {

    if (score > -1) {
        return score;
    }/*from  w  w  w.j  a  v a 2s .  co m*/

    HashSet<AAPosition> residuesOnProteins = new HashSet<>();
    HashSet<AAPosition> residuesOnContacts = new HashSet<>();

    residuesOnProteins.addAll(queryResiduesA);
    residuesOnProteins.addAll(queryResiduesB);

    residuesOnContacts.addAll(structureMapper.getInterfaceAAPositionsA());
    residuesOnContacts.addAll(structureMapper.getInterfaceAAPositionsB());

    if (residuesOnProteins.isEmpty()) {
        return 0;
    }

    float residueScore = ((float) residuesOnContacts.size()) / residuesOnProteins.size();

    this.score = residueScore;

    return residueScore;
}