Example usage for java.util HashSet add

List of usage examples for java.util HashSet add

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Introduction

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

Prototype

public boolean add(E e)

Source Link

Document

Adds the specified element to this set if it is not already present.

Usage

From source file:com.termmed.utils.FileHelper.java

/**
 * Complete file from array./*from   ww w . j  ava  2  s  .  com*/
 *
 * @param filesArray the files array
 * @param fileName the file name
 * @return the string
 */
public static String completeFileFromArray(HashSet<String> filesArray, String fileName) {
    HashSet<File> fileSet = new HashSet<File>();
    for (String sfile : filesArray) {
        File file = new File(sfile);
        if (file.exists()) {
            fileSet.add(file);
        }
    }
    if (fileSet.size() > 0) {
        File outputFile = new File(fileName);
        CommonUtils.concatFile(fileSet, outputFile);
        return outputFile.getAbsolutePath();
    }
    return null;
}

From source file:com.addthis.hydra.job.spawn.JobAlertUtil.java

/**
 * Count the total byte sizes of files along a certain path via mesh
 * @param jobId The job to check//w  ww . j  a v  a 2 s  . c o m
 * @param dirPath The path to check within the jobId, e.g. split/{{now-1}}/importantfiles/*.gz
 * @return A long representing the total size in bytes of files along the specified path
 */
public static long getTotalBytesFromMesh(MeshyClient meshyClient, String jobId, String dirPath) {
    String meshLookupString = "/job*/" + jobId + "/*/gold/" + expandDateMacro(dirPath);
    if (meshyClient != null) {
        try {
            Collection<FileReference> fileRefs = meshyClient.listFiles(new String[] { meshLookupString });
            HashSet<String> fileRefKeysUsed = new HashSet<>();
            long totalBytes = 0;
            for (FileReference fileRef : fileRefs) {
                // Use StreamSourceMeshy to generate a canonical path key. In particular, strip off any multi-minion prefixes if appropriate.
                String meshFileKey = StreamFileUtil.getCanonicalFileReferenceCacheKey(fileRef.name, pathOff,
                        sortToken, pathTokenOffset);
                if (!fileRefKeysUsed.contains(meshFileKey)) {
                    totalBytes += fileRef.size;
                    fileRefKeysUsed.add(meshFileKey);
                }
            }
            return totalBytes;
        } catch (IOException e) {
            log.warn("Job alert mesh look up failed", e);
        }
    } else {
        log.warn(
                "Received mesh lookup request job={} dirPath={} while meshy client was not instantiated; returning zero",
                jobId, dirPath);
    }
    return 0;
}

From source file:com.projity.field.Select.java

public static String toConfigurationXMLOptions(LinkedHashMap map, String keyPrefix) {
    // MapIterator i = map.i();
    Iterator i = map.keySet().iterator();
    StringBuffer buf = new StringBuffer();
    HashSet duplicateSet = new HashSet(); // don't allow duplicate keys
    while (i.hasNext()) {
        String key = (String) i.next();
        // notion of key and value is switched
        String value = (String) map.get(key);
        int dupCount = 2;
        String newKey = key;//from   w w w .j a va 2 s  .co  m
        while (duplicateSet.contains(newKey)) {
            newKey = key + "-" + dupCount++;
        }
        key = newKey;
        duplicateSet.add(key);
        if (key == null || key.length() == 0)
            continue;
        if (value == null || value.length() == 0)
            continue;
        key = keyPrefix + key;
        // String key = "<html>" + keyPrefix + ": " + "<b>" + i.getValue()
        // +"</b></html>";
        buf.append(SelectOption.toConfigurationXML(key, value));
    }
    return buf.toString();
}

From source file:com.jaspersoft.jasperserver.jrsh.operation.PackageScanClassResolver.java

/**
 * Discovers the packages retrieves operation types.
 *
 * @param basePackage package to scan//  w  w w.  ja  v  a  2s .c o m
 * @return operation classes
 */
public static Set<Class<? extends Operation>> findOperationClasses(String basePackage) {
    HashSet<Class<? extends Operation>> operationTypes = new HashSet<>();
    MetadataScannerConfig config = readConfig();
    List<String> externalPackagesToScan = config.getPackagesToScan();
    List<String> classes = config.getClasses();
    FilterBuilder filter = new FilterBuilder().includePackage(basePackage);
    //
    // Discover external operation types from configuration file
    //
    if (classes != null) {
        for (String aClass : classes) {
            try {
                Class clz = Class.forName(aClass);
                if (!Modifier.isAbstract(clz.getModifiers()) && Operation.class.isAssignableFrom(clz)) {
                    operationTypes.add(clz);
                }
            } catch (ClassNotFoundException ignored) {
            }
        }
    }
    //
    // Prepare package filter to avoid unnecessary CP scanning
    //
    if (externalPackagesToScan != null) {
        for (String aPackage : externalPackagesToScan) {
            aPackage = chomp(aPackage, ".*");
            filter.includePackage(aPackage);
        }
    }
    //
    // Retrieve internal operation types
    //
    Reflections ref = new Reflections(new SubTypesScanner(), filter);
    for (val subType : ref.getSubTypesOf(Operation.class)) {
        if (!Modifier.isAbstract(subType.getModifiers())) {
            operationTypes.add(subType);
        }
    }
    return operationTypes;
}

From source file:com.termmed.utils.FileHelper.java

/**
 * Gets the modules.// www.  j  a v  a2s .c o m
 *
 * @param tmpFile the tmp file
 * @return the modules
 * @throws IOException Signals that an I/O exception has occurred.
 */
public static HashSet<String> getModules(String tmpFile) throws IOException {
    BufferedReader br = getReader(tmpFile);
    br.readLine();
    String line;
    String[] spl;
    HashSet<String> modules = new HashSet<String>();
    while ((line = br.readLine()) != null) {
        spl = line.split("\t", -1);
        if (!modules.contains(spl[3])) {
            modules.add(spl[3]);
        }
    }
    br.close();
    return modules;
}

From source file:edu.msu.cme.rdp.readseq.utils.RmDupSeqs.java

public static void filterDuplicates(String inFile, String outFile, int length, boolean debug)
        throws IOException {
    HashMap<String, String> idSet = new HashMap<String, String>();
    IndexedSeqReader reader = new IndexedSeqReader(new File(inFile));
    BufferedWriter outWriter = new BufferedWriter(new FileWriter(new File(outFile)));
    Set<String> allseqIDset = reader.getSeqIdSet();
    Sequence seq;//from w  w w.  java 2 s.c o m
    if (debug) {
        System.out.println("ID\tdescription" + "\tcontained_by_ID\tdescription");
    }
    for (String id : allseqIDset) {
        seq = reader.readSeq(id);
        boolean dup = false;
        HashSet<String> tempdupSet = new HashSet<String>();
        for (String exID : idSet.keySet()) {
            String exSeq = idSet.get(exID);
            if (exSeq.length() >= seq.getSeqString().length()) {
                if (exSeq.contains(seq.getSeqString())) {
                    dup = true;
                    if (debug) {
                        Sequence temp = reader.readSeq(exID);
                        System.out.println(id + "\t" + seq.getDesc() + "\t" + exID + "\t" + temp.getDesc());
                    }
                    break;
                }
            } else if (seq.getSeqString().contains(exSeq)) {
                tempdupSet.add(exID);
            }
        }

        if (!dup) {
            idSet.put(id, seq.getSeqString());
        }
        for (String dupid : tempdupSet) {
            idSet.remove(dupid);
            if (debug) {
                Sequence temp = reader.readSeq(dupid);
                System.out.println(dupid + "\t" + temp.getDesc() + "\t" + id + "\t" + seq.getDesc());
            }
        }
    }
    // get the unique seq
    for (String id : idSet.keySet()) {
        seq = reader.readSeq(id);
        if (seq.getSeqString().length() >= length) {
            outWriter.write(">" + id + "\t" + seq.getDesc() + "\n" + seq.getSeqString() + "\n");
        }
    }
    reader.close();
    outWriter.close();
}

From source file:bookChapter.theoretical.AnalyzeTheoreticalMSMSCalculation.java

/**
 * This method load all sequences in a memory
 *
 * @param databaseName// ww w.  ja  v a 2  s  . c o  m
 * @return
 */
private static HashSet<DBEntry> getDBEntries(String databaseName) throws IOException {
    HashSet<DBEntry> dbEntries = new HashSet<DBEntry>();
    DBLoader loader = DBLoaderLoader.loadDB(new File(databaseName));
    Protein protein = null;
    // get a crossLinkerName object        
    while ((protein = loader.nextProtein()) != null) {
        String sequence = protein.getSequence().getSequence();
        String descrp = protein.getHeader().getDescription(), acc = protein.getHeader().getAccession();
        Peptide tmpPep = new Peptide(sequence, new ArrayList<ModificationMatch>());
        double tmpPepMass = tmpPep.getMass();
        DBEntry dbEntry = new DBEntry(tmpPep, descrp, acc, tmpPepMass);
        dbEntries.add(dbEntry);
    }
    return dbEntries;
}

From source file:edu.wpi.margrave.SQSReader.java

protected static Formula handleStatementCondition(JSONObject obj, Formula theCondition, MVocab vocab)
        throws JSONException, MGEBadIdentifierName, MGEUnknownIdentifier, MGEManagerException {
    // Condition block is a conjunctive list of conditions. all must apply.
    // Each condition is a conjunctive list of value sets. 
    // Each value set is a disjunctive list of values
    // Keys in the condition block are functions to apply
    // Keys in a condition are attribute names. Values are values.

    // Condition block
    //    Function : {}
    //    Function : {}
    // ...//from   w ww . ja v  a 2 s .com

    JSONArray conditionNames = obj.names();
    for (int iCondition = 0; iCondition < conditionNames.length(); iCondition++) {
        String cFunction = (String) conditionNames.get(iCondition);
        JSONObject condition = (JSONObject) obj.get(cFunction);
        //MEnvironment.errorStream.println(cFunction + ": "+condition);

        // condition is a key:value pair or multiple such pairs. The value may be an array.
        // Each sub-condition must be met.
        HashSet<Formula> thisCondition = new HashSet<Formula>();

        JSONArray subConditionNames = condition.names();
        for (int iSubCondition = 0; iSubCondition < subConditionNames.length(); iSubCondition++) {
            String cSubKey = (String) subConditionNames.get(iSubCondition);
            Object subcondition = condition.get(cSubKey);

            // Subcondition: is it an array or a single value?
            if (subcondition instanceof JSONArray) {
                JSONArray subarr = (JSONArray) subcondition;
                HashSet<Formula> valuedisj = new HashSet<Formula>();
                for (int iValue = 0; iValue < subarr.length(); iValue++) {
                    //MEnvironment.errorStream.println(cFunction+"("+cSubKey+", "+subarr.get(iValue)+")");
                    Formula theatom = makeSQSAtom(vocab, "c", "Condition",
                            cFunction + "<" + cSubKey + "><" + subarr.get(iValue) + ">");
                    valuedisj.add(theatom);
                }

                thisCondition.add(MFormulaManager.makeDisjunction(valuedisj));
            } else {
                //MEnvironment.errorStream.println(cFunction+"("+cSubKey+", "+subcondition+")");   
                Formula theatom = makeSQSAtom(vocab, "c", "Condition",
                        cFunction + "<" + cSubKey + "><" + subcondition + ">");
                thisCondition.add(theatom);
            }

        }

        theCondition = MFormulaManager.makeAnd(theCondition, MFormulaManager.makeConjunction(thisCondition));
    }

    return theCondition;
}

From source file:gr.scify.newsum.Utils.java

/**
 * Counts the number of different Sources the Summary refers to
 * @param Summary The summary of interest
 * @return The number of different sources that the summary comes from
 *///from ww  w .j a va  2  s  .c o  m
public static int countDiffArticles(String[] Summary) {
    // Init string set for sources
    HashSet<String> hsSources = new HashSet<String>();
    // Get first entry, i.e. links and labels
    String sAllLinksAndLabels = Summary[0];
    // if only one link
    if (!sAllLinksAndLabels.contains(NewSumServiceClient.getSecondLevelSeparator())) {
        return 1;
    } else {
        // For every pair
        for (String sTmps : sAllLinksAndLabels.split(NewSumServiceClient.getSecondLevelSeparator())) {
            // Get the link (1st field out of 2)  
            hsSources.add(sTmps.split(NewSumServiceClient.getThirdLevelSeparator())[0]);
        }
    }
    // Return unique sources
    return hsSources.size();
}

From source file:com.clustercontrol.repository.util.FacilityTreeCache.java

private static HashSet<String> getAuthorizedRoleIdSet(FacilityInfo facilityInfo,
        FacilityTreeItem parentTreeItem, HashMap<String, ArrayList<String>> objectRoleMap) {

    HashSet<String> roleIdSet = new HashSet<String>();
    // //from   ww  w . ja va 2 s.  com
    roleIdSet.add(RoleIdConstant.ADMINISTRATORS);
    roleIdSet.add(RoleIdConstant.HINEMOS_MODULE);

    // 
    // ???????????????????
    if (facilityInfo.getFacilityType() == FacilityConstant.TYPE_SCOPE) {
        roleIdSet.add(facilityInfo.getOwnerRoleId());
    }

    // ??????
    ArrayList<String> roleIdList = objectRoleMap.get(facilityInfo.getFacilityId());
    if (roleIdList != null) {
        roleIdSet.addAll(roleIdList);
    }

    //???
    if (parentTreeItem != null && parentTreeItem.getData().getFacilityType() == FacilityConstant.TYPE_SCOPE
            && parentTreeItem.getAuthorizedRoleIdSet() != null) {
        roleIdSet.addAll(parentTreeItem.getAuthorizedRoleIdSet());
    }

    return roleIdSet;
}