Example usage for java.util ArrayList toArray

Introduction

In this page you can find the example usage for java.util ArrayList toArray.

Prototype

@SuppressWarnings("unchecked")
public <T> T[] toArray(T[] a) 

Source Link

Document

Returns an array containing all of the elements in this list in proper sequence (from first to last element); the runtime type of the returned array is that of the specified array.

Usage

From source file:annis.CSVHelper.java

public static SortedMap<Integer, SortedSet<String>> exportCSVHeader(Iterator<AnnotatedMatch> matches,
        PrintWriter w) {//  www  .j  a va2s.  c  om
    // figure out what annotations are used at each match position
    SortedMap<Integer, SortedSet<String>> columnsByNodePos = new TreeMap<>();
    while (matches.hasNext()) {
        AnnotatedMatch match = matches.next();
        for (int j = 0; j < match.size(); ++j) {
            AnnotatedSpan span = match.get(j);
            if (columnsByNodePos.get(j) == null) {
                columnsByNodePos.put(j, new TreeSet<String>());
            }
            for (Annotation annotation : span.getAnnotations()) {
                columnsByNodePos.get(j).add("anno_" + annotation.getQualifiedName());
            }

            for (Annotation meta : span.getMetadata()) {
                columnsByNodePos.get(j).add("meta_" + meta.getQualifiedName());
            }

        }
    }

    CSVWriter csvWriter = new CSVWriter(w, '\t', CSVWriter.NO_QUOTE_CHARACTER, '\\');
    // print column names and data types
    int count = columnsByNodePos.keySet().size();
    ArrayList<String> headerLine = new ArrayList<>();

    for (int j = 0; j < count; ++j) {
        headerLine.add(fullColumnName(j + 1, "id"));
        headerLine.add(fullColumnName(j + 1, "span"));

        SortedSet<String> annotationNames = columnsByNodePos.get(j);
        for (String name : annotationNames) {
            headerLine.add(fullColumnName(j + 1, name));
        }
    }
    csvWriter.writeNext(headerLine.toArray(new String[headerLine.size()]));

    return columnsByNodePos;
}

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From source file:com.galenframework.speclang2.reader.pagespec.ForLoop.java

private static Object[] readSequenceForSimpleLoop(String sequenceStatement) {
    sequenceStatement = sequenceStatement.replace(" ", "");
    sequenceStatement = sequenceStatement.replace("\t", "");
    Pattern sequencePattern = Pattern.compile(".*\\-.*");
    try {//from w w w  .  j av a2  s  .c o  m
        String[] values = sequenceStatement.split(",");

        ArrayList<Object> sequence = new ArrayList<>();

        for (String stringValue : values) {
            if (sequencePattern.matcher(stringValue).matches()) {
                sequence.addAll(createSequence(stringValue));
            } else {
                sequence.add(convertValueToIndex(stringValue));
            }
        }

        return sequence.toArray(new Object[] {});
    } catch (Exception ex) {
        throw new SyntaxException(UNKNOWN_LINE, "Incorrect sequence syntax: " + sequenceStatement, ex);
    }
}

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From source file:net.drgnome.virtualpack.util.Util.java

public static <T extends Cloneable> T[] copy(T... objects) {
        ArrayList<T> list = new ArrayList<T>();
        for (T obj : objects) {
            list.add(copy(obj));//  w w  w .  j a v  a 2s  . c  o  m
        }
        return list.toArray(createGenericArray((Class<T>) objects.getClass().getComponentType()));
    }

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From source file:Main.java

/**
 * gets a tokenizer and returns an arraylist with the separated elements of the tokenizer
 * /*from   w  w  w . j av a  2s  . c  o m*/
 * @param strt the tokenizer
 * @param hasToTrim if has to trim every single element of the tokenizer
 * @return the AL with the elements
 */
public static String[] getStringArrayFromString(String strValues, String strSeparator, boolean hasToTrim) {

    // if null
    if (strValues == null)
        return new String[0];

    // creates the AL
    ArrayList<String> al = new ArrayList<String>();
    StringTokenizer strt = new StringTokenizer(strValues, strSeparator);

    while (strt.hasMoreElements()) {
        // gets the next element
        String strElement = (String) strt.nextElement();

        // if is to be trimmed, it does it
        if (hasToTrim)
            strElement = strElement.trim();

        // and adds it to the AL
        al.add(strElement);
    }

    String[] strArray = new String[al.size()];

    // returns the AL
    return al.toArray(strArray);
}

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From source file:com.ricemap.spateDB.core.SpatialSite.java

public static GlobalIndex<Partition> getGlobalIndex(FileSystem fs, Path dir) throws IOException {
    // Retrieve the master file (the only file with the name _master in it)
    FileStatus[] masterFiles = fs.listStatus(dir, new PathFilter() {
        @Override//w  w  w  .jav  a2s .  c  o  m
        public boolean accept(Path path) {
            return path.getName().contains("_master");
        }
    });
    // Check if the given file is indexed
    if (masterFiles.length == 0)
        return null;
    if (masterFiles.length > 1)
        throw new RuntimeException("Found more than one master file in " + dir);
    Path masterFile = masterFiles[0].getPath();
    ShapeRecordReader<Partition> reader = new ShapeRecordReader<Partition>(fs.open(masterFile), 0,
            fs.getFileStatus(masterFile).getLen());
    CellInfo dummy = new CellInfo();
    Partition partition = new Partition();
    ArrayList<Partition> partitions = new ArrayList<Partition>();
    while (reader.next(dummy, partition)) {
        partitions.add(partition.clone());
    }
    GlobalIndex<Partition> globalIndex = new GlobalIndex<Partition>();
    globalIndex.bulkLoad(partitions.toArray(new Partition[partitions.size()]));
    globalIndex.setCompact(masterFile.getName().endsWith("rtree") || masterFile.getName().endsWith("r+tree"));
    globalIndex.setReplicated(masterFile.getName().endsWith("r+tree") || masterFile.getName().endsWith("grid"));
    return globalIndex;
}

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From source file:com.mycsense.carbondb.domain.SourceRelation.java

public static String getHashKey(Dimension dimension, Dimension commonKeywords, Integer alpha) {
    if (alpha == 0) {
        return "#emptyHashKey#";
    }/*  w w w. j  a va 2  s .  c  om*/

    ArrayList<String> keywordInKey = new ArrayList<>();
    for (Keyword keyword : dimension.keywords) {
        if (commonKeywords.contains(keyword)) {
            keywordInKey.add(keyword.toString());
        }
    }
    if (keywordInKey.size() != alpha) {
        return "#nullHashKey#";
    }

    Collections.sort(keywordInKey);
    return implode(",", keywordInKey.toArray(new String[keywordInKey.size()]));
}

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From source file:UtilFunctions.java

public static String[] parseFileTypes(String inputString) {

    //ArrayList to store each parsed filetype
    ArrayList<String> fileTypes = new ArrayList<>();

    //Scanner to iterate over the string filetype by filetype
    Scanner in = new Scanner(inputString);
    in.useDelimiter("[,] | [, ]");

    //Iterate over the string
    while (in.hasNext()) {
        fileTypes.add(in.next());//from  w  ww  .j a va2s. com
    }

    if (fileTypes.size() > 0) {
        //Generate an array from the ArrayList
        String[] returnArray = new String[fileTypes.size()];
        returnArray = fileTypes.toArray(returnArray);

        //Return that magnificent array
        return returnArray;

    } else {
        return null;
    }
}

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From source file:lineage.LineageEngine.java

/**
 * The main pipeline for reconstructing the cell lineage trees
 *///from www.  j  a  v  a2s  .c  om
public static void buildLineage(Args args) {

    // 1. load SNV data
    SNVDataStore db = new SNVDataStore(args.inputFileName, args.clustersFileName, args.normalSampleId);

    // 2. get the SNVs partitioned by group tag and create the appropriate SNV group objects
    HashMap<String, ArrayList<SNVEntry>> snvsByTag = db.getSomaticGroups();
    ArrayList<SNVGroup> groups = new ArrayList<SNVGroup>();
    for (String groupTag : snvsByTag.keySet()) {
        groups.add(new SNVGroup(groupTag, snvsByTag.get(groupTag), db.isRobustGroup(groupTag)));
    }
    if (groups.size() == 0) {
        logger.warning("All SNV groups have been filtered out.");
        return;
    }

    // 3. cluster SNVs in each group
    AAFClusterer clusterer = new AAFClusterer();
    for (SNVGroup group : groups) {
        if (args.clustersFileName == null) {
            Cluster[] clusters = clusterer.clusterSubPopulations(group, ClusteringAlgorithms.EM, 1);
            logger.fine("Clustering results for group: " + group.getTag());
            for (Cluster c : clusters) {
                logger.fine(c.toString());
            }
            group.setSubPopulations(clusters);
        } else {
            ArrayList<Cluster> groupClusters = db.getClusters().get(group.getTag());
            group.subPopulations = new Cluster[groupClusters.size()];
            group.subPopulations = groupClusters.toArray(group.subPopulations);
        }
    }

    // 4. construct the constraint network
    PHYNetwork constrNetwork = new PHYNetwork(groups, db.getNumSamples());
    logger.fine(constrNetwork.toString());

    // 5. find all the lineage trees that pass the VAF constraints
    ArrayList<PHYTree> spanningTrees = constrNetwork.getLineageTrees();
    logger.info("Found " + spanningTrees.size() + " valid tree(s)");

    if (spanningTrees.size() == 0) {
        logger.info("Adjusting the network...");
        // if no valid trees were found, fix the network 
        // remove group nodes that are not robust, complete edges
        int delta = 0;
        do {
            int numNodes = constrNetwork.numNodes;
            constrNetwork = constrNetwork.fixNetwork();
            spanningTrees = constrNetwork.getLineageTrees();
            delta = numNodes - constrNetwork.numNodes;
        } while ((delta != 0) && (spanningTrees.size() <= 0));
        if (spanningTrees.size() <= 0) {
            Parameters.ALL_EDGES = true;
            constrNetwork = new PHYNetwork(groups, db.getNumSamples());
            spanningTrees = constrNetwork.getLineageTrees();
        }
        logger.info("Found " + spanningTrees.size() + " valid trees after network adjustments");
    }

    // 6. evaluate/rank the trees
    if (spanningTrees.size() > 0) {
        constrNetwork.evaluateLineageTrees();
        logger.fine("Top tree\nError score: " + spanningTrees.get(0).getErrorScore());
        logger.fine(spanningTrees.get(0).toString());
    }

    // 7. result visualization
    if (args.showNetwork) {
        constrNetwork.displayNetwork();
    }
    if (spanningTrees.size() > 0) {
        for (int i = 0; i < args.numShow; i++) {
            if (spanningTrees.size() > i) {
                constrNetwork.displayTree(spanningTrees.get(i), db.getSampleNames(), null, null);
            } else {
                break;
            }
        }
        // 8. persistent storage
        if (args.numSave > 0) {
            writeTreesToTxtFile(constrNetwork, spanningTrees, db.getSampleNames(), args);
        }
    }
}

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From source file:Main.java

public static String[] split(String s, String sep) {
    if (s == null) {
        return null;
    }//from   www .  j a  v a2 s.c  om
    ArrayList<String> list = new ArrayList<String>();
    while (s.length() != 0) {
        int pos = s.indexOf(sep);
        if (pos >= 0) {
            list.add(s.substring(0, pos));
            s = s.substring(pos + sep.length(), s.length());
            if (s.length() == 0) {
                list.add(""); // letztes (leeres) Element hinter letztem Trennzeichen
            }
        } else if (s.length() > 0) {
            list.add(s);
            s = "";
        }
    }
    return list.toArray(new String[0]);
}

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From source file:com.amalto.workbench.compare.Utilities.java

public static IFile[] getFiles(ISelection selection) {
    ArrayList tmp = internalGetResources(selection, IFile.class);
    return (IFile[]) tmp.toArray(new IFile[tmp.size()]);
}

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