Example usage for java.util List removeAll

List of usage examples for java.util List removeAll

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Introduction

In this page you can find the example usage for java.util List removeAll.

Prototype

boolean removeAll(Collection<?> c);

Source Link

Document

Removes from this list all of its elements that are contained in the specified collection (optional operation).

Usage

From source file:Main.java

public static void main(String[] argv) throws Exception {
    List list1 = new ArrayList();
    List list2 = new ArrayList();

    list1.addAll(list2);/* w ww.  java2  s . co  m*/

    list1.removeAll(list2);

    list1.retainAll(list2);

    list1.clear();

    int newSize = 2;
    list1.subList(newSize, list1.size()).clear();
}

From source file:MainClass.java

public static void main(String args[]) {
    String init[] = { "One", "Two", "Three", "One", "Two", "Three" };
    List list1 = new ArrayList(Arrays.asList(init));
    List list2 = new ArrayList(Arrays.asList(init));
    list1.remove("One");
    System.out.println(list1);/*from   w w  w  . j ava  2  s.  c  o m*/
    list2.removeAll(Collections.singleton("One"));
    System.out.println(list2);
}

From source file:Main.java

public static void main(String[] argv) throws Exception {
    List<String> list1 = new ArrayList();
    List<String> list2 = new ArrayList();

    list1.addAll(list2);//from   w w w  . j a v  a 2 s  .c o  m

    list1.removeAll(list2);

    list1.retainAll(list2);

    list1.clear();

    int newSize = 2;
    list1.subList(newSize, list1.size()).clear();
}

From source file:Main.java

public static void main(String args[]) {
    String init[] = { "One", "Two", "Three", "One", "Two", "Three" };

    // create two lists
    List<String> list1 = new ArrayList<String>(Arrays.asList(init));
    List<String> list2 = new ArrayList<String>(Arrays.asList(init));

    // remove from list1
    list1.remove("One");
    System.out.println("List1 value: " + list1);

    // remove from list2 using singleton
    list2.removeAll(Collections.singleton("One"));
    System.out.println("The SingletonList is :" + list2);
}

From source file:MainClass.java

public static void main(String args[]) throws Exception {

    List list = new ArrayList();
    list.add("A");
    list.add("A");
    list.add("B");
    list.add("B");
    list.add("C");
    list.add("C");

    List list2 = new ArrayList();
    list2.add("A");
    list2.add("B");
    list2.add("C");
    list.removeAll(list2);

    System.out.println(list);/*from  w ww.  j  a  v  a2  s .  co  m*/
}

From source file:MainClass.java

public static void main(String args[]) throws Exception {

    List list = new ArrayList();
    list.add("A");
    list.add("A");
    list.add("B");
    list.add("B");
    list.add("C");
    list.add("C");
    list.add("D");

    List list2 = new ArrayList();
    list2.add("A");
    list2.add("B");
    list2.add("C");
    list.removeAll(list2);

    System.out.println(list);/*w w w . ja va 2s . co m*/
}

From source file:Main.java

public static void main(String args[]) throws Exception {

    List<String> list = new ArrayList<String>();
    list.add("A");
    list.add("A");
    list.add("B");
    list.add("B");
    list.add("C");
    list.add("C");

    List<String> list2 = new ArrayList<String>();
    list2.add("A");
    list2.add("B");
    list2.add("C");
    list.removeAll(list2);

    System.out.println(list);//  w  w  w . ja  v a 2s .  c o m
}

From source file:com.sangupta.keepwalking.MergeRepo.java

/**
 * @param args//from   ww  w .  j a  v  a2s .c o  m
 * @throws IOException 
 */
public static void main(String[] args) throws IOException {
    if (args.length != 3) {
        usage();
        return;
    }

    final String previousRepo = args[0];
    final String newerRepo = args[1];
    final String mergedRepo = args[2];

    final File previous = new File(previousRepo);
    final File newer = new File(newerRepo);
    final File merged = new File(mergedRepo);

    if (!(previous.exists() && previous.isDirectory())) {
        System.out.println("The previous version does not exists or is not a directory.");
        return;
    }

    if (!(newer.exists() && newer.isDirectory())) {
        System.out.println("The newer version does not exists or is not a directory.");
        return;
    }

    final IOFileFilter directoryFilter = FileFilterUtils.makeCVSAware(FileFilterUtils.makeSVNAware(null));

    final Collection<File> olderFiles = FileUtils.listFiles(previous, TrueFileFilter.TRUE, directoryFilter);
    final Collection<File> newerFiles = FileUtils.listFiles(newer, TrueFileFilter.TRUE, directoryFilter);

    // build a list of unique paths
    System.out.println("Reading files from older version...");
    List<String> olderPaths = new ArrayList<String>();
    for (File oldFile : olderFiles) {
        olderPaths.add(getRelativePath(oldFile, previous));
    }

    System.out.println("Reading files from newer version...");
    List<String> newerPaths = new ArrayList<String>();
    for (File newerFile : newerFiles) {
        newerPaths.add(getRelativePath(newerFile, newer));
    }

    // find which files have been removed from Perforce depot
    List<String> filesRemoved = new ArrayList<String>(olderPaths);
    filesRemoved.removeAll(newerPaths);
    System.out.println("Files removed in newer version: " + filesRemoved.size());
    for (String removed : filesRemoved) {
        System.out.print("    ");
        System.out.println(removed);
    }

    // find which files have been added in Perforce depot
    List<String> filesAdded = new ArrayList<String>(newerPaths);
    filesAdded.removeAll(olderPaths);
    System.out.println("Files added in newer version: " + filesAdded.size());
    for (String added : filesAdded) {
        System.out.print("    ");
        System.out.println(added);
    }

    // find which files are common 
    // now check if they have modified or not
    newerPaths.retainAll(olderPaths);
    List<String> modified = checkModifiedFiles(newerPaths, previous, newer);
    System.out.println("Files modified in newer version: " + modified.size());
    for (String modify : modified) {
        System.out.print("    ");
        System.out.println(modify);
    }

    // clean any previous existence of merged repo
    System.out.println("Cleaning any previous merged repositories...");
    if (merged.exists() && merged.isDirectory()) {
        FileUtils.deleteDirectory(merged);
    }

    System.out.println("Merging from newer to older repository...");
    // copy the original SVN repo to merged
    FileUtils.copyDirectory(previous, merged);

    // now remove all files that need to be
    for (String removed : filesRemoved) {
        File toRemove = new File(merged, removed);
        toRemove.delete();
    }

    // now add all files that are new in perforce
    for (String added : filesAdded) {
        File toAdd = new File(newer, added);
        File destination = new File(merged, added);
        FileUtils.copyFile(toAdd, destination);
    }

    // now over-write modified files
    for (String changed : modified) {
        File change = new File(newer, changed);
        File destination = new File(merged, changed);
        destination.delete();
        FileUtils.copyFile(change, destination);
    }

    System.out.println("Done merging.");
}

From source file:LinkedListTest.java

public static void main(String[] args) {
    List<String> a = new LinkedList<String>();
    a.add("Amy");
    a.add("Carl");
    a.add("Erica");

    List<String> b = new LinkedList<String>();
    b.add("Bob");
    b.add("Doug");
    b.add("Frances");
    b.add("Gloria");

    // merge the words from b into a

    ListIterator<String> aIter = a.listIterator();
    Iterator<String> bIter = b.iterator();

    while (bIter.hasNext()) {
        if (aIter.hasNext())
            aIter.next();//from w  w w  .  java2  s  .c  o  m
        aIter.add(bIter.next());
    }

    System.out.println(a);

    // remove every second word from b

    bIter = b.iterator();
    while (bIter.hasNext()) {
        bIter.next(); // skip one element
        if (bIter.hasNext()) {
            bIter.next(); // skip next element
            bIter.remove(); // remove that element
        }
    }

    System.out.println(b);

    // bulk operation: remove all words in b from a

    a.removeAll(b);

    System.out.println(a);
}

From source file:diffhunter.DiffHunter.java

/**
 * @param args the command line arguments
 * @throws org.apache.commons.cli.ParseException
 * @throws java.io.IOException/*  w ww . j a va2  s .co m*/
 */
public static void main(String[] args) throws ParseException, IOException {

    //String test_ = Paths.get("J:\\VishalData\\additional\\", "Sasan" + "_BDB").toAbsolutePath().toString();

    // TODO code application logic here
    /*args = new String[]
    {
    "-i", "-b", "J:\\VishalData\\additional\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted.bed", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-o", "J:\\VishalData"
    };*/

    /*args = new String[]
    {
    "-c", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-1", "J:\\VishalData\\Ptbp2_Adult_testis_CLIP_mm9_plus_strand_sorted_BDB", "-2", "J:\\VishalData\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted_BDB", "-w", "200", "-s", "50", "-o", "J:\\VishalData"
    };*/
    Options options = new Options();

    // add t option
    options.addOption("i", "index", false, "Indexing BED files.");
    options.addOption("b", "bed", true, "bed file to be indexed");
    options.addOption("o", "output", true, "Folder that the index/comparison file will be created.");
    options.addOption("r", "reference", true, "Reference annotation file to be used for indexing");
    options.addOption("c", "compare", false, "Finding differences between two conditions");
    options.addOption("1", "first", true, "First sample index location");
    options.addOption("2", "second", true, "Second sample index location");
    options.addOption("w", "window", true, "Length of window for identifying differences");
    options.addOption("s", "sliding", true, "Length of sliding");

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = parser.parse(options, args);

    boolean indexing = false;
    boolean comparing = false;

    //Indexing!
    if (cmd.hasOption("i")) {
        //if(cmd.hasOption("1"))
        //System.err.println("sasan");

        //System.out.println("sasa");
        indexing = true;

    } else if (cmd.hasOption("c")) {
        //System.err.println("");
        comparing = true;

    } else {
        //System.err.println("Option is not deteced.");
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("diffhunter", options);
        return;
    }

    //Indexing is selected
    //
    if (indexing == true) {
        //Since indexing is true.
        //User have to provide file for indexing.
        if (!(cmd.hasOption("o") || cmd.hasOption("r") || cmd.hasOption("b"))) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("diffhunter", options);
            return;
        }
        String bedfile_ = cmd.getOptionValue("b");
        String reference_file = cmd.getOptionValue("r");
        String folder_loc = cmd.getOptionValue("o");

        String sample_name = FilenameUtils.getBaseName(bedfile_);

        try (Database B2 = BerkeleyDB_Box.Get_BerkeleyDB(
                Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString(), true, sample_name)) {
            Indexer indexing_ = new Indexer(reference_file);
            indexing_.Make_Index(B2, bedfile_,
                    Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString());
            B2.close();

        }
    } else if (comparing == true) {
        if (!(cmd.hasOption("o") || cmd.hasOption("w") || cmd.hasOption("s") || cmd.hasOption("1")
                || cmd.hasOption("2"))) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("diffhunter", options);
            return;
        }
        String folder_loc = cmd.getOptionValue("o");
        int window_ = Integer.parseInt(cmd.getOptionValue("w"));
        //int window_=600;

        int slide_ = Integer.parseInt(cmd.getOptionValue("s"));

        String first = cmd.getOptionValue("1").replace("_BDB", "");
        String second = cmd.getOptionValue("2").replace("_BDB", "");
        String reference_file = cmd.getOptionValue("r");
        //String folder_loc=cmd.getOptionValue("o");

        String sample_name_first = FilenameUtils.getBaseName(first);
        String sample_name_second = FilenameUtils.getBaseName(second);

        Database B1 = BerkeleyDB_Box.Get_BerkeleyDB(first + "_BDB", false, sample_name_first);
        Database B2 = BerkeleyDB_Box.Get_BerkeleyDB(second + "_BDB", false, sample_name_second);

        List<String> first_condition_genes = Files
                .lines(Paths.get(first + "_BDB", sample_name_first + ".txt").toAbsolutePath())
                .collect(Collectors.toList());
        List<String> second_condition_genes = Files
                .lines(Paths.get(second + "_BDB", sample_name_second + ".txt").toAbsolutePath())
                .collect(Collectors.toList());
        System.out.println("First and second condition are loaded!!! ");
        List<String> intersection_ = new ArrayList<>(first_condition_genes);
        intersection_.retainAll(second_condition_genes);

        BufferedWriter output = new BufferedWriter(
                new FileWriter(Paths.get(folder_loc, "differences_" + window_ + "_s" + slide_ + "_c" + ".txt")
                        .toAbsolutePath().toString(), false));
        List<Result_Window> final_results = Collections.synchronizedList(new ArrayList<>());
        Worker_New worker_class = new Worker_New();
        worker_class.Read_Reference(reference_file);

        while (!intersection_.isEmpty()) {
            List<String> selected_genes = new ArrayList<>();
            //if (intersection_.size()<=10000){selected_genes.addAll(intersection_.subList(0, intersection_.size()));}
            //else selected_genes.addAll(intersection_.subList(0, 10000));
            if (intersection_.size() <= intersection_.size()) {
                selected_genes.addAll(intersection_.subList(0, intersection_.size()));
            } else {
                selected_genes.addAll(intersection_.subList(0, intersection_.size()));
            }
            intersection_.removeAll(selected_genes);
            //System.out.println("Intersection count is:"+intersection_.size());
            //final List<Result_Window> resultssss_=new ArrayList<>();
            IntStream.range(0, selected_genes.size()).parallel().forEach(i -> {
                System.out.println(selected_genes.get(i) + "\tprocessing......");
                String gene_of_interest = selected_genes.get(i);//"ENSG00000142657|PGD";//intersection_.get(6);////"ENSG00000163395|IGFN1";//"ENSG00000270066|SCARNA2";
                int start = worker_class.dic_genes.get(gene_of_interest).start_loc;
                int end = worker_class.dic_genes.get(gene_of_interest).end_loc;

                Map<Integer, Integer> first_ = Collections.EMPTY_MAP;
                try {
                    first_ = BerkeleyDB_Box.Get_Coord_Read(B1, gene_of_interest);
                } catch (IOException | ClassNotFoundException ex) {
                    Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex);
                }

                Map<Integer, Integer> second_ = Collections.EMPTY_MAP;
                try {
                    second_ = BerkeleyDB_Box.Get_Coord_Read(B2, gene_of_interest);
                } catch (IOException | ClassNotFoundException ex) {
                    Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex);
                }
                List<Window> top_windows_first = worker_class.Get_Top_Windows(window_, first_, slide_);
                List<Window> top_windows_second = worker_class.Get_Top_Windows(window_, second_, slide_);
                //System.out.println("passed for window peak call for gene \t"+selected_genes.get(i));
                // System.out.println("top_window_first_Count\t"+top_windows_first.size());
                // System.out.println("top_window_second_Count\t"+top_windows_second.size());
                if (top_windows_first.isEmpty() && top_windows_second.isEmpty()) {
                    return;
                }

                List<Result_Window> res_temp = new Worker_New().Get_Significant_Windows(gene_of_interest, start,
                        end, top_windows_first, top_windows_second, second_, first_, sample_name_first,
                        sample_name_second, 0.01);
                if (!res_temp.isEmpty()) {
                    final_results.addAll(res_temp);//final_results.addAll(worker_class.Get_Significant_Windows(gene_of_interest, start, end, top_windows_first, top_windows_second, second_, first_, first_condition, second_condition, 0.01));

                } //System.out.println(selected_genes.get(i)+"\tprocessed.");

            });

            /*selected_genes.parallelStream().forEach(i ->
             {
                    
                    
             });*/
            List<Double> pvals = new ArrayList<>();

            for (int i = 0; i < final_results.size(); i++) {
                pvals.add(final_results.get(i).p_value);
            }
            List<Double> qvals = MultipleTestCorrection.benjaminiHochberg(pvals);

            System.out.println("Writing to file...");
            output.append("Gene_Symbol\tContributing_Sample\tStart\tEnd\tOddsRatio\tp_Value\tFDR");
            output.newLine();

            for (int i = 0; i < final_results.size(); i++) {
                Result_Window item = final_results.get(i);
                output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t"
                        + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value
                        + "\t" + qvals.get(i)); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non);
                output.newLine();
            }

            /* for (Result_Window item : final_results)
             {
            output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t" + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non);
            output.newLine();
             }
               */
            final_results.clear();

        }
        output.close();

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

}