Example usage for java.util Set isEmpty

Introduction

In this page you can find the example usage for java.util Set isEmpty.

Prototype

boolean isEmpty();

Source Link

Document

Returns true if this set contains no elements.

Usage

From source file:edu.msu.cme.rdp.probematch.cli.SliceToPrimer.java

public static void main(String[] args) throws Exception {
    //args = "--fedit-dist 4 --redit-dist=4 -k --max-length=400 --min-length=280 -o java_sliced_edit4.fasta TGCGAYCCSAARGCBGACTC ATSGCCATCATYTCRCCGGA /scratch/fishjord/tae_kwon_primer_match/all_genomes.fasta".split(" ");
    PatternBitMask64[] fprimers;//ww  w  . j a  va  2s. co m
    String[] fprimerStrs, rprimerStrs;
    PatternBitMask64[] rprimers;

    FastaWriter seqOut;
    PrintStream statsOut;

    int fEdit = 3;
    int rEdit = 3;
    int minLength = Integer.MIN_VALUE;
    int maxLength = Integer.MAX_VALUE;
    boolean allowAmbiguities = true;
    boolean keepPrimers = false;

    SequenceReader inSeqs;

    try {

        CommandLine line = new PosixParser().parse(options, args);

        if (line.hasOption("edit-dist")) {
            fEdit = rEdit = Integer.parseInt(line.getOptionValue("edit-dist"));

            if (line.hasOption("redit-dist") || line.hasOption("fedit-dist")) {
                throw new Exception("edit-dist, [fedit-dist, redit-dist] are mutually exclusive");
            }
        }

        if (line.hasOption("fedit-dist")) {
            fEdit = Integer.parseInt(line.getOptionValue("fedit-dist"));
        }

        if (line.hasOption("no-ambiguities")) {
            allowAmbiguities = false;
        }

        if (line.hasOption("keep-primers")) {
            keepPrimers = true;
        }

        if (line.hasOption("redit-dist")) {
            rEdit = Integer.parseInt(line.getOptionValue("redit-dist"));
        }

        if (line.hasOption("seq-out")) {
            seqOut = new FastaWriter(new File(line.getOptionValue("seq-out")));
        } else {
            throw new Exception("Must specify seq-out");
        }

        if (line.hasOption("stats-out")) {
            statsOut = new PrintStream(new File(line.getOptionValue("stats-out")));
        } else {
            statsOut = System.out;
        }

        if (line.hasOption("min-length")) {
            minLength = Integer.parseInt(line.getOptionValue("min-length"));
        }

        if (line.hasOption("max-length")) {
            maxLength = Integer.parseInt(line.getOptionValue("max-length"));
        }

        args = line.getArgs();

        if (args.length != 3) {
            throw new Exception("Unexpected number of command line arguments");
        }

        fprimers = translateStringPrimers(args[0].split(","), allowAmbiguities, false);
        fprimerStrs = args[0].split(",");
        rprimers = translateStringPrimers(args[1].split(","), allowAmbiguities, true);
        rprimerStrs = args[1].split(",");
        inSeqs = new SequenceReader(new File(args[2]));

    } catch (Exception e) {
        new HelpFormatter().printHelp("SliceToPrimer [options] <f,p,r,i,m,e,r> <r,p,r,i,m,e,r> <in_seq_file>",
                options);
        System.err.println("ERROR: " + e.getMessage());
        return;
    }

    Sequence seq;

    statsOut.println(
            "orig_seqid\tsliced_seqid\tfprimer\tstart\tend\tscore\trprimer\tstart\tend\tscore\tlength");

    ScoringMatrix sccoringMatrix = ScoringMatrix.getDefaultNuclMatrix();

    DPMAligner[] faligners = new DPMAligner[fprimers.length];
    for (int index = 0; index < faligners.length; index++) {
        faligners[index] = new DPMAligner(fprimerStrs[index], Integer.MAX_VALUE);
    }

    try {
        while ((seq = inSeqs.readNextSequence()) != null) {
            Set<PrimerMatch> fprimerMatches = new HashSet();
            Set<PrimerMatch> rprimerMatches = new HashSet();

            for (int index = 0; index < fprimers.length; index++) {
                PatternBitMask64 primer = fprimers[index];

                for (BitVector64Match r : BitVector64.process(seq.getSeqString().toCharArray(), primer, fEdit)
                        .getResults()) {
                    PrimerMatch match = new PrimerMatch();
                    match.start = r.getPosition() - (primer.getPatternLength() + r.getScore());
                    match.end = r.getPosition();
                    match.score = r.getScore();
                    match.primerIndex = index;
                    fprimerMatches.add(match);
                }
            }

            for (int index = 0; index < rprimers.length; index++) {
                PatternBitMask64 primer = rprimers[index];

                for (BitVector64Match r : BitVector64.process(seq.getSeqString().toCharArray(), primer, rEdit)
                        .getResults()) {
                    PrimerMatch match = new PrimerMatch();
                    match.start = r.getPosition() - (primer.getPatternLength() + r.getScore());
                    match.end = r.getPosition();
                    match.score = r.getScore();
                    match.primerIndex = index;
                    rprimerMatches.add(match);
                }
            }

            if (fprimerMatches.isEmpty() || rprimerMatches.isEmpty()) {
                statsOut.println(seq.getSeqName() + "\tEither/or no forward/reverse primer hits");
                continue;
            }
            for (PrimerMatch fmatch : fprimerMatches) {
                PrimerMatch bestReverse = null;
                int bestScore = Integer.MAX_VALUE;
                for (PrimerMatch rmatch : rprimerMatches) {
                    if (rmatch.start > fmatch.end && rmatch.start - fmatch.end < bestScore) {
                        bestReverse = rmatch;
                        bestScore = rmatch.start - fmatch.end;
                    }
                }

                if (bestReverse == null) {
                    statsOut.println(seq.getSeqName() + "\tNo reverse primer before " + fmatch.end);
                    continue;
                }

                String slicedSeq = null;
                if (keepPrimers) {
                    slicedSeq = seq.getSeqString().substring(fmatch.start, bestReverse.end);
                } else {
                    slicedSeq = seq.getSeqString().substring(fmatch.end, bestReverse.start);
                }

                String seqid = seq.getSeqName() + "_" + fmatch.primerIndex + "_" + fmatch.start;
                if (slicedSeq.length() > minLength && slicedSeq.length() < maxLength) {
                    seqOut.writeSeq(seqid, "", slicedSeq);
                }

                DPMAlignment seqs = faligners[fmatch.primerIndex]
                        .align(seq.getSeqString().substring(fmatch.start, fmatch.end));
                System.err.println(">" + seqid);
                System.err.println(fprimerStrs[fmatch.primerIndex]);
                System.err.println(seq.getSeqString().substring(fmatch.start, fmatch.end));
                System.err.println();
                System.err.println(seqs.getAlignedMatchFragment());
                System.err.println(seqs.getAlignedProbe());

                System.err.println();

                statsOut.println(seq.getSeqName() + "\t" + seqid + "\t" + fmatch.primerIndex + "\t"
                        + fmatch.start + "\t" + fmatch.end + "\t" + fmatch.score + "\t"
                        + bestReverse.primerIndex + "\t" + bestReverse.start + "\t" + bestReverse.end + "\t"
                        + bestReverse.score + "\t" + slicedSeq.length());
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
    } finally {
        statsOut.close();
        seqOut.close();
    }
}

From source file:Test.java

private static void displayEntryFlags(Set<AclEntryFlag> flagSet) {
    if (flagSet.isEmpty()) {
        return;//from ww w  .java 2  s . co  m
    }
    for (AclEntryFlag flag : flagSet) {
        System.out.print(flag.name() + " ");
    }
    System.out.println();

}

From source file:Test.java

private static void displayEntryFlags(Set<AclEntryFlag> flagSet) {
    if (flagSet.isEmpty()) {
        System.out.println("No ACL Entry Flags present");
    } else {/*from  www . j a v a 2s  . co  m*/
        System.out.println("ACL Entry Flags");
        for (AclEntryFlag flag : flagSet) {
            System.out.println(flag.name() + " ");
        }
    }
}

From source file:Main.java

public static boolean isSetEmpty(java.util.Set set) {
    if (null == set || set.isEmpty())
        return true;
    return false;
}

From source file:Main.java

public static boolean isNullOrEmpty(Set set) {
    return set == null || set.isEmpty();
}

From source file:Test.java

private static void displayPermissions(Set<AclEntryPermission> permissionSet) {
    if (permissionSet.isEmpty()) {
        return;//from   w ww. j  a  v a 2s .  co m
    }
    for (AclEntryPermission permission : permissionSet) {
        System.out.print(permission.name() + " ");
    }
    System.out.println();

}

From source file:Test.java

private static void displayPermissions(Set<AclEntryPermission> permissionSet) {
    if (permissionSet.isEmpty()) {
        System.out.println("No Permissions present");
    } else {//from   w w w.  ja v  a  2 s  . c  o  m
        System.out.println("Permissions");
        for (AclEntryPermission permission : permissionSet) {
            System.out.println(permission.name() + " ");
        }
    }
}

From source file:Main.java

private static String getPrefix(Set<String> names) {
    if (names.isEmpty()) {
        return "";
    }/*from w ww .ja va 2s.  co m*/

    String name = (String) names.toArray()[0];
    return name.substring(0, name.lastIndexOf("_"));
}

From source file:Main.java

public static boolean isBlank(Set set) {
    return (set == null || set.isEmpty());
}

From source file:Main.java

public static <T> Set<T> nonNullFrom(Set<T> set) {
    if (set == null || set.isEmpty()) {
        return Collections.emptySet();
    }/*from  w w  w  .  ja  va  2  s.  c  om*/
    return Collections.unmodifiableSet(set);
}