Examples with ObjectArrayList cern.colt.list.ObjectArrayList used on opensource projects

Example 1 with ObjectArrayList

use of cern.colt.list.ObjectArrayList in project Gemma by PavlidisLab.

the class LinkAnalysisServiceImpl method writeLinks.

/**
 * Write links as text.
 */
private void writeLinks(final LinkAnalysis la, FilterConfig filterConfig, Writer wr) throws IOException {
    Map<CompositeSequence, Set<Gene>> probeToGeneMap = la.getProbeToGeneMap();
    ObjectArrayList links = la.getKeep();
    double subsetSize = la.getConfig().getSubsetSize();
    List<String> buf = new ArrayList<>();
    if (la.getConfig().isSubset() && links.size() > subsetSize) {
        la.getConfig().setSubsetUsed(true);
    }
    wr.write(la.getConfig().toString());
    wr.write(filterConfig.toString());
    NumberFormat nf = NumberFormat.getInstance();
    nf.setMaximumFractionDigits(4);
    Integer probeDegreeThreshold = la.getConfig().getProbeDegreeThreshold();
    int i = 0;
    int keptLinksCount = 0;
    Random generator = new Random();
    double rand;
    double fraction = subsetSize / links.size();
    int skippedDueToDegree = 0;
    for (int n = links.size(); i < n; i++) {
        Object val = links.getQuick(i);
        if (val == null)
            continue;
        Link m = (Link) val;
        Double w = m.getWeight();
        int x = m.getx();
        int y = m.gety();
        if (probeDegreeThreshold > 0 && (la.getProbeDegree(x) > probeDegreeThreshold || la.getProbeDegree(y) > probeDegreeThreshold)) {
            skippedDueToDegree++;
            continue;
        }
        CompositeSequence p1 = la.getProbe(x);
        CompositeSequence p2 = la.getProbe(y);
        Set<Gene> g1 = probeToGeneMap.get(p1);
        Set<Gene> g2 = probeToGeneMap.get(p2);
        List<String> genes1 = new ArrayList<>();
        for (Gene cluster : g1) {
            String t = cluster.getOfficialSymbol();
            genes1.add(t);
        }
        List<String> genes2 = new ArrayList<>();
        for (Gene cluster : g2) {
            String t = cluster.getOfficialSymbol();
            genes2.add(t);
        }
        if (genes2.size() == 0 || genes1.size() == 0) {
            continue;
        }
        String gene1String = StringUtils.join(genes1.iterator(), "|");
        String gene2String = StringUtils.join(genes2.iterator(), "|");
        if (gene1String.equals(gene2String)) {
            continue;
        }
        if (++keptLinksCount % 50000 == 0) {
            LinkAnalysisServiceImpl.log.info(keptLinksCount + " links retained");
        }
        if (la.getConfig().isSubsetUsed()) {
            rand = generator.nextDouble();
            if (rand > fraction)
                continue;
        }
        buf.add(p1.getId() + "\t" + p2.getId() + "\t" + gene1String + "\t" + gene2String + "\t" + nf.format(w) + // save links
        "\n");
    // wr.write( p1.getId() + "\t" + p2.getId() + "\t" + gene1String + "\t" + gene2String + "\t" + nf.format( w
    // ) + "\n" );
    }
    wr.write("# totalLinks:" + keptLinksCount + "\n");
    wr.write("# printedLinks:" + buf.size() + "\n");
    wr.write("# skippedDueToHighNodeDegree:" + skippedDueToDegree + "\n");
    for (String line : buf) {
        // write links to file
        wr.write(line);
    }
    if (la.getConfig().isSubsetUsed()) {
        // subset option activated
        LinkAnalysisServiceImpl.log.info("Done, " + keptLinksCount + "/" + links.size() + " links kept, " + buf.size() + " links printed");
    // wr.write("# Amount of links before subsetting/after subsetting: " + links.size() + "/" + numPrinted +
    // "\n" );
    } else {
        LinkAnalysisServiceImpl.log.info("Done, " + keptLinksCount + "/" + links.size() + " links printed (some may have been filtered)");
    }
    wr.flush();
}

Example 2 with ObjectArrayList

use of cern.colt.list.ObjectArrayList in project Gemma by PavlidisLab.

the class LinkAnalysisPersisterImpl method saveLinksToDb.

@Override
public void saveLinksToDb(LinkAnalysis la) {
    if (!la.getConfig().isUseDb()) {
        throw new IllegalArgumentException("Analysis is not configured to use the db to persist");
    }
    this.deleteAnalyses(la.getExpressionExperiment());
    // the analysis object will get updated.
    CoexpressionAnalysis analysisObj = la.getAnalysisObj();
    analysisObj.setCoexpCorrelationDistribution(la.getCorrelationDistribution());
    analysisObj = (CoexpressionAnalysis) persisterHelper.persist(analysisObj);
    /*
         * At this point we have the populated analysis object, but no links.
         */
    la.setAnalysisObj(analysisObj);
    StopWatch watch = new StopWatch();
    watch.start();
    ObjectArrayList links = la.getKeep();
    int numSaved = this.saveLinks(la, links);
    LinkAnalysisPersisterImpl.log.info("Seconds to process " + numSaved + " links (plus flipped versions):" + watch.getTime() / 1000.0);
    watch.stop();
}

Example 3 with ObjectArrayList

use of cern.colt.list.ObjectArrayList in project tdq-studio-se by Talend.

the class AbstractLongObjectMap method values.

/**
 * Returns a list filled with all values contained in the receiver.
 * The returned list has a size that equals <tt>this.size()</tt>.
 * Iteration order is guaranteed to be <i>identical</i> to the order used by method {@link #forEachKey(LongProcedure)}.
 * <p>
 * This method can be used to iterate over the values of the receiver.
 *
 * @return the values.
 */
public ObjectArrayList values() {
    ObjectArrayList list = new ObjectArrayList(size());
    values(list);
    return list;
}

Example 4 with ObjectArrayList

use of cern.colt.list.ObjectArrayList in project tdq-studio-se by Talend.

the class OpenLongObjectHashMap method clear.

/**
 * Removes all (key,value) associations from the receiver.
 * Implicitly calls <tt>trimToSize()</tt>.
 */
public void clear() {
    new ByteArrayList(this.state).fillFromToWith(0, this.state.length - 1, FREE);
    // delta
    new ObjectArrayList(values).fillFromToWith(0, state.length - 1, null);
    this.distinct = 0;
    // delta
    this.freeEntries = table.length;
    trimToSize();
}

Example 5 with ObjectArrayList

use of cern.colt.list.ObjectArrayList in project tdq-studio-se by Talend.

the class OpenIntObjectHashMap method clear.

/**
 * Removes all (key,value) associations from the receiver.
 * Implicitly calls <tt>trimToSize()</tt>.
 */
public void clear() {
    new ByteArrayList(this.state).fillFromToWith(0, this.state.length - 1, FREE);
    // delta
    new ObjectArrayList(values).fillFromToWith(0, state.length - 1, null);
    this.distinct = 0;
    // delta
    this.freeEntries = table.length;
    trimToSize();
}