org.mskcc.shenkers.control.track.bam.BamView2.java Source code

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Here is the source code for org.mskcc.shenkers.control.track.bam.BamView2.java

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package org.mskcc.shenkers.control.track.bam;

import htsjdk.samtools.Cigar;
import htsjdk.samtools.CigarElement;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordIterator;
import htsjdk.samtools.SamReader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.concurrent.Semaphore;
import java.util.concurrent.locks.LockSupport;
import javafx.beans.binding.BooleanBinding;
import javafx.beans.property.Property;
import javafx.beans.property.SimpleBooleanProperty;
import javafx.concurrent.Task;
import javafx.scene.Node;
import javafx.scene.control.Label;
import javafx.scene.layout.BorderPane;
import javafx.scene.layout.Pane;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.fxmisc.easybind.EasyBind;
import org.mskcc.shenkers.control.track.View;
import static org.mskcc.shenkers.control.track.bam.BamView1.coverage;
import org.mskcc.shenkers.model.datatypes.GenomeSpan;
import org.mskcc.shenkers.view.LineHistogramView;
import org.mskcc.shenkers.view.SparseLineHistogramView;

/**
 *
 * @author sol
 */
public class BamView2 implements View<BamContext> {

    private final Logger logger = LogManager.getLogger();

    @Override
    public Task<Pane> getContent(BamContext context) {
        return context.spanProperty().getValue().map(i -> {

            String chr = i.getChr();
            int start = i.getStart();
            int end = i.getEnd();

            Task<Pane> task = new PaneTask(context, chr, start, end);

            logger.info("returning task");
            return task;
        }).orElse(new Task<Pane>() {

            @Override
            protected Pane call() throws Exception {
                return new BorderPane(new Label("coordinates not set"));
            }
        }
        //                new BorderPane(new Label("bamview1: span not set"))
        //                new Pane()
        );
    }

    public class PaneTask extends Task<Pane> {

        BamContext context;
        SamReader SAMReader;
        String chr;
        int start;
        int end;
        BooleanBinding flipBinding;
        Semaphore semaphore;

        public PaneTask(BamContext context, String chr, int start, int end) {
            super();
            this.context = context;
            this.SAMReader = context.readerProperty().getValue();
            this.chr = chr;
            this.start = start;
            this.end = end;
        }

        @Override
        protected Pane call() throws Exception {
            SAMRecordIterator sri = null;
            try {
                logger.info("calculating coverage for region {}:{}-{}", chr, start, end);

                logger.info("allocating coverage map");
                Map<Integer, Double> data = new HashMap<>();

                logger.info("acquiring semaphore for sam reader");
                while (!context.acquireReader()) {
                    logger.info("waiting...");
                    Thread.yield();
                }
                logger.info("parsing sam file");
                sri = SAMReader.query(chr, start, end, false);

                while (sri.hasNext()) {

                    if (isCancelled()) {
                        logger.info(Thread.currentThread().getName() + " recieved cancel and terminating");
                        break;
                    }

                    LockSupport.parkNanos(1);

                    SAMRecord sr = sri.next();
                    //                            logger.info("read: " + sr);

                    int alignmentPosition = sr.getAlignmentStart();

                    Cigar cigar = sr.getCigar();

                    for (int i = 0; i < cigar.numCigarElements(); i++) {
                        CigarElement cigarElement = cigar.getCigarElement(i);
                        if (cigarElement.getOperator().consumesReferenceBases()) {
                            boolean consumesReadBases = cigarElement.getOperator().consumesReadBases();
                            for (int j = 0; j < cigarElement.getLength(); j++) {
                                if (consumesReadBases && alignmentPosition >= start && alignmentPosition <= end) {
                                    int k = alignmentPosition - start;
                                    if (!data.containsKey(k)) {
                                        data.put(k, 0.0);
                                    }
                                    data.put(k, data.get(k) + 1);

                                }
                                alignmentPosition++;
                            }
                        }
                    }
                }

                //            double[] data = ArrayUtils.toPrimitive(IntStream.of(cov).mapToDouble(j -> j + 0.).boxed().collect(Collectors.toList()).toArray(new Double[0]));
                logger.info("setting data");
                SparseLineHistogramView lhv = new SparseLineHistogramView();

                class FlipBinding extends BooleanBinding {

                    private final Property<Optional<GenomeSpan>> span;

                    private FlipBinding(Property<Optional<GenomeSpan>> spanProperty) {
                        this.span = spanProperty;
                    }

                    protected boolean computeValue() {

                        if (span.getValue().isPresent()) {
                            return span.getValue().get().isNegativeStrand();
                        } else {
                            return false;
                        }
                    }

                }

                flipBinding = new FlipBinding(context.spanProperty());

                lhv.flipDomainProperty().bind(flipBinding);
                lhv.setData(data, end - start + 1, this);

                logger.info("calculating max");
                data.values().stream().max((Double d1, Double d2) -> Double.compare(d1, d2))
                        .ifPresent(m -> lhv.setMax(m));
                //            IntStream.of(cov).max().ifPresent(m -> lhv.setMax(m));

                logger.info("returning graphic");

                return lhv.getGraphic();
            } catch (Throwable t) {
                logger.info("task {} threw exception {}", this, t.getMessage());
                logger.info("exception: ", t);
                throw t;
            } finally {

                if (sri != null) {
                    sri.close();
                }
                logger.info("{} releasing semaphore for task {}", Thread.currentThread().getName(), this);
                context.releaseReader();
                logger.info("released sam reader semaphore");
            }
        }

        @Override
        protected void cancelled() {
            super.cancelled();
            logger.info("Cancelling task");
        }

    }

}