Examples with Segment org.dishevelled.bio.assembly.gfa2.Segment used on opensource projects

Example 16 with Segment

use of org.dishevelled.bio.assembly.gfa2.Segment in project opencast by opencast.

the class SegmentPreviewsWorkflowOperationHandler method createPreviews.

/**
 * Encode tracks from MediaPackage using profiles stored in properties and updates current MediaPackage.
 *
 * @param mediaPackage
 * @return the operation result containing the updated mediapackage
 * @throws EncoderException
 * @throws ExecutionException
 * @throws InterruptedException
 * @throws IOException
 * @throws NotFoundException
 * @throws WorkflowOperationException
 */
private WorkflowOperationResult createPreviews(final MediaPackage mediaPackage, WorkflowInstance wi) throws EncoderException, InterruptedException, ExecutionException, NotFoundException, MediaPackageException, IOException, WorkflowOperationException {
    long totalTimeInQueue = 0;
    WorkflowOperationInstance operation = wi.getCurrentOperation();
    // Read the configuration properties
    ConfiguredTagsAndFlavors tagsAndFlavors = getTagsAndFlavors(wi, Configuration.many, Configuration.one, Configuration.many, Configuration.one);
    MediaPackageElementFlavor sourceVideoFlavor = tagsAndFlavors.getSingleSrcFlavor();
    List<String> sourceTagSet = tagsAndFlavors.getSrcTags();
    List<String> targetImageTags = tagsAndFlavors.getTargetTags();
    MediaPackageElementFlavor targetImageFlavor = tagsAndFlavors.getSingleTargetFlavor();
    String encodingProfileName = StringUtils.trimToNull(operation.getConfiguration("encoding-profile"));
    String referenceFlavor = StringUtils.trimToNull(operation.getConfiguration("reference-flavor"));
    String referenceTags = StringUtils.trimToNull(operation.getConfiguration("reference-tags"));
    // Find the encoding profile
    EncodingProfile profile = composerService.getProfile(encodingProfileName);
    if (profile == null)
        throw new IllegalStateException("Encoding profile '" + encodingProfileName + "' was not found");
    // Select the tracks based on the tags and flavors
    Set<Track> videoTrackSet = new HashSet<>();
    for (Track track : mediaPackage.getTracksByTags(sourceTagSet)) {
        if (sourceVideoFlavor == null || (track.getFlavor() != null && sourceVideoFlavor.equals(track.getFlavor()))) {
            if (!track.hasVideo())
                continue;
            videoTrackSet.add(track);
        }
    }
    if (videoTrackSet.size() == 0) {
        logger.debug("Mediapackage {} has no suitable tracks to extract images based on tags {} and flavor {}", mediaPackage, sourceTagSet, sourceVideoFlavor);
        return createResult(mediaPackage, Action.CONTINUE);
    } else {
        // Determine the tagset for the reference
        List<String> referenceTagSet = asList(referenceTags);
        // Determine the reference master
        for (Track t : videoTrackSet) {
            // Try to load the segments catalog
            MediaPackageReference trackReference = new MediaPackageReferenceImpl(t);
            Catalog[] segmentCatalogs = mediaPackage.getCatalogs(MediaPackageElements.SEGMENTS, trackReference);
            Mpeg7Catalog mpeg7 = null;
            if (segmentCatalogs.length > 0) {
                mpeg7 = loadMpeg7Catalog(segmentCatalogs[0]);
                if (segmentCatalogs.length > 1)
                    logger.warn("More than one segments catalog found for track {}. Resuming with the first one ({})", t, mpeg7);
            } else {
                logger.debug("No segments catalog found for track {}", t);
                continue;
            }
            // Check the catalog's consistency
            if (mpeg7.videoContent() == null || mpeg7.videoContent().next() == null) {
                logger.info("Segments catalog {} contains no video content", mpeg7);
                continue;
            }
            Video videoContent = mpeg7.videoContent().next();
            TemporalDecomposition<? extends Segment> decomposition = videoContent.getTemporalDecomposition();
            // Are there any segments?
            if (decomposition == null || !decomposition.hasSegments()) {
                logger.info("Segments catalog {} contains no video content", mpeg7);
                continue;
            }
            // Is a derived track with the configured reference flavor available?
            MediaPackageElement referenceMaster = getReferenceMaster(mediaPackage, t, referenceFlavor, referenceTagSet);
            // Create the preview images according to the mpeg7 segments
            if (t.hasVideo() && mpeg7 != null) {
                Iterator<? extends Segment> segmentIterator = decomposition.segments();
                List<MediaTimePoint> timePointList = new LinkedList<>();
                while (segmentIterator.hasNext()) {
                    Segment segment = segmentIterator.next();
                    MediaTimePoint tp = segment.getMediaTime().getMediaTimePoint();
                    timePointList.add(tp);
                }
                // convert to time array
                double[] timeArray = new double[timePointList.size()];
                for (int i = 0; i < timePointList.size(); i++) timeArray[i] = (double) timePointList.get(i).getTimeInMilliseconds() / 1000;
                Job job = composerService.image(t, profile.getIdentifier(), timeArray);
                if (!waitForStatus(job).isSuccess()) {
                    throw new WorkflowOperationException("Extracting preview image from " + t + " failed");
                }
                // Get the latest copy
                try {
                    job = serviceRegistry.getJob(job.getId());
                } catch (ServiceRegistryException e) {
                    throw new WorkflowOperationException(e);
                }
                // add this receipt's queue time to the total
                totalTimeInQueue += job.getQueueTime();
                List<? extends MediaPackageElement> composedImages = MediaPackageElementParser.getArrayFromXml(job.getPayload());
                Iterator<MediaTimePoint> it = timePointList.iterator();
                for (MediaPackageElement element : composedImages) {
                    Attachment composedImage = (Attachment) element;
                    if (composedImage == null)
                        throw new IllegalStateException("Unable to compose image");
                    // Add the flavor, either from the operation configuration or from the composer
                    if (targetImageFlavor != null) {
                        composedImage.setFlavor(targetImageFlavor);
                        logger.debug("Preview image has flavor '{}'", composedImage.getFlavor());
                    }
                    // Set the mimetype
                    try {
                        composedImage.setMimeType(MimeTypes.fromURI(composedImage.getURI()));
                    } catch (UnknownFileTypeException e) {
                        logger.warn("Mime type unknown for file {}. Setting none.", composedImage.getURI(), e);
                    }
                    // Add tags
                    for (String tag : targetImageTags) {
                        logger.trace("Tagging image with '{}'", tag);
                        composedImage.addTag(tag);
                    }
                    // Refer to the original track including a timestamp
                    MediaPackageReferenceImpl ref = new MediaPackageReferenceImpl(referenceMaster);
                    ref.setProperty("time", it.next().toString());
                    composedImage.setReference(ref);
                    // store new image in the mediaPackage
                    mediaPackage.add(composedImage);
                    String fileName = getFileNameFromElements(t, composedImage);
                    composedImage.setURI(workspace.moveTo(composedImage.getURI(), mediaPackage.getIdentifier().toString(), composedImage.getIdentifier(), fileName));
                }
            }
        }
    }
    return createResult(mediaPackage, Action.CONTINUE, totalTimeInQueue);
}

Example 17 with Segment

use of org.dishevelled.bio.assembly.gfa2.Segment in project opencast by opencast.

the class TextAnalysisWorkflowOperationHandler method extractVideoText.

/**
 * Runs the text analysis service on each of the video segments found.
 *
 * @param mediaPackage
 *          the original mediapackage
 * @param operation
 *          the workflow operation
 * @throws ExecutionException
 * @throws InterruptedException
 * @throws NotFoundException
 * @throws WorkflowOperationException
 */
protected WorkflowOperationResult extractVideoText(final MediaPackage mediaPackage, WorkflowOperationInstance operation) throws EncoderException, InterruptedException, ExecutionException, IOException, NotFoundException, MediaPackageException, TextAnalyzerException, WorkflowOperationException, ServiceRegistryException {
    long totalTimeInQueue = 0;
    List<String> sourceTagSet = asList(operation.getConfiguration("source-tags"));
    List<String> targetTagSet = asList(operation.getConfiguration("target-tags"));
    // Select the catalogs according to the tags
    Map<Catalog, Mpeg7Catalog> catalogs = loadSegmentCatalogs(mediaPackage, operation);
    // Was there at least one matching catalog
    if (catalogs.size() == 0) {
        logger.debug("Mediapackage {} has no suitable mpeg-7 catalogs based on tags {} to to run text analysis", mediaPackage, sourceTagSet);
        return createResult(mediaPackage, Action.CONTINUE);
    }
    // Loop over all existing segment catalogs
    for (Entry<Catalog, Mpeg7Catalog> mapEntry : catalogs.entrySet()) {
        Map<VideoSegment, Job> jobs = new HashMap<VideoSegment, Job>();
        List<Attachment> images = new LinkedList<Attachment>();
        Catalog segmentCatalog = mapEntry.getKey();
        try {
            MediaPackageReference catalogRef = segmentCatalog.getReference();
            // Make sure we can figure out the source track
            if (catalogRef == null) {
                logger.info("Skipping catalog {} since we can't determine the source track", segmentCatalog);
            } else if (mediaPackage.getElementByReference(catalogRef) == null) {
                logger.info("Skipping catalog {} since we can't determine the source track", segmentCatalog);
            } else if (!(mediaPackage.getElementByReference(catalogRef) instanceof Track)) {
                logger.info("Skipping catalog {} since it's source was not a track", segmentCatalog);
            }
            logger.info("Analyzing mpeg-7 segments catalog {} for text", segmentCatalog);
            // Create a copy that will contain the segments enriched with the video text elements
            Mpeg7Catalog textCatalog = mapEntry.getValue().clone();
            Track sourceTrack = mediaPackage.getTrack(catalogRef.getIdentifier());
            // Load the temporal decomposition (segments)
            Video videoContent = textCatalog.videoContent().next();
            TemporalDecomposition<? extends Segment> decomposition = videoContent.getTemporalDecomposition();
            Iterator<? extends Segment> segmentIterator = decomposition.segments();
            // For every segment, try to find the still image and run text analysis on it
            List<VideoSegment> videoSegments = new LinkedList<VideoSegment>();
            while (segmentIterator.hasNext()) {
                Segment segment = segmentIterator.next();
                if ((segment instanceof VideoSegment)) {
                    videoSegments.add((VideoSegment) segment);
                }
            }
            // argument array for image extraction
            double[] times = new double[videoSegments.size()];
            for (int i = 0; i < videoSegments.size(); i++) {
                VideoSegment videoSegment = videoSegments.get(i);
                MediaTimePoint segmentTimePoint = videoSegment.getMediaTime().getMediaTimePoint();
                MediaDuration segmentDuration = videoSegment.getMediaTime().getMediaDuration();
                // Choose a time
                MediaPackageReference reference = null;
                if (catalogRef == null) {
                    reference = new MediaPackageReferenceImpl();
                } else {
                    reference = new MediaPackageReferenceImpl(catalogRef.getType(), catalogRef.getIdentifier());
                }
                reference.setProperty("time", segmentTimePoint.toString());
                // Have the time for ocr image created. To circumvent problems with slowly building slides, we take the image
                // that is
                // almost at the end of the segment, it should contain the most content and is stable as well.
                long startTimeSeconds = segmentTimePoint.getTimeInMilliseconds() / 1000;
                long durationSeconds = segmentDuration.getDurationInMilliseconds() / 1000;
                times[i] = Math.max(startTimeSeconds + durationSeconds - stabilityThreshold + 1, 0);
            }
            // Have the ocr image(s) created.
            Job imageJob = composer.image(sourceTrack, IMAGE_EXTRACTION_PROFILE, times);
            if (!waitForStatus(imageJob).isSuccess()) {
                throw new WorkflowOperationException("Extracting scene images from " + sourceTrack + " failed");
            }
            if (imageJob.getPayload() == null) {
                throw new WorkflowOperationException("The payload of extracting images job from " + sourceTrack + " was null");
            }
            totalTimeInQueue += imageJob.getQueueTime();
            for (MediaPackageElement imageMpe : MediaPackageElementParser.getArrayFromXml(imageJob.getPayload())) {
                Attachment image = (Attachment) imageMpe;
                images.add(image);
            }
            if (images.isEmpty() || images.size() != times.length) {
                throw new WorkflowOperationException("There are no images produced for " + sourceTrack + " or the images count isn't equal the count of the video segments.");
            }
            // Run text extraction on each of the images
            Iterator<VideoSegment> it = videoSegments.iterator();
            for (MediaPackageElement element : images) {
                Attachment image = (Attachment) element;
                VideoSegment videoSegment = it.next();
                jobs.put(videoSegment, analysisService.extract(image));
            }
            // Wait for all jobs to be finished
            if (!waitForStatus(jobs.values().toArray(new Job[jobs.size()])).isSuccess()) {
                throw new WorkflowOperationException("Text extraction failed on images from " + sourceTrack);
            }
            // Process the text extraction results
            for (Map.Entry<VideoSegment, Job> entry : jobs.entrySet()) {
                Job job = serviceRegistry.getJob(entry.getValue().getId());
                totalTimeInQueue += job.getQueueTime();
                VideoSegment videoSegment = entry.getKey();
                MediaDuration segmentDuration = videoSegment.getMediaTime().getMediaDuration();
                Catalog catalog = (Catalog) MediaPackageElementParser.getFromXml(job.getPayload());
                if (catalog == null) {
                    logger.warn("Text analysis did not return a valid mpeg7 for segment {}", videoSegment);
                    continue;
                }
                Mpeg7Catalog videoTextCatalog = loadMpeg7Catalog(catalog);
                if (videoTextCatalog == null) {
                    throw new IllegalStateException("Text analysis service did not return a valid mpeg7");
                }
                // Add the spatiotemporal decompositions from the new catalog to the existing video segments
                Iterator<Video> videoTextContents = videoTextCatalog.videoContent();
                if (videoTextContents == null || !videoTextContents.hasNext()) {
                    logger.debug("Text analysis was not able to extract any text from {}", job.getArguments().get(0));
                    break;
                }
                try {
                    Video textVideoContent = videoTextContents.next();
                    VideoSegment textVideoSegment = (VideoSegment) textVideoContent.getTemporalDecomposition().segments().next();
                    VideoText[] videoTexts = textVideoSegment.getSpatioTemporalDecomposition().getVideoText();
                    SpatioTemporalDecomposition std = videoSegment.createSpatioTemporalDecomposition(true, false);
                    for (VideoText videoText : videoTexts) {
                        MediaTime mediaTime = new MediaTimeImpl(new MediaRelTimePointImpl(0), segmentDuration);
                        SpatioTemporalLocator locator = new SpatioTemporalLocatorImpl(mediaTime);
                        videoText.setSpatioTemporalLocator(locator);
                        std.addVideoText(videoText);
                    }
                } catch (Exception e) {
                    logger.warn("The mpeg-7 structure returned by the text analyzer is not what is expected", e);
                    continue;
                }
            }
            // Put the catalog into the workspace and add it to the media package
            MediaPackageElementBuilder builder = MediaPackageElementBuilderFactory.newInstance().newElementBuilder();
            Catalog catalog = (Catalog) builder.newElement(MediaPackageElement.Type.Catalog, MediaPackageElements.TEXTS);
            catalog.setIdentifier(null);
            catalog.setReference(segmentCatalog.getReference());
            // the catalog now has an ID, so we can store the file properly
            mediaPackage.add(catalog);
            InputStream in = mpeg7CatalogService.serialize(textCatalog);
            String filename = "slidetext.xml";
            URI workspaceURI = workspace.put(mediaPackage.getIdentifier().toString(), catalog.getIdentifier(), filename, in);
            catalog.setURI(workspaceURI);
            // Since we've enriched and stored the mpeg7 catalog, remove the original
            try {
                mediaPackage.remove(segmentCatalog);
                workspace.delete(segmentCatalog.getURI());
            } catch (Exception e) {
                logger.warn("Unable to delete segment catalog {}: {}", segmentCatalog.getURI(), e);
            }
            // Add flavor and target tags
            catalog.setFlavor(MediaPackageElements.TEXTS);
            for (String tag : targetTagSet) {
                catalog.addTag(tag);
            }
        } finally {
            // Remove images that were created for text extraction
            logger.debug("Removing temporary images");
            for (Attachment image : images) {
                try {
                    workspace.delete(image.getURI());
                } catch (Exception e) {
                    logger.warn("Unable to delete temporary image {}: {}", image.getURI(), e);
                }
            }
            // Remove the temporary text
            for (Job j : jobs.values()) {
                Catalog catalog = null;
                try {
                    Job job = serviceRegistry.getJob(j.getId());
                    if (!Job.Status.FINISHED.equals(job.getStatus())) {
                        continue;
                    }
                    catalog = (Catalog) MediaPackageElementParser.getFromXml(job.getPayload());
                    if (catalog != null) {
                        workspace.delete(catalog.getURI());
                    }
                } catch (Exception e) {
                    if (catalog != null) {
                        logger.warn("Unable to delete temporary text file {}: {}", catalog.getURI(), e);
                    } else {
                        logger.warn("Unable to parse textextraction payload of job {}", j.getId());
                    }
                }
            }
        }
    }
    logger.debug("Text analysis completed");
    return createResult(mediaPackage, Action.CONTINUE, totalTimeInQueue);
}

Example 18 with Segment

use of org.dishevelled.bio.assembly.gfa2.Segment in project dishevelled by heuermh.

the class ImportGfa2Task method run.

@Override
public void run(final TaskMonitor taskMonitor) throws Exception {
    taskMonitor.setTitle("Import a network in Graphical Fragment Assembly (GFA) 2.0 format");
    final Map<String, Segment> segmentsById = new HashMap<String, Segment>();
    taskMonitor.setStatusMessage("Reading segments from file ...");
    try (BufferedReader readable = new BufferedReader(new FileReader(inputFile))) {
        // stream segments, building cache
        stream(readable, new Gfa2Adapter() {

            @Override
            protected boolean segment(final Segment segment) {
                segmentsById.put(segment.getId(), segment);
                return true;
            }
        });
    }
    taskMonitor.setStatusMessage("Finding reverse orientation references ...");
    final Table<String, Orientation, Segment> segmentsByOrientation = HashBasedTable.create();
    final List<Edge> edges = new ArrayList<Edge>();
    final List<Gap> gaps = new ArrayList<Gap>();
    final List<Path> paths = new ArrayList<Path>();
    try (BufferedReader readable = new BufferedReader(new FileReader(inputFile))) {
        // stream edges, gaps, and paths, looking for reverse orientation references
        stream(readable, new Gfa2Adapter() {

            private void putIfAbsent(final Reference reference) {
                Segment segment = segmentsById.get(reference.getId());
                if (segment == null) {
                    throw new RuntimeException("could not find segment by id " + reference.getId());
                }
                if (!segmentsByOrientation.contains(reference.getId(), reference.getOrientation())) {
                    segmentsByOrientation.put(reference.getId(), reference.getOrientation(), segment);
                }
            }

            @Override
            public boolean edge(final Edge edge) {
                putIfAbsent(edge.getSource());
                putIfAbsent(edge.getTarget());
                edges.add(edge);
                return true;
            }

            @Override
            public boolean gap(final Gap gap) {
                putIfAbsent(gap.getSource());
                putIfAbsent(gap.getTarget());
                gaps.add(gap);
                return true;
            }

            @Override
            public boolean path(final Path path) {
                for (Reference reference : path.getReferences()) {
                    putIfAbsent(reference);
                }
                if (loadPaths) {
                    paths.add(path);
                }
                return true;
            }
        });
    }
    logger.info("read {} segments, {} edges, {} gaps, and {} paths from {}", new Object[] { segmentsById.size(), edges.size(), gaps.size(), paths.size(), inputFile });
    segmentsById.clear();
    taskMonitor.setStatusMessage("Building Cytoscape nodes from segments ...");
    final CyNetwork network = applicationManager.getCurrentNetwork();
    final Map<String, CyNode> nodes = new HashMap<String, CyNode>(segmentsByOrientation.size());
    for (Table.Cell<String, Orientation, Segment> c : segmentsByOrientation.cellSet()) {
        String id = c.getRowKey();
        Orientation orientation = c.getColumnKey();
        Segment segment = c.getValue();
        String name = id + (orientation.isForward() ? "+" : "-");
        if (!nodes.containsKey(name)) {
            CyNode node = network.addNode();
            CyTable nodeTable = network.getDefaultNodeTable();
            CyRow nodeRow = nodeTable.getRow(node.getSUID());
            Integer length = segment.getLength();
            Integer readCount = segment.getReadCountOpt().orElse(null);
            Integer fragmentCount = segment.getFragmentCountOpt().orElse(null);
            Integer kmerCount = segment.getKmerCountOpt().orElse(null);
            String sequenceChecksum = segment.containsSequenceChecksum() ? String.valueOf(segment.getSequenceChecksum()) : null;
            String sequenceUri = segment.getSequenceUriOpt().orElse(null);
            setValue(nodeTable, nodeRow, "name", String.class, name);
            setValue(nodeTable, nodeRow, "length", Integer.class, length);
            setValue(nodeTable, nodeRow, "readCount", Integer.class, readCount);
            setValue(nodeTable, nodeRow, "fragmentCount", Integer.class, fragmentCount);
            setValue(nodeTable, nodeRow, "kmerCount", Integer.class, kmerCount);
            setValue(nodeTable, nodeRow, "sequenceChecksum", String.class, sequenceChecksum);
            setValue(nodeTable, nodeRow, "sequenceUri", String.class, sequenceUri);
            // default display length to length
            Integer displayLength = length;
            String sequence = orientation.isForward() ? segment.getSequence() : reverseComplement(segment.getSequence());
            if (sequence != null) {
                Integer sequenceLength = sequence.length();
                String displaySequence = trimFromMiddle(sequence, displaySequenceLimit);
                Integer displaySequenceLength = displaySequence.length();
                if (loadSequences) {
                    setValue(nodeTable, nodeRow, "sequence", String.class, sequence);
                }
                setValue(nodeTable, nodeRow, "sequenceLength", Integer.class, sequenceLength);
                setValue(nodeTable, nodeRow, "displaySequence", String.class, displaySequence);
                setValue(nodeTable, nodeRow, "displaySequenceLength", Integer.class, displaySequenceLength);
                // override display length with sequence length if necessary
                if (length == null || length != sequenceLength) {
                    displayLength = sequenceLength;
                }
            }
            StringBuilder sb = new StringBuilder();
            sb.append(name);
            if (displayLength != null) {
                sb.append("  ");
                sb.append(displayLength);
                sb.append(" bp");
            }
            String displayName = sb.toString();
            if (readCount != null) {
                sb.append(" ");
                sb.append(readCount);
                sb.append(" reads");
            }
            if (fragmentCount != null) {
                sb.append(" ");
                sb.append(fragmentCount);
                sb.append(" fragments");
            }
            if (kmerCount != null) {
                sb.append(" ");
                sb.append(kmerCount);
                sb.append(" kmers");
            }
            String displayLabel = sb.toString();
            setValue(nodeTable, nodeRow, "displayName", String.class, displayName);
            setValue(nodeTable, nodeRow, "displayLength", Integer.class, displayLength);
            setValue(nodeTable, nodeRow, "displayLabel", String.class, displayLabel);
            nodes.put(name, node);
        }
    }
    logger.info("converted segments and orientation to " + nodes.size() + " nodes");
    segmentsByOrientation.clear();
    taskMonitor.setStatusMessage("Building Cytoscape edges from edges and gaps ...");
    for (Edge edge : edges) {
        String sourceId = edge.getSource().getId();
        String sourceOrientation = edge.getSource().isForwardOrientation() ? "+" : "-";
        String targetId = edge.getTarget().getId();
        String targetOrientation = edge.getTarget().isForwardOrientation() ? "+" : "-";
        CyNode sourceNode = nodes.get(sourceId + sourceOrientation);
        CyNode targetNode = nodes.get(targetId + targetOrientation);
        CyEdge cyEdge = network.addEdge(sourceNode, targetNode, true);
        CyTable edgeTable = network.getDefaultEdgeTable();
        CyRow edgeRow = edgeTable.getRow(cyEdge.getSUID());
        setValue(edgeTable, edgeRow, "id", String.class, edge.getIdOpt().orElse(null));
        setValue(edgeTable, edgeRow, "type", String.class, "edge");
        setValue(edgeTable, edgeRow, "sourceId", String.class, sourceId);
        setValue(edgeTable, edgeRow, "sourceOrientation", String.class, sourceOrientation);
        setValue(edgeTable, edgeRow, "targetId", String.class, targetId);
        setValue(edgeTable, edgeRow, "targetOrientation", String.class, targetOrientation);
        setValue(edgeTable, edgeRow, "sourceStart", String.class, edge.getSourceStart().toString());
        setValue(edgeTable, edgeRow, "sourceEnd", String.class, edge.getSourceEnd().toString());
        setValue(edgeTable, edgeRow, "targetStart", String.class, edge.getTargetStart().toString());
        setValue(edgeTable, edgeRow, "targetEnd", String.class, edge.getTargetEnd().toString());
        setValue(edgeTable, edgeRow, "alignment", String.class, edge.hasAlignment() ? edge.getAlignment().toString() : null);
        setValue(edgeTable, edgeRow, "readCount", Integer.class, edge.getReadCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "fragmentCount", Integer.class, edge.getFragmentCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "kmerCount", Integer.class, edge.getKmerCountOpt().orElse(null));
        setValue(edgeTable, edgeRow, "mappingQuality", Integer.class, edge.getMappingQualityOpt().orElse(null));
        setValue(edgeTable, edgeRow, "mismatchCount", Integer.class, edge.getMismatchCountOpt().orElse(null));
    }
    logger.info("converted edges to " + edges.size() + " edges");
    for (Gap gap : gaps) {
        String sourceId = gap.getSource().getId();
        String sourceOrientation = gap.getSource().isForwardOrientation() ? "+" : "-";
        String targetId = gap.getTarget().getId();
        String targetOrientation = gap.getTarget().isForwardOrientation() ? "+" : "-";
        CyNode sourceNode = nodes.get(sourceId + sourceOrientation);
        CyNode targetNode = nodes.get(targetId + targetOrientation);
        CyEdge edge = network.addEdge(sourceNode, targetNode, true);
        CyTable edgeTable = network.getDefaultEdgeTable();
        CyRow edgeRow = edgeTable.getRow(edge.getSUID());
        setValue(edgeTable, edgeRow, "id", String.class, gap.getIdOpt().orElse(null));
        setValue(edgeTable, edgeRow, "type", String.class, "gap");
        setValue(edgeTable, edgeRow, "sourceId", String.class, sourceId);
        setValue(edgeTable, edgeRow, "sourceOrientation", String.class, sourceOrientation);
        setValue(edgeTable, edgeRow, "targetId", String.class, targetId);
        setValue(edgeTable, edgeRow, "targetOrientation", String.class, targetOrientation);
        setValue(edgeTable, edgeRow, "distance", Integer.class, gap.getDistance());
        setValue(edgeTable, edgeRow, "variance", Integer.class, gap.getVarianceOpt().orElse(null));
    }
    logger.info("converted gaps to " + gaps.size() + " edges");
    nodes.clear();
    edges.clear();
    gaps.clear();
    // pass paths to AssemblyApp if requested
    if (loadPaths && !paths.isEmpty()) {
        taskMonitor.setStatusMessage("Loading paths in path view ...");
        assemblyModel.setInputFileName(inputFile.toString());
    // todo: convert to gfa1 paths?
    // note paths in gfa2 can have references to segments, edges, or other groups
    // assemblyModel.setPaths(paths, traversalsByPathName);
    }
}

Example 19 with Segment

use of org.dishevelled.bio.assembly.gfa2.Segment in project dishevelled-bio by heuermh.

the class CompressRgfa method call.

@Override
public Integer call() throws Exception {
    BufferedReader reader = null;
    PrintWriter writer = null;
    try {
        reader = reader(inputRgfaFile);
        writer = writer(outputRgfaFile);
        final PrintWriter w = writer;
        Gfa1Reader.stream(reader, new Gfa1Listener() {

            @Override
            public boolean record(final Gfa1Record rgfaRecord) {
                if (rgfaRecord instanceof Segment) {
                    Segment segment = (Segment) rgfaRecord;
                    // SN, SO, SR are required for rGFA segments
                    if (!segment.containsStableName()) {
                        throw new IllegalArgumentException("rGFA segment " + segment.getName() + " must contain SN tag");
                    }
                    if (!segment.containsStableOffset()) {
                        throw new IllegalArgumentException("rGFA segment " + segment.getName() + " must contain SO tag");
                    }
                    if (!segment.containsStableRank()) {
                        throw new IllegalArgumentException("rGFA segment " + segment.getName() + " must contain SR tag");
                    }
                }
                Gfa1Writer.write(rgfaRecord, w);
                return true;
            }
        });
        return 0;
    } finally {
        try {
            reader.close();
        } catch (Exception e) {
        // ignore
        }
        try {
            writer.close();
        } catch (Exception e) {
        // ignore
        }
    }
}

Example 20 with Segment

use of org.dishevelled.bio.assembly.gfa2.Segment in project dishevelled-bio by heuermh.

the class SegmentsToPropertyGraph method call.

@Override
public Integer call() throws Exception {
    PrintWriter nodesWriter = null;
    try {
        nodesWriter = writer(outputNodesFile);
        nodesWriter.println(HEADER);
        final PrintWriter nw = nodesWriter;
        Gfa1Reader.stream(reader(inputGfa1File), new Gfa1Adapter() {

            @Override
            public boolean segment(final Segment segment) {
                StringBuilder sb = new StringBuilder();
                sb.append(segment.getName());
                sb.append(",");
                sb.append(segment.getSequenceOpt().orElse(""));
                sb.append(",");
                sb.append(segment.containsLength() ? segment.getLength() : "");
                sb.append(",");
                sb.append(segment.containsReadCount() ? segment.getReadCount() : "");
                sb.append(",");
                sb.append(segment.containsFragmentCount() ? segment.getFragmentCount() : "");
                sb.append(",");
                sb.append(segment.containsKmerCount() ? segment.getKmerCount() : "");
                sb.append(",");
                sb.append(segment.containsSequenceChecksum() ? String.valueOf(segment.getSequenceChecksum()) : "");
                sb.append(",");
                sb.append(segment.getSequenceUriOpt().orElse(""));
                nw.println(sb);
                return true;
            }
        });
        return 0;
    } finally {
        try {
            nodesWriter.close();
        } catch (Exception e) {
        // empty
        }
    }
}