Examples with BandInformation uk.ac.ebi.spot.goci.pussycat.layout.BandInformation used on opensource projects

Example 1 with BandInformation

use of uk.ac.ebi.spot.goci.pussycat.layout.BandInformation in project goci by EBISPOT.

the class AssociationRenderlet method render.

@Override
public void render(RenderletNexus nexus, C context, E associationEntity) {
    getLog().trace("Association: " + associationEntity);
    if (!nexus.bandContextExists(context)) {
        nexus.setBandContext(context, sortBandsWithData(context));
    }
    try {
        BandInformation band = getBandInformation(context, associationEntity);
        if (!nexus.alreadyRendered(band)) {
            // there is no other association in this chromosomal band yet - render
            getLog().trace("This is the first association for band '" + band.getBandName() + "', " + "rendering new line");
            StringBuilder svg = new StringBuilder();
            String transform = getTransformation(band.getChromosome());
            svg.append("<g ").append("id='").append(getAssociationID(context, associationEntity)).append("' ").append("transform='").append(transform).append("' ").append("class='gwas-trait'>");
            // get rendered svg location of the cytogenetic band
            SVGArea location = nexus.getLocationOfRenderedEntity(band);
            if (location != null) {
                // starting x and y co-ords derived from cytogenetic band
                double x1 = location.getX();
                double y1 = location.getY() + (location.getHeight() / 2);
                double dotRadius = 0.35 * location.getWidth();
                // x2 and y2 mark the end of the horizontal line designating the snp location
                double x2 = location.getWidth();
                double y2 = 0;
                // x3 and y3 mark the end of the line - may be fanned to avoid overlaps
                // 0.75 * location.getWidth();
                double x3 = 2 * location.getWidth();
                double y3;
                // fanning algorithm - calculate diagonal part of the line, if necessary
                Map<BandInformation, BandInformation> previousBandMap = nexus.getBandContext(context);
                BandInformation previousBand = previousBandMap.get(band);
                if (previousBand != null && band.getChromosome().equals(previousBand.getChromosome())) {
                    SVGArea previousLocation = getLocationOfPreviousAssociation(nexus, context, associationEntity);
                    if (previousLocation != null) {
                        double previousY = previousLocation.getY() + previousLocation.getHeight();
                        // fan up or down?
                        if (band.getBandName().contains("p")) {
                            // p arm - we need to know how many traits are in this band
                            int traitCount = getNumberOfTraitsInSameBand(nexus, context, associationEntity);
                            int rowCount = ((traitCount - 1) / 20) + 2;
                            double blockSize = rowCount * dotRadius;
                            if (y1 + blockSize > previousY) {
                                // if blockSize takes us down so far it would overlap prevY, move up
                                y3 = previousY - (y1 + blockSize);
                            } else {
                                // otherwise, line can be horizontal
                                y3 = 0;
                            }
                        } else {
                            // q arm - we need to know how many traits were in the previous band (ie. the one above)
                            int traitCount = getNumberOfTraitsInPreviousBand(nexus, context, associationEntity);
                            int rowCount = ((traitCount - 1) / 20) + 2;
                            double blockSize = rowCount * dotRadius;
                            if (previousY + blockSize > y1) {
                                // if the previous blockSize takes us down so far it would overlap y, move down
                                y3 = (previousY + blockSize) - y1;
                            } else {
                                // otherwise, line can be horizontal
                                y3 = 0;
                            }
                        }
                    } else {
                        // no previous location, so line can be horizontal
                        y3 = 0;
                    }
                } else {
                    // no previous band, or isn't in the same chromosome, so line can be horizontal
                    y3 = 0;
                }
                StringBuilder d = new StringBuilder();
                d.append("m ");
                d.append(Double.toString(x1)).append(",").append(Double.toString(y1));
                d.append(" ");
                d.append(Double.toString(x2)).append(",").append(Double.toString(y2));
                d.append(" ");
                d.append(Double.toString(x3)).append(",").append(Double.toString(y3));
                svg.append("<path ").append("d='").append(d.toString()).append("' ").append("style='fill:none;stroke:#211c1d;stroke-width:1.1;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none'").append(" />");
                svg.append("</g>");
                SVGArea currentArea = new SVGArea(x1, y1, x2 + x3, y2 + y3, transform, 0);
                RenderingEvent<E> event = new RenderingEvent<E>(associationEntity, svg.toString(), currentArea, this);
                nexus.renderingEventOccurred(event);
                // add band to renderedBands set
                nexus.setRenderedBand(band, currentArea);
            } else {
                getLog().error("Unable to render association '" + associationEntity + "' - " + "no location for band '" + band.getBandName() + "'");
            }
        } else {
            // we've already rendered the required association line, so we don't need to do it again
            // but we do need to log the rendering event for this association individual
            getLog().trace("Already rendered an association line to band '" + band.getBandName() + "', " + "logging secondary event for association '" + associationEntity + "'");
            SVGArea area = nexus.getRenderedBand(band);
            nexus.renderingEventOccurred(new RenderingEvent<E>(associationEntity, "", area, this));
        }
    } catch (DataIntegrityViolationException e) {
        getLog().error("Cannot render association '" + associationEntity + "'", e);
    }
}

Example 2 with BandInformation

use of uk.ac.ebi.spot.goci.pussycat.layout.BandInformation in project goci by EBISPOT.

the class ChromosomeRenderlet method setChromBands.

protected void setChromBands(Element g, RenderletNexus nexus) {
    NodeList paths = g.getElementsByTagName("path");
    for (int i = 0; i < paths.getLength(); i++) {
        Element path = (Element) paths.item(i);
        String id = path.getAttribute("id");
        String d = path.getAttribute("d");
        if (!id.contains("centre") && !id.contains("outline") && !id.contains("satellite") && !id.contains("-o") && !id.contains("centromere")) {
            StringTokenizer tokenizer = new StringTokenizer(d);
            ArrayList<String> pathElements = new ArrayList<String>();
            while (tokenizer.hasMoreTokens()) {
                pathElements.add(tokenizer.nextToken());
            }
            // bottom left corner of the chromosomal band
            String[] xy = pathElements.get(1).split(",");
            double x = Double.parseDouble(xy[0]);
            double y = Double.parseDouble(xy[1]);
            double width;
            double height = 0;
            // special case for top- and bottom-most bands
            if (pathElements.contains("c")) {
                // top band: starts bottom left -> br -> arc
                if (id.contains("p")) {
                    double original = y;
                    String[] w = pathElements.get(2).split(",");
                    width = Math.abs(Double.parseDouble((w[0])));
                    for (int k = 3; k < pathElements.size() - 1; k++) {
                        String element = pathElements.get(k);
                        if (element.contains("c")) {
                            while (!pathElements.get(k + 1).contains("l") && !pathElements.get(k + 1).contains("z")) {
                                k = k + 3;
                                String point = pathElements.get(k);
                                String[] coords = point.split(",");
                                double temp = Double.parseDouble(coords[1]);
                                if (temp < 0) {
                                    y = y + temp;
                                }
                            }
                        } else if (element.contains("l")) {
                            k = k + 1;
                            String point = pathElements.get(k);
                            String[] coords = point.split(",");
                            double temp = Double.parseDouble(coords[1]);
                            if (temp < 0) {
                                y = y + temp;
                            }
                        } else {
                            String point = pathElements.get(k);
                            String[] coords = point.split(",");
                            double temp = Double.parseDouble(coords[1]);
                            if (temp < 0) {
                                y = y + temp;
                            }
                        }
                        height = original - y;
                    }
                } else // bottom band: starts top left -> arc -> tr
                {
                    int last = pathElements.size() - 2;
                    String[] w = pathElements.get(last).split(",");
                    width = Math.abs(Double.parseDouble(w[0]));
                    height = 0;
                    for (int j = 3; j < pathElements.size() - 1; j++) {
                        String element = pathElements.get(j);
                        if (element.contains("c")) {
                            while (!pathElements.get(j + 1).contains("l")) {
                                j = j + 3;
                                String point = pathElements.get(j);
                                String[] coords = point.split(",");
                                double temp = Double.parseDouble(coords[1]);
                                if (temp > 0) {
                                    height = height + temp;
                                }
                            }
                        } else if (element.contains("l")) {
                            j = j + 1;
                            String point = pathElements.get(j);
                            String[] coords = point.split(",");
                            double temp = Double.parseDouble(coords[1]);
                            if (temp > 0) {
                                height = height + temp;
                            }
                        } else {
                            String point = pathElements.get(j);
                            String[] coords = point.split(",");
                            double temp = Double.parseDouble(coords[1]);
                            if (temp > 0) {
                                height = height + temp;
                            }
                        }
                    }
                }
            } else // all the other bands
            {
                // width of the band
                String[] w = pathElements.get(2).split(",");
                width = Math.abs(Double.parseDouble((w[0])));
                // height of the band
                String[] h = pathElements.get(3).split(",");
                height = Math.abs(Double.parseDouble((h[1])));
                y = y - height;
            }
            // SVG area for the chromosomal bands gives the x&y coordinates for its top left corner, and its width and height
            SVGArea band = new SVGArea(x, y, width, height, 0);
            String chromName = getName().split(" ")[1];
            BandInformation info = new BandInformation(id, chromName);
            nexus.renderingEventOccurred(new RenderingEvent<BandInformation>(info, "", band, this));
        }
    }
}

Example 3 with BandInformation

use of uk.ac.ebi.spot.goci.pussycat.layout.BandInformation in project goci by EBISPOT.

the class SparqlAssociationRenderlet method getNumberOfTraitsInPreviousBand.

/**
 * For the given association, identifies the previous cytogenetic band to the one this association is located in,
 * then identifies the total number of traits located in that cytogenetic band and returns the count
 *
 * @param sparqlTemplate the sparqlTemplate
 * @param association    the association to identify co-located traits for
 * @return the number of traits in the same cytogenetic region as this association
 * @throws DataIntegrityViolationException
 */
protected int getNumberOfTraitsInPreviousBand(RenderletNexus nexus, SparqlTemplate sparqlTemplate, URI association) throws DataIntegrityViolationException {
    BandInformation band = getBandInformation(sparqlTemplate, association);
    if (band != null) {
        BandInformation current = band;
        BandInformation previousBand = null;
        boolean done = false;
        while (!done) {
            previousBand = getPreviousBandMap(nexus, sparqlTemplate).get(current);
            // now find the traits in the previous band
            Set<URI> previousBandAssociations = QueryManager.getCachingInstance().getAssociationsLocatedInCytogeneticBand(sparqlTemplate, previousBand.getBandName(), nexus.getRenderingContext());
            // get first not-null location for an association in the previous band
            for (URI previousBandAssociation : previousBandAssociations) {
                SVGArea prevLocation = nexus.getLocationOfRenderedEntity(previousBandAssociation);
                if (prevLocation != null) {
                    done = true;
                }
            }
            current = previousBand;
        }
        Set<URI> previousBandTraits = QueryManager.getCachingInstance().getTraitsLocatedInCytogeneticBand(sparqlTemplate, previousBand.getBandName(), nexus.getRenderingContext());
        return previousBandTraits.size();
    } else {
        throw new DataIntegrityViolationException("Unable to identify the cytogenetic region where association '" + association + "' is located");
    }
}

Example 4 with BandInformation

use of uk.ac.ebi.spot.goci.pussycat.layout.BandInformation in project goci by EBISPOT.

the class SparqlAssociationRenderlet method getLocationOfPreviousAssociation.

protected SVGArea getLocationOfPreviousAssociation(RenderletNexus nexus, SparqlTemplate sparqlTemplate, URI association) throws DataIntegrityViolationException {
    BandInformation band = getBandInformation(sparqlTemplate, association);
    if (band != null) {
        BandInformation current = band;
        boolean done = false;
        while (!done) {
            BandInformation previousBand = getPreviousBandMap(nexus, sparqlTemplate).get(current);
            if (previousBand == null) {
                done = true;
                return null;
            }
            if (!previousBand.getChromosome().equals(current.getChromosome())) {
                done = true;
                return null;
            }
            // now find the traits in the previous band
            Set<URI> previousBandAssociations = QueryManager.getCachingInstance().getAssociationsLocatedInCytogeneticBand(sparqlTemplate, previousBand.getBandName(), nexus.getRenderingContext());
            // get first not-null location for an association in the previous band
            for (URI previousBandAssociation : previousBandAssociations) {
                SVGArea prevLocation = nexus.getLocationOfRenderedEntity(previousBandAssociation);
                if (prevLocation != null) {
                    done = true;
                    return prevLocation;
                }
            }
            // if we get to here, no associations are located in the previous region so return null
            getLog().trace("Unable to identify any associations in the previous cytogenetic region '" + previousBand.getBandName() + "'");
            current = previousBand;
        }
        return null;
    } else {
        throw new DataIntegrityViolationException("Unable to identify the cytogenetic region where association '" + association + "' is located");
    }
}

Example 5 with BandInformation

use of uk.ac.ebi.spot.goci.pussycat.layout.BandInformation in project goci by EBISPOT.

the class SparqlAssociationRenderlet method sortBandsWithData.

protected Map<BandInformation, BandInformation> sortBandsWithData(SparqlTemplate sparqlTemplate) {
    Map<BandInformation, BandInformation> bandMap = new HashMap<BandInformation, BandInformation>();
    // use the sparqlTemplate to get all individuals of type "cytogenic region"
    getLog().trace("Retrieving all cytogenetic bands to sort into rendering order...");
    List<BandInformation> bands = sparqlTemplate.query("SELECT DISTINCT ?band WHERE { ?bandUri a gt:CytogeneticRegion ; rdfs:label ?band . FILTER (STR(?band) != 'NR') .}", new QuerySolutionMapper<BandInformation>() {

        @Override
        public BandInformation mapQuerySolution(QuerySolution qs) {
            return new BandInformation(qs.getLiteral("band").getLexicalForm());
        }
    });
    getLog().trace("Got " + bands.size() + " bands, starting sorting...");
    // now we've added all band info, sort the set of unique bands
    Collections.sort(bands);
    for (int i = 1; i < bands.size(); i++) {
        BandInformation band = bands.get(i);
        BandInformation previousBand = bands.get(i - 1);
        bandMap.put(band, previousBand);
    }
    getLog().trace("Mapped " + bandMap.keySet().size() + " bands to their 'previous' band");
    return bandMap;
}