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

Example 1 with SVGArea

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

the class ChromosomeRenderlet method render.

public void render(RenderletNexus nexus, C context, E entity) {
    int position = getPosition();
    int height = SVGCanvas.canvasHeight;
    int width = SVGCanvas.canvasWidth;
    double chromWidth = (double) width / 12;
    double chromHeight = (double) height / 2;
    double xCoordinate;
    double yCoordinate = 0;
    if (position < 12) {
        xCoordinate = position * chromWidth;
    } else {
        xCoordinate = (position - 12) * chromWidth;
        yCoordinate = (double) height / 2;
    }
    InputStream in = null;
    try {
        in = getSVGFile().openStream();
        DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
        DocumentBuilder db = dbf.newDocumentBuilder();
        Document chromSVG = db.parse(in);
        Element root = chromSVG.getDocumentElement();
        Element g = (Element) root.getElementsByTagName("g").item(0).cloneNode(true);
        setChromBands(g, nexus);
        StringBuilder builder = new StringBuilder();
        builder.append("translate(");
        builder.append(Double.toString(xCoordinate));
        builder.append(",");
        builder.append(Double.toString(yCoordinate));
        builder.append(")");
        g.setAttribute("transform", builder.toString());
        g.setAttribute("gwasname", getName());
        g.removeAttribute("title");
        SVGArea currentArea = new SVGArea(xCoordinate, yCoordinate, chromWidth, chromHeight, 0);
        TransformerFactory transFactory = TransformerFactory.newInstance();
        Transformer transformer = transFactory.newTransformer();
        StringWriter buffer = new StringWriter();
        transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
        transformer.transform(new DOMSource(g), new StreamResult(buffer));
        String str = buffer.toString();
        RenderingEvent<E> event = new RenderingEvent<E>(entity, str, currentArea, this);
        nexus.renderingEventOccurred(event);
    } catch (ParserConfigurationException e) {
        throw new RuntimeException("Failed to read in template chromosome SVG from original resource", e);
    } catch (SAXException e) {
        throw new RuntimeException("Failed to read in template chromosome SVG from original resource", e);
    } catch (IOException e) {
        throw new RuntimeException("Failed to render chromosome SVG", e);
    } catch (TransformerConfigurationException e) {
        throw new RuntimeException("Failed to render chromosome SVG", e);
    } catch (TransformerException e) {
        throw new RuntimeException("Failed to render chromosome SVG", e);
    } finally {
        if (in != null) {
            try {
                in.close();
            } catch (IOException e) {
            // tried our best!
            }
        }
    }
}

Example 2 with SVGArea

use of uk.ac.ebi.spot.goci.pussycat.layout.SVGArea 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 3 with SVGArea

use of uk.ac.ebi.spot.goci.pussycat.layout.SVGArea 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 SVGArea

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

the class SparqlTraitRenderlet method getLocationsOfOtherTraitsinBand.

protected List<SVGArea> getLocationsOfOtherTraitsinBand(RenderletNexus nexus, SparqlTemplate sparqlTemplate, URI band) throws DataIntegrityViolationException {
    Set<URI> allTraits = QueryManager.getCachingInstance().getTraitsLocatedInCytogeneticBand(sparqlTemplate, band, nexus.getRenderingContext());
    getLog().trace("Identified " + allTraits.size() + " traits in band '" + band + "'");
    List<SVGArea> locations = new ArrayList<SVGArea>();
    // fetch the location of all trait + band pairs that have been rendered so far
    for (URI nextTrait : allTraits) {
        SVGArea location = nexus.getLocationOfRenderedEntity(Arrays.asList(nextTrait, band));
        if (location != null) {
            locations.add(location);
        }
    }
    // now sort
    Collections.sort(locations, new Comparator<SVGArea>() {

        @Override
        public int compare(SVGArea a1, SVGArea a2) {
            Double comp;
            double dY = a2.getY() - a1.getY();
            if (dY == 0) {
                double dX = a2.getX() - a1.getX();
                comp = dX > 0 ? Math.ceil(dX) : Math.floor(dX);
            } else {
                comp = dY > 0 ? Math.ceil(dY) : Math.floor(dY);
            }
            return comp.intValue();
        }
    });
    getLog().trace("Sorted locations for " + allTraits.size() + " traits - " + locations.size() + " have been rendered");
    return locations;
}

Example 5 with SVGArea

use of uk.ac.ebi.spot.goci.pussycat.layout.SVGArea 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) / 10) + 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) / 10) + 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);
    }
}