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

Example 6 with SVGArea

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

the class TraitRenderlet method render.

@Override
public void render(RenderletNexus nexus, C context, E trait) {
    getLog().trace("Trait: " + trait);
    try {
        // collect all the bands for which we need to render this trait, and list all associations in that band
        Map<E, Set<E>> bandToAssociationMap = new HashMap<E, Set<E>>();
        for (E association : getAssociationsForTrait(nexus, context, trait)) {
            try {
                // get the band for this association
                E band = getBandForAssociation(context, association);
                if (!bandToAssociationMap.containsKey(band)) {
                    bandToAssociationMap.put(band, new HashSet<E>());
                }
                bandToAssociationMap.get(band).add(association);
            } catch (DataIntegrityViolationException e) {
                getLog().error("Unable to render trait '" + trait + "' for association '" + association + ": " + e.getMessage());
            }
        }
        for (E band : bandToAssociationMap.keySet()) {
            try {
                // get the location of any traits previously rendered in this band
                List<SVGArea> locations = getLocationsOfOtherTraitsinBand(nexus, context, band);
                StringBuilder svg = new StringBuilder();
                svg.append("<circle ");
                // also grab the location of an association (should all be the same for the same band)
                E association = bandToAssociationMap.get(band).iterator().next();
                SVGArea associationLocation = nexus.getLocationOfRenderedEntity(association);
                if (associationLocation != null) {
                    if (associationLocation.getTransform() != null) {
                        svg.append("transform='").append(associationLocation.getTransform()).append("' ");
                    }
                    double alength = associationLocation.getWidth();
                    //0.2 * alength;
                    double radius = 0.12 * alength;
                    double ax = associationLocation.getX();
                    double ay = associationLocation.getY();
                    double displacement = associationLocation.getHeight();
                    double cx, cy;
                    int position = getTraitPosition(nexus, context, trait, band, locations);
                    int horizontal = position % 10;
                    int vertical = position / 10;
                    if (position == 0) {
                        cx = ax + alength + radius;
                    } else {
                        if (vertical % 2 == 0) {
                            cx = ax + alength + (((2 * horizontal) + 1) * radius);
                        } else {
                            cx = ax + alength + (((2 * horizontal) + 2) * radius);
                        }
                    }
                    cy = ay + displacement + (vertical * radius);
                    svg.append("cx='").append(Double.toString(cx)).append("' ");
                    svg.append("cy='").append(Double.toString(cy)).append("' ");
                    svg.append("r='").append(Double.toString(radius)).append("' ");
                    String colour = getTraitColour(context, trait);
                    svg.append("fill='").append(colour).append("' ");
                    svg.append("stroke='black' ");
                    svg.append("stroke-width='0.5' ");
                    String traitName = getTraitLabel(context, trait);
                    svg.append("gwasname=\"").append(traitName).append("\" ");
                    String traitAttribute = getTraitAttribute(context, trait);
                    getLog().trace("Setting CSS class for trait '" + trait + "' to " + traitAttribute);
                    svg.append("class='gwas-trait ").append(traitAttribute).append("' ");
                    svg.append("fading='false' ");
                    StringBuilder associationAttribute = new StringBuilder();
                    Iterator<E> associationIt = bandToAssociationMap.get(band).iterator();
                    while (associationIt.hasNext()) {
                        associationAttribute.append(getTraitAssociationAttribute(context, associationIt.next()));
                        if (associationIt.hasNext()) {
                            associationAttribute.append(",");
                        }
                    }
                    getLog().trace("Setting gwasassociation attribute for trait '" + trait + "' to " + associationAttribute.toString());
                    svg.append("gwasassociation='").append(associationAttribute.toString()).append("' ");
                    svg.append("priority='").append(vertical).append(// todo - remove this, just for debugging
                    "' ");
                    svg.append("/>");
                    SVGArea currentArea = new SVGArea(cx, cy, 2 * radius, 2 * radius, 0);
                    // this area is a conjunction of trait + band, so store as a List<OWLNamedIndividual> with 2 elements
                    RenderingEvent<List<E>> event = new RenderingEvent<List<E>>(Arrays.asList(trait, band), svg.toString(), currentArea, vertical, this);
                    nexus.renderingEventOccurred(event);
                } else {
                    getLog().error("Cannot render trait '" + trait + "' for association '" + association + "' - " + "failed to identify the location of this association. " + "This could be due to an earlier error rendering the association.");
                }
            } catch (DataIntegrityViolationException e) {
                getLog().error("Cannot render trait '" + trait + "' in band '" + band + "'");
            }
        }
    } catch (DataIntegrityViolationException e) {
        getLog().error("Cannot render trait '" + trait + "'", e);
    }
}

Example 7 with SVGArea

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