Examples with Graph it.uniroma1.dis.wsngroup.gexf4j.core.Graph used on opensource projects

Example 1 with Graph

use of it.uniroma1.dis.wsngroup.gexf4j.core.Graph in project gridss by PapenfussLab.

the class GexfHelper method saveTo.

public static void saveTo(Gexf graph, File file) {
    file.getAbsoluteFile().getParentFile().mkdir();
    GexfWriter graphWriter = new StaxGraphWriter();
    Writer out = null;
    try {
        out = new FileWriter(file, false);
        graphWriter.writeToStream(graph, out, "UTF-8");
    } catch (IOException e) {
        log.error(String.format("Error writing graph visualisation to %s", file), e);
    } finally {
        CloserUtil.close(out);
        CloserUtil.close(graphWriter);
    }
}

Example 2 with Graph

use of it.uniroma1.dis.wsngroup.gexf4j.core.Graph in project gexf4j by francesco-ficarola.

the class DynamicGexfGraph method main.

public static void main(String[] args) {
    Gexf gexf = new GexfImpl();
    Calendar date = Calendar.getInstance();
    gexf.getMetadata().setLastModified(date.getTime()).setCreator("Gephi.org").setDescription("A Web network");
    Graph graph = gexf.getGraph();
    graph.setDefaultEdgeType(EdgeType.UNDIRECTED).setMode(Mode.DYNAMIC).setTimeType(TimeFormat.XSDDATETIME);
    AttributeList attrList = new AttributeListImpl(AttributeClass.NODE);
    graph.getAttributeLists().add(attrList);
    Attribute attUrl = attrList.createAttribute("0", AttributeType.STRING, "url");
    Attribute attIndegree = attrList.createAttribute("1", AttributeType.FLOAT, "indegree");
    Attribute attFrog = attrList.createAttribute("2", AttributeType.BOOLEAN, "frog").setDefaultValue("true");
    /**
     * Node Gephi
     */
    Node gephi = graph.createNode("0");
    gephi.setLabel("Gephi").getAttributeValues().addValue(attUrl, "http://gephi.org").addValue(attIndegree, "1");
    Spell spellGephi = new SpellImpl();
    date.set(2012, 3, 28, 16, 10, 0);
    date.set(Calendar.MILLISECOND, 0);
    spellGephi.setStartValue(date.getTime());
    gephi.getSpells().add(spellGephi);
    /**
     * Node Webatlas
     */
    Node webatlas = graph.createNode("1");
    webatlas.setLabel("Webatlas").getAttributeValues().addValue(attUrl, "http://webatlas.fr").addValue(attIndegree, "2");
    Spell spellWebatlas1 = new SpellImpl();
    date.set(Calendar.MINUTE, 15);
    spellWebatlas1.setStartValue(date.getTime());
    date.set(2012, 3, 28, 18, 57, 2);
    spellWebatlas1.setEndValue(date.getTime());
    webatlas.getSpells().add(spellWebatlas1);
    Spell spellWebatlas2 = new SpellImpl();
    date.set(2012, 3, 28, 20, 31, 10);
    spellWebatlas2.setStartValue(date.getTime()).setStartIntervalType(IntervalType.OPEN);
    date.set(Calendar.MINUTE, 45);
    date.set(Calendar.SECOND, 21);
    spellWebatlas2.setEndValue(date.getTime());
    webatlas.getSpells().add(spellWebatlas2);
    Spell spellWebatlas3 = new SpellImpl();
    date.set(2012, 3, 28, 21, 0, 0);
    spellWebatlas3.setStartValue(date.getTime());
    date.set(2012, 4, 11, 10, 49, 27);
    spellWebatlas3.setEndValue(date.getTime()).setEndIntervalType(IntervalType.OPEN);
    webatlas.getSpells().add(spellWebatlas3);
    /**
     * Node RTGI
     */
    Node rtgi = graph.createNode("2");
    rtgi.setLabel("RTGI").getAttributeValues().addValue(attUrl, "http://rtgi.fr").addValue(attIndegree, "1");
    Spell spellRtgi = new SpellImpl();
    date.set(2012, 3, 27, 6, 0, 0);
    spellRtgi.setStartValue(date.getTime());
    date.set(2012, 4, 19);
    spellRtgi.setEndValue(date.getTime());
    rtgi.getSpells().add(spellRtgi);
    /**
     * Node BarabasiLab
     */
    Node blab = graph.createNode("3");
    blab.setLabel("BarabasiLab").getAttributeValues().addValue(attUrl, "http://barabasilab.com").addValue(attIndegree, "3").addValue(attFrog, "false");
    /**
     * Node foobar
     */
    Node foobar = graph.createNode("4");
    foobar.setLabel("FooBar").getAttributeValues().addValue(attUrl, "http://foo.bar").addValue(attIndegree, "1").addValue(attFrog, "false");
    /**
     * Edge 0 [gephi, webatlas]
     */
    Edge edge0 = gephi.connectTo("0", webatlas);
    Spell spellEdge0 = new SpellImpl();
    date.set(2012, 3, 28, 16, 15, 36);
    spellEdge0.setStartValue(date.getTime());
    date.set(2012, 3, 28, 17, 41, 5);
    spellEdge0.setEndValue(date.getTime());
    edge0.getSpells().add(spellEdge0);
    /**
     * Edge 1 [gephi, rtgi]
     */
    Edge edge1 = gephi.connectTo("1", rtgi);
    Spell spellEdge1 = new SpellImpl();
    date.set(2012, 3, 30, 11, 16, 6);
    spellEdge1.setStartValue(date.getTime());
    date.set(2012, 4, 3, 11, 52, 6);
    spellEdge1.setEndValue(date.getTime());
    edge1.getSpells().add(spellEdge1);
    /**
     * Edge 2 [rtgi, webatlas]
     */
    Edge edge2 = rtgi.connectTo("2", webatlas);
    Spell spellEdge2 = new SpellImpl();
    date.set(2012, 4, 1, 11, 0, 0);
    spellEdge2.setStartValue(date.getTime()).setStartIntervalType(IntervalType.OPEN);
    date.set(2012, 4, 5, 11, 9, 44);
    spellEdge2.setEndValue(date.getTime());
    edge2.getSpells().add(spellEdge2);
    /**
     * Edge 3 [gephi, blab]
     */
    Edge edge3 = gephi.connectTo("3", blab);
    Spell spellEdge3 = new SpellImpl();
    date.set(2012, 3, 30, 12, 13, 22);
    spellEdge3.setStartValue(date.getTime());
    date.set(Calendar.MINUTE, 58);
    date.set(Calendar.SECOND, 24);
    spellEdge3.setEndValue(date.getTime());
    edge3.getSpells().add(spellEdge3);
    /**
     * Edge 4 [webatlas, blab]
     */
    Edge edge4 = webatlas.connectTo("4", blab);
    Spell spellEdge4 = new SpellImpl();
    date.set(2012, 3, 30, 21, 2, 37);
    spellEdge4.setStartValue(date.getTime());
    date.set(Calendar.MINUTE, 13);
    spellEdge4.setEndValue(date.getTime());
    edge4.getSpells().add(spellEdge4);
    /**
     * Edge 5 [foobar, blab]
     */
    foobar.connectTo("5", blab);
    StaxGraphWriter graphWriter = new StaxGraphWriter();
    File f = new File("dynamic_graph_sample.gexf");
    Writer out;
    try {
        out = new FileWriter(f, false);
        graphWriter.writeToStream(gexf, out, "UTF-8");
        System.out.println(f.getAbsolutePath());
    } catch (IOException e) {
        e.printStackTrace();
    }
}

Example 3 with Graph

use of it.uniroma1.dis.wsngroup.gexf4j.core.Graph in project gridss by PapenfussLab.

the class Poc method exportOverlapGraph.

// OverlapGraph { read, read, offset }
// ReadPairGraph { read1, read2 }
// FragmentSizeDistribution
// CompressedOverlapNode { _seq, (read, contig_offset) }
// Algorithm details to resolve:
// - how to allocate read overlap
// - just allocate reads at contig resolution
// - How to generate haplotypes?
// - efficient overlap calculation
// - how to deal with errors
// - sequencing errors
// - chimeric fragments
// Am I just making an OLC haplotype caller? (would that be problematic anyway?)
/**
 * Load overlap string graph
 */
public void exportOverlapGraph(List<SAMRecord> reads, int minOverlap, File file) {
    Gexf gexf = new GexfImpl();
    gexf.getMetadata().setLastModified(new Date()).setCreator("GRIDSS").setDescription("Raw overlap string graph");
    gexf.setVisualization(true);
    Graph graph = gexf.getGraph().setIDType(IDType.STRING).setDefaultEdgeType(EdgeType.DIRECTED).setMode(Mode.STATIC);
    AttributeList nodeAttrList = new AttributeListImpl(AttributeClass.NODE).setMode(Mode.STATIC);
    graph.getAttributeLists().add(nodeAttrList);
    AttributeList edgeAttrList = new AttributeListImpl(AttributeClass.EDGE).setMode(Mode.STATIC);
    Attribute attrSeq = edgeAttrList.createAttribute("seq", AttributeType.STRING, "sequence");
    // Attribute attrOverlap = edgeAttrList.createAttribute("l", AttributeType.INTEGER, "overlap length");
    // Attribute attrMatch = edgeAttrList.createAttribute("m", AttributeType.INTEGER, "base matches");
    // Attribute attrMismatch = edgeAttrList.createAttribute("mm", AttributeType.INTEGER, "base mismatches");
    graph.getAttributeLists().add(edgeAttrList);
    HashMap<Read, Node> startLookup = Maps.newHashMap();
    HashMap<Read, Node> endLookup = Maps.newHashMap();
    OverlapLookup ol = new OverlapLookup(minOverlap);
    for (SAMRecord sam : reads) {
        Read r = Read.create(sam);
        Node startnode = graph.createNode("start_" + sam.getReadName() + "/" + (SAMRecordUtil.getSegmentIndex(sam) + 1));
        Node endnode = graph.createNode("end_" + sam.getReadName() + "/" + (SAMRecordUtil.getSegmentIndex(sam) + 1));
        startLookup.put(r, startnode);
        endLookup.put(r, endnode);
        ol.add(r);
    }
    for (Read r : startLookup.keySet()) {
        Node rend = endLookup.get(r);
        for (Overlap o : ol.successors(r)) {
            Node ostart = startLookup.get(o.read2);
            Edge edge = ostart.connectTo(rend).setEdgeType(EdgeType.DIRECTED);
            edge.setWeight(o.overlap);
            edge.getAttributeValues().createValue(attrSeq, o.read2.getRead().getReadBases().toString().substring(0, o.overlap));
        }
    }
    GexfHelper.saveTo(gexf, file);
}

Example 4 with Graph

use of it.uniroma1.dis.wsngroup.gexf4j.core.Graph in project gexf4j by francesco-ficarola.

the class StaticGexfGraph method main.

public static void main(String[] args) {
    Gexf gexf = new GexfImpl();
    Calendar date = Calendar.getInstance();
    gexf.getMetadata().setLastModified(date.getTime()).setCreator("Gephi.org").setDescription("A Web network");
    gexf.setVisualization(true);
    Graph graph = gexf.getGraph();
    graph.setDefaultEdgeType(EdgeType.UNDIRECTED).setMode(Mode.STATIC);
    AttributeList attrList = new AttributeListImpl(AttributeClass.NODE);
    graph.getAttributeLists().add(attrList);
    Attribute attUrl = attrList.createAttribute("0", AttributeType.STRING, "url");
    Attribute attIndegree = attrList.createAttribute("1", AttributeType.FLOAT, "indegree");
    Attribute attFrog = attrList.createAttribute("2", AttributeType.BOOLEAN, "frog").setDefaultValue("true");
    Node gephi = graph.createNode("0");
    gephi.setLabel("Gephi").setSize(20).getAttributeValues().addValue(attUrl, "http://gephi.org").addValue(attIndegree, "1");
    gephi.getShapeEntity().setNodeShape(NodeShape.DIAMOND).setUri("GephiURI");
    Node webatlas = graph.createNode("1");
    webatlas.setLabel("Webatlas").getAttributeValues().addValue(attUrl, "http://webatlas.fr").addValue(attIndegree, "2");
    Node rtgi = graph.createNode("2");
    rtgi.setLabel("RTGI").getAttributeValues().addValue(attUrl, "http://rtgi.fr").addValue(attIndegree, "1");
    Node blab = graph.createNode("3");
    blab.setLabel("BarabasiLab").getAttributeValues().addValue(attUrl, "http://barabasilab.com").addValue(attIndegree, "1").addValue(attFrog, "false");
    gephi.connectTo("0", webatlas);
    gephi.connectTo("1", rtgi);
    webatlas.connectTo("2", gephi);
    rtgi.connectTo("3", webatlas);
    gephi.connectTo("4", blab);
    StaxGraphWriter graphWriter = new StaxGraphWriter();
    File f = new File("static_graph_sample.gexf");
    Writer out;
    try {
        out = new FileWriter(f, false);
        graphWriter.writeToStream(gexf, out, "UTF-8");
        System.out.println(f.getAbsolutePath());
    } catch (IOException e) {
        e.printStackTrace();
    }
}

Example 5 with Graph

use of it.uniroma1.dis.wsngroup.gexf4j.core.Graph in project gexf4j by francesco-ficarola.

the class GexfImplDefaultTest method testDynamicGexfGraph.

@Test
public void testDynamicGexfGraph() throws IOException, SAXException {
    Gexf gexf = new GexfImpl();
    Calendar date = Calendar.getInstance();
    date.set(2012, 4, 03);
    // date.setTimeZone(TimeZone.getTimeZone("GMT+0300"));
    gexf.getMetadata().setLastModified(date.getTime()).setCreator("Gephi.org").setDescription("A Web network");
    Graph graph = gexf.getGraph();
    graph.setDefaultEdgeType(EdgeType.UNDIRECTED).setMode(Mode.DYNAMIC).setTimeType(TimeFormat.XSDDATETIME);
    AttributeList attrList = new AttributeListImpl(AttributeClass.NODE);
    graph.getAttributeLists().add(attrList);
    Attribute attUrl = attrList.createAttribute("0", AttributeType.STRING, "url");
    Attribute attIndegree = attrList.createAttribute("1", AttributeType.FLOAT, "indegree");
    Attribute attFrog = attrList.createAttribute("2", AttributeType.BOOLEAN, "frog").setDefaultValue("true");
    /**
     * Node Gephi
     */
    Node gephi = graph.createNode("0");
    gephi.setLabel("Gephi").getAttributeValues().addValue(attUrl, "http://gephi.org").addValue(attIndegree, "1");
    Spell spellGephi = new SpellImpl();
    date.set(2012, 3, 28, 16, 10, 0);
    date.set(Calendar.MILLISECOND, 0);
    spellGephi.setStartValue(date.getTime());
    gephi.getSpells().add(spellGephi);
    /**
     * Node Webatlas
     */
    Node webatlas = graph.createNode("1");
    webatlas.setLabel("Webatlas").getAttributeValues().addValue(attUrl, "http://webatlas.fr").addValue(attIndegree, "2");
    Spell spellWebatlas1 = new SpellImpl();
    date.set(Calendar.MINUTE, 15);
    spellWebatlas1.setStartValue(date.getTime());
    date.set(2012, 3, 28, 18, 57, 2);
    spellWebatlas1.setEndValue(date.getTime());
    webatlas.getSpells().add(spellWebatlas1);
    Spell spellWebatlas2 = new SpellImpl();
    date.set(2012, 3, 28, 20, 31, 10);
    spellWebatlas2.setStartValue(date.getTime()).setStartIntervalType(IntervalType.OPEN);
    date.set(Calendar.MINUTE, 45);
    date.set(Calendar.SECOND, 21);
    spellWebatlas2.setEndValue(date.getTime());
    webatlas.getSpells().add(spellWebatlas2);
    Spell spellWebatlas3 = new SpellImpl();
    date.set(2012, 3, 28, 21, 0, 0);
    spellWebatlas3.setStartValue(date.getTime());
    date.set(2012, 4, 11, 10, 49, 27);
    spellWebatlas3.setEndValue(date.getTime()).setEndIntervalType(IntervalType.OPEN);
    webatlas.getSpells().add(spellWebatlas3);
    /**
     * Node RTGI
     */
    Node rtgi = graph.createNode("2");
    rtgi.setLabel("RTGI").getAttributeValues().addValue(attUrl, "http://rtgi.fr").addValue(attIndegree, "1");
    Spell spellRtgi = new SpellImpl();
    date.set(2012, 3, 27, 6, 0, 0);
    spellRtgi.setStartValue(date.getTime());
    date.set(2012, 4, 19);
    spellRtgi.setEndValue(date.getTime());
    rtgi.getSpells().add(spellRtgi);
    /**
     * Node BarabasiLab
     */
    Node blab = graph.createNode("3");
    blab.setLabel("BarabasiLab").getAttributeValues().addValue(attUrl, "http://barabasilab.com").addValue(attIndegree, "3").addValue(attFrog, "false");
    /**
     * Node foobar
     */
    Node foobar = graph.createNode("4");
    foobar.setLabel("FooBar").getAttributeValues().addValue(attUrl, "http://foo.bar").addValue(attIndegree, "1").addValue(attFrog, "false");
    /**
     * Edge 0 [gephi, webatlas]
     */
    Edge edge0 = gephi.connectTo("0", webatlas);
    Spell spellEdge0 = new SpellImpl();
    date.set(2012, 3, 28, 16, 15, 36);
    spellEdge0.setStartValue(date.getTime());
    date.set(2012, 3, 28, 17, 41, 5);
    spellEdge0.setEndValue(date.getTime());
    edge0.getSpells().add(spellEdge0);
    /**
     * Edge 1 [gephi, rtgi]
     */
    Edge edge1 = gephi.connectTo("1", rtgi);
    Spell spellEdge1 = new SpellImpl();
    date.set(2012, 3, 30, 11, 16, 6);
    spellEdge1.setStartValue(date.getTime());
    date.set(2012, 4, 3, 11, 52, 6);
    spellEdge1.setEndValue(date.getTime());
    edge1.getSpells().add(spellEdge1);
    /**
     * Edge 2 [rtgi, webatlas]
     */
    Edge edge2 = rtgi.connectTo("2", webatlas);
    Spell spellEdge2 = new SpellImpl();
    date.set(2012, 4, 1, 11, 0, 0);
    spellEdge2.setStartValue(date.getTime()).setStartIntervalType(IntervalType.OPEN);
    date.set(2012, 4, 5, 11, 9, 44);
    spellEdge2.setEndValue(date.getTime());
    edge2.getSpells().add(spellEdge2);
    /**
     * Edge 3 [gephi, blab]
     */
    Edge edge3 = gephi.connectTo("3", blab);
    Spell spellEdge3 = new SpellImpl();
    date.set(2012, 3, 30, 12, 13, 22);
    spellEdge3.setStartValue(date.getTime());
    date.set(Calendar.MINUTE, 58);
    date.set(Calendar.SECOND, 24);
    spellEdge3.setEndValue(date.getTime());
    edge3.getSpells().add(spellEdge3);
    /**
     * Edge 4 [webatlas, blab]
     */
    Edge edge4 = webatlas.connectTo("4", blab);
    Spell spellEdge4 = new SpellImpl();
    date.set(2012, 3, 30, 21, 2, 37);
    spellEdge4.setStartValue(date.getTime());
    date.set(Calendar.MINUTE, 13);
    spellEdge4.setEndValue(date.getTime());
    edge4.getSpells().add(spellEdge4);
    /**
     * Edge 5 [foobar, blab]
     */
    foobar.connectTo("5", blab);
    StaxGraphWriter graphWriter = new StaxGraphWriter();
    StringWriter stringWriter = new StringWriter();
    graphWriter.writeToStream(gexf, stringWriter, "UTF-8");
    String outputXml = stringWriter.toString();
    InputStream inputStream = GexfImplDefaultTest.class.getResourceAsStream("/dynamicGraph.gexf");
    String myControlXML = IOUtils.toString(inputStream, "UTF-8");
    System.out.println(outputXml);
    System.out.println(myControlXML);
    Diff myDiff = new Diff(myControlXML, outputXml);
    // myDiff.overrideElementQualifier(new ElementNameAndTextQualifier());
    assertTrue("XML similar " + myDiff.toString(), myDiff.similar());
}