/**
   * DOCUMENT ME!
   *
   * @throws Exception DOCUMENT ME!
   */
  public void testReadTable() throws Exception {

    InputStream is = null;
    POIFSFileSystem excelIn;

    try {
      is = getClass().getResource(NETWORK_FILE).openStream();
      excelIn = new POIFSFileSystem(is);
    } finally {
      if (is != null) {
        is.close();
      }
    }

    HSSFWorkbook wb = new HSSFWorkbook(excelIn);

    HSSFSheet sheet = wb.getSheetAt(0);

    List<String> delimiters = new ArrayList<String>();
    delimiters.add(TextFileDelimiters.TAB.toString());

    String[] galAttrName = {
      "Source", "Target", "Interaction", "edge bool attr", "edge string attr", "edge float attr"
    };
    Byte[] galAttrTypes = {
      CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING,
      CyAttributes.TYPE_STRING, CyAttributes.TYPE_BOOLEAN,
      CyAttributes.TYPE_STRING, CyAttributes.TYPE_FLOATING
    };
    NetworkTableMappingParameters mapping =
        new NetworkTableMappingParameters(
            delimiters,
            TextFileDelimiters.PIPE.toString(),
            galAttrName,
            galAttrTypes,
            null,
            null,
            0,
            1,
            2,
            null);

    reader = new ExcelNetworkSheetReader(wb.getSheetName(0), sheet, mapping);

    CyNetwork net = Cytoscape.createNetwork(reader, false, null);

    /*
     * test cases
     */
    assertEquals("Yeast Network Sheet 1", net.getTitle());
    assertEquals(331, net.getNodeCount());
    assertEquals(362, net.getEdgeCount());

    CyAttributes attr = Cytoscape.getEdgeAttributes();
    assertTrue(attr.getBooleanAttribute("YGL122C (pp) YOL123W", "edge bool attr"));
    assertFalse(attr.getBooleanAttribute("YKR026C (pp) YGL122C", "edge bool attr"));

    assertEquals(1.2344543, attr.getDoubleAttribute("YBL026W (pp) YOR167C", "edge float attr"));
    assertEquals("abcd12706", attr.getStringAttribute("YBL026W (pp) YOR167C", "edge string attr"));
    assertEquals("abcd12584", attr.getStringAttribute("YPL248C (pd) ?", "edge string attr"));

    Cytoscape.destroyNetwork(net);
  }
Ejemplo n.º 2
0
    public gpClique[] creategpClique() {
      gpClique[] gps = new gpClique[2];
      gps[0] = new gpClique();
      gps[1] = new gpClique();

      Iterator<Edge> edgeIt = nw.edgesIterator();
      CyAttributes edgeAtt = Cytoscape.getEdgeAttributes();

      ArrayList largeALNodes = new ArrayList();
      ArrayList targetALNodes = new ArrayList();
      ArrayList matchALNodes = new ArrayList();
      while (edgeIt.hasNext()) {

        Edge edge = edgeIt.next();
        if (edgeAtt.getStringAttribute(edge.getIdentifier(), "interaction").equals("p2")) {
          largeALNodes.add(new Integer(nw.getEdgeSourceIndex(edge.getRootGraphIndex())));
          largeALNodes.add(new Integer(nw.getEdgeTargetIndex(edge.getRootGraphIndex())));
          continue; // go directly next step
        }
        if (edgeAtt.getStringAttribute(edge.getIdentifier(), "interaction").equals("p1")) {
          targetALNodes.add(new Integer(nw.getEdgeSourceIndex(edge.getRootGraphIndex())));
          targetALNodes.add(new Integer(nw.getEdgeTargetIndex(edge.getRootGraphIndex())));
          continue;
        }
        if (edgeAtt.getStringAttribute(edge.getIdentifier(), "interaction").equals("pd")) {
          matchALNodes.add(
              new Integer(
                  nw.getEdgeSourceIndex(
                      edge
                          .getRootGraphIndex()))); // the matched node(containing "-") of target
                                                   // network
          matchALNodes.add(
              new Integer(
                  nw.getEdgeTargetIndex(
                      edge
                          .getRootGraphIndex()))); // the matched node(containing "-") of large
                                                   // network
          continue;
        }
        JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "File Format error!");
        return null;
      }

      Iterator matchALNIt = matchALNodes.iterator();
      CyNode node;
      Integer it;
      while (matchALNIt.hasNext()) {
        it = (Integer) matchALNIt.next();
        node =
            Cytoscape.getCyNode(
                nw.getNode(it.intValue()).getIdentifier().substring(1),
                true); // get node according to its identifier
        matchNodes.add(node);
        if (!targetALNodes.contains(
            node.getRootGraphIndex())) // matched node,but not a node of network
        {
          nw.addNode(node);
          targetALNodes.add(node.getRootGraphIndex()); // add to network
        }

        it = (Integer) matchALNIt.next();
        node =
            Cytoscape.getCyNode(
                nw.getNode(it.intValue()).getIdentifier().substring(1),
                true); // get node according to its identifier
        matchNodes.add(node);
        if (!largeALNodes.contains(node.getRootGraphIndex())) {
          nw.addNode(node);
          largeALNodes.add(node.getRootGraphIndex());
        }
      }

      gps[0].setgpNodes(largeALNodes);
      gps[1].setgpNodes(targetALNodes);
      return gps;
    }
  public void testReadTableWithEmptyRows() throws Exception {
    String network = "/empty_attr_row.xls";

    InputStream is = null;
    POIFSFileSystem excelIn;

    try {
      is = getClass().getResource(network).openStream();
      excelIn = new POIFSFileSystem(is);
    } finally {
      if (is != null) {
        is.close();
      }
    }

    HSSFWorkbook wb = new HSSFWorkbook(excelIn);

    HSSFSheet sheet = wb.getSheetAt(0);

    List<String> delimiters = new ArrayList<String>();
    delimiters.add(TextFileDelimiters.TAB.toString());

    String[] galAttrName = {"Gene 1", "Gene 2", "Interaction Type", "Gene", "GO Group"};
    Byte[] galAttrTypes = {
      CyAttributes.TYPE_STRING,
      CyAttributes.TYPE_STRING,
      CyAttributes.TYPE_STRING,
      CyAttributes.TYPE_STRING,
      CyAttributes.TYPE_STRING
    };
    NetworkTableMappingParameters mapping =
        new NetworkTableMappingParameters(
            delimiters,
            TextFileDelimiters.PIPE.toString(),
            galAttrName,
            galAttrTypes,
            null,
            null,
            0,
            1,
            2,
            null);

    CyNetwork net = null;
    try {
      reader = new ExcelNetworkSheetReader(wb.getSheetName(0), sheet, mapping, 1);
      net = Cytoscape.createNetwork(reader, false, null);
    } catch (Exception ee) {
      ee.printStackTrace();
      fail("Caught exception");
    }

    assertEquals(222, net.getNodeCount());
    assertEquals(443, net.getEdgeCount());

    CyAttributes attr = Cytoscape.getEdgeAttributes();

    // test some random edges
    assertEquals("cc", attr.getStringAttribute("YDR459C (cc) YNL271C", "interaction"));
    assertEquals("Transport", attr.getStringAttribute("YDR459C (cc) YNL271C", "GO Group"));
    assertEquals("YPR011C", attr.getStringAttribute("YDR459C (cc) YNL271C", "Gene"));

    assertNull(attr.getStringAttribute("YEL040W (cc) YER016W", "GO Group"));
    assertNull(attr.getStringAttribute("YEL040W (cc) YER016W", "Gene"));

    Cytoscape.destroyNetwork(net);
  }