List of usage examples for org.apache.commons.collections4 BidiMap containsKey
boolean containsKey(Object key);
From source file:research.NetworkAligner.java
public void align_networks_from_data(AlignmentNetwork network0, AlignmentNetwork network1, AlignmentNetwork aligned, TaskMonitor tm) throws Exception { String name = network0.get_suggested_name() + "_" + network1.get_suggested_name(); aligned.set_suggested_name(name);//w ww . j a va2 s.co m if (tm != null) { tm.setStatusMessage("aligning " + name + "..."); } List<CyRow> rows = m_table.getAllRows(); // keep track of progress int j = 0; int total = rows.size() + network0.get_node_count() + network0.get_edge_count() + network1.get_node_count() + network1.get_edge_count(); // Create the bidirectional maps for lookup BidiMap<String, String> network0_1 = new DualHashBidiMap<>(); for (CyRow row : rows) { List<String> sigs = row.getList(c_NodesSignatureSlot, String.class); network0_1.put(sigs.get(0), sigs.get(1)); Util.advance_progress(tm, j, total); } NodeSignatureManager sig_mgr = new NodeSignatureManager(); // Update the signatures with the one in the real network for (AlignmentNetwork.NodeIterator i = network0.NodeIterator(); i.hasNext();) { String real_sig = i.next(); sig_mgr.override_with(real_sig); String plain_sig = the_only_element_in(sig_mgr.get_all_node_signatures()); String val = network0_1.get(plain_sig); if (val != null) { network0_1.remove(plain_sig); network0_1.put(real_sig, val); } } for (AlignmentNetwork.NodeIterator i = network1.NodeIterator(); i.hasNext();) { String real_sig = i.next(); sig_mgr.override_with(real_sig); String plain_sig = the_only_element_in(sig_mgr.get_all_node_signatures()); String key = network0_1.getKey(plain_sig); if (key != null) { network0_1.removeValue(plain_sig); network0_1.put(key, real_sig); } } // Add all the data from the first network, and add belongings according to alignment data // Add nodes 0 for (AlignmentNetwork.NodeIterator i = network0.NodeIterator(); i.hasNext();) { String sig = i.next(); sig_mgr.override_with(sig); CyNode node = aligned.make_node(sig_mgr); if (network0_1.containsKey(sig)) { // This node can be aligned aligned.add_node_belongings(node, network0.get_network()); aligned.add_node_belongings(node, network1.get_network()); } else { // This node cannot be aligned aligned.add_node_belongings(node, network0.get_network()); } Util.advance_progress(tm, j, total); } // Add edges 0 for (AlignmentNetwork.EdgeIterator i = network0.EdgeIterator(); i.hasNext();) { AlignmentNetwork.Edge edge_sig = i.next(); CyNode node0, node1; sig_mgr.override_with(edge_sig.m_e0); node0 = aligned.get_node_from_signature(sig_mgr); sig_mgr.override_with(edge_sig.m_e1); node1 = aligned.get_node_from_signature(sig_mgr); if (node0 == null || node1 == null) { throw new Exception(getClass() + " - Edge and node doesn't match: The pair (node0:" + edge_sig.m_e0 + "node1:" + edge_sig.m_e1 + ") cannot be found"); } CyEdge edge = aligned.make_edge(node0, node1); aligned.add_edge_belongings(edge, network0.get_network()); if (network0_1.containsKey(edge_sig.m_e0) && network0_1.containsKey(edge_sig.m_e1)) { // This edge can be aligned aligned.add_edge_belongings(edge, network1.get_network()); } Util.advance_progress(tm, j, total); } // Add second network but exclude nodes and edges that are already in the first network // Add nodes 1 for (AlignmentNetwork.NodeIterator i = network1.NodeIterator(); i.hasNext();) { String sig = i.next(); if (!network0_1.containsValue(sig)) { // This node is not aligned sig_mgr.override_with(sig); CyNode node = aligned.make_node(sig_mgr); aligned.add_node_belongings(node, network1.get_network()); } Util.advance_progress(tm, j, total); } // Add edges 1 for (AlignmentNetwork.EdgeIterator i = network1.EdgeIterator(); i.hasNext();) { AlignmentNetwork.Edge edge_sig = i.next(); CyNode node0, node1; if (network0_1.containsValue(edge_sig.m_e0)) { String translated = network0_1.getKey(edge_sig.m_e0); sig_mgr.override_with(translated); node0 = aligned.get_node_from_signature(sig_mgr); } else { sig_mgr.override_with(edge_sig.m_e0); node0 = aligned.get_node_from_signature(sig_mgr); } if (network0_1.containsValue(edge_sig.m_e1)) { String translated = network0_1.getKey(edge_sig.m_e1); sig_mgr.override_with(translated); node1 = aligned.get_node_from_signature(sig_mgr); } else { sig_mgr.override_with(edge_sig.m_e1); node1 = aligned.get_node_from_signature(sig_mgr); } if (node0 == null) { if (network0_1.containsValue(edge_sig.m_e0)) { // throw new Exception(" - node0 not found from the g0 network: " // + edge_sig.m_e0 + "->" + network0_1.get(edge_sig.m_e0)); System.out.println(getClass() + " - node0 not found from the g0 network: " + edge_sig.m_e0 + "->" + network0_1.get(edge_sig.m_e0)); } else { // throw new Exception(" - node0 not found from the g1 network: " // + edge_sig.m_e0); System.out.println(getClass() + " - node0 not found from the g1 network: " + edge_sig.m_e0); } continue; } if (node1 == null) { if (network0_1.containsValue(edge_sig.m_e1)) { // throw new Exception(" - node1 not found from the g0 network: " // + edge_sig.m_e1 + "->" + network0_1.get(edge_sig.m_e1)); System.out.println(getClass() + " - node1 not found from the g0 network: " + edge_sig.m_e1 + "->" + network0_1.get(edge_sig.m_e1)); } else { // throw new Exception(" - node1 not found from the g1 network: " // + edge_sig.m_e1); System.out.println(getClass() + " - node1 not found from the g1 network: " + edge_sig.m_e1); } continue; } if (!network0_1.containsValue(edge_sig.m_e0) || !network0_1.containsValue(edge_sig.m_e1)) { // This edge is not aligned CyEdge edge = aligned.make_edge(node0, node1); aligned.add_edge_belongings(edge, network1.get_network()); } Util.advance_progress(tm, j, total); } // Finally adjust the aligned node name by adding the signature from network1 for (AlignmentNetwork.NodeIterator i = network1.NodeIterator(); i.hasNext();) { String sig = i.next(); if (network0_1.containsValue(sig)) { // This node is aligned but we shall change the signature // to reflect the relation of the aligned node String translated = network0_1.getKey(sig); sig_mgr.override_with(translated); CyNode node = aligned.get_node_from_signature(sig_mgr); if (node == null) { // have to skip the incorrect node. continue; } sig_mgr.append_with(sig); aligned.mutate_node_signature(node, sig_mgr); } Util.advance_progress(tm, j, total); } }