Java tutorial
/* * Copyright (C) 2015 Wen, Chifeng <https://sourceforge.net/u/daviesx/profile/> * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */ package research; import java.util.ArrayList; import java.util.List; import org.apache.commons.collections4.BidiMap; import org.apache.commons.collections4.bidimap.DualHashBidiMap; import org.cytoscape.model.CyEdge; import org.cytoscape.model.CyNode; import org.cytoscape.model.CyRow; import org.cytoscape.model.CyTable; import org.cytoscape.model.CyTableFactory; import org.cytoscape.work.TaskMonitor; import research.NodeSignatureManager.NodeSignature; /** * Aligning networks from given data * * @author Wen, Chifeng <https://sourceforge.net/u/daviesx/profile/> */ public class NetworkAligner { private CyTable m_table = null; // This table stores majority of the alignment data private final String c_PrimaryKeySlot = "AlignPrimaryKey"; private final String c_NodesSignatureSlot = "AlignNodesSig"; private final String c_DataTitle = "AlignmentData"; private Long m_size; private void build_attributes(CyTable table) { m_table = table; m_size = new Long(0); if (null == m_table.getColumn(c_PrimaryKeySlot)) { m_table.createColumn(c_PrimaryKeySlot, Long.class, true); } if (null == m_table.getColumn(c_NodesSignatureSlot)) { m_table.createListColumn(c_NodesSignatureSlot, String.class, true); } } public NetworkAligner(CyTableFactory fact) { build_attributes(fact.createTable(c_DataTitle, c_PrimaryKeySlot, Long.class, true, true)); } public NetworkAligner(CyTable table) { build_attributes(table); } CyTable get_data() { return m_table; } void set_data_name(String name) { m_table.setTitle(name); } public void add_data_aligned_node_pair(String sig0, String sig1) { CyRow row = m_table.getRow(m_size); row.set(c_PrimaryKeySlot, m_size); ArrayList<String> list = new ArrayList<>(2); list.add(sig0); list.add(sig1); row.set(c_NodesSignatureSlot, list); m_size++; } public String the_only_element_in(ArrayList<NodeSignature> set) { return set.get(0).id; } 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); 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); } } public void align_networks_from_data(AlignmentNetwork network0, AlignmentNetwork network1, AlignmentNetwork aligned) throws Exception { align_networks_from_data(network0, network1, aligned, null); } }