/* Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org) The Cytoscape Consortium is: - Institute for Systems Biology - University of California San Diego - Memorial Sloan-Kettering Cancer Center - Institut Pasteur - Agilent Technologies This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or any later version. This library 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. The software and documentation provided hereunder is on an "as is" basis, and the Institute for Systems Biology and the Whitehead Institute have no obligations to provide maintenance, support, updates, enhancements or modifications. In no event shall the Institute for Systems Biology and the Whitehead Institute be liable to any party for direct, indirect, special, incidental or consequential damages, including lost profits, arising out of the use of this software and its documentation, even if the Institute for Systems Biology and the Whitehead Institute have been advised of the possibility of such damage. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. */ package csplugins.id.mapping.ui; import csplugins.id.mapping.AttributeBasedIDMappingImpl; import csplugins.id.mapping.util.DataSourceWrapper; import cytoscape.task.Task; import cytoscape.task.TaskMonitor; import cytoscape.CyNetwork; import java.util.Set; import java.util.Map; /** * */ public class AttributeBasedIDMappingTask implements Task { private final Set<CyNetwork> networks; private final Map<String,Set<DataSourceWrapper>> mapSrcAttrIDTypes; private final Map<String, DataSourceWrapper> mapTgtAttrNameIDType; private final AttributeBasedIDMappingImpl service; private final Map<String,Byte> mapTgtAttrNameAttrType; private TaskMonitor taskMonitor; private boolean success; /** * * @param networks * @param mapSrcAttrIDTypes * @param mapTgtAttrNameIDType */ public AttributeBasedIDMappingTask(final Set<CyNetwork> networks, final Map<String,Set<DataSourceWrapper>> mapSrcAttrIDTypes, final Map<String, DataSourceWrapper> mapTgtAttrNameIDType, Map<String,Byte> mapTgtAttrNameAttrType) { this.networks = networks; this.mapSrcAttrIDTypes = mapSrcAttrIDTypes; this.mapTgtAttrNameIDType = mapTgtAttrNameIDType; this.mapTgtAttrNameAttrType = mapTgtAttrNameAttrType; service = new AttributeBasedIDMappingImpl(); success = false; } /** * Executes Task. */ //@Override public void run() { try { service.setTaskMonitor(taskMonitor); service.suggestTgtAttrType(mapTgtAttrNameAttrType); service.map(networks, mapSrcAttrIDTypes, mapTgtAttrNameIDType); } catch (Exception e) { taskMonitor.setPercentCompleted(100); taskMonitor.setStatus("ID mapping failed.\n"); e.printStackTrace(); } success = true; } public boolean success() { return success; } /** * Halts the Task: Not Currently Implemented. */ //@Override public void halt() { service.interrupt(); } /** * Sets the Task Monitor. * * @param taskMonitor * TaskMonitor Object. */ //@Override public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException { this.taskMonitor = taskMonitor; } /** * Gets the Task Title. * * @return Task Title. */ //@Override public String getTitle() { return new String("ID mapping"); } }