/*
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;
import csplugins.id.mapping.util.DataSourceWrapper;
import csplugins.id.mapping.util.IDMapperWrapper;
import csplugins.id.mapping.util.XrefWrapper;
import cytoscape.Cytoscape;
import cytoscape.CyNetwork;
import cytoscape.data.CyAttributes;
import cytoscape.data.attr.MultiHashMapDefinition;
import cytoscape.task.TaskMonitor;
import giny.model.Node;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
import java.util.Vector;
/**
*
* @author gjj
*/
public class AttributeBasedIDMappingImpl
implements AttributeBasedIDMapping{
protected TaskMonitor taskMonitor;
protected boolean interrupted;
protected String report;
protected Map<String,Byte> attrNameType = null;
public void setTaskMonitor(TaskMonitor taskMonitor) {
this.taskMonitor = taskMonitor;
interrupted = false;
}
public void interrupt() {
interrupted = true;
report = "Aborted!";
}
public String getReport() {
return report;
}
/**
* Define target attributes.
* Call this method first before mapping if necessary.
* @param attrNameType
*/
public void suggestTgtAttrType(Map<String,Byte> attrNameType) {
this.attrNameType = attrNameType;
CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
MultiHashMapDefinition mmapDef = nodeAttributes.getMultiHashMapDefinition();
for (Map.Entry<String,Byte> entry : attrNameType.entrySet()) {
String attrname = entry.getKey();
byte attrtype = entry.getValue();
//hack to allow overwriting existing attributes
boolean skip = false;
for (String existingName : nodeAttributes.getAttributeNames()){
if (attrname.equals(existingName)){
skip = true;
}
}
if(skip)
break;
byte[] keyTypes;
if (attrtype==CyAttributes.TYPE_STRING) {
keyTypes = null;
} else if (attrtype==CyAttributes.TYPE_SIMPLE_LIST ) {
keyTypes = new byte[] { MultiHashMapDefinition.TYPE_INTEGER };
} else {
keyTypes = null;
}
mmapDef.defineAttribute(attrname,
MultiHashMapDefinition.TYPE_STRING,
keyTypes);
}
}
/**
* {@inheritDoc}
*/
public void map(Set<CyNetwork> networks, Map<String,Set<DataSourceWrapper>> mapSrcAttrIDTypes,
Map<String, DataSourceWrapper> mapTgtAttrNameIDType) {
// prepare source xrefs
Set<Node> nodes = nodesUnion(networks);
Map<Node,Set<XrefWrapper>> mapNodeSrcXrefs = prepareNodeSrcXrefs(nodes, mapSrcAttrIDTypes);
Set<XrefWrapper> srcXrefs = srcXrefUnion(mapNodeSrcXrefs);
// target id types
Set<DataSourceWrapper> tgtTypes = new HashSet(mapTgtAttrNameIDType.values());
// id mapping
updateTaskMonitor("Mapping IDs...",-1);
Map<XrefWrapper, Set<XrefWrapper>> mapping = IDMapperWrapper.mapID(srcXrefs, tgtTypes);
// define target attribute
defineTgtAttributes(mapTgtAttrNameIDType.keySet());
// set target attribute
Map<Node,Set<XrefWrapper>> mapNodeTgtXrefs = getNodeTgtXrefs(mapNodeSrcXrefs, mapping);
setTgtAttribute(mapNodeTgtXrefs, mapTgtAttrNameIDType);
report = "Identifiers mapped for "+mapNodeTgtXrefs.size()+" nodes (out of "+nodes.size()+")!";
updateTaskMonitor(report,100);
}
private Set<Node> nodesUnion(Set<CyNetwork> networks) {
int nNode = 0;
for (CyNetwork network : networks) {
nNode += network.getNodeCount();
}
Set nodes = new HashSet();
int i = 0;
for (CyNetwork network : networks) {
for (Iterator<Node> nodeIt = network.nodesIterator(); nodeIt.hasNext();) {
if (interrupted) return null;
updateTaskMonitor("Retrieving nodes...\n"+i+"/"+nNode,(i+1)*100/nNode);
i++;
nodes.add(nodeIt.next());
}
}
return nodes;
}
private Map<Node,Set<XrefWrapper>> prepareNodeSrcXrefs(Set<Node> nodes, Map<String,Set<DataSourceWrapper>> mapSrcAttrIDTypes) {
Map<Node,Set<XrefWrapper>> ret = new HashMap();
CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
int nNode = nodes.size();
int i=0;
for (Node node : nodes) {
if (interrupted) return null;
updateTaskMonitor("Preparing cross reference for nodes...\n"+i+"/"+nNode,(i+1)*100/nNode);
i++;
Set<XrefWrapper> xrefs = new HashSet();
ret.put(node, xrefs);
String nodeID = node.getIdentifier();
for (Map.Entry<String,Set<DataSourceWrapper>> entryAttrIDTypes : mapSrcAttrIDTypes.entrySet()) {
String attrName = entryAttrIDTypes.getKey();
Set<DataSourceWrapper> dss = entryAttrIDTypes.getValue();
//TODO: remove this in Cy3
if (attrName.compareTo("ID")==0) {
for (DataSourceWrapper ds : dss) {
xrefs.add(new XrefWrapper(nodeID, ds));
}
continue;
}
byte attrType = nodeAttributes.getType(attrName);
if (attrType == CyAttributes.TYPE_SIMPLE_LIST) {
List attr = nodeAttributes.getListAttribute(nodeID, attrName);
for (Object obj : attr) {
String str = obj.toString();
for (DataSourceWrapper ds : dss) {
xrefs.add(new XrefWrapper(str, ds));
}
}
} else {
Object obj = nodeAttributes.getAttribute(nodeID, attrName);
if (obj!=null) {
String str = obj.toString();
if (str.length()>0) {
for (DataSourceWrapper ds : dss) {
xrefs.add(new XrefWrapper(str, ds));
}
}
}
}
}
}
return ret;
}
private Set<XrefWrapper> srcXrefUnion(Map<Node,Set<XrefWrapper>> mapNodeSrcXrefs) {
Set<XrefWrapper> ret = new HashSet();
for (Set<XrefWrapper> xrefs : mapNodeSrcXrefs.values()) {
ret.addAll(xrefs);
}
return ret;
}
private Map<Node,Set<XrefWrapper>> getNodeTgtXrefs (Map<Node,Set<XrefWrapper>> mapNodeSrcXrefs,
Map<XrefWrapper, Set<XrefWrapper>> idMapping) {
Map<Node,Set<XrefWrapper>> mapNodeTgtXrefs = new HashMap();
for (Map.Entry<Node,Set<XrefWrapper>> entryNodeXrefs : mapNodeSrcXrefs.entrySet()) {
Node node = entryNodeXrefs.getKey();
Set<XrefWrapper> tgtXrefs = new HashSet();
Set<XrefWrapper> srcXrefs = entryNodeXrefs.getValue();
//TODO: deal with ambiguity--same node, same attribute, different data source
for (XrefWrapper srcXref : srcXrefs) {
Set<XrefWrapper> xrefs = idMapping.get(srcXref);
if (xrefs!=null) {
tgtXrefs.addAll(xrefs);
}
}
if (!tgtXrefs.isEmpty())
mapNodeTgtXrefs.put(node, tgtXrefs);
}
return mapNodeTgtXrefs;
}
private void defineTgtAttributes(Set<String> attrs) {
CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
List<String> attrNames = java.util.Arrays.asList(nodeAttributes.getAttributeNames());
MultiHashMapDefinition mmapDef = nodeAttributes.getMultiHashMapDefinition();
for (String attr : attrs) {
if (attrNames.contains(attr)) {
// for existing attribute, check if its type is String or List
byte attrType = nodeAttributes.getType(attr);
if (attrType!=CyAttributes.TYPE_STRING && attrType!=CyAttributes.TYPE_SIMPLE_LIST) {
throw new java.lang.UnsupportedOperationException("Only String and List target attributes are supported.");
}
} else {
// define the new attribute as List
// only if it is explicitly defined as String, o.w. default is list of string
byte[] keyTypes;
if (attrNameType!=null && attrNameType.get(attr)==CyAttributes.TYPE_STRING) {
keyTypes = null;
}
keyTypes = new byte[] { MultiHashMapDefinition.TYPE_INTEGER };
mmapDef.defineAttribute(attr,
MultiHashMapDefinition.TYPE_STRING,
keyTypes);
}
}
}
private void setTgtAttribute(Map<Node,Set<XrefWrapper>> mapNodeTgtXrefs,
Map<String, DataSourceWrapper> mapTgtAttrNameIDType) {
CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
Map<String, Byte> mapAttrNameType = new HashMap();
Map<DataSourceWrapper, Set<String>> mapIDTypeAttrName = new HashMap();
for (String attrName : mapTgtAttrNameIDType.keySet()) {
mapAttrNameType.put(attrName, nodeAttributes.getType(attrName));
DataSourceWrapper idType = mapTgtAttrNameIDType.get(attrName);
Set<String> names = mapIDTypeAttrName.get(idType);
if (names==null) {
names = new HashSet();
mapIDTypeAttrName.put(idType, names);
}
names.add(attrName);
}
int i = 0;
int nNode = mapNodeTgtXrefs.size();
for (Map.Entry<Node,Set<XrefWrapper>> entryNodeXrefs : mapNodeTgtXrefs.entrySet()) {
if (interrupted) return;
updateTaskMonitor("Preparing cross reference for nodes...\n"+i+"/"+nNode,(i+1)*100/nNode);
i++;
// type wise
Map<DataSourceWrapper, Set<String>> mapDsIds = new HashMap();
Set<XrefWrapper> tgtXrefs = entryNodeXrefs.getValue();
for (XrefWrapper xref : tgtXrefs) {
DataSourceWrapper ds = xref.getDataSource();
Set<String> ids = mapDsIds.get(ds);
if (ids==null) {
ids = new TreeSet(); // alphabetically
mapDsIds.put(ds, ids);
}
ids.add(xref.getValue());
}
// set attribute
Node node = entryNodeXrefs.getKey();
String nodeID = node.getIdentifier();
for (Map.Entry<DataSourceWrapper, Set<String>> entryDsIds : mapDsIds.entrySet()) {
DataSourceWrapper ds = entryDsIds.getKey();
Set<String> attrNames = mapIDTypeAttrName.get(ds);
if (attrNames==null) {
// TODO: what happened?
continue;
}
for (String attrName : attrNames) {
byte attrType = mapAttrNameType.get(attrName);
Set<String> ids = entryDsIds.getValue();
if (attrType==CyAttributes.TYPE_SIMPLE_LIST) {
List<String> values = new Vector(ids);
nodeAttributes.setListAttribute(nodeID, attrName, values);
} else if (attrType==CyAttributes.TYPE_STRING) {
// only returns the first ID
//TODO: is that a way to get the "best" one?
if (!ids.isEmpty()) {
nodeAttributes.setAttribute(nodeID, attrName, ids.iterator().next());
}
}
}
}
}
}
private void updateTaskMonitor(String status, int percentage) {
if (this.taskMonitor!=null) {
taskMonitor.setStatus(status);
taskMonitor.setPercentCompleted(percentage);
}
}
private void updateTaskMonitor(String status) {
if (this.taskMonitor!=null) {
taskMonitor.setStatus(status);
}
}
}