This workflow renders gene expression data onto an SBML model of the glycolysis metabolic pathway using classes and methods from the Java bindng to libsbml. http://dbkgroup.org/peter/mcisb_glycolysis3-edited.xml import java.util.ArrayList; ArrayList AffyIdGeneNameMap = new ArrayList(); System.out.println("Size of AffyIds: " + AffyIds.size()); System.out.println("Size of GeneNames: " + GeneNames.size()); //if(!AffyIds.size() = GeneNames.size()) // System.out.println("Number of affyids does NOT equal number of gene names!"); for(x =0; x < AffyIds.size(); x ++) { ArrayList map = new ArrayList(); String affyId = AffyIds.get(x); if(affyId.equals("")) continue; String geneName = GeneNames.get(x); map.add(affyId); map.add(geneName); AffyIdGeneNameMap.add(map); } AffyIds GeneNames AffyIdGeneNameMap import java.util.ArrayList; //Output ArrayList NewExpressionValues = new ArrayList(); //Create hashmap for easier querying of affy Ids HashMap mappings = new HashMap(); for(int i = 0; i < affyIdGeneNameMap.size(); i ++) { ArrayList map = affyIdGeneNameMap.get(i); String affyId = map.get(0); String genename = map.get(1); mappings.put(affyId, genename); } //System.out.println("Number of items in expressionValues list: " + expressionValues.size()); //Exchange affyIds in expression values for(x = 0; x < expressionValues.size(); x ++) { ArrayList pair = expressionValues.get(x); String affy = pair.get(0); affy = affy.substring(12); System.out.println("Affy Id: " + affy); String value = pair.get(1); System.out.println("Exp value: " + value); String geneName = mappings.get(affy); System.out.println("Gene name: " + geneName); ArrayList newPair = new ArrayList(); newPair.add(geneName); newPair.add(value); NewExpressionValues.add(newPair); } affyIdGeneNameMap expressionValues NewExpressionValues import org.xml.sax.InputSource; import javax.xml.namespace.QName; import javax.xml.transform.sax.SAXSource; import javax.xml.xpath.*; import java.io.BufferedReader; import java.io.File; import java.io.InputStreamReader; import java.util.Iterator; import java.util.List; import org.w3c.dom.*; import org.w3c.dom.NodeList; class XPathWorker implements XPathVariableResolver { NodeList evaluateXPath(InputSource is) { XPathFactory factory = XPathFactory.newInstance(); XPath xPath = factory.newXPath(); String expression = "//*[@Name]"; NodeList nodes = (NodeList) xPath.evaluate(expression, is, XPathConstants.NODESET); NodeList nodeList = (NodeList) nodes; return nodeList; } } ArrayList ExpressionValues = new ArrayList(); ArrayList pair; try { XPath xpath = XPathFactory.newInstance().newXPath(); InputSource s = new InputSource(new StringReader(maxdBrowseXMLOutput)); //Saxon specific XPathWorker xpathWorker = new XPathWorker(); NodeList nodes = xpathWorker.evaluateXPath(s); System.out.println("Expression values from MaxD:\n"); if (nodes != null) { int count = 0; for(int i = 0; i < nodes.getLength(); i ++) { Node n = nodes.item(i); String str = n.getTextContent().trim(); if(count == 0) { pair = new ArrayList(); } if(!str.equals("") && !str.startsWith("Affy:YG_S98:F:") && !str.startsWith("Affy:YG_S98:R:")) { System.out.println(str); pair.add(str); count ++; } if(count == 2) { ExpressionValues.add(pair); count = 0; } } } System.out.println("Size of ExpressionValues list: " + ExpressionValues.size()); } catch (XPathExpressionException e) { e.printStackTrace(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } maxdBrowseXMLOutput ExpressionValues libsbmlj.jar //Output ArrayList ColorCodedExpressionValues = new ArrayList(); for(int i = 0; i < expressionValues.size(); i++) { ArrayList pair = expressionValues.get(i); String geneName = pair.get(0); float value = Float.parseFloat(pair.get(1)); String colorValue = ""; System.out.println("Gene: " + geneName); //Match color to expression value for(int v = 0; v < colorcode.size(); v++) { ArrayList colors = colorcode.get(v); Float f = new Float(colors.get(0)); float expValue = f.floatValue(); if(value < expValue) { System.out.println("Gene expression value: " + value); System.out.println("Colour value: " + expValue); colorValue = colors.get(1); break; } if(value > expValue) colorValue = "ff33ff00"; } //Add to new arraylist ArrayList triple = new ArrayList(); triple.add(geneName); triple.add(value); triple.add(colorValue); ColorCodedExpressionValues.add(triple); } colorcode expressionValues ColorCodedExpressionValues /** * Concatenates the affy ids into one String * delimited by commas */ StringBuffer final_sb = new StringBuffer(); for(int i = 0; i < ids.size(); i ++) { String str = "Affy:YG_S98:" + (String)ids.get(i); final_sb.append(str); if(i < ids.size()) final_sb.append(","); else continue; } //Output String mergedIds = final_sb.toString(); ids mergedIds //Output String range = ""; float lowestValue = 500.00; float highestValue = 0.00; System.out.println("Calculating gene expression value range..."); for(int i = 0; i < expressionValues.size(); i++) { ArrayList pair = expressionValues.get(i); String value = pair.get(1); //System.out.println("Value is: " + value); float x = java.lang.Float.parseFloat(value); if(x < lowestValue) lowestValue = x; if(x > highestValue) highestValue = x; } System.out.println("Calculating colour intervals..."); //Create list of color codes float intervals = highestValue / 6; ArrayList colorcode = new ArrayList(); for(int i = 0 ; i < 6; i++) { float e = intervals * (i + 1); String color = ""; if(i == 0) color = "ff330000"; else if(i == 1) color = "ff333300"; else if(i == 2) color = "ff336600"; else if(i == 3) color = "ff339900"; else if(i == 4) color = "ff33CC00"; else if(i == 5) color = "ff33FF00"; ArrayList colormap = new ArrayList(); colormap.add(e); colormap.add(color); colorcode.add(colormap); } //Check //for(int m = 0; m < colorcode.size(); m ++) // System.out.println(colorcode.get(m)); expressionValues colorcode http://dbk-ed.mib.man.ac.uk:8080/CellDesignerViz/services/CellDesignerViz?wsdl createImage Will take a list of Gene names, a list of Measurement names and a list of Column Types and produce a table. All values are coloured in relation to the a reference. In the list of Measurement names, the first Measurement listed is taken to be the reference. Formatted as text. * JC_S-0.07-1_Measurement , BigEx:9dj2n5g7l http://dbkgroup.org/software/maxd/maxdBrowse/sequences/GeneHunterXHTMLCoreOutput/wsdl.xml query org.embl.ebi.escience.scuflworkers.java.WebPageFetcher http://dbk-ed.mib.man.ac.uk:8080/YeastAffymapper/services/YeastAffymapper?wsdl getAffyId import org.sbml.libsbml.*; import org.xml.sax.InputSource; import javax.xml.xpath.XPath; import javax.xml.xpath.XPathFactory; import javax.xml.xpath.XPathExpressionException; import java.util.ArrayList; //System.loadLibrary("sbmlj"); //Output ArrayList geneNames = new ArrayList(); //For some reason, Taverna is converting NumOfSpecies into a String //Need to parse into an int int speciesNumber = Integer.parseInt(NumOfSpecies); for(int i = 0; i < speciesNumber; i ++) { Species species = (Species) listOfSpecies.get(i); //System.out.println(species.getName()); String annotation = species.getAnnotation(); annotation = annotation.replaceAll("celldesigner:", ""); //System.out.println(annotation); try { XPath xpath = XPathFactory.newInstance().newXPath(); String expression = "//class"; InputSource s = new InputSource(new StringReader(annotation)); String speciesClass = xpath.evaluate(expression, s); if (speciesClass.equals("PROTEIN")) geneNames.add(species.getName()); } catch (XPathExpressionException e) { e.printStackTrace(); } } NumOfSpecies listOfSpecies geneNames libsbmlj.jar Creates a new SBMLReader and returns it. By default schema validation is off (XML_SCHEMA_VALIDATION_NONE) and schemaFilenames are empty. Creates a new SBMLReader and returns it. By default schema validation is off (XML_SCHEMA_VALIDATION_NONE) and schemaFilenames are empty. libsbmlj.jar libsbmlj.jar libsbmlj.jar Reads an SBML document from the given XML string. The XML string must be complete and legal XML document. Among other things, it must start with an XML processing instruction. For e.g.,: <?xml version='1.0' encoding='UTF-8'?> This method will log a fatal error if the XML string is not SBML. See the method documentation for readSBML(filename) for example error checking code. Reads an SBML document from the given XML string. The XML string must be complete and legal XML document. Among other things, it must start with an XML processing instruction. For e.g.,: <?xml version='1.0' encoding='UTF-8'?> This method will log a fatal error if the XML string is not SBML. See the method documentation for readSBML(filename) for example error checking code. libsbmlj.jar libsbmlj.jar import org.sbml.libsbml.*; import org.xml.sax.InputSource; import org.xml.sax.SAXException; import org.w3c.dom.*; import javax.xml.transform.*; import javax.xml.transform.stream.StreamResult; import javax.xml.transform.dom.DOMSource; import com.sun.org.apache.xerces.internal.parsers.DOMParser; import java.io.OutputStreamWriter; //Output String NewSBMLFile = ""; //System.loadLibrary("sbmlj"); //Create hashmap mapping gene names to colour values HashMap geneColorMappings = new HashMap(); for(int h = 0; h < ExpressionValues.size(); h ++) { ArrayList l = ExpressionValues.get(h); String genename = l.get(0); Float value = l.get(1); String color = l.get(2); geneColorMappings.put(genename, color); } //SBMLReader reader = new SBMLReader(); //SBMLDocument document = reader.readSBMLFromString(SBMLFile); //odel model = document.getModel(); //String annotation = model.getAnnotation(); //Get rid of prefix celldesigner: in XML tags annotation = annotation.replaceAll("celldesigner:", ""); try { DOMParser parser = new DOMParser(); InputSource s = new InputSource(new StringReader(annotation)); parser.parse(s); Document doc = parser.getDocument(); NodeList nodes1 = doc.getElementsByTagName("speciesAlias"); System.out.println("Number of speciesAlias nodes: " + nodes1.getLength()); for (int i = 0; i < nodes1.getLength(); i++) { Element speciesAliasElem = (Element) nodes1.item(i); //System.out.println(speciesAliasElem.getAttribute("id")); String id = speciesAliasElem.getAttribute("id"); if (id.startsWith("sa")) continue; System.out.println("Id is: " + id); NodeList nodes2 = speciesAliasElem.getElementsByTagName("usualView"); for (int v = 0; v < nodes2.getLength(); v++) { Element usualViewElem = (Element) nodes2.item(v); NodeList nodes3 = usualViewElem.getElementsByTagName("paint"); //System.out.println("Number of paint nodes: " + nodes3.getLength()); //If id is a gene name which is not measured in the experiment or not found by YeastAffymapper //, colour it white!!! if(!geneColorMappings.containsKey(id)) { System.out.println("Gene name: " + id + " was not found in MaxD database or by YeastAffymapper"); for (int g = 0; g < nodes3.getLength(); g++) { Element paintElem = (Element) nodes3.item(g); paintElem.removeAttribute("color"); paintElem.setAttribute("color", "fff9f2f0"); } } else { for (int g = 0; g < nodes3.getLength(); g++) { Element paintElem = (Element) nodes3.item(g); paintElem.removeAttribute("color"); paintElem.setAttribute("color", geneColorMappings.get(speciesAliasElem.getAttribute("id"))); } } } } // Prepare the DOM document for writing - use a Transformer for output StringWriter sw = new StringWriter(); TransformerFactory tFactory = TransformerFactory.newInstance(); Transformer transformer = tFactory.newTransformer(); DOMSource source = new DOMSource(doc); StreamResult result = new StreamResult(sw); transformer.transform(source, result); StringBuffer output = new StringBuffer(); String stuff = sw.toString(); String[] lines = stuff.split("\n"); //Sort out first line //output.append("<annotation>\n"); output.append("<annotation>"); for (int i = 2; i < lines.length; i++) //Miss first line { String line = lines[i]; if (line.trim().startsWith("<html") || line.trim().startsWith("</html") || line.trim().startsWith("<body") || line.trim().startsWith("</body") || line.trim().startsWith("</annotation")) { output.append("\n" + line); continue; } if (line.trim().startsWith("<") && !line.trim().startsWith("</")) line = line.replaceFirst("<", "<celldesigner:"); line = line.replaceAll("</", "</celldesigner:"); output.append("\n" + line); //if(i < 20) // System.out.println("Line is: " + line); } NewSBMLFile = output.toString(); //Need to add into SBML model /* //model.unsetAnnotation(); //model.setAnnotation(output.toString()); //SBMLDocument document = new SBMLDocument(2); //document.getNamespaces().add("celldesigner", "http://www.sbml.org/2001/ns/celldesigner"); //document.setModel(model); //New!!!!!!!!!!!!!!!!!! //SBMLWriter writer = new SBMLWriter(); String str = writer.writeToString(document); writer.delete(); writer = null; NewSBMLFile = str.replaceAll("\t", " "); */ } catch (SAXException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } catch (TransformerException e) { e.printStackTrace(); } annotation ExpressionValues NewSBMLFile libsbmlj.jar Creates a new SBMLReader and returns it. By default schema validation is off (XML_SCHEMA_VALIDATION_NONE) and schemaFilenames are empty. Creates a new SBMLReader and returns it. By default schema validation is off (XML_SCHEMA_VALIDATION_NONE) and schemaFilenames are empty. libsbmlj.jar Reads an SBML document from the given XML string. The XML string must be complete and legal XML document. Among other things, it must start with an XML processing instruction. For e.g.,: <?xml version='1.0' encoding='UTF-8'?> This method will log a fatal error if the XML string is not SBML. See the method documentation for readSBML(filename) for example error checking code. Reads an SBML document from the given XML string. The XML string must be complete and legal XML document. Among other things, it must start with an XML processing instruction. For e.g.,: <?xml version='1.0' encoding='UTF-8'?> This method will log a fatal error if the XML string is not SBML. See the method documentation for readSBML(filename) for example error checking code. libsbmlj.jar Writes the given SBML document to an in-memory string and returns a pointer to it. The string is owned by the caller and should be freed (with free()) when no longer needed. Writes the given SBML document to an in-memory string and returns a pointer to it. The string is owned by the caller and should be freed (with free()) when no longer needed. libsbmlj.jar Creates a new SBMLDocument. The SBML level defaults to 2 and version defaults to 1. Creates a new SBMLDocument. The SBML level defaults to 2 and version defaults to 1. libsbmlj.jar libsbmlj.jar libsbmlj.jar libsbmlj.jar libsbmlj.jar libsbmlj.jar Adds (prefix, URI) to this list of XML namespaces. If prefix starts with 'xmlns:' (case-insensitive), it will be removed. celldesigner http://www.sbml.org/2001/ns/celldesigner Adds (prefix, URI) to this list of XML namespaces. If prefix starts with 'xmlns:' (case-insensitive), it will be removed. libsbmlj.jar Creates a new SBMLWriter. Creates a new SBMLWriter. libsbmlj.jar Sets the Model of this SBMLDocument to the given Model. Any previously defined model is unset and freed. Sets the Model of this SBMLDocument to the given Model. Any previously defined model is unset and freed. libsbmlj.jar Completed getAnnotation unsetAnnotation Scheduled Running Completed add setModel Scheduled Running Completed setAnnotation setModel Scheduled Running Completed setModel writeToString Scheduled Running image/png