Java tutorial
/* * Genoogle: Similar DNA Sequences Searching Engine and Tools. (http://genoogle.pih.bio.br) * Copyright (C) 2008,2009 Felipe Fernandes Albrecht (felipe.albrecht@gmail.com) * * For further information check the LICENSE file. */ package bio.pih.genoogle.io; import java.util.Formatter; import java.util.List; import java.util.Locale; import java.util.Map; import org.dom4j.Document; import org.dom4j.DocumentFactory; import org.dom4j.DocumentHelper; import org.dom4j.Element; import org.dom4j.ProcessingInstruction; import bio.pih.genoogle.Genoogle; import bio.pih.genoogle.search.SearchParams; import bio.pih.genoogle.search.results.HSP; import bio.pih.genoogle.search.results.Hit; import bio.pih.genoogle.search.results.SearchResults; import bio.pih.genoogle.seq.RichSequence; import bio.pih.genoogle.seq.SymbolList; import com.google.common.collect.Maps; /** * * Visitator class that create a XML with the results. * * @author albrecht */ public class Output { private final static String SIMPLE_DOUBLE_FORMAT = "%.3f"; private final static String SCIENTIFIC_DOUBLE_FORMAT = "%5e"; /** * @param searchResults * * @return {@link Document} containing the {@link SearchResults} in XML form. */ public static Document genoogleOutputToXML(List<SearchResults> searchResults) { assert searchResults != null; DocumentFactory factory = DocumentFactory.getInstance(); Document doc = factory.createDocument(); doc.setName("genoogle"); Element output = doc.addElement(Genoogle.SOFTWARE_NAME); output.addAttribute("version", Genoogle.VERSION.toString()); output.addAttribute("copyright", Genoogle.COPYRIGHT); Element iterationsElement = output.addElement("iterations"); for (int i = 0; i < searchResults.size(); i++) { SearchResults searchResult = searchResults.get(i); Element iterationElement = iterationsElement.addElement("iteration"); iterationElement.addAttribute("number", String.valueOf(i)); SymbolList query = searchResult.getParams().getQuery(); if (query instanceof RichSequence) { iterationElement.addAttribute("query", ((RichSequence) query).getHeader()); } iterationElement.add(searchResultToXML(searchResult)); } return doc; } /** * @param searchResult * * @return {@link Document} containing the {@link SearchResults} in XML form. */ public static Document genoogleOutputToXML(SearchResults searchResult) { assert searchResult != null; Element output = genoogleXmlHeader(); output.add(searchResultToXML(searchResult)); return output.getDocument(); } public static Element genoogleXmlHeader() { DocumentFactory factory = DocumentFactory.getInstance(); Document doc = factory.createDocument(); doc.setName("genoogle"); Map<String, String> xslProcessing = Maps.newHashMap(); xslProcessing.put("type", "text/xsl"); xslProcessing.put("href", "results.xsl"); ProcessingInstruction xsltInstruction = DocumentHelper.createProcessingInstruction("xml-stylesheet", xslProcessing); doc.add(xsltInstruction); Element output = doc.addElement("genoogle"); output.addElement("references").addAttribute("program", Genoogle.SOFTWARE_NAME) .addAttribute("version", Double.toString(Genoogle.VERSION)) .addAttribute("copyright", Genoogle.COPYRIGHT); return output; } /** * @param searchResult * @return {@link Element} containing the {@link SearchResults} at XML form. */ public static Element searchResultToXML(SearchResults searchResult) { assert searchResult != null; // TODO: Revise this behavor to throws the exception before. if (searchResult.hasFail()) { for (Throwable e : searchResult.getFails()) { e.printStackTrace(System.err); } } DocumentFactory factory = DocumentFactory.getInstance(); Element resultsElement = factory.createElement("results"); resultsElement.add(paramsToXML(searchResult.getParams())); resultsElement.add(hitsToXML(searchResult.getHits())); return resultsElement; } /** * @param params * @return {@link Element} containing the {@link SearchParams} at XML form. */ public static Element paramsToXML(SearchParams params) { assert params != null; DocumentFactory factory = DocumentFactory.getInstance(); Element paramsElement = factory.createElement("params"); paramsElement.addAttribute("databank", params.getDatabank()); paramsElement.addAttribute("maxSubSequencesDistance", Integer.toString(params.getMaxSubSequencesDistance())); paramsElement.addAttribute("minHspLength", Integer.toString(params.getMinHspLength())); paramsElement.addAttribute("maxHitsResults", Integer.toString(params.getMaxHitsResults())); paramsElement.addAttribute("sequencesExtendDropoff", Integer.toString(params.getSequencesExtendDropoff())); paramsElement.addAttribute("matchScore", Integer.toString(params.getMatchScore())); paramsElement.addAttribute("mismatchScore", Integer.toString(params.getMismatchScore())); return paramsElement; } /** * @param hits * @return {@link Element} containing the {@link List} of {@link Hit} at XML form. */ public static Element hitsToXML(List<Hit> hits) { assert hits != null; DocumentFactory factory = DocumentFactory.getInstance(); Element hitsElement = factory.createElement("hits"); for (Hit hit : hits) { hitsElement.add(hitToXML(hit)); } return hitsElement; } /** * @param hit * @return {@link Element} containing the {@link Hit} at XML form. */ public static Element hitToXML(Hit hit) { assert hit != null; DocumentFactory factory = DocumentFactory.getInstance(); Element hitElement = factory.createElement("hit"); hitElement.addAttribute("id", hit.getId()); hitElement.addAttribute("gi", hit.getGi()); hitElement.addAttribute("description", hit.getDescription()); hitElement.addAttribute("accession", hit.getAccession()); hitElement.addAttribute("length", Integer.toString(hit.getLength())); hitElement.addAttribute("databank", hit.getDatabankName()); hitElement.add(hspsToXML(hit.getHSPs())); return hitElement; } /** * @param hsps * @return {@link Element} containing the {@link List} of {@link HSP} at XML form. */ public static Element hspsToXML(List<HSP> hsps) { assert hsps != null; DocumentFactory factory = DocumentFactory.getInstance(); Element hspsElement = factory.createElement("hsps"); for (HSP hsp : hsps) { hspsElement.add(hspToXML(hsp)); } return hspsElement; } /** * @param hsp * @return {@link Element} containing the {@link HSP} at XML form. */ public static Element hspToXML(HSP hsp) { assert hsp != null; DocumentFactory factory = DocumentFactory.getInstance(); Element hspElement = factory.createElement("hsp"); hspElement.addAttribute("score", Integer.toString((int) hsp.getScore())); hspElement.addAttribute("normalized-score", Integer.toString((int) hsp.getNormalizedScore())); hspElement.addAttribute("e-value", eValueToString(hsp.getEValue())); hspElement.addAttribute("query-from", Integer.toString(hsp.getQueryFrom())); hspElement.addAttribute("query-to", Integer.toString(hsp.getQueryTo())); hspElement.addAttribute("hit-from", Integer.toString(hsp.getHitFrom())); hspElement.addAttribute("hit-to", Integer.toString(hsp.getHitTo())); hspElement.addAttribute("identity-len", Integer.toString(hsp.getIdentityLength())); hspElement.addAttribute("align-len", Integer.toString(hsp.getAlignLength())); hspElement.addElement("query").addText(hsp.getQuerySeq()); hspElement.addElement("align").addText(hsp.getPathSeq()); hspElement.addElement("targt").addText(hsp.getTargetSeq()); return hspElement; } public static String doubleToString(double value) { StringBuilder sb = new StringBuilder(); Formatter formatter = new Formatter(sb); formatter.format(Locale.US, SIMPLE_DOUBLE_FORMAT, value); return sb.toString(); } public static String doubleToScientificString(double value) { StringBuilder sb = new StringBuilder(); Formatter formatter = new Formatter(sb); formatter.format(Locale.US, SCIENTIFIC_DOUBLE_FORMAT, value); return sb.toString(); } public static String eValueToString(double eValue) { if (eValue >= 0.001) { return doubleToString(eValue); } else { if (Double.isNaN(eValue)) { return "NaN"; } String string = doubleToScientificString(eValue); int indexOf = string.indexOf('-'); if (indexOf == -1) { indexOf = string.indexOf('+'); } return string.substring(indexOf - 1); } } }