Java tutorial
/* * The Gemma project * * Copyright (c) 2010 University of British Columbia * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ package ubic.gemma.loader.protein.string; import java.util.ArrayList; import java.util.Collection; import java.util.HashSet; import org.apache.commons.lang.StringUtils; import ubic.gemma.loader.protein.StringProteinInteractionEvidenceCodeEnum; import ubic.gemma.loader.protein.string.model.StringProteinProteinInteraction; import ubic.gemma.loader.util.parser.BasicLineParser; import ubic.gemma.loader.util.parser.FileFormatException; import ubic.gemma.model.genome.Taxon; /** * Class that is responsible for parsing the string protein protein interaction file (protein.links.detailed.txt). * String has the following line format: * <p> * protein1 protein2 neighborhood fusion cooccurence coexpression experimental database textmining combined_score. * <p> * The first two fields are strings and represent ensembl protein ids, the other 8 fields represent evidence for the * interactions. Currently no logic connected to the evidence and any evidence is taken as is. The file is large and * contains over 600 taxon as of version 8.2, the file is filtered based on ncbi id which is appended to the start of * the protein1 and protein 2. Thus filtering involves only parsing those lines that contain taxon of interest. * * @author ldonnison * @version $Id: StringProteinProteinInteractionFileParser.java,v 1.5 2011/10/31 13:07:06 paul Exp $ */ public class StringProteinProteinInteractionFileParser extends BasicLineParser<StringProteinProteinInteraction> { /** String file format which has 10 columns */ private int STRING_PROTEINPROTEININTERACTION_FIELDS_PER_ROW = 10; /** String uses space as the delimter */ private static final char FIELD_DELIM = ' '; /** * The Collection of StringProteinProteinInteraction of taxon that are of interest note * StringProteinProteinInteraction has hashCode method overriden as HashSet uses this method to test for equality */ Collection<StringProteinProteinInteraction> proteinProteinInteractions = new HashSet<StringProteinProteinInteraction>(); /** Taxon of interest in the string file */ private Collection<Taxon> taxa = new ArrayList<Taxon>(); /** * Parse a string file line into an array representing the components, on successful validation create a * StringProteinProteinInteraction value object. * * @param The line to parse * @return StringProteinProteinInteraction the value object. */ @Override public StringProteinProteinInteraction parseOneLine(String line) { // header line skip or empty line if (line.startsWith("protein") || line.isEmpty()) { return null; } String[] fields = StringUtils.splitPreserveAllTokens(line, FIELD_DELIM); if (fields.length != STRING_PROTEINPROTEININTERACTION_FIELDS_PER_ROW) { log.info("check file format"); throw new FileFormatException("Line + " + line + " is not in the right format: has " + fields.length + " fields, expected " + STRING_PROTEINPROTEININTERACTION_FIELDS_PER_ROW); } try { return createStringProteinProteinInteraction(fields); } catch (NumberFormatException e) { throw new RuntimeException(e); } catch (FileFormatException e) { throw new RuntimeException(e); } } /** * Typical line of string file is of the following format: * * <pre> * 882.DVU0001 882.DVU0002 707 0 0 0 0 0 172 742 * </pre> * * 882.DVU0001 and 882.DVU0002 refer to protein 1 and protein2 Note the 882 is the ncbi taxon id, the other part is * an external id (ensembl). Method takes the array representing a line of string file and creates a * StringProteinProteinInteraction object. * * @param fields Line split on delimiter * @return StringProteinProteinInteraction value object. */ public StringProteinProteinInteraction createStringProteinProteinInteraction(String[] fields) { // validate if (fields == null) { return null; } if (fields[0] == null || fields[1] == null || fields[0].isEmpty() || fields[1].isEmpty()) { return null; } String[] protein1AndTaxa = StringUtils.split(fields[0], "."); int taxonIdProtein1 = Integer.parseInt(protein1AndTaxa[0]); String[] protein2AndTaxa = StringUtils.split(fields[1], "."); int taxonIdProtein2 = Integer.parseInt(protein2AndTaxa[0]); // Check that the two proteins taxa match that is the taxon appended to protein name match if (taxonIdProtein1 != taxonIdProtein2) { throw new FileFormatException( "Protein 1 " + fields[0] + " protein 2 " + fields[1] + " do not contain matching taxons"); } // taxon not supported skip it if (!(getNcbiValidTaxon()).contains(taxonIdProtein1)) { return null; } // always ensure that protein 1 and protein 2 are set same alphabetical order makes matching much easier later // hashcode equality method relies on them being in consistent order. // use hashcode as mixed alphanumeric code Integer protein1Infile = Integer.valueOf(fields[0].hashCode()); Integer protein2InFile = Integer.valueOf(fields[1].hashCode()); StringProteinProteinInteraction stringProteinProteinInteraction = null; if (protein1Infile.compareTo(protein2InFile) < 0) { stringProteinProteinInteraction = new StringProteinProteinInteraction(fields[0], fields[1]); } else { stringProteinProteinInteraction = new StringProteinProteinInteraction(fields[1], fields[0]); } stringProteinProteinInteraction.setNcbiTaxonId(taxonIdProtein1); // validate the line make sure these fields are numeric for (int i = 2; i < fields.length; i++) { if (!StringUtils.isNumeric(fields[i])) { throw new FileFormatException("This line does not contain valid number "); } } stringProteinProteinInteraction.addEvidenceCodeScoreToMap( StringProteinInteractionEvidenceCodeEnum.NEIGHBORHOOD, Integer.valueOf(fields[2])); stringProteinProteinInteraction.addEvidenceCodeScoreToMap( StringProteinInteractionEvidenceCodeEnum.GENEFUSION, Integer.valueOf(fields[3])); stringProteinProteinInteraction.addEvidenceCodeScoreToMap( StringProteinInteractionEvidenceCodeEnum.COOCCURENCE, Integer.valueOf(fields[4])); stringProteinProteinInteraction.addEvidenceCodeScoreToMap( StringProteinInteractionEvidenceCodeEnum.COEXPRESSION, Integer.valueOf(fields[5])); stringProteinProteinInteraction.addEvidenceCodeScoreToMap( StringProteinInteractionEvidenceCodeEnum.EXPERIMENTAL, Integer.valueOf(fields[6])); stringProteinProteinInteraction.addEvidenceCodeScoreToMap(StringProteinInteractionEvidenceCodeEnum.DATABASE, Integer.valueOf(fields[7])); stringProteinProteinInteraction.addEvidenceCodeScoreToMap( StringProteinInteractionEvidenceCodeEnum.TEXTMINING, Integer.valueOf(fields[8])); stringProteinProteinInteraction.setCombined_score(Double.valueOf(fields[9])); return stringProteinProteinInteraction; } /** * Method to add a StringProteinProteinInteraction the map objects. * * @param StringProteinProteinInteraction value oobject representing parsed line */ @Override protected void addResult(StringProteinProteinInteraction obj) { proteinProteinInteractions.add(obj); } @Override public Collection<StringProteinProteinInteraction> getResults() { return proteinProteinInteractions; } /** * Method to generate a collection of ncbi ids for the taxon which are to be used. * * @return Collection of integers representing the ncbis to use. */ private Collection<Integer> getNcbiValidTaxon() { Collection<Integer> taxaNcibi = new HashSet<Integer>(); for (Taxon taxon : this.taxa) { taxaNcibi.add(taxon.getNcbiId()); if (taxon.getSecondaryNcbiId() != null) taxaNcibi.add(taxon.getSecondaryNcbiId()); } return taxaNcibi; } /** * Getter for taxon that are to be selected for in the string file * * @return taxon to be parsed */ public Collection<Taxon> getTaxa() { return taxa; } /** * Setter for the taxon that are to be selected for in the string file * * @param taxa to be parsed */ public void setTaxa(Collection<Taxon> taxa) { this.taxa = taxa; } }