001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 */ 021package org.biojava.nbio.core.search.io.blast; 022 023import org.biojava.nbio.core.search.io.Hit; 024import java.util.HashMap; 025import java.util.List; 026import org.biojava.nbio.core.sequence.template.Sequence; 027 028/** 029 * Designed by Paolo Pavan. 030 * You may want to find my contacts on Github and LinkedIn for code info 031 * or discuss major changes. 032 * https://github.com/paolopavan 033 * 034 * @author Paolo Pavan 035 */ 036 037public class BlastResultBuilder { 038 private String program; 039 private String version; 040 private String reference; 041 private String dbFile; 042 private HashMap<String, String> programSpecificParameters; 043 private int iterationNumber; 044 private String queryID; 045 private String queryDef; 046 private int queryLength; 047 private Sequence querySequence; 048 private List<Hit> hits; 049 050 public BlastResultBuilder() { 051 } 052 053 public BlastResultBuilder setProgram(String program) { 054 this.program = program; 055 return this; 056 } 057 058 public BlastResultBuilder setVersion(String version) { 059 this.version = version; 060 return this; 061 } 062 063 public BlastResultBuilder setReference(String reference) { 064 this.reference = reference; 065 return this; 066 } 067 068 public BlastResultBuilder setDbFile(String dbFile) { 069 this.dbFile = dbFile; 070 return this; 071 } 072 073 public BlastResultBuilder setProgramSpecificParameters(HashMap<String, String> programSpecificParameters) { 074 this.programSpecificParameters = programSpecificParameters; 075 return this; 076 } 077 078 public BlastResultBuilder setIterationNumber(int iterationNumber) { 079 this.iterationNumber = iterationNumber; 080 return this; 081 } 082 083 public BlastResultBuilder setQueryID(String queryID) { 084 this.queryID = queryID; 085 return this; 086 } 087 088 public BlastResultBuilder setQueryDef(String queryDef) { 089 this.queryDef = queryDef; 090 return this; 091 } 092 093 public BlastResultBuilder setQueryLength(int queryLength) { 094 this.queryLength = queryLength; 095 return this; 096 } 097 098 public BlastResultBuilder setHits(List<Hit> hits) { 099 this.hits = hits; 100 return this; 101 } 102 103 public BlastResultBuilder setQuerySequence(Sequence s) { 104 this.querySequence = s; 105 return this; 106 } 107 108 public BlastResult createBlastResult() { 109 return new BlastResult(program, version, reference, dbFile, programSpecificParameters, iterationNumber, queryID, queryDef, queryLength, hits, querySequence); 110 } 111 112}