Java tutorial
/** * * Copyright 2010 Matthew Z DeMaere. * * This file is part of SHAP. * * SHAP is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * SHAP 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. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with SHAP. If not, see <http://www.gnu.org/licenses/>. * */ package org.mzd.shap.analysis.hmmer.bean; import org.apache.commons.lang.builder.EqualsBuilder; import org.apache.commons.lang.builder.HashCodeBuilder; import org.apache.commons.lang.builder.ToStringBuilder; import org.apache.commons.lang.builder.ToStringStyle; import com.thoughtworks.xstream.annotations.XStreamAlias; @XStreamAlias("hit") public class DomainHit { @XStreamAlias("model") private String model; @XStreamAlias("index") private Integer index; @XStreamAlias("ndom") private Integer ndom; @XStreamAlias("seq-from") private Integer seqFrom; @XStreamAlias("seq-to") private Integer seqTo; @XStreamAlias("seq-start") private Boolean seqStart; @XStreamAlias("seq-end") private Boolean seqEnd; @XStreamAlias("hmm-from") private Integer hmmFrom; @XStreamAlias("hmm-to") private Integer hmmTo; @XStreamAlias("hmm-start") private Boolean hmmStart; @XStreamAlias("hmm-end") private Boolean hmmEnd; @XStreamAlias("score") private Double score; @XStreamAlias("evalue") private Double evalue; @XStreamAlias("query-seq") private String querySeq; @XStreamAlias("subject-seq") private String subjectSeq; @XStreamAlias("consensus-seq") private String consensusSeq; public DomainHit() { /*...*/} public DomainHit(String model, Integer index, Integer ndom, Integer seqFrom, Integer seqTo, Boolean seqStart, Boolean seqEnd, Integer hmmFrom, Integer hmmTo, Boolean hmmStart, Boolean hmmEnd, Double score, Double evalue) { this.model = model; this.index = index; this.ndom = ndom; this.seqFrom = seqFrom; this.seqTo = seqTo; this.seqStart = seqStart; this.seqEnd = seqEnd; this.hmmFrom = hmmFrom; this.hmmTo = hmmTo; this.hmmStart = hmmStart; this.hmmEnd = hmmEnd; this.score = score; this.evalue = evalue; } @Override public String toString() { return new ToStringBuilder(this, ToStringStyle.MULTI_LINE_STYLE).append("model", getModel()) .append("index", getIndex()).append("ndom", getNdom()).append("seqFrom", getSeqFrom()) .append("seqTo", getSeqTo()).append("seqStart", getSeqStart()).append("seqEnd", getSeqEnd()) .append("hmmFrom", getHmmFrom()).append("hmmTo", getHmmTo()).append("hmmStart", getHmmStart()) .append("hmmEnd", getHmmEnd()).append("score", getScore()).append("evalue", getEvalue()) .append("querySeq", getQuerySeq()).append("subjectSeq", getSubjectSeq()) .append("consensusSeq", getConsensusSeq()).toString(); } @Override public int hashCode() { return new HashCodeBuilder(17, 31).append(getModel()).append(getIndex()).append(getNdom()) .append(getSeqFrom()).append(getSeqTo()).append(getSeqStart()).append(getSeqEnd()) .append(getHmmFrom()).append(getHmmTo()).append(getHmmStart()).append(getHmmEnd()) .append(getScore()).append(getEvalue()).append(getQuerySeq()).append(getSubjectSeq()) .append(getConsensusSeq()).toHashCode(); } @Override public boolean equals(Object obj) { if (obj instanceof DomainHit == false) { return false; } if (obj == this) { return true; } DomainHit rhs = (DomainHit) obj; return new EqualsBuilder().append(getModel(), rhs.getModel()).append(getIndex(), rhs.getIndex()) .append(getNdom(), rhs.getNdom()).append(getSeqFrom(), rhs.getSeqFrom()) .append(getSeqTo(), rhs.getSeqTo()).append(getSeqStart(), rhs.getSeqStart()) .append(getSeqEnd(), rhs.getSeqEnd()).append(getHmmFrom(), rhs.getHmmFrom()) .append(getHmmTo(), rhs.getHmmTo()).append(getHmmStart(), rhs.getHmmStart()) .append(getHmmEnd(), rhs.getHmmEnd()).append(getScore(), rhs.getScore()) .append(getEvalue(), rhs.getEvalue()).append(getQuerySeq(), rhs.getQuerySeq()) .append(getSubjectSeq(), rhs.getSubjectSeq()).append(getConsensusSeq(), rhs.getConsensusSeq()) .isEquals(); } public Double getEvalue() { return evalue; } public void setEvalue(Double evalue) { this.evalue = evalue; } public Integer getHmmFrom() { return hmmFrom; } public void setHmmFrom(Integer hmmFrom) { this.hmmFrom = hmmFrom; } public Integer getHmmTo() { return hmmTo; } public void setHmmTo(Integer hmmTo) { this.hmmTo = hmmTo; } public Integer getIndex() { return index; } public void setIndex(Integer index) { this.index = index; } public String getModel() { return model; } public void setModel(String model) { this.model = model; } public Integer getNdom() { return ndom; } public void setNdom(Integer ndom) { this.ndom = ndom; } public Double getScore() { return score; } public void setScore(Double score) { this.score = score; } public Integer getSeqFrom() { return seqFrom; } public void setSeqFrom(Integer seqFrom) { this.seqFrom = seqFrom; } public Integer getSeqTo() { return seqTo; } public void setSeqTo(Integer seqTo) { this.seqTo = seqTo; } public Boolean getHmmEnd() { return hmmEnd; } public void setHmmEnd(Boolean hmmEnd) { this.hmmEnd = hmmEnd; } public Boolean getHmmStart() { return hmmStart; } public void setHmmStart(Boolean hmmStart) { this.hmmStart = hmmStart; } public Boolean getSeqEnd() { return seqEnd; } public void setSeqEnd(Boolean seqEnd) { this.seqEnd = seqEnd; } public Boolean getSeqStart() { return seqStart; } public void setSeqStart(Boolean seqStart) { this.seqStart = seqStart; } public String getConsensusSeq() { return consensusSeq; } public void setConsensusSeq(String consensusSeq) { this.consensusSeq = consensusSeq; } public String getQuerySeq() { return querySeq; } public void setQuerySeq(String querySeq) { this.querySeq = querySeq; } public String getSubjectSeq() { return subjectSeq; } public void setSubjectSeq(String subjectSeq) { this.subjectSeq = subjectSeq; } }