/*
 $Id: OMSSAParameterSet.java 3207 2009-04-09 06:48:11Z gregory $

 Copyright (C) 2008 Gregory Vincic, Olle Mansson

 Files are copyright by their respective authors. The contributions to
 files where copyright is not explicitly stated can be traced with the
 source code revision system.

 This file is part of Proteios.
 Available at http://www.proteios.org/

 Proteios-2.x 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 2
 of the License, or (at your option) any later version.

 Proteios 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 this program; if not, write to the Free Software
 Foundation, Inc., 59 Temple Place - Suite 330,
 Boston, MA  02111-1307, USA.
 */
package org.proteios.io;


/**
 * This file API should be used to get parameter data from OMSSA input files.
 * 
 * @author olle
 */
public class OMSSAParameterSet
{
        private String species = null;
        private String searchSpectrumType = null;
        private String precursorSearchType = null;
        private String productSearchType = null;
        private String ionsToSearch1 = null;
        private String ionsToSearch2 = null;
        private String pepTol = null;
        private String msMsTol = null;
        private String zDep = null;
        private String cutoff = null;
        private String cutLo = null;
        private String cutHi = null;
        private String cutInc = null;
        private String singleWin = null;
        private String doubleWin = null;
        private String singleNum = null;
        private String doubleNum = null;
        private String fixed = null;
        private String variable = null;
        private String enzyme = null;
        private String missedCleave = null;
        private String hitListLen = null;
        private String db = null;
        private String topHitNum = null;
        private String minHit = null;
        private String minSpectra = null;
        private String scale = null;
        private String maxMods = null;
        private String msCalcPlusOne = null;
        private String msCalcCharge = null;
        private String minCharge = null;
        private String maxCharge = null;
        private String considerMult = null;
        private String plusOne = null;
        private String maxProductCharge = null;
        private String pseudoCount = null;
        private String searchB1 = null;
        private String searchCTermProduct = null;
        private String maxProductions = null;
        private String minNoEnzyme = null;
        private String maxNoEnzyme = null;
        private String exactMass = null;
        private String settingId = null;
        private String researchThresh = null;
        private String subsetThresh = null;
        private String replaceThresh = null;
        private String precursorCull = null;
        private String noCorrelationScore = null;
        private String probFollowingIon = null;
        private String nMethionineAttribute = null;
        private String autoMassAdjust = null;

        /**
         * @return String search species.
         */
        public String getSpecies()
        {
                return species;
        }


        /**
         * @param species String.
         */
        public void setSpecies(String species)
        {
                this.species = species;
        }


        /**
         * @return String search spectrum type (iontrap or etd).
         */
        public String getSearchSpectrumType()
        {
                return searchSpectrumType;
        }


        /**
         * @param searchSpectrumType String search spectrum type (iontrap or etd).
         */
        public void setSearchSpectrumType(String searchSpectrumType)
        {
                this.searchSpectrumType = searchSpectrumType;
        }


        /**
         * @return String precursor search type.
         */
        public String getPrecursorSearchType()
        {
                return precursorSearchType;
        }


        /**
         * @param precursorSearchType String precursor search type.
         */
        public void setPrecursorSearchType(String precursorSearchType)
        {
                this.precursorSearchType = precursorSearchType;
        }


        /**
         * @return String product search type.
         */
        public String getProductSearchType()
        {
                return productSearchType;
        }


        /**
         * @param productSearchType String product search type.
         */
        public void setProductSearchType(String productSearchType)
        {
                this.productSearchType = productSearchType;
        }


        /**
         * @return String ions to search 1.
         */
        public String getIonsToSearch1()
        {
                return ionsToSearch1;
        }


        /**
         * @param ionsToSearch1 String ions to search 1.
         */
        public void setIonsToSearch1(String ionsToSearch1)
        {
                this.ionsToSearch1 = ionsToSearch1;
        }


        /**
         * @return String ions to search 2.
         */
        public String getIonsToSearch2()
        {
                return ionsToSearch2;
        }


        /**
         * @param ionsToSearch2 String ions to search 2.
         */
        public void setIonsToSearch2(String ionsToSearch2)
        {
                this.ionsToSearch2 = ionsToSearch2;
        }


        /**
         * Precursor mass tolerance (Da).
         * 
         * @return String peptide tolerance.
         */
        public String getPepTol()
        {
                return pepTol;
        }
        
        
        /**
         * Precursor mass tolerance (Da).
         * 
         * @param pepTol String peptide tolerance.
         */
        public void setPepTol(String pepTol)
        {
                this.pepTol = pepTol;
        }
        
        
        /**
         * Product mass tolerance (Da).
         * 
         * @return String ms-ms tolerance.
         */
        public String getMsMsTol()
        {
                return msMsTol;
        }
        
        
        /**
         * Product mass tolerance (Da).
         * 
         * @param msMsTol String ms-ms tolerance.
         */
        public void setMsMsTol(String msMsTol)
        {
                this.msMsTol = msMsTol;
        }
        
        
        /**
         * @return String z-dep.
         */
        public String getZDep()
        {
                return zDep;
        }
        
        
        /**
         * @param zDep String z-dep.
         */
        public void setZDep(String zDep)
        {
                this.zDep = zDep;
        }
        
        
        /**
         * @return String cutoff.
         */
        public String getCutoff()
        {
                return cutoff;
        }
        
        
        /**
         * @param cutoff String cutoff.
         */
        public void setCutoff(String cutoff)
        {
                this.cutoff = cutoff;
        }
        
        
        /**
         * Peak low intensity cutoff (fraction of most intense)
         * 
         * @return String cut low.
         */
        public String getCutLo()
        {
                return cutLo;
        }
        
        
        /**
         * Peak low intensity cutoff (fraction of most intense)
         * 
         * @param cutLo String cut low.
         */
        public void setCutLo(String cutLo)
        {
                this.cutLo = cutLo;
        }
        
        
        /**
         * Peak high intensity cutoff (fraction of most intense)
         * 
         * @return String cut high.
         */
        public String getCutHi()
        {
                return cutHi;
        }
        
        
        /**
         * Peak high intensity cutoff (fraction of most intense)
         * 
         * @param cutHi String cutHi.
         */
        public void setCutHi(String cutHi)
        {
                this.cutHi = cutHi;
        }
        
        
        /**
         * @return String cut inc.
         */
        public String getCutInc()
        {
                return cutInc;
        }
        
        
        /**
         * @param cutInc String cut inc.
         */
        public void setCutInc(String cutInc)
        {
                this.cutInc = cutInc;
        }
        
        
        /**
         * @return String single window.
         */
        public String getSingleWin()
        {
                return singleWin;
        }


        /**
         * @param singleWin String single window.
         */
        public void setSingleWin(String singleWin)
        {
                this.singleWin = singleWin;
        }


        /**
         * @return String double window.
         */
        public String getDoubleWin()
        {
                return doubleWin;
        }


        /**
         * @param doubleWin String double window.
         */
        public void setDoubleWin(String doubleWin)
        {
                this.doubleWin = doubleWin;
        }


        /**
         * @return String single number.
         */
        public String getSingleNum()
        {
                return singleNum;
        }


        /**
         * @param singleNum String single number.
         */
        public void setSingleNum(String singleNum)
        {
                this.singleNum = singleNum;
        }


        /**
         * @return String double number.
         */
        public String getDoubleNum()
        {
                return doubleNum;
        }


        /**
         * @param doubleNum String double number.
         */
        public void setDoubleNum(String doubleNum)
        {
                this.doubleNum = doubleNum;
        }


        /**
         * @return String fixed.
         */
        public String getFixed()
        {
                return fixed;
        }


        /**
         * @param fixed String fixed.
         */
        public void setFixed(String fixed)
        {
                this.fixed = fixed;
        }


        /**
         * @return String variable.
         */
        public String getVariable()
        {
                return variable;
        }


        /**
         * @param variable String variable.
         */
        public void setVariable(String variable)
        {
                this.variable = variable;
        }


        /**
         * @return String enzyme.
         */
        public String getEnzyme()
        {
                return enzyme;
        }


        /**
         * @param enzyme String enzyme.
         */
        public void setEnzyme(String enzyme)
        {
                this.enzyme = enzyme;
        }


        /**
         * @return String missed cleavages.
         */
        public String getMissedCleave()
        {
                return missedCleave;
        }


        /**
         * @param missedCleave String missed cleavages.
         */
        public void setMissedCleave(String missedCleave)
        {
                this.missedCleave = missedCleave;
        }


        /**
         * @return String hit list length.
         */
        public String getHitListLen()
        {
                return hitListLen;
        }


        /**
         * @param hitListLen String hit list length.
         */
        public void setHitListLen(String hitListLen)
        {
                this.hitListLen = hitListLen;
        }


        /**
         * @return String db.
         */
        public String getDb()
        {
                return db;
        }


        /**
         * @param db String db.
         */
        public void setDb(String db)
        {
                this.db = db;
        }


        /**
         * Number of top intensity peaks in first pass
         * 
         * @return String top hit number.
         */
        public String getTopHitNum()
        {
                return topHitNum;
        }


        /**
         * Number of top intensity peaks in first pass
         * 
         * @param topHitNum String top hit number.
         */
        public void setTopHitNum(String topHitNum)
        {
                this.topHitNum = topHitNum;
        }


        /**
         * @return String minHit.
         */
        public String getMinHit()
        {
                return minHit;
        }


        /**
         * @param minHit String minHit.
         */
        public void setMinHit(String minHit)
        {
                this.minHit = minHit;
        }


        /**
         * @return String minSpectra.
         */
        public String getMinSpectra()
        {
                return minSpectra;
        }


        /**
         * @param minSpectra String minSpectra.
         */
        public void setMinSpectra(String minSpectra)
        {
                this.minSpectra = minSpectra;
        }


        /**
         * @return String scale.
         */
        public String getScale()
        {
                return scale;
        }


        /**
         * @param scale String scale.
         */
        public void setScale(String scale)
        {
                this.scale = scale;
        }


        /**
         * @return String max modifications.
         */
        public String getMaxMods()
        {
                return maxMods;
        }


        /**
         * @param maxMods String max modifications.
         */
        public void setMaxMods(String maxMods)
        {
                this.maxMods = maxMods;
        }


        /**
         * @return String msCalcPlusOne.
         */
        public String getMsCalcPlusOne()
        {
                return msCalcPlusOne;
        }


        /**
         * @param msCalcPlusOne String msCalcPlusOne.
         */
        public void setMsCalcPlusOne(String msCalcPlusOne)
        {
                this.msCalcPlusOne = msCalcPlusOne;
        }


        /**
         * @return String msCalcCharge.
         */
        public String getMsCalcCharge()
        {
                return msCalcCharge;
        }


        /**
         * @param msCalcCharge String msCalcCharge.
         */
        public void setMsCalcCharge(String msCalcCharge)
        {
                this.msCalcCharge = msCalcCharge;
        }


        /**
         * Lower bound of precursor charge
         * 
         * @return String min charge.
         */
        public String getMinCharge()
        {
                return minCharge;
        }


        /**
         * Lower bound of precursor charge
         * 
         * @param minCharge String min charge.
         */
        public void setMinCharge(String minCharge)
        {
                this.minCharge = minCharge;
        }


        /**
         * Upper bound of precursor charge
         * 
         * @return String max charge.
         */
        public String getMaxCharge()
        {
                return maxCharge;
        }


        /**
         * Upper bound of precursor charge
         * 
         * @param maxCharge String max charge.
         */
        public void setMaxCharge(String maxCharge)
        {
                this.maxCharge = maxCharge;
        }


        /**
         * Minimum charge to start using multiply charged products
         * 
         * @return String considerMult.
         */
        public String getConsiderMult()
        {
                return considerMult;
        }


        /**
         * Minimum charge to start using multiply charged products
         * 
         * @param considerMult String considerMult.
         */
        public void setConsiderMult(String considerMult)
        {
                this.considerMult = considerMult;
        }


        /**
         * Fraction of product peaks below precursor to determine +1 precursor
         * 
         * @return String plusOne.
         */
        public String getPlusOne()
        {
                return plusOne;
        }


        /**
         * Fraction of product peaks below precursor to determine +1 precursor
         * 
         * @param plusOne String plusOne.
         */
        public void setPlusOne(String plusOne)
        {
                this.plusOne = plusOne;
        }


        /**
         * @return String max product charge.
         */
        public String getMaxProductCharge()
        {
                return maxProductCharge;
        }


        /**
         * @param maxProductCharge String max product charge.
         */
        public void setMaxProductCharge(String maxProductCharge)
        {
                this.maxProductCharge = maxProductCharge;
        }


        /**
         * @return String pseudo count.
         */
        public String getPseudoCount()
        {
                return pseudoCount;
        }


        /**
         * @param pseudoCount String pseudo count.
         */
        public void setPseudoCount(String pseudoCount)
        {
                this.pseudoCount = pseudoCount;
        }


        /**
         * @return String search b1.
         */
        public String getSearchB1()
        {
                return searchB1;
        }


        /**
         * @param searchB1 String search b1.
         */
        public void setSearchB1(String searchB1)
        {
                this.searchB1 = searchB1;
        }


        /**
         * @return String search C term product.
         */
        public String getSearchCTermProduct()
        {
                return searchCTermProduct;
        }


        /**
         * @param searchCTermProduct String search C term product.
         */
        public void setSearchCTermProduct(String searchCTermProduct)
        {
                this.searchCTermProduct = searchCTermProduct;
        }


        /**
         * @return String max productions.
         */
        public String getMaxProductions()
        {
                return maxProductions;
        }


        /**
         * @param maxProductions String max productions.
         */
        public void setMaxProductions(String maxProductions)
        {
                this.maxProductions = maxProductions;
        }


        /**
         * @return String min number of enzymes.
         */
        public String getMinNoEnzyme()
        {
                return minNoEnzyme;
        }


        /**
         * @param minNoEnzyme String min number of enzymes.
         */
        public void setMinNoEnzyme(String minNoEnzyme)
        {
                this.minNoEnzyme = minNoEnzyme;
        }


        /**
         * @return String max number of enzymes.
         */
        public String getMaxNoEnzyme()
        {
                return maxNoEnzyme;
        }


        /**
         * @param maxNoEnzyme String max number of enzymes.
         */
        public void setMaxNoEnzyme(String maxNoEnzyme)
        {
                this.maxNoEnzyme = maxNoEnzyme;
        }


        /**
         * @return String exact mass.
         */
        public String getExactMass()
        {
                return exactMass;
        }


        /**
         * @param exactMass String exact mass.
         */
        public void setExactMass(String exactMass)
        {
                this.exactMass = exactMass;
        }


        /**
         * @return String setting id.
         */
        public String getSettingId()
        {
                return settingId;
        }


        /**
         * @param settingId String setting id.
         */
        public void setSettingId(String settingId)
        {
                this.settingId = settingId;
        }


        /**
         * @return String research threshold.
         */
        public String getResearchThresh()
        {
                return researchThresh;
        }


        /**
         * @param researchThresh String research threshold.
         */
        public void setResearchThresh(String researchThresh)
        {
                this.researchThresh = researchThresh;
        }


        /**
         * @return String subset threshold.
         */
        public String getSubsetThresh()
        {
                return subsetThresh;
        }


        /**
         * @param subsetThresh String subset threshold.
         */
        public void setSubsetThresh(String subsetThresh)
        {
                this.subsetThresh = subsetThresh;
        }


        /**
         * @return String replace threshold.
         */
        public String getReplaceThresh()
        {
                return replaceThresh;
        }


        /**
         * @param replaceThresh String replace threshold.
         */
        public void setReplaceThresh(String replaceThresh)
        {
                this.replaceThresh = replaceThresh;
        }


        /**
         * @return String precursor cull.
         */
        public String getPrecursorCull()
        {
                return precursorCull;
        }


        /**
         * @param precursorCull String precursor cull.
         */
        public void setPrecursorCull(String precursorCull)
        {
                this.precursorCull = precursorCull;
        }


        /**
         * @return String noCorrelationScore.
         */
        public String getNoCorrelationScore()
        {
                return noCorrelationScore;
        }


        /**
         * @param noCorrelationScore String noCorrelationScore.
         */
        public void setNoCorrelationScore(String noCorrelationScore)
        {
                this.noCorrelationScore = noCorrelationScore;
        }


        /**
         * @return String probFollowingIon.
         */
        public String getProbFollowingIon()
        {
                return probFollowingIon;
        }


        /**
         * @param probFollowingIon String probFollowingIon.
         */
        public void setProbFollowingIon(String probFollowingIon)
        {
                this.probFollowingIon = probFollowingIon;
        }


        /**
         * @return String nMethionine.
         */
        public String getNMethionineAttribute()
        {
                return nMethionineAttribute;
        }


        /**
         * @param nMethionineAttribute String nMethionineAttribute.
         */
        public void setNMethionineAttribute(String nMethionineAttribute)
        {
                this.nMethionineAttribute = nMethionineAttribute;
        }


        /**
         * @return String auto mass adjustment.
         */
        public String getAutoMassAdjust()
        {
                return autoMassAdjust;
        }


        /**
         * @param autoMassAdjust String auto mass adjustment.
         */
        public void setAutoMassAdjust(String autoMassAdjust)
        {
                this.autoMassAdjust = autoMassAdjust;
        }
}