/*
* EuroCarbDB, a framework for carbohydrate bioinformatics
*
* Copyright (c) 2006-2009, Eurocarb project, or third-party contributors as
* indicated by the @author tags or express copyright attribution
* statements applied by the authors.
*
* This copyrighted material is made available to anyone wishing to use, modify,
* copy, or redistribute it subject to the terms and conditions of the GNU
* Lesser General Public License, as published by the Free Software Foundation.
* A copy of this license accompanies this distribution in the file LICENSE.txt.
*
* This program 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 Lesser General Public License
* for more details.
*
* Last commit: $Rev: 1549 $ by $Author: glycoslave $ on $Date:: 2009-07-19 #$
*/
package org.eurocarbdb.action.hplc;
import java.io.*;
import java.util.*;
import java.lang.*;
import org.apache.log4j.Logger;
import org.apache.commons.io.FileUtils;
import org.eurocarbdb.action.*;
import org.eurocarbdb.dataaccess.*;
import org.eurocarbdb.dataaccess.core.*;
import org.eurocarbdb.dataaccess.hplc.*;
import static org.eurocarbdb.dataaccess.Eurocarb.getEntityManager;
import org.eurocarbdb.dataaccess.EntityManager;
import org.hibernate.*;
import org.hibernate.cfg.*;
import org.hibernate.criterion.*;
import com.opensymphony.xwork.Action;
import com.opensymphony.xwork.Preparable;
public class digestAssign extends EurocarbAction {
//SessionFactory sessionFactory = new Configuration().configure().buildSessionFactory();
//Session session =sessionFactory.openSession();
String a1s = "(G.a1 = 1 AND G.s = 1)";
String a1f = "(G.a1 = 1 AND G.f6 =1)";
String a1b = "(G.a1 = 1 AND G.b = 1)";
String a1bgal = "(G.a1 = 1 AND G.bgal = 1)";
String a1agal = "(G.a1 = 1 AND G.agal = 1)";
String a1galnac = "(G.a1 = 1 AND G.galnac = 1)";
String a1polylac = "(G.a1 = 1 AND G.polylac = 1)";
String a1fouterarm = "(G.a1 = 1 AND G.fouterarm = 1)";
String a1hybrid = "(G.a1 = 1 AND G.hybrid = 1)";
String a1mannose = "(G.a1 = 1 AND G.mannose = 1)";
short classA1;
String A1S;
short assignA1S;
short assigna1s = 1;
String A1F;
short assignA1F;
short assigna1f =1;
String A1B;
short assignA1B;
short assigna1b =1;
String A1BGAL;
short assignA1BGAL;
short assigna1bgal;
String A1AGAL;
short assignA1AGAL;
short assigna1agal =1;
String A1GALNAC;
short assignA1GALNAC;
short assigna1galnac =1;
String A1POLYLAC;
short assignA1POLYLAC;
short assigna1polylac =1;
String A1FOUTERARM;
short assignA1FOUTERARM;
short assigna1fouterarm =1;
String A1HYBRID;
short assignA1HYBRID;
short assigna1hybrid =1;
String A1MANNOSE;
short assignA1MANNOSE;
short assigna1mannose =1;
String a2s = "(G.a2 = 1 AND G.s = 1)";
String a2f = "(G.a2 = 1 AND G.f6 =1)";
String a2b = "(G.a2 = 1 AND G.b = 1)";
String a2bgal = "(G.a2 = 1 AND G.bgal = 1)";
String a2agal = "(G.a2 = 1 AND G.agal = 1)";
String a2galnac = "(G.a2 = 1 AND G.galnac = 1)";
String a2polylac = "(G.a2 = 1 AND G.polylac = 1)";
String a2fouterarm = "(G.a2 = 1 AND G.fouterarm = 1)";
String a2hybrid = "(G.a2 = 1 AND G.hybrid = 1)";
String a2mannose = "(G.a2 = 1 AND G.mannose = 1)";
short classA2;
String A2S;
short assignA2S;
short assigna2s = 1;
String A2F;
short assignA2F;
short assigna2f =1;
String A2B;
short assignA2B;
short assigna2b =1;
String A2BGAL;
short assignA2BGAL;
short assigna2bgal;
String A2AGAL;
short assignA2AGAL;
short assigna2agal =1;
String A2GALNAC;
short assignA2GALNAC;
short assigna2galnac =1;
String A2POLYLAC;
short assignA2POLYLAC;
short assigna2polylac =1;
String A2FOUTERARM;
short assignA2FOUTERARM;
short assigna2fouterarm =1;
String A2HYBRID;
short assignA2HYBRID;
short assigna2hybrid =1;
String A2MANNOSE;
short assignA2MANNOSE;
short assigna2mannose =1;
String a3s = "(G.a3 = 1 AND G.s = 1)";
String a3f = "(G.a3 = 1 AND G.f6 =1)";
String a3b = "(G.a3 = 1 AND G.b = 1)";
String a3bgal = "(G.a3 = 1 AND G.bgal = 1)";
String a3agal = "(G.a3 = 1 AND G.agal = 1)";
String a3galnac = "(G.a3 = 1 AND G.galnac = 1)";
String a3polylac = "(G.a3 = 1 AND G.polylac = 1)";
String a3fouterarm = "(G.a3 = 1 AND G.fouterarm = 1)";
String a3hybrid = "(G.a3 =1 AND G.hybrid = 1)";
String a3mannose = "(G.a3 =1 AND G.mannose = 1)";
short classA3;
String A3S;
short assignA3S;
short assigna3s = 1;
String A3F;
short assignA3F;
short assigna3f =1;
String A3B;
short assignA3B;
short assigna3b =1;
String A3BGAL;
short assignA3BGAL;
short assigna3bgal;
String A3AGAL;
short assignA3AGAL;
short assigna3agal =1;
String A3GALNAC;
short assignA3GALNAC;
short assigna3galnac =1;
String A3POLYLAC;
short assignA3POLYLAC;
short assigna3polylac =1;
String A3FOUTERARM;
short assignA3FOUTERARM;
short assigna3fouterarm =1;
String A3HYBRID;
short assignA3HYBRID;
short assigna3hybrid =1;
String A3MANNOSE;
short assignA3MANNOSE;
short assigna3mannose =1;;
String a4s = "(G.a4 = 1 AND G.s = 1)";
String a4f = "(G.a4 = 1 AND G.f6 =1)";
String a4b = "(G.a4 = 1 AND G.b = 1)";
String a4bgal = "(G.a4 = 1 AND G.bgal = 1)";
String a4agal = "(G.a4 = 1 AND G.agal = 1)";
String a4galnac = "(G.a4 = 1 AND G.galnac = 1)";
String a4polylac = "(G.a4 = 1 AND G.polylac = 1)";
String a4fouterarm = "(G.a4 = 1 AND G.fouterarm = 1)";
String a4hybrid = "(G.a4 =1 AND G.hybrid = 1)";
String a4mannose = "(G.a4 =1 AND G.mannose = 1)";
short classA4;
String A4S;
short assignA4S;
short assigna4s = 1;
String A4F;
short assignA4F;
short assigna4f =1;
String A4B;
short assignA4B;
short assigna4b =1;
String A4BGAL;
short assignA4BGAL;
short assigna4bgal;
String A4AGAL;
short assignA4AGAL;
short assigna4agal =1;
String A4GALNAC;
short assignA4GALNAC;
short assigna4galnac =1;
String A4POLYLAC;
short assignA4POLYLAC;
short assigna4polylac =1;
String A4FOUTERARM;
short assignA4FOUTERARM;
short assigna4fouterarm =1;
String A4HYBRID;
short assignA4HYBRID;
short assigna4hybrid =1;
String A4MANNOSE;
short assignA4MANNOSE;
short assigna4mannose =1;
private Profile parent = null;
private Instrument instrument = null;
private DigestProfile digestprofile;
private int instrument_id;
private int profile_id;
private int digest_id;
private String enzyme;
short classType = 1;
private String refineAssignment;
short replaceSearch = 100;
private int delete_entry;
private int criteriaResults;
protected static final Logger logger = Logger.getLogger ( preAssign.class.getName());
private List<Glycan> preliminary; // = new List();
private List<HplcPeaksAnnotated> display;
private List<DigestProfile> preliminaryenz;
private HplcPeaksAnnotated peaksannotated;
private List<HplcPeaksAnnotated> displayDigest;
private List<HplcPeaksAnnotated> showCriteria;
private int refineDigestId;
public String execute() throws Exception {
refineDigestId = digest_id;
if (classA1 == 0) {
classA1 = replaceSearch;
}
if (classA2 == 0) {
classA2 = replaceSearch;
}
if (classA3 == 0) {
classA3 = replaceSearch;
}
if (classA4 == 0) {
classA4 = replaceSearch;
}
if( refineAssignment!=null ) {
SessionFactory sessionFactory = new Configuration().configure().buildSessionFactory();
Session session =sessionFactory.openSession();
logger.info("user whats a refinement displayed");
logger.info("confirm digest id for criteria" + refineDigestId);
Criteria criteria = session.createCriteria(HplcPeaksAnnotated.class);
Disjunction disjunction = Restrictions.disjunction();
ProjectionList proList = Projections.projectionList();
criteria.add(Expression.eq("profileId", profile_id));
criteria.add(Expression.eq("digestId", refineDigestId));
criteria.createAlias("glycan", "G");
proList.add(Projections.property("nameAbbreviation"));
proList.add(Projections.property("gu"));
proList.add(Projections.property("dbGu"));
proList.add(Projections.property("peakArea"));
proList.add(Projections.property("G.ogbitranslation"));
proList.add(Projections.property("hplcPeaksAnnotatedId"));
criteria.setProjection(proList);
if(assignA3S==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a3", classA3),
Expression.eq("G.s", assignA3S)
));
}
if(assignA3F ==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a3", classA3),
Expression.eq("G.f6", assignA3F)
));
logger.info("assigned a3 f");
}
if(assignA3FOUTERARM ==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a3", classA3),
Expression.eq("G.fouterarm", assignA3FOUTERARM)
));
}
if(assignA3B ==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a3", classA3),
Expression.eq("G.b", assignA3B)
));
logger.info("assigned a3 b");
}
if(assignA3BGAL==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a3", classA3),
Expression.eq("G.bgal", assignA3BGAL)
));
}
if(assignA3AGAL==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a3", classA3),
Expression.eq("G.agal", assignA3AGAL)
));
}
if(assignA3GALNAC==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a3", classA3),
Expression.eq("G.galnac", assignA3GALNAC)
));
}
if(assignA3POLYLAC==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a3", classA3),
Expression.eq("G.polylac", assignA3POLYLAC)
));
}
if(assignA3HYBRID==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a3", classA3),
Expression.eq("G.hybrid", assignA3HYBRID)
));
}
if(assignA3MANNOSE==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a3", classA3),
Expression.eq("G.mannose", assignA3MANNOSE)
));
}
if(assignA2S==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a2", classA2),
Expression.eq("G.s", assignA2S)
));
}
if(assignA2F==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a2", classA2),
Expression.eq("G.f6", assignA2F)
));
}
if(assignA2FOUTERARM==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a2", classA2),
Expression.eq("G.fouterarm", assignA2FOUTERARM)
));
}
if(assignA2B==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a2", classA2),
Expression.eq("G.b", assignA2B)
));
}
if(assignA2BGAL==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a2", classA2),
Expression.eq("G.bgal", assignA2BGAL)
));
}
if(assignA2AGAL==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a2", classA2),
Expression.eq("G.agal", assignA2AGAL)
));
}
if(assignA2GALNAC==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a2", classA2),
Expression.eq("G.galnac", assignA2GALNAC)
));
}
if(assignA2POLYLAC==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a2", classA2),
Expression.eq("G.polylac", assignA2POLYLAC)
));
}
if(assignA2HYBRID==1){
disjunction.add(Restrictions.and(
Expression.eq("G.a2", classA2),
Expression.eq("G.hybrid", assignA2HYBRID)
));
}
if(assignA2MANNOSE==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a2", classA2),
Expression.eq("G.mannose", assignA2MANNOSE)
));
}
if(assignA1S==1){
disjunction.add(Restrictions.and(
Expression.eq("G.a1", classA1),
Expression.eq("G.s", assignA1S)
));
}
if(assignA1F==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a1", classA1),
Expression.eq("G.f6", assignA1F)
));
}
if(assignA1FOUTERARM==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a1", classA1),
Expression.eq("G.fouterarm", assignA1FOUTERARM)
));
}
if(assignA1B==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a1", classA1),
Expression.eq("G.b", assignA1B)
));
}
if(assignA1BGAL==1){
disjunction.add(Restrictions.and(
Expression.eq("G.a1", classA1),
Expression.eq("G.bgal", assignA1BGAL)
));
}
if(assignA1AGAL==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a1", classA1),
Expression.eq("G.agal", assignA1AGAL)
));
}
if(assignA1GALNAC==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a1", classA1),
Expression.eq("G.galnac", assignA1GALNAC)
));
}
if(assignA1POLYLAC==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a1", classA1),
Expression.eq("G.polylac", assignA1POLYLAC)
));
}
if(assignA1HYBRID==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a1", classA1),
Expression.eq("G.hybrid", assignA1HYBRID)
));
}
if(assignA1MANNOSE==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a1", classA1),
Expression.eq("G.mannose", assignA1MANNOSE)
));
}
if(assignA4S==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a4", classA4),
Expression.eq("G.s", assignA4S)
));
}
if(assignA4F==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a4", classA4),
Expression.eq("G.f6", assignA4F)
));
}
if(assignA4FOUTERARM==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a4", classA4),
Expression.eq("G.fouterarm", assignA4FOUTERARM)
));
}
if(assignA4B==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a4", classA4),
Expression.eq("G.b", assignA4B)
));
}
if(assignA4BGAL==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a4", classA4),
Expression.eq("G.bgal", assignA4BGAL)
));
}
if(assignA4AGAL==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a4", classA4),
Expression.eq("G.agal", assignA4AGAL)
));
}
if(assignA4GALNAC==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a4", classA4),
Expression.eq("G.galnac", assignA4GALNAC)
));
}
if(assignA4POLYLAC==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a4", classA4),
Expression.eq("G.polylac", assignA4POLYLAC)
));
}
if(assignA4HYBRID==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a4", classA4),
Expression.eq("G.hybrid", assignA4HYBRID)
));
}
if(assignA4MANNOSE==1) {
disjunction.add(Restrictions.and(
Expression.eq("G.a4", classA4),
Expression.eq("G.mannose", assignA4MANNOSE)
));
}
criteria.add(disjunction);
List displayCriteria = criteria.list();
showCriteria = displayCriteria;
int criteriaSelection = showCriteria.size();
logger.info("lets lookup at refinement" + criteriaSelection);
//What if the refinement lists nothing
if (criteriaSelection <= 0) {
logger.info("selection criteria generated no results");
criteriaResults = 0;
List display = getEntityManager().getQuery("org.eurocarbdb.dataaccess.hplc.HplcPeaksAnnotated.DIGEST_DISPLAY")
.setParameter("parent", profile_id)
.setParameter("digest", digest_id)
.list();
displayDigest = display;
}
Iterator iterCrit = showCriteria.iterator();
while (iterCrit.hasNext()) {
Object [] tempcrit = (Object[])iterCrit.next();
String namecrit = (String) tempcrit[0];
}
}
if( refineAssignment==null && delete_entry >0) {
logger.info("record for deleting" + delete_entry);
HplcPeaksAnnotated deletedRecord = HplcPeaksAnnotated.deleteById(delete_entry);
List afterDelete = getEntityManager().getQuery("org.eurocarbdb.dataaccess.hplc.HplcPeaksAnnotated.DIGEST_ASSIGN_DISPLAY")
.setParameter("parent", profile_id)
.setParameter("digest", refineDigestId)
.list();
displayDigest = afterDelete;
}
if( refineAssignment == null && delete_entry == 0) {
File file = new File ("/tmp/digest" + profile_id + digest_id + ".txt");
//Session s = HibernateUtil.getSession();
//Transaction tx = s.beginTransaction();
EntityManager em = getEntityManager();
ArrayList<Double> arrayGu = new ArrayList<Double>();
FileReader input = new FileReader(file);
BufferedReader bufRead = new BufferedReader(input);
String line; // String that holds current file line
int count = 0; // Line number of count
// Read first line
line = bufRead.readLine();
while (line != null){
String rec = line;
String [] gu = rec.split("\t");
double gu_c = Double.parseDouble(gu[1]);
arrayGu.add(gu_c);
double area = Double.parseDouble(gu[0]);
line = bufRead.readLine();
// for (Double gu_value : arrayGu) {
// logger.info("print gu value" + gu_c);
List list = getEntityManager().getQuery("org.eurocarbdb.dataaccess.hplc.Glycan.PRELIM_ASSIGN") .setParameter( "gu_value", gu_c) .list();
preliminary = list;
logger.info("sizeofprel" + preliminary.size());
Iterator iter = preliminary.iterator();
while (iter.hasNext()) {
Glycan temp = (Glycan) iter.next();
//logger.info("print contents" + temp);
peaksannotated = new HplcPeaksAnnotated();
//peaksannotated.setGlycan(temp);
peaksannotated.setPeakArea(area);
peaksannotated.setGu(gu_c);
peaksannotated.setDbGu(temp.getGu());
peaksannotated.setProfileId(profile_id);
peaksannotated.setDigestId(digest_id);
//peaksannotated.setGlycanId(temp.getGlycanId());
//modification to support relationship change
peaksannotated.setGlycan(temp);
peaksannotated.setNameAbbreviation(temp.getName());
//getEntityManager().store(peaksannotated);
//peaksannotated.setContributor(Contributor.getCurrentContributor());
//peaksannotated.setTechnique(Technique.lookupAbbrev("hplc"));
getEntityManager().store(peaksannotated);
logger.info("check storage process");
} //close the iteration over the query result
} // end gu value loop
bufRead.close(); //close the gu file
Profile p = Profile.lookupById(profile_id);
logger.info("themagic is" + p);
DigestProfile dp = new DigestProfile();
dp.setDigestId(digest_id);
dp.setSequentialDigest(enzyme);
dp.setProfile(p);
getEntityManager().store(dp);
int idTest = p.getProfileId();
logger.info("the value of idTest:" + idTest);
//note: due to use of evidenceId relationships the profileId in DIgestProfile is the evidenceId
//to get the corresponfing profileId from Profile use the getProfileId()
//get the enzymes used
logger.info ("check profile id" + profile_id);
logger.info ("check digest id" + digest_id);
List enzymelist = getEntityManager().getQuery("org.eurocarbdb.dataaccess.hplc.DigestProfile.GET_ENZYMES") //.setParameter("parent", parent) .list(); // .setParameter("digest_id", digest_id) .list();
//recurring problem with the use of evidence id
//if use evidence id instead of profile id for HplcPeaks... will cause core probs
.setParameter("parent", p).list();
logger.info ("enzymelist" + enzymelist);
//loop over the enzymes
preliminaryenz = enzymelist;
logger.info("size report" + preliminaryenz.size());
//delete records which have a digest product for that given enzyme
for (Object enzymeused : enzymelist) {
logger.info("loopstufftoheckenz" + enzymeused);
List annolist = getEntityManager().getQuery("org.eurocarbdb.dataaccess.hplc.HplcPeaksAnnotated.ATTEMPT")
.setParameter("parent", profile_id)
.setParameter("digest", digest_id)
.setParameter("enzymeused", enzymeused)
.list();
logger.info("what now");
Iterator iteraa = annolist.iterator();
while (iteraa.hasNext()) {
HplcPeaksAnnotated tempanno = (HplcPeaksAnnotated) iteraa.next();
logger.info ("whatshouldberemoved" + tempanno);
//tx.begin();
//s.delete( tempanno );
Eurocarb.getEntityManager().remove( tempanno);
//tx.commit();
}
}
//preview the results
List display = getEntityManager().getQuery("org.eurocarbdb.dataaccess.hplc.HplcPeaksAnnotated.DIGEST_DISPLAY")
.setParameter("parent", profile_id)
.setParameter("digest", digest_id)
.list();
displayDigest = display;
logger.info(displayDigest.size());
digest_id++;
}
return SUCCESS;
}
//getter and setters
public List<HplcPeaksAnnotated> getQuery() {
return displayDigest;
}
public void setQuery( List<HplcPeaksAnnotated> displayDigest) {
this.displayDigest = displayDigest;
}
public List getDisplayDigest()
{
return this.displayDigest;
}
public List getDisplay()
{
return this.display;
}
/*
public List<Glycan> getQuery() {
return preliminary;
}
public void setQuery( List<Glycan> preliminary) {
this.preliminary = preliminary;
}
public List getPreliminary()
{
return this.preliminary;
}
*/
public Profile getProfile() {
return parent;
}
public void setProfile (Profile parent) {
this.parent = parent;
}
public void setProfileId(int id) {
this.profile_id = id;
}
public int getProfileId() {
return this.profile_id;
}
public void setDigestId(int id) {
this.digest_id = id;
this.refineDigestId = digest_id - 1;
}
public int getDigestId() {
return this.digest_id;
}
public List getShowCriteria()
{
return this.showCriteria;
}
public int getDeleteEntry() {
return this.delete_entry;
}
public void setDeleteEntry(int deleteId){
this.delete_entry = deleteId;
}
public Instrument getInstrument() {
return instrument;
}
public void setInstrument (Instrument instrument) {
this.instrument = instrument;
}
public void setInstrumentId(int id) {
this.instrument_id = id;
}
public int getInstrumentId() {
return this.instrument_id;
}
public void setSequentialDigest(String enzymeused) {
this.enzyme = enzymeused;
}
public String getSequentialDigest() {
return this.enzyme;
}
public String getRefineAssignment() {
return this.refineAssignment;
}
public void setRefineAssignment( String refine) {
this.refineAssignment = refine;
}
public int getRefineDigestId() {
return this.refineDigestId;
}
public void setRefineDigestId ( int digest_id) {
this.refineDigestId = digest_id;
}
public void setCriteriaResults ( int criteriaResults) {
this.criteriaResults = criteriaResults;
}
public int getCriteriaResults() {
return this.criteriaResults;
}
public void setA1s(String tempa1s) {
this.A1S = a1s;
this. assignA1S = assigna1s;
this.classA1 = classType;
}
public void setA1f(String tempa1f) {
this.A1F = a1f;
this. assignA1F = assigna1f;
this.classA1 = classType;
}
public void setA1b(String tempa1b) {
this.A1B = a1b;
this. assignA1B = assigna1b;
this.classA1 = classType;
}
public void setA1bgal(String tempa1bgal) {
this.A1BGAL = a1bgal;
this. assignA1BGAL = assigna1bgal;
this.classA1 = classType;
}
public void setA1agal(String tempa1agal) {
this.A1AGAL = a1agal;
this. assignA1AGAL = assigna1agal;
this.classA1 = classType;
}
public void setA1galnac(String tempa1galnac) {
this.A1GALNAC = a1galnac;
this. assignA1GALNAC = assigna1galnac;
this.classA1 = classType;
}
public void setA1polylac(String tempa1polylac) {
this.A1POLYLAC = a1polylac;
this. assignA1POLYLAC = assigna1polylac;
this.classA1 = classType;
}
public void setA1fouterarm(String tempa1fouterarm) {
this.A1FOUTERARM = a1fouterarm;
this. assignA1FOUTERARM = assigna1fouterarm;
this.classA1 = classType;
}
public void setA1hybrid(String tempa1hybrid) {
this.A1HYBRID = a1hybrid;
this. assignA1HYBRID = assigna1hybrid;
this.classA1 = classType;
}
public void setA1mannose(String tempa1mannose) {
this.A1MANNOSE = a1mannose;
this. assignA1MANNOSE = assigna1mannose;
this.classA1 = classType;
}
public void setA2s(String tempa2s) {
this.A2S = a2s;
this. assignA2S = assigna2s;
this.classA2 = classType;
}
public void setA2f(String tempa2f) {
this.A2F = a2f;
this. assignA2F = assigna2f;
this.classA2 = classType;
}
public void setA2b(String tempa2b) {
this.A2B = a2b;
this. assignA2B = assigna2b;
this.classA2 = classType;
}
public void setA2bgal(String tempa2bgal) {
this.A2BGAL = a2bgal;
this. assignA2BGAL = assigna2bgal;
this.classA2 = classType;
}
public void setA2agal(String tempa2agal) {
this.A2AGAL = a2agal;
this. assignA2AGAL = assigna2agal;
this.classA2 = classType;
}
public void setA2galnac(String tempa2galnac) {
this.A2GALNAC = a2galnac;
this. assignA2GALNAC = assigna2galnac;
this.classA2 = classType;
}
public void setA2polylac(String tempa2polylac) {
this.A2POLYLAC = a2polylac;
this. assignA2POLYLAC = assigna2polylac;
this.classA2 = classType;
}
public void setA2fouterarm(String tempa2fouterarm) {
this.A2FOUTERARM = a2fouterarm;
this. assignA2FOUTERARM = assigna2fouterarm;
this.classA2 = classType;
}
public void setA2hybrid(String tempa2hybrid) {
this.A2HYBRID = a2hybrid;
this. assignA2HYBRID = assigna2hybrid;
this.classA2 = classType;
}
public void setA2mannose(String tempa2mannose) {
this.A2MANNOSE = a2mannose;
this. assignA2MANNOSE = assigna2mannose;
this.classA2 = classType;
}
public void setA3s(String tempa3s) {
this.A3S = a3s;
this. assignA3S = assigna3s;
this.classA3 = classType;
}
public void setA3f(String tempa3f) {
this.A3F = a3f;
this. assignA3F = assigna3f;
this.classA3 = classType;
}
public void setA3b(String tempa3b) {
this.A3B = a3b;
this. assignA3B = assigna3b;
this.classA3 = classType;
}
public void setA3bgal(String tempa3bgal) {
this.A3BGAL = a3bgal;
this. assignA3BGAL = assigna3bgal;
this.classA3 = classType;
}
public void setA3agal(String tempa3agal) {
this.A3AGAL = a3agal;
this. assignA3AGAL = assigna3agal;
this.classA3 = classType;
}
public void setA3galnac(String tempa3galnac) {
this.A3GALNAC = a3galnac;
this. assignA3GALNAC = assigna3galnac;
this.classA3 = classType;
}
public void setA3polylac(String tempa3polylac) {
this.A3POLYLAC = a3polylac;
this. assignA3POLYLAC = assigna3polylac;
this.classA3 = classType;
}
public void setA3fouterarm(String tempa3fouterarm) {
this.A3FOUTERARM = a3fouterarm;
this. assignA3FOUTERARM = assigna3fouterarm;
this.classA3 = classType;
}
public void setA3hybrid(String tempa3hybrid) {
this.A3HYBRID = a3hybrid;
this. assignA3HYBRID = assigna3hybrid;
this.classA3 = classType;
}
public void setA3mannose(String tempa3mannose) {
this.A3MANNOSE = a3mannose;
this. assignA3MANNOSE = assigna3mannose;
this.classA3 = classType;
}
public void setA4s(String tempa4s) {
this.A4S = a4s;
this. assignA4S = assigna4s;
this.classA4 = classType;
}
public void setA4f(String tempa4f) {
this.A4F = a4f;
this. assignA4F = assigna4f;
this.classA4 = classType;
}
public void setA4b(String tempa4b) {
this.A4B = a4b;
this. assignA4B = assigna4b;
this.classA4 = classType;
}
public void setA4bgal(String tempa4bgal) {
this.A4BGAL = a4bgal;
this. assignA4BGAL = assigna4bgal;
this.classA4 = classType;
}
public void setA4agal(String tempa4agal) {
this.A4AGAL = a4agal;
this. assignA4AGAL = assigna4agal;
this.classA4 = classType;
}
public void setA4galnac(String tempa4galnac) {
this.A4GALNAC = a4galnac;
this. assignA4GALNAC = assigna4galnac;
this.classA4 = classType;
}
public void setA4polylac(String tempa4polylac) {
this.A4POLYLAC = a4polylac;
this. assignA4POLYLAC = assigna4polylac;
this.classA4 = classType;
}
public void setA4fouterarm(String tempa4fouterarm) {
this.A4FOUTERARM = a4fouterarm;
this. assignA4FOUTERARM = assigna2fouterarm;
this.classA4 = classType;
}
public void setA4hybrid(String tempa4hybrid) {
this.A4HYBRID = a4hybrid;
this. assignA4HYBRID = assigna4hybrid;
this.classA4 = classType;
}
public void setA4mannose(String tempa4mannose) {
this.A4MANNOSE = a4mannose;
this. assignA2MANNOSE = assigna2mannose;
this.classA4 = classType;
}
}