Java tutorial
/* * 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 java.math.*; import org.apache.log4j.Logger; import org.apache.commons.io.FileUtils; import org.eurocarbdb.action.*; import org.hibernate.*; import org.hibernate.cfg.*; import org.hibernate.criterion.*; import org.eurocarbdb.dataaccess.EntityManager; import org.eurocarbdb.dataaccess.hplc.*; import static org.eurocarbdb.dataaccess.Eurocarb.getEntityManager; public class preAssign extends BrowseAction<Glycan> { EntityManager em = getEntityManager(); //string required for refining displayed glycans 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 int instrument_id; private int profile_id; private int delete_entry; private String imageStyle; protected static final Logger logger = Logger.getLogger(preAssign.class.getName()); private List<Glycan> preliminary; private List<HplcPeaksAnnotated> display; // = new List(); private List<HplcPeaksAnnotated> prelimarytwo; private List<HplcPeaksAnnotated> showCriteria; private HplcPeaksAnnotated peaksannotated; int digest_id = 0; short classType = 1; short replaceSearch = 100; private String refineAssignment; public String execute() throws Exception { logger.info("before zeros" + classA3); if (classA1 == 0) { classA1 = replaceSearch; } if (classA2 == 0) { classA2 = replaceSearch; } if (classA3 == 0) { classA3 = replaceSearch; } if (classA4 == 0) { classA4 = replaceSearch; } logger.info("some zeros" + classA1 + classA2 + classA3 + classA4); if (refineAssignment != null) { logger.info("user whats a refinement displayed"); logger.info("was a2f assigned = " + assignA2F + "ws a2 class done" + classA2 + "just to insure" + assignA4F); String queryRefine = A2S + A2F + A2B + A2BGAL + A2AGAL + A2GALNAC + A2POLYLAC + A2FOUTERARM + A2HYBRID + A2MANNOSE + A1B + A1BGAL + A1AGAL + A1GALNAC + A1POLYLAC + A1FOUTERARM + A1HYBRID + A1MANNOSE + A1S + A1F + A3S + A3F + A3B + A3BGAL + A3AGAL + A3GALNAC + A3POLYLAC + A3FOUTERARM + A3HYBRID + A3MANNOSE + A4S + A4F + A4B + A4BGAL + A4AGAL + A4GALNAC + A4POLYLAC + A4FOUTERARM + A4HYBRID + A4MANNOSE; String queryReplace = queryRefine.replaceAll("null", ""); String queryAnd = queryReplace.replaceAll("\\)\\(", ") OR ("); logger.info("query string again:" + queryAnd); int len = queryAnd.length(); //String queryRefineComplete = "SELECT HP.glycan, HP.peakArea, HP.gu, HP.dbGu, HP.nameAbbreviation, (select g.ogbitranslation from Glycan g where g.glycanId = HP.glycan) as ogbitranslation from HplcPeaksAnnotated HP where HP.profileId = " + profile_id + " and HP.digestId = 0 and HP.glycan IN (SELECT G.glycanId from Glycan G WHERE " + queryAnd + " and G.glycanId = HP.glycan) ORDER BY HP.gu"; String queryRefineComplete = "from HplcPeaksAnnotated HP join HP.glycan G where HP.profileId = 46 and " + queryAnd + " order by HP.gu"; logger.info("check new query" + queryRefineComplete); SessionFactory sessionFactory = new Configuration().configure().buildSessionFactory(); Session session = sessionFactory.openSession(); Query query = session.createQuery(queryRefineComplete); List<HplcPeaksAnnotated> display = query.list(); //display = query.list(); //prelimarytwo = display; int tempint = 1140; int tempprofile = 48; short tempintr = 1; /*Disjunction disc = Expression.disjunction(); */ /*List displaytest = session.createCriteria(HplcPeaksAnnotated.class) .createAlias("glycan", "G") .add( Expression.eq("profileId", tempprofile)) .add(Restrictions.and( Expression.eq("G.a3", classA3), Expression.eq("G.s", assignA3S) )) .add(Restrictions.and( Expression.eq("G.a3", classA3), Expression.eq("G.f6", assignA3F) ))//.add ( Expression.eq("G.glycanId", tempint)) .add(Expression.or( Expression.eq("G.a1", classA1), Expression.eq("G.s", assignA1S) )) .add(Expression.or( Expression.eq("G.a2", classA2), Expression.eq("G.s", assignA2S) )) .add(Expression.or( Expression.and( Expression.eq("G.a3", classA3), Expression.eq("G.s", assignA3S) ) .add(Expression.and( Expression.eq("G.a3", classA3), Expression.eq("G.f6", assignA3F) )) )) .add(Expression.or( Expression.eq("G.a4", classA4), Expression.eq("G.s", assignA4S) )) //.AddOrder( Order.Asc("gu") ) // .list(); */ logger.info("variables check" + classA3 + "core f" + assignA3F + "s" + assignA3S); Criteria criteria = session.createCriteria(HplcPeaksAnnotated.class); Disjunction disjunction = Restrictions.disjunction(); ProjectionList proList = Projections.projectionList(); criteria.add(Expression.eq("profileId", profile_id)); 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"); display = getEntityManager() .getQuery("org.eurocarbdb.dataaccess.hplc.HplcPeaksAnnotated.PRE_ASSIGN_DISPLAY") .setParameter("parent", profile_id).list(); prelimarytwo = display; } Iterator iterCrit = showCriteria.iterator(); while (iterCrit.hasNext()) { Object[] tempcrit = (Object[]) iterCrit.next(); String namecrit = (String) tempcrit[0]; logger.info("here" + namecrit); } } //test deleting records 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.PRE_ASSIGN_DISPLAY") .setParameter("parent", profile_id).list(); prelimarytwo = afterDelete; } if (refineAssignment == null && delete_entry == 0) { logger.info("i shouldnt be seeing this message"); File file = new File("/tmp/undigested" + profile_id + ".txt"); 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]); double area = Double.parseDouble(gu[0]); arrayGu.add(gu_c); line = bufRead.readLine(); // } // for (Double gu_value : arrayGu) { // logger.info("the value is" + gu_value); List list = getEntityManager().getQuery("org.eurocarbdb.dataaccess.hplc.Glycan.PRELIM_ASSIGN") .setParameter("gu_value", gu_c).list(); preliminary = list; // logger.info("gu value print" + gu_value); logger.info(preliminary.size()); Iterator iter = preliminary.iterator(); while (iter.hasNext()) { Glycan temp = (Glycan) iter.next(); peaksannotated = new HplcPeaksAnnotated(); //peaksannotated.setGlycan(temp); // peaksannotated.setGu(gu_value); peaksannotated.setPeakArea(area); peaksannotated.setGu(gu_c); peaksannotated.setDbGu(temp.getGu()); peaksannotated.setProfileId(profile_id); peaksannotated.setGlycan(temp); peaksannotated.setNameAbbreviation(temp.getName()); peaksannotated.setDigestId(digest_id); //peaksannotated.setContributor(Contributor.getCurrentContributor()); //peaksannotated.setTechnique(Technique.lookupAbbrev("hplc")); getEntityManager().store(peaksannotated); } } bufRead.close(); /* test ArrayList <Double> test = new ArrayList(); test.addAll(arrayGu); for (Double testing : test) {} */ //need to do a query to grap inserted data above for displaying to user //logger.info("check the profile id number here:" + profile_id); display = getEntityManager() .getQuery("org.eurocarbdb.dataaccess.hplc.HplcPeaksAnnotated.PRE_ASSIGN_DISPLAY") .setParameter("parent", profile_id).list(); prelimarytwo = display; logger.info(prelimarytwo.size()); } return SUCCESS; } //getter and setters /* public List<Glycan> getQuery() { return preliminary; } public void setQuery( List<Glycan> preliminary) { this.preliminary = preliminary; } public List getPreliminary() { return this.preliminary; } */ public List<HplcPeaksAnnotated> getQuery() { return prelimarytwo; } public void setQuery(List<HplcPeaksAnnotated> prelimarytwo) { this.prelimarytwo = prelimarytwo; } public List getPrelimarytwo() { return this.prelimarytwo; } public List getShowCriteria() { return this.showCriteria; } public List getDisplay() { return this.display; } public int getDeleteEntry() { return this.delete_entry; } public void setDeleteEntry(int deleteId) { this.delete_entry = deleteId; } 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 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 String getImageStyle() { return this.imageStyle; } public void setImageStyle(String pic_image_style) { this.imageStyle = pic_image_style; } public String getRefineAssignment() { return this.refineAssignment; } public void setRefineAssignment(String refine) { this.refineAssignment = refine; } 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; } public final Class<Glycan> getIndexableType() { return Glycan.class; } }