reagent1[i].getTreatment().add(new Treatment());

Treatment treatment = new Treatment();
treatment.setReagent(reagent1[i]);
reagent1[i].getTreatment().add(treatment);

<ui:repeat value="#{quantExperimentHome.reagent1}" var="info" >
<h:inputText id="pname1" required="true" value="#{info.pname}"/>
   ....
<ui:repeat value="#{info.treatment}" var="itreat">   
<h:inputText id="treatmentCompoundName" value="#{itreat.treatmentCompoundName}"/>
         ......
</ui:repeat>   
<h:commandLink action="#{quantExperimentHome.addTreatmentLink}" 
   value="Add treatments" immediate="true" >
<f:param name="re_hashcode" value="#{info.hashCode()}"/>                                                      </h:commandLink>
</ui:repeat>

@Name("quantExperimentHome")
public class QuantExperimentHome extends EntityHome<QuantExperiment> {

   @In(create = true)
   ProjectHome projectHome;
   
   @Out(required=false)
   @In(required=false)
   TreatmentHome treatmentHome;


   public void setQuantExperimentHjid(Long id) {
      setId(id);
   }

   public Long getQuantExperimentHjid() {
      return (Long) getId();
   }

   @Override
   protected QuantExperiment createInstance() {
      QuantExperiment quantExperiment = new QuantExperiment();
      return quantExperiment;
   }

   public void wire() {
      getInstance();
      Project project = projectHome.getDefinedInstance();
      if (project != null) {
         getInstance().setProject(project);
      }
   }

   public boolean isWired() {
      if (getInstance().getProject() == null)
         return false;
      return true;
   }

   public QuantExperiment getDefinedInstance() {
      return isIdDefined() ? getInstance() : null;
   }

   public List<Reagent> getReagent() {
      return getInstance() == null ? null : new ArrayList<Reagent>(
            getInstance().getReagent());
   }
   
   //CUSTOM FUNCTIONALITY STARTS here
   @Out(required=false)
   @In(required=false)   
    ReagentHome reagentHome=new ReagentHome();
   
   @In(create=true)   
    private FacesMessages facesMessages;

   @In
   private EntityManager entityManager;

    private Reagent[] reagent1=new Reagent[]{new Reagent()};
   
   private Reagent initializeReagent(Reagent re){
      List<Treatment> t=re.getTreatment();
      if(t.size()<1){
         t.add(new Treatment());         
      }
      re.setTreatment(t);
      return re;
   }
   
    public QuantExperimentHome(){
   super();
   Identity.setSecurityEnabled(true);
   for(int i=0;i<reagent1.length;i++){
   reagent1[i]=initializeReagent(reagent1[i]);
   }
   }

      
  public String addTreatmentLink(){
javax.faces.context.FacesContext facesContext = (new org.jboss.seam.faces.FacesContext()).getContext();
javax.servlet.http.HttpServletRequest hsr=(javax.servlet.http.HttpServletRequest)facesContext.getCurrentInstance().getExternalContext().getRequest();
String reagentHashcode=hsr.getParameter("re_hashcode");
for(int i=0;i<reagent1.length;i++){
if(reagent1[i].hashCode()==Integer.parseInt(reagentHashcode)){
   /////////////
   Treatment treatment = new Treatment();
   treatment.setReagent(reagent1[i]);
   reagent1[i].getTreatment().add(treatment);
   ///////////
   //reagent1[i].getTreatment().add(new Treatment());
break;
}
}
return "";   
}   
   
public String persist(){       
java.util.ArrayList<QuantExperiment> arrListQuantExp=new java.util.ArrayList<QuantExperiment>();
QuantExperiment qe=getInstance();      
ArrayList<Reagent> arrListReagent=new ArrayList<Reagent>();            
for(int i=0;i<reagent1.length;i++){      
arrListReagent.add(reagent1[i]);   
}
      
super.persist();
return "";
}
   
  public void editProject(){
    List<Reagent> liRe=getInstance().getReagent();
   reagent1 = new Reagent[liRe.size()];
      
   for(int i=0;i<reagent1.length;i++){
   reagent1[i]=liRe.get(i);
   ReagentHome rh=new ReagentHome();
   rh.setInstance(reagent1[i]);
   rh.treatmentHome=new TreatmentHome();
   rh.treatmentHome.setTreatmentHjid(reagent1[i].getHjid());
   //rh.wire();
   }
  }
   
  private boolean findMatchingReagent(Reagent re){
  boolean bl=false;
  for(int j=0;j<this.reagent1.length;j++){
   if(reagent1[j].getHjid()==re.getHjid()){
   bl=true;
   break;
  }
}
return bl;
}
   
    @Override
    public String update(){            
      QuantExperiment qeUpdate = getInstance();         

      List<Reagent> re=getInstance().getReagent();
      int xs=re.size();
      for(int i=0;i<xs;i++){
         Reagent reg=re.get(i);
         if(!findMatchingReagent(reg)){
            List<Treatment> trs=reg.getTreatment();
            int xt=trs.size();
            for(int k=0;k<xt;k++){
               entityManager.remove(trs.get(k));
            }
            entityManager.remove(reg);
            //rh.remove();
         }else{
            System.out.println(reg.getHjid()+"  has not been removed");
         }
      }
      re.clear();
     
      for(int i=0;i<this.reagent1.length;i++){
         reagent1[i].setLabel(qeUpdate.getQuantitationType());
         reagent1[i].setEntryPoint(reagent1[i].getAffinityCompound());
         re.add(reagent1[i]);
      }
      return super.update();
    }
   
   /**
    * @return the reagent1
    */
   public Reagent[] getReagent1() {
      return reagent1;
   }

   /**
    * @param reagent1 the reagent1 to set
    */
   public void setReagent1(Reagent[] reagent1) {
      this.reagent1 = reagent1;
   }
}

protected List<Treatment> treatment;
@OneToMany(cascade = {CascadeType.ALL}, mappedBy="reagent")
public List<Treatment> getTreatment() {
        if (treatment == null) {
            treatment = new ArrayList<Treatment>();
        }
        return this.treatment;
    }
public void setTreatment(List<Treatment> treatment) {
          for(Treatment t : treatment){
             t.setReagent(this);
          }
           this.treatment = treatment}

public class Treatment impl...{
protected Reagent reagent;
@ManyToOne(optional=false)
   public Reagent getReagent() {
      return reagent;
   }
public void setReagent(Reagent reagent) {
      this.reagent = reagent;
   }