package org.molgenis.mutation.ui.search;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import org.molgenis.framework.ui.EasyPluginModel;
import org.molgenis.mutation.MutationGene;
import org.molgenis.mutation.ui.LimitOffsetPager;
import org.molgenis.mutation.ui.search.form.DisplayOptionsForm;
import org.molgenis.mutation.ui.search.form.ExpertSearchForm;
import org.molgenis.mutation.ui.search.form.ListAllMutationsForm;
import org.molgenis.mutation.ui.search.form.ListAllPatientsForm;
import org.molgenis.mutation.ui.search.form.ShowMutationForm;
import org.molgenis.mutation.ui.search.form.SimpleSearchForm;
import org.molgenis.mutation.ui.search.form.ToExpertSearchForm;
import org.molgenis.mutation.ui.search.form.ToSimpleSearchForm;
import org.molgenis.mutation.vo.ExonSearchCriteriaVO;
import org.molgenis.mutation.vo.ExonSummaryVO;
import org.molgenis.mutation.vo.MBrowseVO;
import org.molgenis.mutation.vo.MutationSearchCriteriaVO;
import org.molgenis.mutation.vo.MutationSummaryVO;
import org.molgenis.mutation.vo.PatientSearchCriteriaVO;
import org.molgenis.mutation.vo.PatientSummaryVO;
import org.molgenis.mutation.vo.PhenotypeDetailsVO;
import org.molgenis.mutation.vo.ProteinDomainSummaryVO;
import org.molgenis.mutation.vo.QueryParametersVO;
import org.molgenis.news.MolgenisNews;
public class SearchModel extends EasyPluginModel
{
private static final long serialVersionUID = 1L;
private String geneName;
private String patientPager;
private String mutationPager;
private String patientViewer;
private String action = "init";
private String result = "mutations"; // Initially search/display mutations
private String header;
private int numPatients;
private int numUnpublished;
private int numMutations;
private SimpleSearchForm simpleSearchForm = new SimpleSearchForm();
private ListAllMutationsForm listAllMutationsForm = new ListAllMutationsForm();
private ListAllPatientsForm listAllPatientsForm = new ListAllPatientsForm();
private ToExpertSearchForm toExpertSearchForm = new ToExpertSearchForm();
private ToSimpleSearchForm toSimpleSearchForm = new ToSimpleSearchForm();
private ExpertSearchForm expertSearchForm = new ExpertSearchForm();
private ShowMutationForm showMutationForm = new ShowMutationForm();
private DisplayOptionsForm displayOptionsForm = new DisplayOptionsForm();
private ExonSearchCriteriaVO exonSearchCriteriaVO = new ExonSearchCriteriaVO();
private MutationSearchCriteriaVO mutationSearchCriteriaVO = new MutationSearchCriteriaVO();
private PatientSearchCriteriaVO patientSearchCriteriaVO = new PatientSearchCriteriaVO();
private QueryParametersVO queryParametersVO = new QueryParametersVO();
private MutationGene gene;
private ExonSummaryVO exonSummaryVO;
private MutationSummaryVO mutationSummaryVO;
private List<MutationSummaryVO> mutationSummaryVOs = new ArrayList<MutationSummaryVO>();
private HashMap<String, String> mutationSummaryVOHash;
private List<PatientSummaryVO> patientSummaryVOs = new ArrayList<PatientSummaryVO>();
private ProteinDomainSummaryVO proteinDomainSummaryVO;
private List<ProteinDomainSummaryVO> proteinDomainList;
private PatientSummaryVO patientSummaryVO;
// private List<PatientDetailsVO> patientDetailsVO;
private PhenotypeDetailsVO phenotypeDetailsVO;
private HashMap<String, String> patientSummaryVOHash;
private String rawOutput; // for output from included sources
private List<MolgenisNews> news;
private LimitOffsetPager<?> pager;
private MBrowseVO mBrowseVO = new MBrowseVO();
private String textWelcome = "";
private String textSearch = "";
private String textRemarks = "";
private String textCollaborations = "";
private List<MutationSummaryVO> positionMutations;
private List<MutationSummaryVO> codonMutations;
public String getGeneName()
{
return geneName;
}
public void setGeneName(String geneName)
{
this.geneName = geneName;
}
public String getPatientPager()
{
return patientPager;
}
public void setPatientPager(String patientPager)
{
this.patientPager = patientPager;
}
public String getMutationPager()
{
return mutationPager;
}
public void setMutationPager(String mutationPager)
{
this.mutationPager = mutationPager;
}
public String getPatientViewer()
{
return patientViewer;
}
public void setPatientViewer(String patientViewer)
{
this.patientViewer = patientViewer;
}
public String getAction()
{
return action;
}
public void setAction(String action)
{
this.action = action;
}
public String getResult()
{
return result;
}
public void setResult(String result)
{
this.result = result;
}
public String getHeader()
{
return header;
}
public void setHeader(String header)
{
this.header = header;
}
public int getNumPatients()
{
return numPatients;
}
public void setNumPatients(int numPatients)
{
this.numPatients = numPatients;
}
public int getNumUnpublished()
{
return numUnpublished;
}
public void setNumUnpublished(int numUnpublished)
{
this.numUnpublished = numUnpublished;
}
public int getNumMutations()
{
return numMutations;
}
public void setNumMutations(int numMutations)
{
this.numMutations = numMutations;
}
public SimpleSearchForm getSimpleSearchForm()
{
return simpleSearchForm;
}
public void setSimpleSearchForm(SimpleSearchForm simpleSearchForm)
{
this.simpleSearchForm = simpleSearchForm;
}
public ListAllMutationsForm getListAllMutationsForm()
{
return listAllMutationsForm;
}
public void setListAllMutationsForm(ListAllMutationsForm listAllMutationsForm)
{
this.listAllMutationsForm = listAllMutationsForm;
}
public ListAllPatientsForm getListAllPatientsForm()
{
return listAllPatientsForm;
}
public void setListAllPatientsForm(ListAllPatientsForm listAllPatientsForm)
{
this.listAllPatientsForm = listAllPatientsForm;
}
public ToExpertSearchForm getToExpertSearchForm()
{
return toExpertSearchForm;
}
public void setToExpertSearchForm(ToExpertSearchForm toExpertSearchForm)
{
this.toExpertSearchForm = toExpertSearchForm;
}
public ToSimpleSearchForm getToSimpleSearchForm()
{
return toSimpleSearchForm;
}
public void setToSimpleSearchForm(ToSimpleSearchForm toSimpleSearchForm)
{
this.toSimpleSearchForm = toSimpleSearchForm;
}
public ExpertSearchForm getExpertSearchForm()
{
return expertSearchForm;
}
public void setExpertSearchForm(ExpertSearchForm expertSearchForm)
{
this.expertSearchForm = expertSearchForm;
}
public ShowMutationForm getShowMutationForm()
{
return showMutationForm;
}
public void setShowMutationForm(ShowMutationForm showMutationForm)
{
this.showMutationForm = showMutationForm;
}
public DisplayOptionsForm getDisplayOptionsForm()
{
return displayOptionsForm;
}
public void setDisplayOptionsForm(DisplayOptionsForm displayOptionsForm)
{
this.displayOptionsForm = displayOptionsForm;
}
public ExonSearchCriteriaVO getExonSearchCriteriaVO()
{
return exonSearchCriteriaVO;
}
public void setExonSearchCriteriaVO(ExonSearchCriteriaVO exonSearchCriteriaVO)
{
this.exonSearchCriteriaVO = exonSearchCriteriaVO;
}
public MutationSearchCriteriaVO getMutationSearchCriteriaVO()
{
return mutationSearchCriteriaVO;
}
public void setMutationSearchCriteriaVO(MutationSearchCriteriaVO mutationSearchCriteriaVO)
{
this.mutationSearchCriteriaVO = mutationSearchCriteriaVO;
}
public PatientSearchCriteriaVO getPatientSearchCriteriaVO()
{
return patientSearchCriteriaVO;
}
public void setPatientSearchCriteriaVO(PatientSearchCriteriaVO patientSearchCriteriaVO)
{
this.patientSearchCriteriaVO = patientSearchCriteriaVO;
}
public QueryParametersVO getQueryParametersVO()
{
return queryParametersVO;
}
public void setQueryParametersVO(QueryParametersVO queryParametersVO)
{
this.queryParametersVO = queryParametersVO;
}
public void setGene(MutationGene gene)
{
this.gene = gene;
}
public MutationGene getGene()
{
return gene;
}
public ExonSummaryVO getExonSummaryVO()
{
return exonSummaryVO;
}
public void setExonSummaryVO(ExonSummaryVO exonSummaryVO)
{
this.exonSummaryVO = exonSummaryVO;
}
public MutationSummaryVO getMutationSummaryVO()
{
return mutationSummaryVO;
}
public void setMutationSummaryVO(MutationSummaryVO mutationSummaryVO)
{
this.mutationSummaryVO = mutationSummaryVO;
}
public List<MutationSummaryVO> getMutationSummaryVOs()
{
return mutationSummaryVOs;
}
public void setMutationSummaryVOs(List<MutationSummaryVO> mutationSummaryVOs)
{
this.mutationSummaryVOs = mutationSummaryVOs;
}
public HashMap<String, String> getMutationSummaryVOHash()
{
return mutationSummaryVOHash;
}
public void setMutationSummaryVOHash(HashMap<String, String> mutationSummaryVOHash)
{
this.mutationSummaryVOHash = mutationSummaryVOHash;
}
public List<PatientSummaryVO> getPatientSummaryVOs()
{
return patientSummaryVOs;
}
public void setPatientSummaryVOs(List<PatientSummaryVO> patientSummaryVOs)
{
this.patientSummaryVOs = patientSummaryVOs;
}
// public List<PatientDetailsVO> getPatientDetailsVO() {
// return patientDetailsVO;
// }
//
// public void setPatientDetailsVO(List<PatientDetailsVO> patientDetailsVO)
// {
// this.patientDetailsVO = patientDetailsVO;
// }
public ProteinDomainSummaryVO getProteinDomainSummaryVO()
{
return proteinDomainSummaryVO;
}
public void setProteinDomainSummaryVO(ProteinDomainSummaryVO proteinDomainSummaryVO)
{
this.proteinDomainSummaryVO = proteinDomainSummaryVO;
}
public List<ProteinDomainSummaryVO> getProteinDomainList()
{
return proteinDomainList;
}
public void setProteinDomainList(List<ProteinDomainSummaryVO> proteinDomainList)
{
this.proteinDomainList = proteinDomainList;
}
public PatientSummaryVO getPatientSummaryVO()
{
return patientSummaryVO;
}
public void setPatientSummaryVO(PatientSummaryVO patientSummaryVO)
{
this.patientSummaryVO = patientSummaryVO;
}
public PhenotypeDetailsVO getPhenotypeDetailsVO()
{
return phenotypeDetailsVO;
}
public void setPhenotypeDetailsVO(PhenotypeDetailsVO phenotypeDetailsVO)
{
this.phenotypeDetailsVO = phenotypeDetailsVO;
}
public HashMap<String, String> getPatientSummaryVOHash()
{
return patientSummaryVOHash;
}
public void setPatientSummaryVOHash(HashMap<String, String> patientSummaryVOHash)
{
this.patientSummaryVOHash = patientSummaryVOHash;
}
public String getRawOutput()
{
return rawOutput;
}
public void setRawOutput(String rawOutput)
{
this.rawOutput = rawOutput;
}
public List<MolgenisNews> getNews()
{
return news;
}
public void setNews(List<MolgenisNews> news)
{
this.news = news;
}
public LimitOffsetPager<?> getPager()
{
return pager;
}
public void setPager(LimitOffsetPager<?> pager)
{
this.pager = pager;
}
public MBrowseVO getmBrowseVO()
{
return mBrowseVO;
}
public void setmBrowseVO(MBrowseVO mBrowseVO)
{
this.mBrowseVO = mBrowseVO;
}
public String getTextWelcome()
{
return textWelcome;
}
public void setTextWelcome(String textWelcome)
{
this.textWelcome = textWelcome;
}
public String getTextSearch()
{
return textSearch;
}
public void setTextSearch(String textSearch)
{
this.textSearch = textSearch;
}
public String getTextRemarks()
{
return textRemarks;
}
public void setTextRemarks(String textRemarks)
{
this.textRemarks = textRemarks;
}
public String getTextCollaborations()
{
return textCollaborations;
}
public void setTextCollaborations(String textCollaborations)
{
this.textCollaborations = textCollaborations;
}
public List<MutationSummaryVO> getPositionMutations()
{
return positionMutations;
}
public void setPositionMutations(List<MutationSummaryVO> positionMutations)
{
this.positionMutations = positionMutations;
}
public List<MutationSummaryVO> getCodonMutations()
{
return codonMutations;
}
public void setCodonMutations(List<MutationSummaryVO> codonMutations)
{
this.codonMutations = codonMutations;
}
public SearchModel(SearchPlugin controller)
{
super(controller);
// TODO Auto-generated constructor stub
}
}