SearchModel.java

package org.molgenis.mutation.ui.search;

import java.util.ArrayList;
import java.util.List;
import java.util.Map;

import org.molgenis.framework.ui.EasyPluginModel;
import org.molgenis.framework.ui.html.HtmlInput;
import org.molgenis.mutation.dto.ExonDTO;
import org.molgenis.mutation.dto.GeneDTO;
import org.molgenis.mutation.dto.MutationSearchCriteriaDTO;
import org.molgenis.mutation.dto.MutationSummaryDTO;
import org.molgenis.mutation.dto.PatientSummaryDTO;
import org.molgenis.mutation.dto.ProteinDomainDTO;
import org.molgenis.mutation.dto.QueryParametersDTO;
import org.molgenis.mutation.dto.VariantDTO;
import org.molgenis.mutation.ui.HtmlFormWrapper;
import org.molgenis.mutation.ui.LimitOffsetPager;
import org.molgenis.mutation.ui.html.MBrowse;
import org.molgenis.mutation.ui.search.form.DisplayOptionsForm;
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.pheno.dto.ObservationElementDTO;

public class SearchModel extends EasyPluginModel
{
	private static final long serialVersionUID = 1L;
	private String patientPager;
	private String mutationPager;
	private String patientViewer;
	private String mutationViewer;
	private String action = "init";
	private String result = "mutations"; // Initially search/display mutations
	private String searchTerm = ""; // Initially search term is empty
	private String header;
	private int numPatients;
	private int numUnpublished;
	private int numMutations;
	private Map<String, Integer> numMutationsByPathogenicity;
	private Map<String, Integer> numPatientsByPathogenicity;
	private HtmlFormWrapper expertSearchFormWrapper;
	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 ShowMutationForm showMutationForm                 = new ShowMutationForm();
	private DisplayOptionsForm displayOptionsForm             = new DisplayOptionsForm();
	private HtmlInput<?> topPanel;
	private HtmlInput<?> mBrowsePanel;
	private MutationSearchCriteriaDTO mutationSearchCriteriaVO = new MutationSearchCriteriaDTO();
	private QueryParametersDTO queryParametersVO = new QueryParametersDTO();

	private GeneDTO geneDTO;
	private List<GeneDTO> geneDTOList;
	private ExonDTO exonDTO;
	private List<ExonDTO> exonDTOList;
	private MutationSummaryDTO mutationSummaryVO;
	private List<MutationSummaryDTO> mutationSummaryDTOList = new ArrayList<MutationSummaryDTO>();
	private Map<String, String> mutationSummaryVOHash;
	private List<PatientSummaryDTO> patientSummaryVOs = new ArrayList<PatientSummaryDTO>();
	private ProteinDomainDTO proteinDomainDTO;
	private List<ProteinDomainDTO> proteinDomainDTOList;
	private PatientSummaryDTO patientSummaryVO;
	private ObservationElementDTO individualDTO;
	private Map<String, String> patientSummaryVOHash;
	private String rawOutput; // for output from included sources

	private LimitOffsetPager<?> pager;

	private MBrowse mbrowse;

	private String textWelcome = "";
	private String textSearch = "";
	private String textRemarks = "";
	private String textCollaborations = "";

	private List<VariantDTO> positionMutations;
	private List<VariantDTO> codonMutations;

	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 getMutationViewer()
	{
		return mutationViewer;
	}

	public void setMutationViewer(String mutationViewer)
	{
		this.mutationViewer = mutationViewer;
	}

	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 getSearchTerm()
	{
		return searchTerm;
	}

	public void setSearchTerm(String searchTerm)
	{
		this.searchTerm = searchTerm;
	}

	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 Integer getNumMutationsByPathogenicity(String pathogenicity)
	{
		if (this.numMutationsByPathogenicity.containsKey(pathogenicity)) return this.numMutationsByPathogenicity
				.get(pathogenicity);
		else
			return 0;
	}

	public void setNumMutationsByPathogenicity(Map<String, Integer> numMutationsByPathogenicity)
	{
		this.numMutationsByPathogenicity = numMutationsByPathogenicity;
	}

	public Integer getNumPatientsByPathogenicity(String pathogenicity)
	{
		if (this.numPatientsByPathogenicity.containsKey(pathogenicity)) return this.numPatientsByPathogenicity
				.get(pathogenicity);
		else
			return 0;
	}

	public void setNumPatientsByPathogenicity(Map<String, Integer> numPatientsByPathogenicity)
	{
		this.numPatientsByPathogenicity = numPatientsByPathogenicity;
	}

	public HtmlFormWrapper getExpertSearchFormWrapper()
	{
		return expertSearchFormWrapper;
	}

	public void setExpertSearchFormWrapper(HtmlFormWrapper expertSearchFormWrapper)
	{
		this.expertSearchFormWrapper = expertSearchFormWrapper;
	}

	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 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 HtmlInput<?> getTopPanel()
	{
		return topPanel;
	}

	public void setTopPanel(HtmlInput<?> topPanel)
	{
		this.topPanel = topPanel;
	}

	public HtmlInput<?> getMBrowsePanel()
	{
		return mBrowsePanel;
	}

	public void setMBrowsePanel(HtmlInput<?> mBrowsePanel)
	{
		this.mBrowsePanel = mBrowsePanel;
	}

	public MutationSearchCriteriaDTO getMutationSearchCriteriaVO()
	{
		return mutationSearchCriteriaVO;
	}

	public void setMutationSearchCriteriaVO(MutationSearchCriteriaDTO mutationSearchCriteriaVO)
	{
		this.mutationSearchCriteriaVO = mutationSearchCriteriaVO;
	}

	public QueryParametersDTO getQueryParametersVO()
	{
		return queryParametersVO;
	}

	public void setQueryParametersVO(QueryParametersDTO queryParametersVO)
	{
		this.queryParametersVO = queryParametersVO;
	}

	public void setGeneDTO(GeneDTO geneDTO)
	{
		this.geneDTO = geneDTO;
	}

	public GeneDTO getGeneDTO()
	{
		return geneDTO;
	}

	public List<GeneDTO> getGeneDTOList()
	{
		return geneDTOList;
	}

	public void setGeneDTOList(List<GeneDTO> geneDTOList)
	{
		this.geneDTOList = geneDTOList;
	}

	public ExonDTO getExonDTO()
	{
		return exonDTO;
	}

	public void setExonDTO(ExonDTO exonDTO)
	{
		this.exonDTO = exonDTO;
	}

	public List<ExonDTO> getExonDTOList()
	{
		return exonDTOList;
	}

	public void setExonDTOList(List<ExonDTO> exonDTOList)
	{
		this.exonDTOList = exonDTOList;
	}

	public MutationSummaryDTO getMutationSummaryVO()
	{
		return mutationSummaryVO;
	}

	public void setMutationSummaryVO(MutationSummaryDTO mutationSummaryVO)
	{
		this.mutationSummaryVO = mutationSummaryVO;
	}

	public List<MutationSummaryDTO> getMutationSummaryDTOList()
	{
		return mutationSummaryDTOList;
	}

	public void setMutationSummaryDTOList(List<MutationSummaryDTO> mutationSummaryDTOList)
	{
		this.mutationSummaryDTOList = mutationSummaryDTOList;
	}

	public Map<String, String> getMutationSummaryVOHash()
	{
		return mutationSummaryVOHash;
	}

	public void setMutationSummaryVOHash(Map<String, String> mutationSummaryVOHash)
	{
		this.mutationSummaryVOHash = mutationSummaryVOHash;
	}

	public List<PatientSummaryDTO> getPatientSummaryVOs()
	{
		return patientSummaryVOs;
	}

	public void setPatientSummaryVOs(List<PatientSummaryDTO> patientSummaryVOs)
	{
		this.patientSummaryVOs = patientSummaryVOs;
	}

	public ProteinDomainDTO getProteinDomainDTO()
	{
		return proteinDomainDTO;
	}

	public void setProteinDomainDTO(ProteinDomainDTO proteinDomainDTO)
	{
		this.proteinDomainDTO = proteinDomainDTO;
	}

	public List<ProteinDomainDTO> getProteinDomainDTOList()
	{
		return proteinDomainDTOList;
	}

	public void setProteinDomainDTOList(List<ProteinDomainDTO> proteinDomainDTOList)
	{
		this.proteinDomainDTOList = proteinDomainDTOList;
	}

	public PatientSummaryDTO getPatientSummaryVO()
	{
		return patientSummaryVO;
	}

	public void setPatientSummaryVO(PatientSummaryDTO patientSummaryVO)
	{
		this.patientSummaryVO = patientSummaryVO;
	}

	public ObservationElementDTO getIndividualDTO()
	{
		return individualDTO;
	}

	public void setIndividualDTO(ObservationElementDTO individualDTO)
	{
		this.individualDTO = individualDTO;
	}

	public Map<String, String> getPatientSummaryVOHash()
	{
		return patientSummaryVOHash;
	}

	public void setPatientSummaryVOHash(Map<String, String> patientSummaryVOHash)
	{
		this.patientSummaryVOHash = patientSummaryVOHash;
	}

	public String getRawOutput()
	{
		return rawOutput;
	}

	public void setRawOutput(String rawOutput)
	{
		this.rawOutput = rawOutput;
	}

	public LimitOffsetPager<?> getPager()
	{
		return pager;
	}

	public void setPager(LimitOffsetPager<?> pager)
	{
		this.pager = pager;
	}

	public MBrowse getMbrowse()
	{
		return mbrowse;
	}

	public void setMbrowse(MBrowse mbrowse)
	{
		this.mbrowse = mbrowse;
	}

	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<VariantDTO> getPositionMutations()
	{
		return positionMutations;
	}

	public void setPositionMutations(List<VariantDTO> positionMutations)
	{
		this.positionMutations = positionMutations;
	}

	public List<VariantDTO> getCodonMutations()
	{
		return codonMutations;
	}

	public void setCodonMutations(List<VariantDTO> codonMutations)
	{
		this.codonMutations = codonMutations;
	}

	public SearchModel(SearchPlugin controller)
	{
		super(controller);
	}

}