/*
 * mzTab-M reference implementation and validation API.
 * This is the mzTab-M reference implementation and validation API service.
 *
 * OpenAPI spec version: 2.0.0
 * Contact: nils.hoffmann@isas.de
 *
 * NOTE: This class is auto generated by the swagger code generator program.
 * https://github.com/swagger-api/swagger-codegen.git
 * Do not edit the class manually.
 */


package de.isas.mztab2.model;

import java.util.Objects;
import java.util.Arrays;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.annotation.JsonCreator;
import com.fasterxml.jackson.annotation.JsonValue;
import de.isas.mztab2.model.Comment;
import de.isas.mztab2.model.Metadata;
import de.isas.mztab2.model.SmallMoleculeEvidence;
import de.isas.mztab2.model.SmallMoleculeFeature;
import de.isas.mztab2.model.SmallMoleculeSummary;
import io.swagger.annotations.ApiModel;
import io.swagger.annotations.ApiModelProperty;
import java.util.ArrayList;
import java.util.List;
import com.fasterxml.jackson.dataformat.xml.annotation.*;
import javax.xml.bind.annotation.*;
import javax.validation.constraints.*;
import javax.validation.Valid;
import de.isas.lipidomics.mztab2.validation.constraints.*;
/**
 * 
 * mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches.

This format is further intended to provide local LIMS systems as well as MS metabolomics repositories a simple way to share and combine basic information.

The mzTab-M format consists of four cross-referenced data tables:
    
    * Metadata (MTD), 
    * Small Molecule (SML), 
    * Small Molecule Feature (SMF) and the 
    * Small Molecule Evidence (SME). 

The MTD and SML tables are mandatory, and for a file to contain any evidence about how molecules were quantified or identified by software, then all four tables must be present. The tables must follow the order MTD, SML, SMF and SME, with a blank line separating each table. 

The structure of each table, in terms of the rows and columns that must be present is tightly specified and formally defined and explained in the mzTab-M specification document.
mzTab-M files MUST have one Metadata (MTD) section and one Small Molecule (SML) Section. In practice, we expect that most files SHOULD also include one Small Molecule Feature (SMF) section, and one Small Molecule Evidence (SME) Section. 
Files lacking SMF and SME sections can only present summary data about quantified molecules, without any evidence trail for how those values were derived. It will be left to reading software to determine whether additional validation will be requested such that SMF and SME tables MUST be present.

 * 
 *
 * 
 *
 */
@ApiModel(description = "mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches.  This format is further intended to provide local LIMS systems as well as MS metabolomics repositories a simple way to share and combine basic information.  The mzTab-M format consists of four cross-referenced data tables:          * Metadata (MTD),      * Small Molecule (SML),      * Small Molecule Feature (SMF) and the      * Small Molecule Evidence (SME).   The MTD and SML tables are mandatory, and for a file to contain any evidence about how molecules were quantified or identified by software, then all four tables must be present. The tables must follow the order MTD, SML, SMF and SME, with a blank line separating each table.   The structure of each table, in terms of the rows and columns that must be present is tightly specified and formally defined and explained in the mzTab-M specification document. mzTab-M files MUST have one Metadata (MTD) section and one Small Molecule (SML) Section. In practice, we expect that most files SHOULD also include one Small Molecule Feature (SMF) section, and one Small Molecule Evidence (SME) Section.  Files lacking SMF and SME sections can only present summary data about quantified molecules, without any evidence trail for how those values were derived. It will be left to reading software to determine whether additional validation will be requested such that SMF and SME tables MUST be present. ")
@javax.annotation.Generated(value = "io.swagger.codegen.languages.JavaClientCodegen", date = "2019-08-07T11:09:24.487+02:00")
@XmlRootElement(name = "MzTab")
@XmlAccessorType(XmlAccessType.FIELD)
@JacksonXmlRootElement(localName = "MzTab")
public class MzTab {

  /**
   * Property enumeration for MzTab.
   */
  public static enum Properties {
      metadata("metadata"), 
      smallMoleculeSummary("smallMoleculeSummary"), 
      smallMoleculeFeature("smallMoleculeFeature"), 
      smallMoleculeEvidence("smallMoleculeEvidence"), 
      comment("comment");

    private final String propertyName;

    private Properties(String propertyName) {
      this.propertyName = propertyName;
    }

    public String getPropertyName() {
      return propertyName;
    }

    public String toString() {
      return propertyName;
    }

    public String toUpper() {
      return propertyName.toUpperCase();
    }

    public static Properties of(String value) {
      if(value==null) {
        throw new NullPointerException("Argument value must not be null!");
      }
      return Arrays.asList(Properties.values()).stream().filter(m -> m.propertyName.equals(value.toLowerCase())).findAny().orElseThrow(IllegalArgumentException::new);
    }
  };
  
  @JsonProperty("metadata")
  @JacksonXmlProperty(localName = "metadata")
  @XmlElement(name = "metadata")
  private Metadata metadata = null;
  @JsonProperty("smallMoleculeSummary")
  // Is a container wrapped=false
  // items.name=smallMoleculeSummary items.baseName=smallMoleculeSummary items.xmlName= items.xmlNamespace=
  // items.example= items.type=SmallMoleculeSummary
  @XmlElement(name = "smallMoleculeSummary")
  private List<SmallMoleculeSummary> smallMoleculeSummary = new ArrayList<>();
  @JsonProperty("smallMoleculeFeature")
  // Is a container wrapped=false
  // items.name=smallMoleculeFeature items.baseName=smallMoleculeFeature items.xmlName= items.xmlNamespace=
  // items.example= items.type=SmallMoleculeFeature
  @XmlElement(name = "smallMoleculeFeature")
  private List<SmallMoleculeFeature> smallMoleculeFeature = new ArrayList<>();
  @JsonProperty("smallMoleculeEvidence")
  // Is a container wrapped=false
  // items.name=smallMoleculeEvidence items.baseName=smallMoleculeEvidence items.xmlName= items.xmlNamespace=
  // items.example= items.type=SmallMoleculeEvidence
  @XmlElement(name = "smallMoleculeEvidence")
  private List<SmallMoleculeEvidence> smallMoleculeEvidence = new ArrayList<>();
  @JsonProperty("comment")
  // Is a container wrapped=false
  // items.name=comment items.baseName=comment items.xmlName= items.xmlNamespace=
  // items.example= items.type=Comment
  @XmlElement(name = "comment")
  private List<Comment> comment = null;

 /**
   * Builder method for metadata.
   *
   * @see MzTab#setMetadata MzTab#setMetadata for specification examples
   * @see MzTab#getMetadata MzTab#getMetadata for validation constraints
   * @param metadata a {@code Metadata} parameter.
   * @return MzTab
  **/
  public MzTab metadata(Metadata metadata) {
   this.metadata = metadata;
   return this;
  }

   /**
   * <p>Get metadata.</p>
   *
   * @return metadata
  **/
  @NotNull
  @Valid
  @ApiModelProperty(required = true, value = "")
  public Metadata getMetadata() {
    return metadata;
  }

 /**
   * Set metadata.
   *
   * 
   * 
   * @see #getMetadata MzTab#getMetadata for validation constraints
   * @param metadata a {@code Metadata} parameter.
  **/
  public void setMetadata(Metadata metadata) {
    this.metadata = metadata;
  }


 /**
   * Builder method for smallMoleculeSummary.
   *
   * @see MzTab#setSmallMoleculeSummary MzTab#setSmallMoleculeSummary for specification examples
   * @see MzTab#getSmallMoleculeSummary MzTab#getSmallMoleculeSummary for validation constraints
   * @param smallMoleculeSummary a {@code List<SmallMoleculeSummary>} parameter.
   * @return MzTab
  **/
  public MzTab smallMoleculeSummary(List<SmallMoleculeSummary> smallMoleculeSummary) {
   this.smallMoleculeSummary = smallMoleculeSummary;
   return this;
  }

  /**
   * Add a single smallMoleculeSummaryItem to the smallMoleculeSummary collection.
   *
   * @see MzTab#getSmallMoleculeSummary MzTab#getSmallMoleculeSummary for validation constraints
   * @param smallMoleculeSummaryItem a {@code SmallMoleculeSummary} parameter.
   * @return MzTab
   */
  public MzTab addSmallMoleculeSummaryItem(SmallMoleculeSummary smallMoleculeSummaryItem) {
    this.smallMoleculeSummary.add(smallMoleculeSummaryItem);
    return this;
  }

   /**
   * The small molecule section is table-based. The small molecule section MUST always come after the metadata section. All table columns MUST be Tab separated. There MUST NOT be any empty cells; missing values MUST be reported using “null” for columns where Is Nullable &#x3D; “True”.

Each row of the small molecule section is intended to report one final result to be communicated in terms of a molecule that has been quantified. In many cases, this may be the molecule of biological interest, although in some cases, the final result could be a derivatized form as appropriate – although it is desirable for the database identifier(s) to reference to the biological (non-derivatized) form. In general, different adduct forms would generally be reported in the Small Molecule Feature section.

The order of columns MUST follow the order specified below.

All columns are MANDATORY except for “opt_” columns.

   *
   * @return smallMoleculeSummary
  **/
  @NotNull
  @Valid
 @Size(min=1)  @ApiModelProperty(required = true, value = "The small molecule section is table-based. The small molecule section MUST always come after the metadata section. All table columns MUST be Tab separated. There MUST NOT be any empty cells; missing values MUST be reported using “null” for columns where Is Nullable = “True”.  Each row of the small molecule section is intended to report one final result to be communicated in terms of a molecule that has been quantified. In many cases, this may be the molecule of biological interest, although in some cases, the final result could be a derivatized form as appropriate – although it is desirable for the database identifier(s) to reference to the biological (non-derivatized) form. In general, different adduct forms would generally be reported in the Small Molecule Feature section.  The order of columns MUST follow the order specified below.  All columns are MANDATORY except for “opt_” columns. ")
  public List<SmallMoleculeSummary> getSmallMoleculeSummary() {
    return smallMoleculeSummary;
  }

 /**
   * Set smallMoleculeSummary.
   *
   * 
   * 
   * @see #getSmallMoleculeSummary MzTab#getSmallMoleculeSummary for validation constraints
   * @param smallMoleculeSummary a {@code List<SmallMoleculeSummary>} parameter.
  **/
  public void setSmallMoleculeSummary(List<SmallMoleculeSummary> smallMoleculeSummary) {
    this.smallMoleculeSummary = smallMoleculeSummary;
  }


 /**
   * Builder method for smallMoleculeFeature.
   *
   * @see MzTab#setSmallMoleculeFeature MzTab#setSmallMoleculeFeature for specification examples
   * @see MzTab#getSmallMoleculeFeature MzTab#getSmallMoleculeFeature for validation constraints
   * @param smallMoleculeFeature a {@code List<SmallMoleculeFeature>} parameter.
   * @return MzTab
  **/
  public MzTab smallMoleculeFeature(List<SmallMoleculeFeature> smallMoleculeFeature) {
   this.smallMoleculeFeature = smallMoleculeFeature;
   return this;
  }

  /**
   * Add a single smallMoleculeFeatureItem to the smallMoleculeFeature collection.
   *
   * @see MzTab#getSmallMoleculeFeature MzTab#getSmallMoleculeFeature for validation constraints
   * @param smallMoleculeFeatureItem a {@code SmallMoleculeFeature} parameter.
   * @return MzTab
   */
  public MzTab addSmallMoleculeFeatureItem(SmallMoleculeFeature smallMoleculeFeatureItem) {
    this.smallMoleculeFeature.add(smallMoleculeFeatureItem);
    return this;
  }

   /**
   * The small molecule feature section is table-based, representing individual MS regions (generally considered to be the elution profile for all isotopomers formed from a single charge state of a molecule), that have been measured/quantified. However, for approaches that quantify individual isotopomers e.g. stable isotope labelling/flux studies, then each SMF row SHOULD represent a single isotopomer.

Different adducts or derivatives and different charge states of individual molecules should be reported as separate SMF rows.

The small molecule feature section MUST always come after the Small Molecule Table. All table columns MUST be Tab separated. There MUST NOT be any empty cells. Missing values MUST be reported using “null”.

The order of columns MUST follow the order specified below.

All columns are MANDATORY except for “opt_” columns.

   *
   * @return smallMoleculeFeature
  **/
  @NotNull
  @Valid
  @ApiModelProperty(required = true, value = "The small molecule feature section is table-based, representing individual MS regions (generally considered to be the elution profile for all isotopomers formed from a single charge state of a molecule), that have been measured/quantified. However, for approaches that quantify individual isotopomers e.g. stable isotope labelling/flux studies, then each SMF row SHOULD represent a single isotopomer.  Different adducts or derivatives and different charge states of individual molecules should be reported as separate SMF rows.  The small molecule feature section MUST always come after the Small Molecule Table. All table columns MUST be Tab separated. There MUST NOT be any empty cells. Missing values MUST be reported using “null”.  The order of columns MUST follow the order specified below.  All columns are MANDATORY except for “opt_” columns. ")
  public List<SmallMoleculeFeature> getSmallMoleculeFeature() {
    return smallMoleculeFeature;
  }

 /**
   * Set smallMoleculeFeature.
   *
   * 
   * 
   * @see #getSmallMoleculeFeature MzTab#getSmallMoleculeFeature for validation constraints
   * @param smallMoleculeFeature a {@code List<SmallMoleculeFeature>} parameter.
  **/
  public void setSmallMoleculeFeature(List<SmallMoleculeFeature> smallMoleculeFeature) {
    this.smallMoleculeFeature = smallMoleculeFeature;
  }


 /**
   * Builder method for smallMoleculeEvidence.
   *
   * @see MzTab#setSmallMoleculeEvidence MzTab#setSmallMoleculeEvidence for specification examples
   * @see MzTab#getSmallMoleculeEvidence MzTab#getSmallMoleculeEvidence for validation constraints
   * @param smallMoleculeEvidence a {@code List<SmallMoleculeEvidence>} parameter.
   * @return MzTab
  **/
  public MzTab smallMoleculeEvidence(List<SmallMoleculeEvidence> smallMoleculeEvidence) {
   this.smallMoleculeEvidence = smallMoleculeEvidence;
   return this;
  }

  /**
   * Add a single smallMoleculeEvidenceItem to the smallMoleculeEvidence collection.
   *
   * @see MzTab#getSmallMoleculeEvidence MzTab#getSmallMoleculeEvidence for validation constraints
   * @param smallMoleculeEvidenceItem a {@code SmallMoleculeEvidence} parameter.
   * @return MzTab
   */
  public MzTab addSmallMoleculeEvidenceItem(SmallMoleculeEvidence smallMoleculeEvidenceItem) {
    this.smallMoleculeEvidence.add(smallMoleculeEvidenceItem);
    return this;
  }

   /**
   * The small molecule evidence section is table-based, representing evidence for identifications of small molecules/features, from database search or any other process used to give putative identifications to molecules. In a typical case, each row represents one result from a single search or intepretation of a piece of evidence e.g. a database search with a fragmentation spectrum. Multiple results from a given input data item (e.g. one fragment spectrum) SHOULD share the same value under evidence_input_id.

The small molecule evidence section MUST always come after the Small Molecule Feature Table. All table columns MUST be Tab separated. There MUST NOT be any empty cells. Missing values MUST be reported using “null”.

The order of columns MUST follow the order specified below.

All columns are MANDATORY except for “opt_” columns.

   *
   * @return smallMoleculeEvidence
  **/
  @NotNull
  @Valid
  @ApiModelProperty(required = true, value = "The small molecule evidence section is table-based, representing evidence for identifications of small molecules/features, from database search or any other process used to give putative identifications to molecules. In a typical case, each row represents one result from a single search or intepretation of a piece of evidence e.g. a database search with a fragmentation spectrum. Multiple results from a given input data item (e.g. one fragment spectrum) SHOULD share the same value under evidence_input_id.  The small molecule evidence section MUST always come after the Small Molecule Feature Table. All table columns MUST be Tab separated. There MUST NOT be any empty cells. Missing values MUST be reported using “null”.  The order of columns MUST follow the order specified below.  All columns are MANDATORY except for “opt_” columns. ")
  public List<SmallMoleculeEvidence> getSmallMoleculeEvidence() {
    return smallMoleculeEvidence;
  }

 /**
   * Set smallMoleculeEvidence.
   *
   * 
   * 
   * @see #getSmallMoleculeEvidence MzTab#getSmallMoleculeEvidence for validation constraints
   * @param smallMoleculeEvidence a {@code List<SmallMoleculeEvidence>} parameter.
  **/
  public void setSmallMoleculeEvidence(List<SmallMoleculeEvidence> smallMoleculeEvidence) {
    this.smallMoleculeEvidence = smallMoleculeEvidence;
  }


 /**
   * Builder method for comment.
   *
   * @see MzTab#setComment MzTab#setComment for specification examples
   * @see MzTab#getComment MzTab#getComment for validation constraints
   * @param comment a {@code List<Comment>} parameter.
   * @return MzTab
  **/
  public MzTab comment(List<Comment> comment) {
   this.comment = comment;
   return this;
  }

  /**
   * Add a single commentItem to the comment collection.
   *
   * @see MzTab#getComment MzTab#getComment for validation constraints
   * @param commentItem a {@code Comment} parameter.
   * @return MzTab
   */
  public MzTab addCommentItem(Comment commentItem) {
    if (this.comment == null) {
      this.comment = new ArrayList<>();
    }
    this.comment.add(commentItem);
    return this;
  }

   /**
   * Comment lines can be placed anywhere in an mzTab file. These lines must start with the three-letter code COM and are ignored by most parsers. Empty lines can also occur anywhere in an mzTab file and are ignored.

   *
   * @return comment
  **/
  @Valid
  @ApiModelProperty(value = "Comment lines can be placed anywhere in an mzTab file. These lines must start with the three-letter code COM and are ignored by most parsers. Empty lines can also occur anywhere in an mzTab file and are ignored. ")
  public List<Comment> getComment() {
    return comment;
  }

 /**
   * Set comment.
   *
   * 
   * 
   * @see #getComment MzTab#getComment for validation constraints
   * @param comment a {@code List<Comment>} parameter.
  **/
  public void setComment(List<Comment> comment) {
    this.comment = comment;
  }


  @Override
  public boolean equals(java.lang.Object o) {
    if (this == o) {
      return true;
    }
    if (o == null || getClass() != o.getClass()) {
      return false;
    }
    MzTab mzTab = (MzTab) o;
    return Objects.equals(this.metadata, mzTab.metadata) &&
        Objects.equals(this.smallMoleculeSummary, mzTab.smallMoleculeSummary) &&
        Objects.equals(this.smallMoleculeFeature, mzTab.smallMoleculeFeature) &&
        Objects.equals(this.smallMoleculeEvidence, mzTab.smallMoleculeEvidence) &&
        Objects.equals(this.comment, mzTab.comment);
  }

  @Override
  public int hashCode() {
    return Objects.hash(metadata, smallMoleculeSummary, smallMoleculeFeature, smallMoleculeEvidence, comment);
  }


  @Override
  public String toString() {
    StringBuilder sb = new StringBuilder();
    sb.append("class MzTab {\n");
    
    sb.append("    metadata: ").append(toIndentedString(metadata)).append("\n");
    sb.append("    smallMoleculeSummary: ").append(toIndentedString(smallMoleculeSummary)).append("\n");
    sb.append("    smallMoleculeFeature: ").append(toIndentedString(smallMoleculeFeature)).append("\n");
    sb.append("    smallMoleculeEvidence: ").append(toIndentedString(smallMoleculeEvidence)).append("\n");
    sb.append("    comment: ").append(toIndentedString(comment)).append("\n");
    sb.append("}");
    return sb.toString();
  }

  /**
   * Convert the given object to string with each line indented by 4 spaces
   * (except the first line).
   */
  private String toIndentedString(java.lang.Object o) {
    if (o == null) {
      return "null";
    }
    return o.toString().replace("\n", "\n    ");
  }

}