001/*
002 * mzTab-M reference implementation and validation API.
003 * This is the mzTab-M reference implementation and validation API service.
004 *
005 * OpenAPI spec version: 2.0.0
006 * Contact: nils.hoffmann@isas.de
007 *
008 * NOTE: This class is auto generated by the swagger code generator program.
009 * https://github.com/swagger-api/swagger-codegen.git
010 * Do not edit the class manually.
011 */
012
013
014package de.isas.mztab2.model;
015
016import java.util.Objects;
017import java.util.Arrays;
018import com.fasterxml.jackson.annotation.JsonProperty;
019import com.fasterxml.jackson.annotation.JsonCreator;
020import com.fasterxml.jackson.annotation.JsonValue;
021import de.isas.mztab2.model.IndexedElement;
022import de.isas.mztab2.model.Parameter;
023import io.swagger.annotations.ApiModel;
024import io.swagger.annotations.ApiModelProperty;
025import java.util.ArrayList;
026import java.util.List;
027import com.fasterxml.jackson.dataformat.xml.annotation.*;
028import javax.xml.bind.annotation.*;
029import javax.validation.constraints.*;
030import javax.validation.Valid;
031import de.isas.lipidomics.mztab2.validation.constraints.*;
032/**
033 * 
034 * Specification of sample.
035(empty) name: A name for each sample to serve as a list of the samples that MUST be reported in the following tables. Samples MUST be reported if a statistical design is being captured (i.e. bio or tech replicates). If the type of replicates are not known, samples SHOULD NOT be reported. 
036species: The respective species of the samples analysed. For more complex cases, such as metagenomics, optional columns and userParams should be used. 
037tissue: The respective tissue(s) of the sample. 
038cell_type: The respective cell type(s) of the sample. 
039disease: The respective disease(s) of the sample. 
040description: A human readable description of the sample. 
041custom: Custom parameters describing the sample's additional properties. Dates MUST be provided in ISO-8601 format.
042
043 * 
044 *
045 * <p>mzTab-M specification example(s):</p>
046 * <pre><code>COM       Experiment where all samples consisted of the same two species
047MTD     sample[1]       individual number 1
048MTD     sample[1]-species[1]    [NCBITaxon, NCBITaxon:9606, Homo sapiens, ]
049MTD     sample[1]-tissue[1]     [BTO, BTO:0000759, liver, ]
050MTD     sample[1]-cell_type[1]  [CL, CL:0000182, hepatocyte, ]
051MTD     sample[1]-disease[1]    [DOID, DOID:684, hepatocellular carcinoma, ]
052MTD     sample[1]-disease[2]    [DOID, DOID:9451, alcoholic fatty liver, ]
053MTD     sample[1]-description   Hepatocellular carcinoma samples.
054MTD     sample[1]-custom[1]     [,,Extraction date, 2011-12-21]
055MTD     sample[1]-custom[2]     [,,Extraction reason, liver biopsy]
056MTD     sample[2]       individual number 2
057MTD     sample[2]-species[1]    [NCBITaxon, NCBITaxon:9606, Homo sapiens, ]
058MTD     sample[2]-tissue[1]     [BTO, BTO:0000759, liver, ]
059MTD     sample[2]-cell_type[1]  [CL, CL:0000182, hepatocyte, ]
060MTD     sample[2]-description   Healthy control samples.
061</code></pre>
062 * 
063 *
064 */
065@ApiModel(description = "Specification of sample. (empty) name: A name for each sample to serve as a list of the samples that MUST be reported in the following tables. Samples MUST be reported if a statistical design is being captured (i.e. bio or tech replicates). If the type of replicates are not known, samples SHOULD NOT be reported.  species: The respective species of the samples analysed. For more complex cases, such as metagenomics, optional columns and userParams should be used.  tissue: The respective tissue(s) of the sample.  cell_type: The respective cell type(s) of the sample.  disease: The respective disease(s) of the sample.  description: A human readable description of the sample.  custom: Custom parameters describing the sample's additional properties. Dates MUST be provided in ISO-8601 format. ")
066@javax.annotation.Generated(value = "io.swagger.codegen.languages.JavaClientCodegen", date = "2019-08-07T11:09:24.487+02:00")
067@XmlRootElement(name = "Sample")
068@XmlAccessorType(XmlAccessType.FIELD)
069@JacksonXmlRootElement(localName = "Sample")
070public class Sample extends IndexedElement {
071
072  /**
073   * Property enumeration for Sample.
074   */
075  public static enum Properties {
076      name("name"), 
077      custom("custom"), 
078      species("species"), 
079      tissue("tissue"), 
080      cellType("cell_type"), 
081      disease("disease"), 
082      description("description");
083
084    private final String propertyName;
085
086    private Properties(String propertyName) {
087      this.propertyName = propertyName;
088    }
089
090    public String getPropertyName() {
091      return propertyName;
092    }
093
094    public String toString() {
095      return propertyName;
096    }
097
098    public String toUpper() {
099      return propertyName.toUpperCase();
100    }
101
102    public static Properties of(String value) {
103      if(value==null) {
104        throw new NullPointerException("Argument value must not be null!");
105      }
106      return Arrays.asList(Properties.values()).stream().filter(m -> m.propertyName.equals(value.toLowerCase())).findAny().orElseThrow(IllegalArgumentException::new);
107    }
108  };
109  
110  @JsonProperty("name")
111  @JacksonXmlProperty(localName = "name")
112  @XmlElement(name = "name")
113  private String name = null;
114  @JsonProperty("custom")
115  // Is a container wrapped=false
116  // items.name=custom items.baseName=custom items.xmlName= items.xmlNamespace=
117  // items.example= items.type=Parameter
118  @XmlElement(name = "custom")
119  private List<Parameter> custom = null;
120  @JsonProperty("species")
121  // Is a container wrapped=false
122  // items.name=species items.baseName=species items.xmlName= items.xmlNamespace=
123  // items.example= items.type=Parameter
124  @XmlElement(name = "species")
125  private List<Parameter> species = null;
126  @JsonProperty("tissue")
127  // Is a container wrapped=false
128  // items.name=tissue items.baseName=tissue items.xmlName= items.xmlNamespace=
129  // items.example= items.type=Parameter
130  @XmlElement(name = "tissue")
131  private List<Parameter> tissue = null;
132  @JsonProperty("cell_type")
133  // Is a container wrapped=false
134  // items.name=cellType items.baseName=cellType items.xmlName= items.xmlNamespace=
135  // items.example= items.type=Parameter
136  @XmlElement(name = "cellType")
137  private List<Parameter> cellType = null;
138  @JsonProperty("disease")
139  // Is a container wrapped=false
140  // items.name=disease items.baseName=disease items.xmlName= items.xmlNamespace=
141  // items.example= items.type=Parameter
142  @XmlElement(name = "disease")
143  private List<Parameter> disease = null;
144  @JsonProperty("description")
145  @JacksonXmlProperty(localName = "description")
146  @XmlElement(name = "description")
147  private String description = null;
148  
149  @Override
150  public Sample id(Integer id) {
151   super.setId(id);
152   return this;
153  }
154  
155  @Override
156  public Sample elementType(String elementType) {
157   super.setElementType(elementType);
158   return this;
159  }
160
161 /**
162   * Builder method for name.
163   *
164   * @see Sample#setName Sample#setName for specification examples
165   * @see Sample#getName Sample#getName for validation constraints
166   * @param name a {@code String} parameter.
167   * @return Sample
168  **/
169  public Sample name(String name) {
170   this.name = name;
171   return this;
172  }
173
174   /**
175   * The sample&#39;s name.
176   *
177   * @return name
178  **/
179  @ApiModelProperty(value = "The sample's name.")
180  public String getName() {
181    return name;
182  }
183
184 /**
185   * Set name.
186   *
187   * 
188   * 
189   * @see #getName Sample#getName for validation constraints
190   * @param name a {@code String} parameter.
191  **/
192  public void setName(String name) {
193    this.name = name;
194  }
195
196
197 /**
198   * Builder method for custom.
199   *
200   * @see Sample#setCustom Sample#setCustom for specification examples
201   * @see Sample#getCustom Sample#getCustom for validation constraints
202   * @param custom a {@code List<Parameter>} parameter.
203   * @return Sample
204  **/
205  public Sample custom(List<Parameter> custom) {
206   this.custom = custom;
207   return this;
208  }
209
210  /**
211   * Add a single customItem to the custom collection.
212   *
213   * @see Sample#getCustom Sample#getCustom for validation constraints
214   * @param customItem a {@code Parameter} parameter.
215   * @return Sample
216   */
217  public Sample addCustomItem(Parameter customItem) {
218    if (this.custom == null) {
219      this.custom = new ArrayList<>();
220    }
221    this.custom.add(customItem);
222    return this;
223  }
224
225   /**
226   * Additional user or cv parameters.
227   *
228   * @return custom
229  **/
230  @Valid
231  @ApiModelProperty(value = "Additional user or cv parameters.")
232  public List<Parameter> getCustom() {
233    return custom;
234  }
235
236 /**
237   * Set custom.
238   *
239   * 
240   * 
241   * @see #getCustom Sample#getCustom for validation constraints
242   * @param custom a {@code List<Parameter>} parameter.
243  **/
244  public void setCustom(List<Parameter> custom) {
245    this.custom = custom;
246  }
247
248
249 /**
250   * Builder method for species.
251   *
252   * @see Sample#setSpecies Sample#setSpecies for specification examples
253   * @see Sample#getSpecies Sample#getSpecies for validation constraints
254   * @param species a {@code List<Parameter>} parameter.
255   * @return Sample
256  **/
257  public Sample species(List<Parameter> species) {
258   this.species = species;
259   return this;
260  }
261
262  /**
263   * Add a single speciesItem to the species collection.
264   *
265   * @see Sample#getSpecies Sample#getSpecies for validation constraints
266   * @param speciesItem a {@code Parameter} parameter.
267   * @return Sample
268   */
269  public Sample addSpeciesItem(Parameter speciesItem) {
270    if (this.species == null) {
271      this.species = new ArrayList<>();
272    }
273    this.species.add(speciesItem);
274    return this;
275  }
276
277   /**
278   * Biological species information on the sample.
279   *
280   * @return species
281  **/
282  @Valid
283  @ApiModelProperty(value = "Biological species information on the sample.")
284  public List<Parameter> getSpecies() {
285    return species;
286  }
287
288 /**
289   * Set species.
290   *
291   * 
292   * 
293   * @see #getSpecies Sample#getSpecies for validation constraints
294   * @param species a {@code List<Parameter>} parameter.
295  **/
296  public void setSpecies(List<Parameter> species) {
297    this.species = species;
298  }
299
300
301 /**
302   * Builder method for tissue.
303   *
304   * @see Sample#setTissue Sample#setTissue for specification examples
305   * @see Sample#getTissue Sample#getTissue for validation constraints
306   * @param tissue a {@code List<Parameter>} parameter.
307   * @return Sample
308  **/
309  public Sample tissue(List<Parameter> tissue) {
310   this.tissue = tissue;
311   return this;
312  }
313
314  /**
315   * Add a single tissueItem to the tissue collection.
316   *
317   * @see Sample#getTissue Sample#getTissue for validation constraints
318   * @param tissueItem a {@code Parameter} parameter.
319   * @return Sample
320   */
321  public Sample addTissueItem(Parameter tissueItem) {
322    if (this.tissue == null) {
323      this.tissue = new ArrayList<>();
324    }
325    this.tissue.add(tissueItem);
326    return this;
327  }
328
329   /**
330   * Biological tissue information on the sample.
331   *
332   * @return tissue
333  **/
334  @Valid
335  @ApiModelProperty(value = "Biological tissue information on the sample.")
336  public List<Parameter> getTissue() {
337    return tissue;
338  }
339
340 /**
341   * Set tissue.
342   *
343   * 
344   * 
345   * @see #getTissue Sample#getTissue for validation constraints
346   * @param tissue a {@code List<Parameter>} parameter.
347  **/
348  public void setTissue(List<Parameter> tissue) {
349    this.tissue = tissue;
350  }
351
352
353 /**
354   * Builder method for cellType.
355   *
356   * @see Sample#setCellType Sample#setCellType for specification examples
357   * @see Sample#getCellType Sample#getCellType for validation constraints
358   * @param cellType a {@code List<Parameter>} parameter.
359   * @return Sample
360  **/
361  public Sample cellType(List<Parameter> cellType) {
362   this.cellType = cellType;
363   return this;
364  }
365
366  /**
367   * Add a single cellTypeItem to the cellType collection.
368   *
369   * @see Sample#getCellType Sample#getCellType for validation constraints
370   * @param cellTypeItem a {@code Parameter} parameter.
371   * @return Sample
372   */
373  public Sample addCellTypeItem(Parameter cellTypeItem) {
374    if (this.cellType == null) {
375      this.cellType = new ArrayList<>();
376    }
377    this.cellType.add(cellTypeItem);
378    return this;
379  }
380
381   /**
382   * Biological cell type information on the sample.
383   *
384   * @return cellType
385  **/
386  @Valid
387  @ApiModelProperty(value = "Biological cell type information on the sample.")
388  public List<Parameter> getCellType() {
389    return cellType;
390  }
391
392 /**
393   * Set cellType.
394   *
395   * 
396   * 
397   * @see #getCellType Sample#getCellType for validation constraints
398   * @param cellType a {@code List<Parameter>} parameter.
399  **/
400  public void setCellType(List<Parameter> cellType) {
401    this.cellType = cellType;
402  }
403
404
405 /**
406   * Builder method for disease.
407   *
408   * @see Sample#setDisease Sample#setDisease for specification examples
409   * @see Sample#getDisease Sample#getDisease for validation constraints
410   * @param disease a {@code List<Parameter>} parameter.
411   * @return Sample
412  **/
413  public Sample disease(List<Parameter> disease) {
414   this.disease = disease;
415   return this;
416  }
417
418  /**
419   * Add a single diseaseItem to the disease collection.
420   *
421   * @see Sample#getDisease Sample#getDisease for validation constraints
422   * @param diseaseItem a {@code Parameter} parameter.
423   * @return Sample
424   */
425  public Sample addDiseaseItem(Parameter diseaseItem) {
426    if (this.disease == null) {
427      this.disease = new ArrayList<>();
428    }
429    this.disease.add(diseaseItem);
430    return this;
431  }
432
433   /**
434   * Disease information on the sample.
435   *
436   * @return disease
437  **/
438  @Valid
439  @ApiModelProperty(value = "Disease information on the sample.")
440  public List<Parameter> getDisease() {
441    return disease;
442  }
443
444 /**
445   * Set disease.
446   *
447   * 
448   * 
449   * @see #getDisease Sample#getDisease for validation constraints
450   * @param disease a {@code List<Parameter>} parameter.
451  **/
452  public void setDisease(List<Parameter> disease) {
453    this.disease = disease;
454  }
455
456
457 /**
458   * Builder method for description.
459   *
460   * @see Sample#setDescription Sample#setDescription for specification examples
461   * @see Sample#getDescription Sample#getDescription for validation constraints
462   * @param description a {@code String} parameter.
463   * @return Sample
464  **/
465  public Sample description(String description) {
466   this.description = description;
467   return this;
468  }
469
470   /**
471   * A free form description of the sample.
472   *
473   * @return description
474  **/
475  @ApiModelProperty(value = "A free form description of the sample.")
476  public String getDescription() {
477    return description;
478  }
479
480 /**
481   * Set description.
482   *
483   * 
484   * 
485   * @see #getDescription Sample#getDescription for validation constraints
486   * @param description a {@code String} parameter.
487  **/
488  public void setDescription(String description) {
489    this.description = description;
490  }
491
492
493  @Override
494  public boolean equals(java.lang.Object o) {
495    if (this == o) {
496      return true;
497    }
498    if (o == null || getClass() != o.getClass()) {
499      return false;
500    }
501    Sample sample = (Sample) o;
502    return Objects.equals(this.name, sample.name) &&
503        Objects.equals(this.custom, sample.custom) &&
504        Objects.equals(this.species, sample.species) &&
505        Objects.equals(this.tissue, sample.tissue) &&
506        Objects.equals(this.cellType, sample.cellType) &&
507        Objects.equals(this.disease, sample.disease) &&
508        Objects.equals(this.description, sample.description) &&
509        super.equals(o);
510  }
511
512  @Override
513  public int hashCode() {
514    return Objects.hash(name, custom, species, tissue, cellType, disease, description, super.hashCode());
515  }
516
517
518  @Override
519  public String toString() {
520    StringBuilder sb = new StringBuilder();
521    sb.append("class Sample {\n");
522    sb.append("    ").append(toIndentedString(super.toString())).append("\n");
523    sb.append("    name: ").append(toIndentedString(name)).append("\n");
524    sb.append("    custom: ").append(toIndentedString(custom)).append("\n");
525    sb.append("    species: ").append(toIndentedString(species)).append("\n");
526    sb.append("    tissue: ").append(toIndentedString(tissue)).append("\n");
527    sb.append("    cellType: ").append(toIndentedString(cellType)).append("\n");
528    sb.append("    disease: ").append(toIndentedString(disease)).append("\n");
529    sb.append("    description: ").append(toIndentedString(description)).append("\n");
530    sb.append("}");
531    return sb.toString();
532  }
533
534  /**
535   * Convert the given object to string with each line indented by 4 spaces
536   * (except the first line).
537   */
538  private String toIndentedString(java.lang.Object o) {
539    if (o == null) {
540      return "null";
541    }
542    return o.toString().replace("\n", "\n    ");
543  }
544
545}
546