cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenRow.java

   1 /**
   2 * Copyright (C) 2009 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.io.specimen.excel.in;
  11
  12 import java.util.ArrayList;
  13 import java.util.List;
  14 import java.util.TreeMap;
  15
  16 import org.apache.log4j.Logger;
  17
  18 import eu.etaxonomy.cdm.io.excel.common.ExcelRowBase;
  19 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  20 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  21 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
  22 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  23 import eu.etaxonomy.cdm.model.reference.Reference;
  24
  25 /**
  26  * @author a.mueller
  27  * @created 08.04.2011
  28  * @version 1.0
  29  */
  30 public class SpecimenRow extends ExcelRowBase{
  31         @SuppressWarnings("unused")
  32         private static final Logger logger = Logger.getLogger(SpecimenRow.class);
  33
  34         private String basisOfRecord;
  35
  36         private String country;
  37         private String isoCountry;
  38         private String locality;
  39         private String latitude;
  40         private String longitude;
  41         private String referenceSystem;
  42         private String errorRadius;
  43         private String altitude;
  44         private String altitudeMax;
  45         private String fieldNotes;
  46         private String collectingDate;
  47         private String collectingDateEnd;
  48         private String collectorsNumber;
  49
  50         private String sex;
  51
  52         private String accessionNumber;
  53         private String barcode;
  54
  55         //      private String author;
  56
  57 //      private String family;
  58 //      private String genus;
  59 //      private String specificEpithet;
  60         private String collectionCode;
  61         private String collection;
  62
  63
  64         private TreeMap<Integer, IdentifiableSource> sources = new TreeMap<Integer, IdentifiableSource>();
  65         private TreeMap<Integer, String> collectors = new TreeMap<Integer, String>();
  66         private TreeMap<Integer, String> unitNotes = new TreeMap<Integer, String>();
  67         private TreeMap<Integer, SpecimenTypeDesignation> types = new TreeMap<Integer, SpecimenTypeDesignation>();
  68         private TreeMap<Integer, DeterminationLight> determinations = new TreeMap<Integer, DeterminationLight>();
  69         private List<PostfixTerm> levels  = new ArrayList<PostfixTerm>();
  70
  71
  72
  73         public SpecimenRow() {
  74         }
  75
  76
  77
  78         //      may be public if necessary
  79         protected class DeterminationLight{
  80                 String family;
  81                 String genus;
  82                 String rank;
  83                 String fullName;
  84                 String speciesEpi;
  85                 String infraSpeciesEpi;
  86                 String author;
  87                 String modifier;
  88                 String determinedBy;
  89                 String determinedWhen;
  90                 String notes;
  91         }
  92
  93
  94 // **************************** GETTER / SETTER *********************************/
  95
  96         public void setBasisOfRecord(String basisOfRecord) {
  97                 this.basisOfRecord = basisOfRecord;
  98         }
  99
 100
 101         public String getBasisOfRecord() {
 102                 return basisOfRecord;
 103         }
 104
 105
 106         public void setCountry(String country) {
 107                 this.country = country;
 108         }
 109
 110
 111         public String getCountry() {
 112                 return country;
 113         }
 114
 115
 116         public void setIsoCountry(String isoCountry) {
 117                 this.isoCountry = isoCountry;
 118         }
 119
 120
 121         public String getIsoCountry() {
 122                 return isoCountry;
 123         }
 124
 125
 126         public void setLocality(String locality) {
 127                 this.locality = locality;
 128         }
 129
 130
 131         public String getLocality() {
 132                 return locality;
 133         }
 134
 135
 136         public void setFieldNotes(String fieldNotes) {
 137                 this.fieldNotes = fieldNotes;
 138         }
 139
 140
 141         public String getFieldNotes() {
 142                 return fieldNotes;
 143         }
 144
 145
 146         public void setAccessionNumber(String accessionNumber) {
 147                 this.accessionNumber = accessionNumber;
 148         }
 149
 150
 151         public String getAccessionNumber() {
 152                 return accessionNumber;
 153         }
 154
 155
 156         public void setBarcode(String barcode) {
 157                 this.barcode = barcode;
 158         }
 159 //
 160 //      /**
 161 //       * @return the author
 162 //       */
 163 //      public String getAuthor() {
 164 //              return author;
 165 //      }
 166 //
 167 //
 168 //      /**
 169 //       * @param author the author to set
 170 //       */
 171 //      public void setAuthor(String author) {
 172 //              this.author = author;
 173 //      }
 174
 175
 176         /**
 177          * @return the absoluteElevation
 178          */
 179         public String getAltitude() {
 180                 return altitude;
 181         }
 182
 183
 184         /**
 185          * @param absoluteElevation the absoluteElevation to set
 186          */
 187         public void setAltitude(String altitude) {
 188                 this.altitude = altitude;
 189         }
 190
 191
 192         /**
 193          * @return the collectionCode
 194          */
 195         public String getCollectionCode() {
 196                 return collectionCode;
 197         }
 198
 199
 200         /**
 201          * @param collectionCode the collectionCode to set
 202          */
 203         public void setCollectionCode(String collectionCode) {
 204                 this.collectionCode = collectionCode;
 205         }
 206
 207
 208         /**
 209          * @return the collectingDate
 210          */
 211         public String getCollectingDate() {
 212                 return collectingDate;
 213         }
 214
 215
 216         /**
 217          * @param collectingDate the collectingDate to set
 218          */
 219         public void setCollectingDate(String collectingDate) {
 220                 this.collectingDate = collectingDate;
 221         }
 222
 223
 224         /**
 225          * @return the collectorsNumber
 226          */
 227         public String getCollectorsNumber() {
 228                 return collectorsNumber;
 229         }
 230
 231
 232         /**
 233          * @param collectorsNumber the collectorsNumber to set
 234          */
 235         public void setCollectorsNumber(String collectorsNumber) {
 236                 this.collectorsNumber = collectorsNumber;
 237         }
 238
 239
 240         /**
 241          * @return the barcode
 242          */
 243         public String getBarcode() {
 244                 return barcode;
 245         }
 246
 247
 248         /**
 249          * @return the collectingDateEnd
 250          */
 251         public String getCollectingDateEnd() {
 252                 return collectingDateEnd;
 253         }
 254
 255
 256         /**
 257          * @param collectingDateEnd the collectingDateEnd to set
 258          */
 259         public void setCollectingDateEnd(String collectingDateEnd) {
 260                 this.collectingDateEnd = collectingDateEnd;
 261         }
 262
 263
 264         /**
 265          * @return the latitude
 266          */
 267         public String getLatitude() {
 268                 return latitude;
 269         }
 270
 271
 272         /**
 273          * @param latitude the latitude to set
 274          */
 275         public void setLatitude(String latitude) {
 276                 this.latitude = latitude;
 277         }
 278
 279
 280         /**
 281          * @return the longitude
 282          */
 283         public String getLongitude() {
 284                 return longitude;
 285         }
 286
 287
 288         /**
 289          * @param longitude the longitude to set
 290          */
 291         public void setLongitude(String longitude) {
 292                 this.longitude = longitude;
 293         }
 294
 295
 296         public void putIdInSource(int key, String id){
 297                 IdentifiableSource source = getOrMakeSource(key);
 298                 source.setIdInSource(id);
 299         }
 300         public void putSourceReference(int key, Reference<?> reference){
 301                 IdentifiableSource source = getOrMakeSource(key);
 302                 source.setCitation(reference);
 303         }
 304
 305         public List<IdentifiableSource> getSources() {
 306                 return getOrdered(sources);
 307         }
 308
 309         public void putCollector(int key, String collector){
 310                 this.collectors.put(key, collector);
 311         }
 312
 313         public List<String> getCollectors() {
 314                 return getOrdered(collectors);
 315         }
 316
 317         public void putUnitNote(int key, String unitNote){
 318                 this.unitNotes.put(key, unitNote);
 319         }
 320
 321         public List<String> getUnitNotes() {
 322                 return getOrdered(unitNotes);
 323         }
 324
 325
 326
 327         /**
 328          * @param key
 329          * @return
 330          */
 331         private IdentifiableSource getOrMakeSource(int key) {
 332                 IdentifiableSource  source = sources.get(key);
 333                 if (source == null){
 334                         source = IdentifiableSource.NewInstance();
 335                         sources.put(key, source);
 336                 }
 337                 return source;
 338         }
 339
 340
 341         public void putTypeCategory(int key, SpecimenTypeDesignationStatus status){
 342                 SpecimenTypeDesignation designation = getOrMakeTypeDesignation(key);
 343                 designation.setTypeStatus(status);
 344         }
 345         public void putTypifiedName(int key, TaxonNameBase<?,?> name){
 346                 if (name != null){
 347                         SpecimenTypeDesignation designation = getOrMakeTypeDesignation(key);
 348                         name.addTypeDesignation(designation, false);
 349                 }
 350         }
 351
 352         public List<SpecimenTypeDesignation> getTypeDesignations() {
 353                 return getOrdered(types);
 354         }
 355
 356
 357         private SpecimenTypeDesignation getOrMakeTypeDesignation(int key) {
 358                 SpecimenTypeDesignation designation = types.get(key);
 359                 if (designation == null){
 360                         designation = SpecimenTypeDesignation.NewInstance();
 361                         types.put(key, designation);
 362                 }
 363                 return designation;
 364         }
 365
 366         public void putDeterminationFamily(int key, String family){
 367                 DeterminationLight determinationEvent = getOrMakeDetermination(key);
 368                 determinationEvent.family = family;
 369         }
 370
 371         public void putDeterminationFullName(int key, String fullName){
 372                 DeterminationLight determinationEvent = getOrMakeDetermination(key);
 373                 determinationEvent.fullName = fullName;
 374         }
 375
 376         public void putDeterminationRank(int key, String rank){
 377                 DeterminationLight determinationEvent = getOrMakeDetermination(key);
 378                 determinationEvent.rank = rank;
 379         }
 380
 381         public void putDeterminationGenus(int key, String genus){
 382                 DeterminationLight determinationEvent = getOrMakeDetermination(key);
 383                 determinationEvent.genus = genus;
 384         }
 385
 386         public void putDeterminationSpeciesEpi(int key, String speciesEpi){
 387                 DeterminationLight determinationEvent = getOrMakeDetermination(key);
 388                 determinationEvent.speciesEpi = speciesEpi;
 389         }
 390
 391         public void putDeterminationInfraSpeciesEpi(int key, String infraSpeciesEpi){
 392                 DeterminationLight determinationEvent = getOrMakeDetermination(key);
 393                 determinationEvent.infraSpeciesEpi = infraSpeciesEpi;
 394         }
 395
 396         public void putDeterminationAuthor(int key, String author){
 397                 DeterminationLight determinationEvent = getOrMakeDetermination(key);
 398                 determinationEvent.author = author;
 399         }
 400
 401         public void putDeterminationDeterminedBy(int key, String determinedBy){
 402                 DeterminationLight determinationEvent = getOrMakeDetermination(key);
 403                 determinationEvent.determinedBy = determinedBy;
 404         }
 405
 406         public void putDeterminationDeterminedWhen(int key, String determinedWhen){
 407                 DeterminationLight determinationEvent = getOrMakeDetermination(key);
 408                 determinationEvent.determinedWhen = determinedWhen;
 409         }
 410
 411         public void putDeterminationDeterminationNotes(int key, String notes){
 412                 DeterminationLight determinationEvent = getOrMakeDetermination(key);
 413                 determinationEvent.notes = notes;
 414         }
 415
 416         public void putDeterminationDeterminationModifier(int key, String modifier){
 417                 DeterminationLight determinationEvent = getOrMakeDetermination(key);
 418                 determinationEvent.modifier = modifier;
 419         }
 420
 421         public List<DeterminationLight> getDetermination() {
 422                 return getOrdered(determinations);
 423         }
 424
 425
 426
 427         private DeterminationLight getOrMakeDetermination(int key) {
 428                 DeterminationLight determination = this.determinations.get(key);
 429                 if (determination == null){
 430                         determination = new DeterminationLight();
 431                         this.determinations.put(key, determination);
 432                 }
 433                 return determination;
 434         }
 435
 436
 437         private<T extends Object> List<T> getOrdered(TreeMap<?, T> tree) {
 438                 List<T> result = new ArrayList<T>();
 439                 for (T value : tree.values()){
 440                         result.add(value);
 441                 }
 442                 return result;
 443         }
 444
 445         public void setSex(String sex) {
 446                 this.sex = sex;
 447         }
 448
 449
 450         public String getSex() {
 451                 return sex;
 452         }
 453
 454
 455         /**
 456          * @return the referenceSystem
 457          */
 458         public String getReferenceSystem() {
 459                 return referenceSystem;
 460         }
 461
 462
 463         /**
 464          * @param referenceSystem the referenceSystem to set
 465          */
 466         public void setReferenceSystem(String referenceSystem) {
 467                 this.referenceSystem = referenceSystem;
 468         }
 469
 470
 471         /**
 472          * @return the errorRadius
 473          */
 474         public String getErrorRadius() {
 475                 return errorRadius;
 476         }
 477
 478
 479         /**
 480          * @param errorRadius the errorRadius to set
 481          */
 482         public void setErrorRadius(String errorRadius) {
 483                 this.errorRadius = errorRadius;
 484         }
 485
 486
 487         public void setCollection(String collection) {
 488                 this.collection = collection;
 489         }
 490
 491
 492         public String getCollection() {
 493                 return collection;
 494         }
 495
 496
 497         public void addLeveledArea(String levelPostfix, String value) {
 498                 PostfixTerm area = new PostfixTerm();
 499                 area.term = value;
 500                 area.postfix = levelPostfix;
 501                 this.levels.add(area);
 502         }
 503
 504         public List<PostfixTerm> getLeveledAreas(){
 505                 return levels;
 506         }
 507
 508         public void setAltitudeMax(String altitudeMax) {
 509                 this.altitudeMax = altitudeMax;
 510         }
 511
 512
 513         public String getAltitudeMax() {
 514                 return altitudeMax;
 515         }
 516
 517
 518 }