Source code

001package com.hfg.bio.seq.genomic.assembly;
002
003import java.io.BufferedReader;
004import java.io.File;
005import java.io.FileReader;
006import java.io.IOException;
007import java.text.ParseException;
008import java.text.SimpleDateFormat;
009import java.util.ArrayList;
010import java.util.Date;
011import java.util.HashMap;
012import java.util.List;
013import java.util.Map;
014
015import com.hfg.bio.taxonomy.ncbi.NCBITaxon;
016import com.hfg.util.BooleanUtil;
017import com.hfg.util.CompareUtil;
018import com.hfg.util.StringBuilderPlus;
019import com.hfg.util.io.TSV;
020import com.hfg.xml.HfgXML;
021import com.hfg.xml.XMLName;
022import com.hfg.xml.XMLTag;
023
024//------------------------------------------------------------------------------
025/**
026 * Information about an NCBI genomic assembly.
027 * See ftp://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt for a description of the fields.
028 * <div>
029 * @author J. Alex Taylor, hairyfatguy.com
030 * </div>
031 */
032//------------------------------------------------------------------------------
033// com.hfg XML/HTML Coding Library
034//
035// This library is free software; you can redistribute it and/or
036// modify it under the terms of the GNU Lesser General Public
037// License as published by the Free Software Foundation; either
038// version 2.1 of the License, or (at your option) any later version.
039//
040// This library is distributed in the hope that it will be useful,
041// but WITHOUT ANY WARRANTY; without even the implied warranty of
042// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
043// Lesser General Public License for more details.
044//
045// You should have received a copy of the GNU Lesser General Public
046// License along with this library; if not, write to the Free Software
047// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
048//
049// J. Alex Taylor, President, Founder, CEO, COO, CFO, OOPS hairyfatguy.com
050// jataylor@hairyfatguy.com
051//------------------------------------------------------------------------------
052
053public class NCBIGenomicAssemblyInfo implements Comparable<NCBIGenomicAssemblyInfo>
054{
055   // Tag names
056   private static final XMLName NCBI_GENOMIC_ASSEMBLY_INFO = new XMLName("NCBIGenomicAssemblyInfo", HfgXML.HFG_NAMESPACE);
057   private static final XMLName ASSEMBLY_ACCESSION          = new XMLName("AssemblyAccession",    HfgXML.HFG_NAMESPACE);
058   private static final XMLName BIOPROJECT_ACCESSION        = new XMLName("BioprojectAccession",    HfgXML.HFG_NAMESPACE);
059   private static final XMLName BIOSAMPLE_ACCESSION         = new XMLName("BiosampleAccession",    HfgXML.HFG_NAMESPACE);
060   private static final XMLName WGS_ACCESSION               = new XMLName("WGS_Accession",    HfgXML.HFG_NAMESPACE);
061   private static final XMLName REFSEQ_CATEGORY             = new XMLName("RefseqCategory",    HfgXML.HFG_NAMESPACE);
062   private static final XMLName ORGANISM_TAXON              = new XMLName("OrganismTaxon",    HfgXML.HFG_NAMESPACE);
063   private static final XMLName SPECIES_TAXON               = new XMLName("SpeciesTaxon",    HfgXML.HFG_NAMESPACE);
064   private static final XMLName INFRASPECIFIC_NAME          = new XMLName("InfraspecificName",    HfgXML.HFG_NAMESPACE);
065   private static final XMLName ISOLATE                     = new XMLName("Isolate",    HfgXML.HFG_NAMESPACE);
066   private static final XMLName ASSEMBLY_VERSION_STATUS     = new XMLName("AssemblyVersionStatus",    HfgXML.HFG_NAMESPACE);
067   private static final XMLName ASSEMBLY_LEVEL              = new XMLName("AssemblyLevel",    HfgXML.HFG_NAMESPACE);
068   private static final XMLName ASSEMBLY_RELEASE_TYPE       = new XMLName("AssemblyReleaseType",    HfgXML.HFG_NAMESPACE);
069   private static final XMLName GENOMIC_REPRESENTATION      = new XMLName("GenomicRepresentation",    HfgXML.HFG_NAMESPACE);
070   private static final XMLName RELEASE_DATE                = new XMLName("ReleaseDate",    HfgXML.HFG_NAMESPACE);
071   private static final XMLName ASSEMBLY_NAME               = new XMLName("AssemblyName",    HfgXML.HFG_NAMESPACE);
072   private static final XMLName SUBMITTER                   = new XMLName("Submitter",    HfgXML.HFG_NAMESPACE);
073   private static final XMLName GENBANK_REFSEQ_PAIRED_ASSEMBLY = new XMLName("GenBankRefseqPairedAssembly",    HfgXML.HFG_NAMESPACE);
074   private static final XMLName GENOMIC_PAIRED_ASSEMBLY_COMPARISON = new XMLName("GenomicPairedAssemblyComparison",    HfgXML.HFG_NAMESPACE);
075   private static final XMLName FTP_PATH                    = new XMLName("FTP_Path",    HfgXML.HFG_NAMESPACE);
076   private static final XMLName EXCLUDED_FROM_REFSEQ        = new XMLName("ExcludedFromRefseq",    HfgXML.HFG_NAMESPACE);
077   private static final XMLName GENOMIC_RELATION_TO_TYPE_MATERIAL = new XMLName("GenomicRelationToTypeMaterial",    HfgXML.HFG_NAMESPACE);
078
079   private String mAssemblyAccession;
080   private String mBioprojectAccession;
081   private String mBiosampleAccession;
082   private String mWGSAccession;
083   private GenomicRefSeqCategory mRefseqCategory;
084   private NCBITaxon mOrganismNCBITaxon;
085   private NCBITaxon mSpeciesNCBITaxon; // The species taxid will differ from the
086                                        // organism taxid (column 6) only when the
087                                        // organism was reported at a sub-species or strain level.
088   private String mInfraspecificName;
089   private String mIsolate;
090   private GenomicAssemblyVersionStatus mAssemblyVersionStatus;
091   private GenomicAssemblyLevel mAssemblyLevel;
092   private GenomicAssemblyReleaseType mAssemblyReleaseType;
093   private GenomicRepresentation mGenomicRepresentation;
094   private Date mReleaseDate;
095   private String mAssemblyName;
096   private String mSubmitter;
097   private String mGenBankRefSeqPairedAssembly;
098   private GenomicPairedAssemblyComparison mGenomicPairedAssemblyComparison;
099   private String mFTP_Path;
100   private Boolean mExcludedFromRefSeq;
101   private GenomicRelationToTypeMaterial mGenomicRelationToTypeMaterial;
102
103
104   private SimpleDateFormat mDateFormat = new SimpleDateFormat("YYYY-MM-dd");
105
106   //##########################################################################
107   // CONSTRUCTORS
108   //##########################################################################
109
110   //---------------------------------------------------------------------------
111   public NCBIGenomicAssemblyInfo()
112   {
113
114   }
115
116   //---------------------------------------------------------------------------
117   public NCBIGenomicAssemblyInfo(XMLTag inXMLTag)
118   {
119      inXMLTag.verifyTagName(NCBI_GENOMIC_ASSEMBLY_INFO);
120
121      XMLTag assemblyAccessionTag = inXMLTag.getRequiredSubtagByName(ASSEMBLY_ACCESSION);
122      setAssemblyAccession(assemblyAccessionTag.getContent().trim());
123
124      XMLTag bioprojectAccessionTag = inXMLTag.getRequiredSubtagByName(BIOPROJECT_ACCESSION);
125      setBioprojectAccession(bioprojectAccessionTag.getContent().trim());
126
127      XMLTag biosampleAccessionTag = inXMLTag.getRequiredSubtagByName(BIOSAMPLE_ACCESSION);
128      setBioprojectAccession(biosampleAccessionTag.getContent().trim());
129
130      XMLTag wgsAccessionTag = inXMLTag.getRequiredSubtagByName(WGS_ACCESSION);
131      setWGSAccession(wgsAccessionTag.getContent().trim());
132
133      XMLTag refseqCategoryTag = inXMLTag.getRequiredSubtagByName(REFSEQ_CATEGORY);
134      setRefSeqCategory(GenomicRefSeqCategory.valueOf(refseqCategoryTag.getContent().trim()));
135
136      XMLTag organismTaxonTag = inXMLTag.getRequiredSubtagByName(ORGANISM_TAXON);
137      setOrganismTaxon(NCBITaxon.getByTaxonId(Integer.parseInt(organismTaxonTag.getContent().trim())));
138
139      XMLTag speciesTaxonTag = inXMLTag.getRequiredSubtagByName(SPECIES_TAXON);
140      setSpeciesTaxon(NCBITaxon.getByTaxonId(Integer.parseInt(speciesTaxonTag.getContent().trim())));
141
142      XMLTag infraspecificNameTag = inXMLTag.getOptionalSubtagByName(INFRASPECIFIC_NAME);
143      if (infraspecificNameTag != null)
144      {
145         setInfraspecificName(infraspecificNameTag.getContent().trim());
146      }
147
148      XMLTag isolateTag = inXMLTag.getOptionalSubtagByName(ISOLATE);
149      if (isolateTag != null)
150      {
151         setIsolate(isolateTag.getContent().trim());
152      }
153
154      XMLTag assemblyVersionStatusTag = inXMLTag.getRequiredSubtagByName(ASSEMBLY_VERSION_STATUS);
155      setAssemblyVersionStatus(GenomicAssemblyVersionStatus.valueOf(assemblyVersionStatusTag.getContent().trim()));
156
157      XMLTag assemblyLevelTag = inXMLTag.getRequiredSubtagByName(ASSEMBLY_LEVEL);
158      setAssemblyLevel(GenomicAssemblyLevel.valueOf(assemblyLevelTag.getContent().trim()));
159
160      XMLTag assemblyReleaseTypeTag = inXMLTag.getRequiredSubtagByName(ASSEMBLY_RELEASE_TYPE);
161      setAssemblyReleaseType(GenomicAssemblyReleaseType.valueOf(assemblyReleaseTypeTag.getContent().trim()));
162
163      XMLTag genomicRepresentationTag = inXMLTag.getRequiredSubtagByName(GENOMIC_REPRESENTATION);
164      setGenomicRepresentation(GenomicRepresentation.valueOf(genomicRepresentationTag.getContent().trim()));
165
166      XMLTag releaseDateTag = inXMLTag.getRequiredSubtagByName(RELEASE_DATE);
167      try
168      {
169         setReleaseDate(mDateFormat.parse(releaseDateTag.getContent().trim()));
170      }
171      catch (ParseException e)
172      {
173         throw new RuntimeException(e);
174      }
175
176      XMLTag assemblyNameTag = inXMLTag.getRequiredSubtagByName(ASSEMBLY_NAME);
177      setAssemblyName(assemblyNameTag.getContent().trim());
178
179      XMLTag submitterTag = inXMLTag.getRequiredSubtagByName(SUBMITTER);
180      setSubmitter(submitterTag.getContent().trim());
181
182      XMLTag genbankRefseqPairedAssemblyTag = inXMLTag.getOptionalSubtagByName(GENBANK_REFSEQ_PAIRED_ASSEMBLY);
183      if (genbankRefseqPairedAssemblyTag != null)
184      {
185         setGenBankRefSeqPairedAssembly(genbankRefseqPairedAssemblyTag.getContent().trim());
186      }
187
188      XMLTag genomicPairedAssemblyComparisonTag = inXMLTag.getOptionalSubtagByName(GENOMIC_PAIRED_ASSEMBLY_COMPARISON);
189      if (genomicPairedAssemblyComparisonTag != null)
190      {
191         setPairedAssemblyComparison(GenomicPairedAssemblyComparison.valueOf(genomicPairedAssemblyComparisonTag.getContent().trim()));
192      }
193
194      XMLTag ftpPathTag = inXMLTag.getRequiredSubtagByName(FTP_PATH);
195      setFTP_Path(ftpPathTag.getContent().trim());
196
197      XMLTag excludedFromRefseqTag = inXMLTag.getRequiredSubtagByName(EXCLUDED_FROM_REFSEQ);
198      setExcludedFromRefSeq(BooleanUtil.valueOf(excludedFromRefseqTag.getContent().trim()));
199
200      XMLTag genomicRelationToTypeMaterialTag = inXMLTag.getOptionalSubtagByName(GENOMIC_RELATION_TO_TYPE_MATERIAL);
201      if (genomicRelationToTypeMaterialTag != null)
202      {
203         setRelationToTypeMaterial(GenomicRelationToTypeMaterial.valueOf(genomicRelationToTypeMaterialTag.getContent().trim()));
204      }
205   }
206
207   //##########################################################################
208   // PUBLIC METHODS
209   //##########################################################################
210
211   //---------------------------------------------------------------------------
212   /**
213    * Use for processing an assembly_summary.txt file from the NCBI ftp site.
214    * @param inFile the assembly_summary.txt file
215    * @return a Map with species taxons as the keys
216    * @throws IOException
217    * @throws ParseException
218    */
219   public static Map<NCBITaxon, List<NCBIGenomicAssemblyInfo>> extractInfoFromAssemblySummaryFile(File inFile)
220         throws IOException, ParseException
221   {
222      List<String[]> tsvData = TSV.parse(new BufferedReader(new FileReader(inFile)));
223
224      Map<NCBITaxon, List<NCBIGenomicAssemblyInfo>> assemblyMap = new HashMap<>(tsvData.size());
225
226      String[] headerCols = tsvData.get(1);
227      if (headerCols.length != 22)
228      {
229         throw new IOException("The assembly_summary.txt file does not have the expected number of columns!");
230      }
231
232      SimpleDateFormat YYYYMMDD_format = new SimpleDateFormat("yyyy/MM/dd");
233
234      // Build the map of assembly data
235      for (int i = 2; i < tsvData.size(); i++)
236      {
237         String[] fields = tsvData.get(i);
238
239         NCBIGenomicAssemblyInfo assemblyInfo = new NCBIGenomicAssemblyInfo()
240               .setAssemblyAccession(fields[0])
241               .setBioprojectAccession(fields[1])
242               .setBiosampleAccession(fields[2])
243               .setWGSAccession(fields[3])
244               .setRefSeqCategory(GenomicRefSeqCategory.valueOf(fields[4]))
245               .setOrganismTaxon(NCBITaxon.getByTaxonId(Integer.parseInt(fields[5])))
246               .setSpeciesTaxon(NCBITaxon.getByTaxonId(Integer.parseInt(fields[6])))
247               // Skipping field 7 (the species name) since is part of the taxon info
248               .setInfraspecificName(fields[8])
249               .setIsolate(fields[9])
250               .setAssemblyVersionStatus(GenomicAssemblyVersionStatus.valueOf(fields[10]))
251               .setAssemblyLevel(GenomicAssemblyLevel.valueOf(fields[11]))
252               .setAssemblyReleaseType(GenomicAssemblyReleaseType.valueOf(fields[12]))
253               .setGenomicRepresentation(GenomicRepresentation.valueOf(fields[13]))
254               .setReleaseDate(YYYYMMDD_format.parse(fields[14]))  // Ex: 2019/07/30
255               .setAssemblyName(fields[15])
256               .setSubmitter(fields[16])
257               .setGenBankRefSeqPairedAssembly(fields[17])
258               .setPairedAssemblyComparison(GenomicPairedAssemblyComparison.valueOf(fields[18]))
259               .setFTP_Path(fields[19])
260               .setExcludedFromRefSeq(BooleanUtil.valueOf(fields[20]))
261               .setRelationToTypeMaterial(GenomicRelationToTypeMaterial.valueOf(fields[21]));
262
263         List<NCBIGenomicAssemblyInfo> infoList = assemblyMap.get(assemblyInfo.getSpeciesTaxon());
264         if (null == infoList)
265         {
266            infoList = new ArrayList<>(2);
267            assemblyMap.put(assemblyInfo.getSpeciesTaxon(), infoList);
268         }
269
270         infoList.add(assemblyInfo);
271      }
272
273      return assemblyMap;
274   }
275
276
277   //---------------------------------------------------------------------------
278   @Override
279   public String toString()
280   {
281      StringBuilderPlus buffer = new StringBuilderPlus().setDelimiter("\n")
282         .delimitedAppend("assembly_accession: " + getAssemblyAccession())
283         .delimitedAppend("bioproject: " + getBioprojectAccession())
284         .delimitedAppend("biosample: " + getBiosampleAccession())
285         .delimitedAppend("wgs_master: " + getWGSAccession())
286         .delimitedAppend("refseq_category: " + getRefSeqCategory())
287         .delimitedAppend("taxid: " + getOrganismTaxon().getTaxonId())
288         .delimitedAppend("species_taxid: " + getSpeciesTaxon().getTaxonId())
289         .delimitedAppend("organism_name: " + getSpeciesTaxon().getScientificName())
290         .delimitedAppend("infraspecific_name: " + getInfraspecificName())
291         .delimitedAppend("isolate: " + getIsolate())
292         .delimitedAppend("version_status: " + getAssemblyVersionStatus())
293         .delimitedAppend("assembly_level: " + getAssemblyLevel())
294         .delimitedAppend("release_type: " + getAssemblyReleaseType())
295         .delimitedAppend("genome_rep: " + getGenomicRepresentation())
296         .delimitedAppend("seq_rel_date: " + getReleaseDate())
297         .delimitedAppend("asm_name: " + getAssemblyName())
298         .delimitedAppend("submitter: " + getSubmitter())
299         .delimitedAppend("gbrs_paired_asm: " + getGenBankRefSeqPairedAssembly())
300         .delimitedAppend("paired_asm_comp: " + getPairedAssemblyComparison())
301         .delimitedAppend("ftp_path: " + getFTP_Path())
302         .delimitedAppend("excluded_from_refseq: " + getExcludedFromRefSeq())
303         .delimitedAppend("relation_to_type_material: " + (getRelationToTypeMaterial() != null ? getRelationToTypeMaterial() : ""));
304
305      return buffer.toString();
306   }
307
308   //---------------------------------------------------------------------------
309   public XMLTag toXMLTag()
310   {
311      XMLTag rootTag = new XMLTag(NCBI_GENOMIC_ASSEMBLY_INFO);
312
313      rootTag.addSubtag(ASSEMBLY_ACCESSION).setContent(getAssemblyAccession());
314      rootTag.addSubtag(BIOPROJECT_ACCESSION).setContent(getBioprojectAccession());
315      rootTag.addSubtag(BIOSAMPLE_ACCESSION).setContent(getBiosampleAccession());
316      rootTag.addSubtag(WGS_ACCESSION).setContent(getWGSAccession());
317      rootTag.addSubtag(REFSEQ_CATEGORY).setContent(getRefSeqCategory().name());
318      rootTag.addSubtag(ORGANISM_TAXON).setContent(getOrganismTaxon().getTaxonId());
319      rootTag.addSubtag(SPECIES_TAXON).setContent(getSpeciesTaxon().getTaxonId());
320
321      if (getInfraspecificName() != null)
322      {
323         rootTag.addSubtag(INFRASPECIFIC_NAME).setContent(getInfraspecificName());
324      }
325
326      if (getIsolate() != null)
327      {
328         rootTag.addSubtag(ISOLATE).setContent(getIsolate());
329      }
330
331      rootTag.addSubtag(ASSEMBLY_VERSION_STATUS).setContent(getAssemblyVersionStatus().name());
332      rootTag.addSubtag(ASSEMBLY_LEVEL).setContent(getAssemblyLevel().name());
333      rootTag.addSubtag(ASSEMBLY_RELEASE_TYPE).setContent(getAssemblyReleaseType().name());
334      rootTag.addSubtag(GENOMIC_REPRESENTATION).setContent(getGenomicRepresentation().name());
335      rootTag.addSubtag(RELEASE_DATE).setContent(mDateFormat.format(getReleaseDate()));
336      rootTag.addSubtag(ASSEMBLY_NAME).setContent(getAssemblyName());
337      rootTag.addSubtag(SUBMITTER).setContent(getSubmitter());
338
339
340      if (getGenBankRefSeqPairedAssembly() != null)
341      {
342         rootTag.addSubtag(GENBANK_REFSEQ_PAIRED_ASSEMBLY).setContent(getGenBankRefSeqPairedAssembly());
343      }
344
345      if (getPairedAssemblyComparison() != null)
346      {
347         rootTag.addSubtag(GENOMIC_PAIRED_ASSEMBLY_COMPARISON).setContent(getPairedAssemblyComparison().name());
348      }
349
350      rootTag.addSubtag(FTP_PATH).setContent(getFTP_Path());
351      rootTag.addSubtag(EXCLUDED_FROM_REFSEQ).setContent(getExcludedFromRefSeq() ? "true" : "false");
352
353      if (getRelationToTypeMaterial() != null)
354      {
355         rootTag.addSubtag(GENOMIC_RELATION_TO_TYPE_MATERIAL).setContent(getRelationToTypeMaterial().name());
356      }
357
358      return rootTag;
359   }
360
361   //---------------------------------------------------------------------------
362   public NCBIGenomicAssemblyInfo setAssemblyAccession(String inValue)
363   {
364      mAssemblyAccession = inValue;
365      return this;
366   }
367
368   //---------------------------------------------------------------------------
369   public String getAssemblyAccession()
370   {
371      return mAssemblyAccession;
372   }
373
374
375   //---------------------------------------------------------------------------
376   public NCBIGenomicAssemblyInfo setBioprojectAccession(String inValue)
377   {
378      mBioprojectAccession = inValue;
379      return this;
380   }
381
382   //---------------------------------------------------------------------------
383   public String getBioprojectAccession()
384   {
385      return mBioprojectAccession;
386   }
387
388
389   //---------------------------------------------------------------------------
390   public NCBIGenomicAssemblyInfo setBiosampleAccession(String inValue)
391   {
392      mBiosampleAccession = inValue;
393      return this;
394   }
395
396   //---------------------------------------------------------------------------
397   public String getBiosampleAccession()
398   {
399      return mBiosampleAccession;
400   }
401
402
403   //---------------------------------------------------------------------------
404   public NCBIGenomicAssemblyInfo setWGSAccession(String inValue)
405   {
406      mWGSAccession = inValue;
407      return this;
408   }
409
410   //---------------------------------------------------------------------------
411   public String getWGSAccession()
412   {
413      return mWGSAccession;
414   }
415
416
417   //---------------------------------------------------------------------------
418   public NCBIGenomicAssemblyInfo setRefSeqCategory(GenomicRefSeqCategory inValue)
419   {
420      mRefseqCategory = inValue;
421      return this;
422   }
423
424   //---------------------------------------------------------------------------
425   public GenomicRefSeqCategory getRefSeqCategory()
426   {
427      return mRefseqCategory;
428   }
429
430
431   //---------------------------------------------------------------------------
432   public NCBIGenomicAssemblyInfo setOrganismTaxon(NCBITaxon inValue)
433   {
434      mOrganismNCBITaxon = inValue;
435      return this;
436   }
437
438   //---------------------------------------------------------------------------
439   public NCBITaxon getOrganismTaxon()
440   {
441      return mOrganismNCBITaxon;
442   }
443
444
445   //---------------------------------------------------------------------------
446   public NCBIGenomicAssemblyInfo setSpeciesTaxon(NCBITaxon inValue)
447   {
448      mSpeciesNCBITaxon = inValue;
449      return this;
450   }
451
452   //---------------------------------------------------------------------------
453   public NCBITaxon getSpeciesTaxon()
454   {
455      return mSpeciesNCBITaxon;
456   }
457
458
459   //---------------------------------------------------------------------------
460   public NCBIGenomicAssemblyInfo setInfraspecificName(String inValue)
461   {
462      mInfraspecificName = inValue;
463      return this;
464   }
465
466   //---------------------------------------------------------------------------
467   public String getInfraspecificName()
468   {
469      return mInfraspecificName;
470   }
471
472
473   //---------------------------------------------------------------------------
474   public NCBIGenomicAssemblyInfo setIsolate(String inValue)
475   {
476      mIsolate = inValue;
477      return this;
478   }
479
480   //---------------------------------------------------------------------------
481   public String getIsolate()
482   {
483      return mIsolate;
484   }
485
486
487   //---------------------------------------------------------------------------
488   public NCBIGenomicAssemblyInfo setAssemblyVersionStatus(GenomicAssemblyVersionStatus inValue)
489   {
490      mAssemblyVersionStatus = inValue;
491      return this;
492   }
493
494   //---------------------------------------------------------------------------
495   public GenomicAssemblyVersionStatus getAssemblyVersionStatus()
496   {
497      return mAssemblyVersionStatus;
498   }
499
500
501   //---------------------------------------------------------------------------
502   public NCBIGenomicAssemblyInfo setAssemblyLevel(GenomicAssemblyLevel inValue)
503   {
504      mAssemblyLevel = inValue;
505      return this;
506   }
507
508   //---------------------------------------------------------------------------
509   public GenomicAssemblyLevel getAssemblyLevel()
510   {
511      return mAssemblyLevel;
512   }
513
514
515   //---------------------------------------------------------------------------
516   public NCBIGenomicAssemblyInfo setAssemblyReleaseType(GenomicAssemblyReleaseType inValue)
517   {
518      mAssemblyReleaseType = inValue;
519      return this;
520   }
521
522   //---------------------------------------------------------------------------
523   public GenomicAssemblyReleaseType getAssemblyReleaseType()
524   {
525      return mAssemblyReleaseType;
526   }
527
528
529   //---------------------------------------------------------------------------
530   public NCBIGenomicAssemblyInfo setGenomicRepresentation(GenomicRepresentation inValue)
531   {
532      mGenomicRepresentation = inValue;
533      return this;
534   }
535
536   //---------------------------------------------------------------------------
537   public GenomicRepresentation getGenomicRepresentation()
538   {
539      return mGenomicRepresentation;
540   }
541
542
543   //---------------------------------------------------------------------------
544   public NCBIGenomicAssemblyInfo setReleaseDate(Date inValue)
545   {
546      mReleaseDate = inValue;
547      return this;
548   }
549
550   //---------------------------------------------------------------------------
551   public Date getReleaseDate()
552   {
553      return mReleaseDate;
554   }
555
556
557   //---------------------------------------------------------------------------
558   public NCBIGenomicAssemblyInfo setAssemblyName(String inValue)
559   {
560      mAssemblyName = inValue;
561      return this;
562   }
563
564   //---------------------------------------------------------------------------
565   public String getAssemblyName()
566   {
567      return mAssemblyName;
568   }
569
570
571   //---------------------------------------------------------------------------
572   public NCBIGenomicAssemblyInfo setSubmitter(String inValue)
573   {
574      mSubmitter = inValue;
575      return this;
576   }
577
578   //---------------------------------------------------------------------------
579   public String getSubmitter()
580   {
581      return mSubmitter;
582   }
583
584
585   //---------------------------------------------------------------------------
586   public NCBIGenomicAssemblyInfo setGenBankRefSeqPairedAssembly(String inValue)
587   {
588      mGenBankRefSeqPairedAssembly = inValue;
589      return this;
590   }
591
592   //---------------------------------------------------------------------------
593   public String getGenBankRefSeqPairedAssembly()
594   {
595      return mGenBankRefSeqPairedAssembly;
596   }
597
598
599   //---------------------------------------------------------------------------
600   public NCBIGenomicAssemblyInfo setPairedAssemblyComparison(GenomicPairedAssemblyComparison inValue)
601   {
602      mGenomicPairedAssemblyComparison = inValue;
603      return this;
604   }
605
606   //---------------------------------------------------------------------------
607   public GenomicPairedAssemblyComparison getPairedAssemblyComparison()
608   {
609      return mGenomicPairedAssemblyComparison;
610   }
611
612
613   //---------------------------------------------------------------------------
614   public NCBIGenomicAssemblyInfo setFTP_Path(String inValue)
615   {
616      mFTP_Path = inValue;
617      return this;
618   }
619
620   //---------------------------------------------------------------------------
621   public String getFTP_Path()
622   {
623      return mFTP_Path;
624   }
625
626
627   //---------------------------------------------------------------------------
628   public NCBIGenomicAssemblyInfo setExcludedFromRefSeq(boolean inValue)
629   {
630      mExcludedFromRefSeq = inValue;
631      return this;
632   }
633
634   //---------------------------------------------------------------------------
635   public boolean getExcludedFromRefSeq()
636   {
637      return mExcludedFromRefSeq;
638   }
639
640
641   //---------------------------------------------------------------------------
642   public NCBIGenomicAssemblyInfo setRelationToTypeMaterial(GenomicRelationToTypeMaterial inValue)
643   {
644      mGenomicRelationToTypeMaterial = inValue;
645      return this;
646   }
647
648   //---------------------------------------------------------------------------
649   public GenomicRelationToTypeMaterial getRelationToTypeMaterial()
650   {
651      return mGenomicRelationToTypeMaterial;
652   }
653
654
655   //---------------------------------------------------------------------------
656   /**
657    * Compares this object with the specified object for order.  Returns a
658    * negative integer, zero, or a positive integer as this object is less
659    * than, equal to, or greater than the specified object.
660    *
661    * <p>The implementor must ensure
662    * {@code sgn(x.compareTo(y)) == -sgn(y.compareTo(x))}
663    * for all {@code x} and {@code y}.  (This
664    * implies that {@code x.compareTo(y)} must throw an exception iff
665    * {@code y.compareTo(x)} throws an exception.)
666    *
667    * <p>The implementor must also ensure that the relation is transitive:
668    * {@code (x.compareTo(y) > 0 && y.compareTo(z) > 0)} implies
669    * {@code x.compareTo(z) > 0}.
670    *
671    * <p>Finally, the implementor must ensure that {@code x.compareTo(y)==0}
672    * implies that {@code sgn(x.compareTo(z)) == sgn(y.compareTo(z))}, for
673    * all {@code z}.
674    *
675    * <p>It is strongly recommended, but <i>not</i> strictly required that
676    * {@code (x.compareTo(y)==0) == (x.equals(y))}.  Generally speaking, any
677    * class that implements the {@code Comparable} interface and violates
678    * this condition should clearly indicate this fact.  The recommended
679    * language is "Note: this class has a natural ordering that is
680    * inconsistent with equals."
681    *
682    * <p>In the foregoing description, the notation
683    * {@code sgn(}<i>expression</i>{@code )} designates the mathematical
684    * <i>signum</i> function, which is defined to return one of {@code -1},
685    * {@code 0}, or {@code 1} according to whether the value of
686    * <i>expression</i> is negative, zero, or positive, respectively.
687    *
688    * @param inObj2 the object to be compared.
689    * @return a negative integer, zero, or a positive integer as this object
690    * is less than, equal to, or greater than the specified object.
691    * @throws ClassCastException   if the specified object's type prevents it
692    *                              from being compared to this object.
693    */
694   @Override
695   public int compareTo(NCBIGenomicAssemblyInfo inObj2)
696   {
697      int result = -1;
698      if (inObj2 != null)
699      {
700         result = CompareUtil.compare(getSpeciesTaxon(), inObj2.getSpeciesTaxon());
701
702         if (0 == result)
703         {
704            result = CompareUtil.compare(getOrganismTaxon(), inObj2.getOrganismTaxon());
705
706            if (0 == result)
707            {
708               result = CompareUtil.compare(getRefSeqCategory(), inObj2.getRefSeqCategory());
709
710               if (0 == result)
711               {
712                  result = CompareUtil.compare(getGenomicRepresentation(), inObj2.getGenomicRepresentation());
713
714                  if (0 == result)
715                  {
716                     result = CompareUtil.compare(getAssemblyReleaseType(), inObj2.getAssemblyReleaseType());
717
718                     if (0 == result)
719                     {
720                        result = CompareUtil.compare(getAssemblyVersionStatus(), inObj2.getAssemblyVersionStatus());
721                     }
722                  }
723               }
724            }
725         }
726      }
727
728      return result;
729   }
730}