001/*
002 $Id: OMSSAParameterSet.java 3207 2009-04-09 06:48:11Z gregory $
003
004 Copyright (C) 2008 Gregory Vincic, Olle Mansson
005
006 Files are copyright by their respective authors. The contributions to
007 files where copyright is not explicitly stated can be traced with the
008 source code revision system.
009
010 This file is part of Proteios.
011 Available at http://www.proteios.org/
012
013 Proteios-2.x is free software; you can redistribute it and/or
014 modify it under the terms of the GNU General Public License
015 as published by the Free Software Foundation; either version 2
016 of the License, or (at your option) any later version.
017
018 Proteios is distributed in the hope that it will be useful,
019 but WITHOUT ANY WARRANTY; without even the implied warranty of
020 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
021 GNU General Public License for more details.
022
023 You should have received a copy of the GNU General Public License
024 along with this program; if not, write to the Free Software
025 Foundation, Inc., 59 Temple Place - Suite 330,
026 Boston, MA  02111-1307, USA.
027 */
028package org.proteios.io;
029
030
031/**
032 * This file API should be used to get parameter data from OMSSA input files.
033 * 
034 * @author olle
035 */
036public class OMSSAParameterSet
037{
038        private String species = null;
039        private String searchSpectrumType = null;
040        private String precursorSearchType = null;
041        private String productSearchType = null;
042        private String ionsToSearch1 = null;
043        private String ionsToSearch2 = null;
044        private String pepTol = null;
045        private String msMsTol = null;
046        private String zDep = null;
047        private String cutoff = null;
048        private String cutLo = null;
049        private String cutHi = null;
050        private String cutInc = null;
051        private String singleWin = null;
052        private String doubleWin = null;
053        private String singleNum = null;
054        private String doubleNum = null;
055        private String fixed = null;
056        private String variable = null;
057        private String enzyme = null;
058        private String missedCleave = null;
059        private String hitListLen = null;
060        private String db = null;
061        private String topHitNum = null;
062        private String minHit = null;
063        private String minSpectra = null;
064        private String scale = null;
065        private String maxMods = null;
066        private String msCalcPlusOne = null;
067        private String msCalcCharge = null;
068        private String minCharge = null;
069        private String maxCharge = null;
070        private String considerMult = null;
071        private String plusOne = null;
072        private String maxProductCharge = null;
073        private String pseudoCount = null;
074        private String searchB1 = null;
075        private String searchCTermProduct = null;
076        private String maxProductions = null;
077        private String minNoEnzyme = null;
078        private String maxNoEnzyme = null;
079        private String exactMass = null;
080        private String settingId = null;
081        private String researchThresh = null;
082        private String subsetThresh = null;
083        private String replaceThresh = null;
084        private String precursorCull = null;
085        private String noCorrelationScore = null;
086        private String probFollowingIon = null;
087        private String nMethionineAttribute = null;
088        private String autoMassAdjust = null;
089
090        /**
091         * @return String search species.
092         */
093        public String getSpecies()
094        {
095                return species;
096        }
097
098
099        /**
100         * @param species String.
101         */
102        public void setSpecies(String species)
103        {
104                this.species = species;
105        }
106
107
108        /**
109         * @return String search spectrum type (iontrap or etd).
110         */
111        public String getSearchSpectrumType()
112        {
113                return searchSpectrumType;
114        }
115
116
117        /**
118         * @param searchSpectrumType String search spectrum type (iontrap or etd).
119         */
120        public void setSearchSpectrumType(String searchSpectrumType)
121        {
122                this.searchSpectrumType = searchSpectrumType;
123        }
124
125
126        /**
127         * @return String precursor search type.
128         */
129        public String getPrecursorSearchType()
130        {
131                return precursorSearchType;
132        }
133
134
135        /**
136         * @param precursorSearchType String precursor search type.
137         */
138        public void setPrecursorSearchType(String precursorSearchType)
139        {
140                this.precursorSearchType = precursorSearchType;
141        }
142
143
144        /**
145         * @return String product search type.
146         */
147        public String getProductSearchType()
148        {
149                return productSearchType;
150        }
151
152
153        /**
154         * @param productSearchType String product search type.
155         */
156        public void setProductSearchType(String productSearchType)
157        {
158                this.productSearchType = productSearchType;
159        }
160
161
162        /**
163         * @return String ions to search 1.
164         */
165        public String getIonsToSearch1()
166        {
167                return ionsToSearch1;
168        }
169
170
171        /**
172         * @param ionsToSearch1 String ions to search 1.
173         */
174        public void setIonsToSearch1(String ionsToSearch1)
175        {
176                this.ionsToSearch1 = ionsToSearch1;
177        }
178
179
180        /**
181         * @return String ions to search 2.
182         */
183        public String getIonsToSearch2()
184        {
185                return ionsToSearch2;
186        }
187
188
189        /**
190         * @param ionsToSearch2 String ions to search 2.
191         */
192        public void setIonsToSearch2(String ionsToSearch2)
193        {
194                this.ionsToSearch2 = ionsToSearch2;
195        }
196
197
198        /**
199         * Precursor mass tolerance (Da).
200         * 
201         * @return String peptide tolerance.
202         */
203        public String getPepTol()
204        {
205                return pepTol;
206        }
207        
208        
209        /**
210         * Precursor mass tolerance (Da).
211         * 
212         * @param pepTol String peptide tolerance.
213         */
214        public void setPepTol(String pepTol)
215        {
216                this.pepTol = pepTol;
217        }
218        
219        
220        /**
221         * Product mass tolerance (Da).
222         * 
223         * @return String ms-ms tolerance.
224         */
225        public String getMsMsTol()
226        {
227                return msMsTol;
228        }
229        
230        
231        /**
232         * Product mass tolerance (Da).
233         * 
234         * @param msMsTol String ms-ms tolerance.
235         */
236        public void setMsMsTol(String msMsTol)
237        {
238                this.msMsTol = msMsTol;
239        }
240        
241        
242        /**
243         * @return String z-dep.
244         */
245        public String getZDep()
246        {
247                return zDep;
248        }
249        
250        
251        /**
252         * @param zDep String z-dep.
253         */
254        public void setZDep(String zDep)
255        {
256                this.zDep = zDep;
257        }
258        
259        
260        /**
261         * @return String cutoff.
262         */
263        public String getCutoff()
264        {
265                return cutoff;
266        }
267        
268        
269        /**
270         * @param cutoff String cutoff.
271         */
272        public void setCutoff(String cutoff)
273        {
274                this.cutoff = cutoff;
275        }
276        
277        
278        /**
279         * Peak low intensity cutoff (fraction of most intense)
280         * 
281         * @return String cut low.
282         */
283        public String getCutLo()
284        {
285                return cutLo;
286        }
287        
288        
289        /**
290         * Peak low intensity cutoff (fraction of most intense)
291         * 
292         * @param cutLo String cut low.
293         */
294        public void setCutLo(String cutLo)
295        {
296                this.cutLo = cutLo;
297        }
298        
299        
300        /**
301         * Peak high intensity cutoff (fraction of most intense)
302         * 
303         * @return String cut high.
304         */
305        public String getCutHi()
306        {
307                return cutHi;
308        }
309        
310        
311        /**
312         * Peak high intensity cutoff (fraction of most intense)
313         * 
314         * @param cutHi String cutHi.
315         */
316        public void setCutHi(String cutHi)
317        {
318                this.cutHi = cutHi;
319        }
320        
321        
322        /**
323         * @return String cut inc.
324         */
325        public String getCutInc()
326        {
327                return cutInc;
328        }
329        
330        
331        /**
332         * @param cutInc String cut inc.
333         */
334        public void setCutInc(String cutInc)
335        {
336                this.cutInc = cutInc;
337        }
338        
339        
340        /**
341         * @return String single window.
342         */
343        public String getSingleWin()
344        {
345                return singleWin;
346        }
347
348
349        /**
350         * @param singleWin String single window.
351         */
352        public void setSingleWin(String singleWin)
353        {
354                this.singleWin = singleWin;
355        }
356
357
358        /**
359         * @return String double window.
360         */
361        public String getDoubleWin()
362        {
363                return doubleWin;
364        }
365
366
367        /**
368         * @param doubleWin String double window.
369         */
370        public void setDoubleWin(String doubleWin)
371        {
372                this.doubleWin = doubleWin;
373        }
374
375
376        /**
377         * @return String single number.
378         */
379        public String getSingleNum()
380        {
381                return singleNum;
382        }
383
384
385        /**
386         * @param singleNum String single number.
387         */
388        public void setSingleNum(String singleNum)
389        {
390                this.singleNum = singleNum;
391        }
392
393
394        /**
395         * @return String double number.
396         */
397        public String getDoubleNum()
398        {
399                return doubleNum;
400        }
401
402
403        /**
404         * @param doubleNum String double number.
405         */
406        public void setDoubleNum(String doubleNum)
407        {
408                this.doubleNum = doubleNum;
409        }
410
411
412        /**
413         * @return String fixed.
414         */
415        public String getFixed()
416        {
417                return fixed;
418        }
419
420
421        /**
422         * @param fixed String fixed.
423         */
424        public void setFixed(String fixed)
425        {
426                this.fixed = fixed;
427        }
428
429
430        /**
431         * @return String variable.
432         */
433        public String getVariable()
434        {
435                return variable;
436        }
437
438
439        /**
440         * @param variable String variable.
441         */
442        public void setVariable(String variable)
443        {
444                this.variable = variable;
445        }
446
447
448        /**
449         * @return String enzyme.
450         */
451        public String getEnzyme()
452        {
453                return enzyme;
454        }
455
456
457        /**
458         * @param enzyme String enzyme.
459         */
460        public void setEnzyme(String enzyme)
461        {
462                this.enzyme = enzyme;
463        }
464
465
466        /**
467         * @return String missed cleavages.
468         */
469        public String getMissedCleave()
470        {
471                return missedCleave;
472        }
473
474
475        /**
476         * @param missedCleave String missed cleavages.
477         */
478        public void setMissedCleave(String missedCleave)
479        {
480                this.missedCleave = missedCleave;
481        }
482
483
484        /**
485         * @return String hit list length.
486         */
487        public String getHitListLen()
488        {
489                return hitListLen;
490        }
491
492
493        /**
494         * @param hitListLen String hit list length.
495         */
496        public void setHitListLen(String hitListLen)
497        {
498                this.hitListLen = hitListLen;
499        }
500
501
502        /**
503         * @return String db.
504         */
505        public String getDb()
506        {
507                return db;
508        }
509
510
511        /**
512         * @param db String db.
513         */
514        public void setDb(String db)
515        {
516                this.db = db;
517        }
518
519
520        /**
521         * Number of top intensity peaks in first pass
522         * 
523         * @return String top hit number.
524         */
525        public String getTopHitNum()
526        {
527                return topHitNum;
528        }
529
530
531        /**
532         * Number of top intensity peaks in first pass
533         * 
534         * @param topHitNum String top hit number.
535         */
536        public void setTopHitNum(String topHitNum)
537        {
538                this.topHitNum = topHitNum;
539        }
540
541
542        /**
543         * @return String minHit.
544         */
545        public String getMinHit()
546        {
547                return minHit;
548        }
549
550
551        /**
552         * @param minHit String minHit.
553         */
554        public void setMinHit(String minHit)
555        {
556                this.minHit = minHit;
557        }
558
559
560        /**
561         * @return String minSpectra.
562         */
563        public String getMinSpectra()
564        {
565                return minSpectra;
566        }
567
568
569        /**
570         * @param minSpectra String minSpectra.
571         */
572        public void setMinSpectra(String minSpectra)
573        {
574                this.minSpectra = minSpectra;
575        }
576
577
578        /**
579         * @return String scale.
580         */
581        public String getScale()
582        {
583                return scale;
584        }
585
586
587        /**
588         * @param scale String scale.
589         */
590        public void setScale(String scale)
591        {
592                this.scale = scale;
593        }
594
595
596        /**
597         * @return String max modifications.
598         */
599        public String getMaxMods()
600        {
601                return maxMods;
602        }
603
604
605        /**
606         * @param maxMods String max modifications.
607         */
608        public void setMaxMods(String maxMods)
609        {
610                this.maxMods = maxMods;
611        }
612
613
614        /**
615         * @return String msCalcPlusOne.
616         */
617        public String getMsCalcPlusOne()
618        {
619                return msCalcPlusOne;
620        }
621
622
623        /**
624         * @param msCalcPlusOne String msCalcPlusOne.
625         */
626        public void setMsCalcPlusOne(String msCalcPlusOne)
627        {
628                this.msCalcPlusOne = msCalcPlusOne;
629        }
630
631
632        /**
633         * @return String msCalcCharge.
634         */
635        public String getMsCalcCharge()
636        {
637                return msCalcCharge;
638        }
639
640
641        /**
642         * @param msCalcCharge String msCalcCharge.
643         */
644        public void setMsCalcCharge(String msCalcCharge)
645        {
646                this.msCalcCharge = msCalcCharge;
647        }
648
649
650        /**
651         * Lower bound of precursor charge
652         * 
653         * @return String min charge.
654         */
655        public String getMinCharge()
656        {
657                return minCharge;
658        }
659
660
661        /**
662         * Lower bound of precursor charge
663         * 
664         * @param minCharge String min charge.
665         */
666        public void setMinCharge(String minCharge)
667        {
668                this.minCharge = minCharge;
669        }
670
671
672        /**
673         * Upper bound of precursor charge
674         * 
675         * @return String max charge.
676         */
677        public String getMaxCharge()
678        {
679                return maxCharge;
680        }
681
682
683        /**
684         * Upper bound of precursor charge
685         * 
686         * @param maxCharge String max charge.
687         */
688        public void setMaxCharge(String maxCharge)
689        {
690                this.maxCharge = maxCharge;
691        }
692
693
694        /**
695         * Minimum charge to start using multiply charged products
696         * 
697         * @return String considerMult.
698         */
699        public String getConsiderMult()
700        {
701                return considerMult;
702        }
703
704
705        /**
706         * Minimum charge to start using multiply charged products
707         * 
708         * @param considerMult String considerMult.
709         */
710        public void setConsiderMult(String considerMult)
711        {
712                this.considerMult = considerMult;
713        }
714
715
716        /**
717         * Fraction of product peaks below precursor to determine +1 precursor
718         * 
719         * @return String plusOne.
720         */
721        public String getPlusOne()
722        {
723                return plusOne;
724        }
725
726
727        /**
728         * Fraction of product peaks below precursor to determine +1 precursor
729         * 
730         * @param plusOne String plusOne.
731         */
732        public void setPlusOne(String plusOne)
733        {
734                this.plusOne = plusOne;
735        }
736
737
738        /**
739         * @return String max product charge.
740         */
741        public String getMaxProductCharge()
742        {
743                return maxProductCharge;
744        }
745
746
747        /**
748         * @param maxProductCharge String max product charge.
749         */
750        public void setMaxProductCharge(String maxProductCharge)
751        {
752                this.maxProductCharge = maxProductCharge;
753        }
754
755
756        /**
757         * @return String pseudo count.
758         */
759        public String getPseudoCount()
760        {
761                return pseudoCount;
762        }
763
764
765        /**
766         * @param pseudoCount String pseudo count.
767         */
768        public void setPseudoCount(String pseudoCount)
769        {
770                this.pseudoCount = pseudoCount;
771        }
772
773
774        /**
775         * @return String search b1.
776         */
777        public String getSearchB1()
778        {
779                return searchB1;
780        }
781
782
783        /**
784         * @param searchB1 String search b1.
785         */
786        public void setSearchB1(String searchB1)
787        {
788                this.searchB1 = searchB1;
789        }
790
791
792        /**
793         * @return String search C term product.
794         */
795        public String getSearchCTermProduct()
796        {
797                return searchCTermProduct;
798        }
799
800
801        /**
802         * @param searchCTermProduct String search C term product.
803         */
804        public void setSearchCTermProduct(String searchCTermProduct)
805        {
806                this.searchCTermProduct = searchCTermProduct;
807        }
808
809
810        /**
811         * @return String max productions.
812         */
813        public String getMaxProductions()
814        {
815                return maxProductions;
816        }
817
818
819        /**
820         * @param maxProductions String max productions.
821         */
822        public void setMaxProductions(String maxProductions)
823        {
824                this.maxProductions = maxProductions;
825        }
826
827
828        /**
829         * @return String min number of enzymes.
830         */
831        public String getMinNoEnzyme()
832        {
833                return minNoEnzyme;
834        }
835
836
837        /**
838         * @param minNoEnzyme String min number of enzymes.
839         */
840        public void setMinNoEnzyme(String minNoEnzyme)
841        {
842                this.minNoEnzyme = minNoEnzyme;
843        }
844
845
846        /**
847         * @return String max number of enzymes.
848         */
849        public String getMaxNoEnzyme()
850        {
851                return maxNoEnzyme;
852        }
853
854
855        /**
856         * @param maxNoEnzyme String max number of enzymes.
857         */
858        public void setMaxNoEnzyme(String maxNoEnzyme)
859        {
860                this.maxNoEnzyme = maxNoEnzyme;
861        }
862
863
864        /**
865         * @return String exact mass.
866         */
867        public String getExactMass()
868        {
869                return exactMass;
870        }
871
872
873        /**
874         * @param exactMass String exact mass.
875         */
876        public void setExactMass(String exactMass)
877        {
878                this.exactMass = exactMass;
879        }
880
881
882        /**
883         * @return String setting id.
884         */
885        public String getSettingId()
886        {
887                return settingId;
888        }
889
890
891        /**
892         * @param settingId String setting id.
893         */
894        public void setSettingId(String settingId)
895        {
896                this.settingId = settingId;
897        }
898
899
900        /**
901         * @return String research threshold.
902         */
903        public String getResearchThresh()
904        {
905                return researchThresh;
906        }
907
908
909        /**
910         * @param researchThresh String research threshold.
911         */
912        public void setResearchThresh(String researchThresh)
913        {
914                this.researchThresh = researchThresh;
915        }
916
917
918        /**
919         * @return String subset threshold.
920         */
921        public String getSubsetThresh()
922        {
923                return subsetThresh;
924        }
925
926
927        /**
928         * @param subsetThresh String subset threshold.
929         */
930        public void setSubsetThresh(String subsetThresh)
931        {
932                this.subsetThresh = subsetThresh;
933        }
934
935
936        /**
937         * @return String replace threshold.
938         */
939        public String getReplaceThresh()
940        {
941                return replaceThresh;
942        }
943
944
945        /**
946         * @param replaceThresh String replace threshold.
947         */
948        public void setReplaceThresh(String replaceThresh)
949        {
950                this.replaceThresh = replaceThresh;
951        }
952
953
954        /**
955         * @return String precursor cull.
956         */
957        public String getPrecursorCull()
958        {
959                return precursorCull;
960        }
961
962
963        /**
964         * @param precursorCull String precursor cull.
965         */
966        public void setPrecursorCull(String precursorCull)
967        {
968                this.precursorCull = precursorCull;
969        }
970
971
972        /**
973         * @return String noCorrelationScore.
974         */
975        public String getNoCorrelationScore()
976        {
977                return noCorrelationScore;
978        }
979
980
981        /**
982         * @param noCorrelationScore String noCorrelationScore.
983         */
984        public void setNoCorrelationScore(String noCorrelationScore)
985        {
986                this.noCorrelationScore = noCorrelationScore;
987        }
988
989
990        /**
991         * @return String probFollowingIon.
992         */
993        public String getProbFollowingIon()
994        {
995                return probFollowingIon;
996        }
997
998
999        /**
1000         * @param probFollowingIon String probFollowingIon.
1001         */
1002        public void setProbFollowingIon(String probFollowingIon)
1003        {
1004                this.probFollowingIon = probFollowingIon;
1005        }
1006
1007
1008        /**
1009         * @return String nMethionine.
1010         */
1011        public String getNMethionineAttribute()
1012        {
1013                return nMethionineAttribute;
1014        }
1015
1016
1017        /**
1018         * @param nMethionineAttribute String nMethionineAttribute.
1019         */
1020        public void setNMethionineAttribute(String nMethionineAttribute)
1021        {
1022                this.nMethionineAttribute = nMethionineAttribute;
1023        }
1024
1025
1026        /**
1027         * @return String auto mass adjustment.
1028         */
1029        public String getAutoMassAdjust()
1030        {
1031                return autoMassAdjust;
1032        }
1033
1034
1035        /**
1036         * @param autoMassAdjust String auto mass adjustment.
1037         */
1038        public void setAutoMassAdjust(String autoMassAdjust)
1039        {
1040                this.autoMassAdjust = autoMassAdjust;
1041        }
1042}