Checkstyle Results

The following document contains the results of Checkstyle.

Summary

Files	Infos	Warnings	Errors
16	0	0	3135

Files

Files	I	W	E
uk/ac/ebi/intenz/mapper/AuditPackageMapper.java	0	0	10
uk/ac/ebi/intenz/mapper/CommonProceduresMapper.java	0	0	10
uk/ac/ebi/intenz/mapper/EnzymeClassMapper.java	0	0	69
uk/ac/ebi/intenz/mapper/EnzymeCofactorMapper.java	0	0	344
uk/ac/ebi/intenz/mapper/EnzymeCommentMapper.java	0	0	134
uk/ac/ebi/intenz/mapper/EnzymeEntryMapper.java	0	0	798
uk/ac/ebi/intenz/mapper/EnzymeFutureMapper.java	0	0	81
uk/ac/ebi/intenz/mapper/EnzymeHistoryMapper.java	0	0	53
uk/ac/ebi/intenz/mapper/EnzymeLinkMapper.java	0	0	375
uk/ac/ebi/intenz/mapper/EnzymeNameMapper.java	0	0	200
uk/ac/ebi/intenz/mapper/EnzymeReactionMapper.java	0	0	263
uk/ac/ebi/intenz/mapper/EnzymeReferenceMapper.java	0	0	353
uk/ac/ebi/intenz/mapper/EnzymeSubSubclassMapper.java	0	0	126
uk/ac/ebi/intenz/mapper/EnzymeSubclassMapper.java	0	0	80
uk/ac/ebi/intenz/mapper/EventPackageMapper.java	0	0	100
uk/ac/ebi/intenz/mapper/HistoryEventMapper.java	0	0	139

Rules

Rules	Violations	Severity
JavadocPackage allowLegacy: `"true"`	0	Error
NewlineAtEndOfFile	0	Error
Translation	0	Error
FileLength	0	Error
FileTabCharacter eachLine: `"true"`	592	Error
RegexpSingleline message: `"Line has trailing spaces."` format: `"\s+$"`	71	Error
JavadocMethod	308	Error
JavadocType	1	Error
JavadocVariable	52	Error
JavadocStyle	1	Error
ConstantName	0	Error
LocalFinalVariableName	0	Error
LocalVariableName	0	Error
MemberName	1	Error
MethodName	0	Error
PackageName	0	Error
ParameterName	0	Error
StaticVariableName	0	Error
TypeName	0	Error
AvoidStarImport	0	Error
IllegalImport	0	Error
RedundantImport	0	Error
UnusedImports	0	Error
LineLength	512	Error
MethodLength	0	Error
ParameterNumber	2	Error
EmptyForIteratorPad	0	Error
MethodParamPad	0	Error
NoWhitespaceAfter	1	Error
NoWhitespaceBefore	0	Error
OperatorWrap	87	Error
ParenPad	0	Error
TypecastParenPad	0	Error
WhitespaceAfter	2	Error
WhitespaceAround	85	Error
ModifierOrder	0	Error
RedundantModifier	0	Error
AvoidNestedBlocks	0	Error
EmptyBlock	1	Error
LeftCurly	0	Error
NeedBraces	506	Error
RightCurly	0	Error
AvoidInlineConditionals	10	Error
EmptyStatement	0	Error
EqualsHashCode	0	Error
HiddenField	1	Error
IllegalInstantiation	0	Error
InnerAssignment	0	Error
MagicNumber	298	Error
MissingSwitchDefault	1	Error
RedundantThrows	4	Error
SimplifyBooleanExpression	0	Error
SimplifyBooleanReturn	0	Error
DesignForExtension	123	Error
FinalClass	0	Error
HideUtilityClassConstructor	0	Error
InterfaceIsType	0	Error
VisibilityModifier	2	Error
ArrayTypeStyle	0	Error
FinalParameters	473	Error
TodoComment	2	Error
UpperEll	0	Error

Details

uk/ac/ebi/intenz/mapper/AuditPackageMapper.java

Violation	Message	Line
	Missing a Javadoc comment.	16
	Missing a Javadoc comment.	18
	Missing a Javadoc comment.	21
	Method 'setRemark' is not designed for extension - needs to be abstract, final or empty.	32
	Parameter remark should be final.	32
	Parameter con should be final.	32
	Expected @throws tag for 'SQLException'.	32
	'{' is not preceded with whitespace.	37
	Line contains a tab character.	38
	Line contains a tab character.	40

uk/ac/ebi/intenz/mapper/CommonProceduresMapper.java

Violation	Message	Line
	Missing a Javadoc comment.	16
	Missing a Javadoc comment.	19
	Expected an @return tag.	30
	Method 'createClone' is not designed for extension - needs to be abstract, final or empty.	30
	Parameter enzymeId should be final.	30
	Parameter con should be final.	30
	Expected @throws tag for 'SQLException'.	30
	'3' is a magic number.	38
	'4' is a magic number.	39
	'if' construct must use '{}'s.	44

uk/ac/ebi/intenz/mapper/EnzymeClassMapper.java

Violation	Message	Line
	Missing a Javadoc comment.	27
	Line has trailing spaces.	28
	Line is longer than 80 characters (found 81).	29
	Missing a Javadoc comment.	29
	Missing a Javadoc comment.	31
	Line contains a tab character.	32
	Missing a Javadoc comment.	34
	Missing a Javadoc comment.	37
	Missing a Javadoc comment.	41
	Line is longer than 80 characters (found 97).	50
	Unused @throws tag for 'NullPointerException'.	51
	Line is longer than 80 characters (found 119).	53
	Line is longer than 80 characters (found 92).	55
	Method 'find' is not designed for extension - needs to be abstract, final or empty.	55
	Parameter ec1 should be final.	55
	Parameter con should be final.	55
	'if' construct must use '{}'s.	56
	Line is longer than 80 characters (found 89).	56
	'if' construct must use '{}'s.	57
	Line is longer than 80 characters (found 89).	57
	'if' construct must use '{}'s.	77
	Line contains a tab character.	77
	'if' construct must use '{}'s.	78
	Line has trailing spaces.	83
	Line has trailing spaces.	85
	Line has trailing spaces.	89
	Line has trailing spaces.	90
	Unused @throws tag for 'EcException'.	90
	Line is longer than 80 characters (found 88).	92
	Method 'findAll' is not designed for extension - needs to be abstract, final or empty.	92
	Parameter con should be final.	92
	Expected @param tag for 'con'.	92
	Expected @throws tag for 'DomainException'.	92
	'{' is not preceded with whitespace.	92
	'{' is not preceded with whitespace.	99
	'if' construct must use '{}'s.	103
	Line contains a tab character.	103
	'if' construct must use '{}'s.	104
	Method 'findNumberOfClasses' is not designed for extension - needs to be abstract, final or empty.	116
	Parameter con should be final.	116
	Expected @throws tag for 'SQLException'.	116
	'if' construct must use '{}'s.	117
	Line is longer than 80 characters (found 89).	117
	'if' construct must use '{}'s.	129
	Line contains a tab character.	129
	'if' construct must use '{}'s.	130
	Line contains a tab character.	130
	Method 'classExists' is not designed for extension - needs to be abstract, final or empty.	144
	Parameter ec1 should be final.	144
	Parameter con should be final.	144
	Expected @throws tag for 'SQLException'.	144
	'if' construct must use '{}'s.	145
	Line is longer than 80 characters (found 89).	145
	'if' construct must use '{}'s.	146
	Line is longer than 80 characters (found 89).	146
	'if' construct must use '{}'s.	157
	Line contains a tab character.	157
	'if' construct must use '{}'s.	158
	Line contains a tab character.	158
	Parameter rs should be final.	173
	Parameter subclasses should be final.	173
	Expected @param tag for 'subclasses'.	173
	Expected @throws tag for 'SQLException'.	174
	Expected @throws tag for 'EcException'.	174
	Line has trailing spaces.	176
	'if' construct must use '{}'s.	181
	'if' construct must use '{}'s.	182
	'if' construct must use '{}'s.	183
	Line is longer than 80 characters (found 87).	183

uk/ac/ebi/intenz/mapper/EnzymeCofactorMapper.java

Violation	Message	Line
	Missing a Javadoc comment.	39
	Line contains a tab character.	40
	Missing a Javadoc comment.	42
	'{' is not preceded with whitespace.	42
	Line has trailing spaces.	44
	Missing a Javadoc comment.	45
	'{' is not preceded with whitespace.	45
	Line contains a tab character.	48
	Method 'finalize' is not designed for extension - needs to be abstract, final or empty.	48
	Line contains a tab character.	49
	Line contains a tab character.	50
	Line contains a tab character.	51
	Missing a Javadoc comment.	53
	Line is longer than 80 characters (found 104).	54
	Line contains a tab character.	54
	Missing a Javadoc comment.	56
	Line is longer than 80 characters (found 99).	57
	Line contains a tab character.	57
	'+' should be on a new line.	57
	Line contains a tab character.	58
	Line has trailing spaces.	59
	Missing a Javadoc comment.	60
	Missing a Javadoc comment.	64
	Line contains a tab character.	65
	'+' should be on a new line.	65
	Line is longer than 80 characters (found 109).	66
	'+' should be on a new line.	66
	Line has trailing spaces.	68
	Missing a Javadoc comment.	69
	Line is longer than 80 characters (found 95).	70
	Line contains a tab character.	70
	'+' should be on a new line.	70
	Line is longer than 80 characters (found 107).	71
	Line contains a tab character.	71
	'+' should be on a new line.	71
	Line contains a tab character.	72
	Line has trailing spaces.	73
	Missing a Javadoc comment.	74
	Missing a Javadoc comment.	78
	Line is longer than 80 characters (found 87).	79
	Line contains a tab character.	79
	Missing a Javadoc comment.	81
	Line has trailing spaces.	85
	Missing a Javadoc comment.	86
	Line has trailing spaces.	88
	Missing a Javadoc comment.	89
	Line contains a tab character.	90
	Line has trailing spaces.	91
	Missing a Javadoc comment.	92
	Line is longer than 80 characters (found 90).	93
	Line contains a tab character.	93
	Line is longer than 80 characters (found 88).	101
	Line contains a tab character.	101
	Line contains a tab character.	102
	Method 'find' is not designed for extension - needs to be abstract, final or empty.	106
	Parameter enzymeId should be final.	106
	Parameter con should be final.	106
	'if' construct must use '{}'s.	108
	Line is longer than 80 characters (found 99).	108
	'if' construct must use '{}'s.	109
	Line is longer than 80 characters (found 89).	109
	'if' construct must use '{}'s.	122
	Line contains a tab character.	122
	'if' construct must use '{}'s.	123
	Line has trailing spaces.	132
	Method 'findByChebiId' is not designed for extension - needs to be abstract, final or empty.	141
	Parameter chebiId should be final.	141
	Parameter con should be final.	141
	'{' is not preceded with whitespace.	142
	'{' is not preceded with whitespace.	150
	'if' construct must use '{}'s.	155
	'if' construct must use '{}'s.	156
	Line is longer than 80 characters (found 108).	168
	Line is longer than 80 characters (found 83).	171
	Unused @throws tag for 'NullPointerException'.	171
	Method 'exportSibCofactors' is not designed for extension - needs to be abstract, final or empty.	173
	Parameter enzymeId should be final.	173
	Parameter con should be final.	173
	'if' construct must use '{}'s.	175
	Line is longer than 80 characters (found 99).	175
	'if' construct must use '{}'s.	176
	Line is longer than 80 characters (found 89).	176
	'if' construct must use '{}'s.	189
	Line contains a tab character.	189
	'if' construct must use '{}'s.	190
	Line contains a tab character.	190
	Line has trailing spaces.	195
	Line is longer than 80 characters (found 82).	197
	Method 'findAll' is not designed for extension - needs to be abstract, final or empty.	205
	Parameter con should be final.	205
	Line is longer than 80 characters (found 97).	207
	Line contains a tab character.	207
	Line contains a tab character.	208
	Line contains a tab character.	209
	Line contains a tab character.	210
	Line contains a tab character.	211
	Line contains a tab character.	212
	Line contains a tab character.	213
	Line contains a tab character.	214
	Line contains a tab character.	215
	'{' is not preceded with whitespace.	215
	Line contains a tab character.	216
	Line contains a tab character.	217
	Line contains a tab character.	218
	Line contains a tab character.	219
	'{' is not preceded with whitespace.	219
	Line contains a tab character.	220
	Line is longer than 80 characters (found 83).	221
	Line contains a tab character.	221
	Line contains a tab character.	222
	Line contains a tab character.	223
	Line contains a tab character.	224
	Line contains a tab character.	225
	Line contains a tab character.	226
	Line contains a tab character.	227
	Line contains a tab character.	228
	'if' construct must use '{}'s.	229
	Line contains a tab character.	229
	'if' construct must use '{}'s.	230
	Line contains a tab character.	230
	Line contains a tab character.	231
	Line contains a tab character.	232
	Line is longer than 80 characters (found 96).	244
	Method 'insert' is not designed for extension - needs to be abstract, final or empty.	244
	Parameter cofactors should be final.	244
	Parameter enzymeId should be final.	244
	Parameter status should be final.	244
	Expected @param tag for 'status'.	244
	Parameter con should be final.	244
	Expected @throws tag for 'SQLException'.	245
	'if' construct must use '{}'s.	246
	Line is longer than 80 characters (found 107).	246
	Line contains a tab character.	246
	'if' construct must use '{}'s.	247
	Line is longer than 80 characters (found 105).	247
	Line contains a tab character.	247
	'if' construct must use '{}'s.	248
	Line is longer than 80 characters (found 101).	248
	Line contains a tab character.	248
	'if' construct must use '{}'s.	249
	Line is longer than 80 characters (found 95).	249
	Line contains a tab character.	249
	Line contains a tab character.	251
	Line contains a tab character.	253
	Line contains a tab character.	254
	Line contains a tab character.	255
	Line contains a tab character.	256
	Line contains a tab character.	257
	'{' is not preceded with whitespace.	257
	Line contains a tab character.	258
	Line is longer than 80 characters (found 107).	259
	Line contains a tab character.	259
	Line contains a tab character.	260
	Line contains a tab character.	261
	'{' is not preceded with whitespace.	261
	Line contains a tab character.	262
	Line is longer than 80 characters (found 97).	263
	Line contains a tab character.	263
	Line contains a tab character.	264
	Line contains a tab character.	265
	Line contains a tab character.	266
	Line contains a tab character.	267
	Line contains a tab character.	268
	Line contains a tab character.	269
	Method 'insertCompound' is not designed for extension - needs to be abstract, final or empty.	280
	Parameter compound should be final.	280
	Parameter con should be final.	280
	'{' is followed by whitespace.	287
	'{' is not preceded with whitespace.	291
	'{' is not preceded with whitespace.	293
	'if' construct must use '{}'s.	302
	'if' construct must use '{}'s.	303
	Line has trailing spaces.	306
	Method 'deleteCompound' is not designed for extension - needs to be abstract, final or empty.	314
	Parameter compoundId should be final.	314
	Parameter con should be final.	314
	'{' is not preceded with whitespace.	315
	'if' construct must use '{}'s.	323
	Line has trailing spaces.	326
	Line is longer than 80 characters (found 96).	336
	Method 'reload' is not designed for extension - needs to be abstract, final or empty.	336
	Parameter cofactors should be final.	336
	Parameter enzymeId should be final.	336
	Parameter status should be final.	336
	Expected @param tag for 'status'.	336
	Parameter con should be final.	336
	Expected @throws tag for 'SQLException'.	337
	'if' construct must use '{}'s.	338
	Line is longer than 80 characters (found 101).	338
	'if' construct must use '{}'s.	339
	Line is longer than 80 characters (found 99).	339
	'if' construct must use '{}'s.	340
	Line is longer than 80 characters (found 95).	340
	'if' construct must use '{}'s.	341
	Line is longer than 80 characters (found 89).	341
	Line has trailing spaces.	346
	Method 'update' is not designed for extension - needs to be abstract, final or empty.	354
	Parameter oldCf should be final.	354
	Parameter newCf should be final.	354
	Parameter con should be final.	354
	Expected @param tag for 'con'.	354
	Expected @throws tag for 'SQLException'.	355
	'{' is not preceded with whitespace.	355
	Line contains a tab character.	356
	Line contains a tab character.	357
	Line contains a tab character.	358
	Line contains a tab character.	359
	Line contains a tab character.	360
	Line contains a tab character.	361
	'3' is a magic number.	361
	Line contains a tab character.	362
	Line contains a tab character.	363
	'if' construct must use '{}'s.	364
	Line contains a tab character.	364
	Line contains a tab character.	365
	Method 'deleteAll' is not designed for extension - needs to be abstract, final or empty.	375
	Parameter enzymeId should be final.	375
	Parameter con should be final.	375
	Expected @throws tag for 'SQLException'.	375
	'if' construct must use '{}'s.	376
	Line is longer than 80 characters (found 99).	376
	'if' construct must use '{}'s.	377
	Line is longer than 80 characters (found 89).	377
	Parameter rs should be final.	400
	'if' construct must use '{}'s.	408
	Line is longer than 80 characters (found 94).	408
	'if' construct must use '{}'s.	409
	'if' construct must use '{}'s.	410
	Line contains a tab character.	414
	'{' is not preceded with whitespace.	414
	Line is longer than 80 characters (found 83).	415
	Line contains a tab character.	415
	Line contains a tab character.	416
	Line contains a tab character.	417
	Line contains a tab character.	418
	Line contains a tab character.	419
	Line contains a tab character.	420
	Line is longer than 80 characters (found 110).	421
	Method 'getCompound' is not designed for extension - needs to be abstract, final or empty.	431
	Parameter connection should be final.	431
	Expected @param tag for 'connection'.	431
	Parameter compoundId should be final.	431
	Expected @throws tag for 'SQLException'.	432
	'{' is not preceded with whitespace.	440
	'?' is not preceded with whitespace.	449
	Avoid inline conditionals.	449
	'if' construct must use '{}'s.	452
	Line contains a tab character.	452
	'if' construct must use '{}'s.	453
	Line contains a tab character.	453
	Missing a Javadoc comment.	458
	Parameter rs should be final.	459
	Line contains a tab character.	461
	Line contains a tab character.	462
	Line contains a tab character.	463
	'if' construct must use '{}'s.	465
	Line is longer than 80 characters (found 82).	465
	Line contains a tab character.	465
	Line contains a tab character.	466
	Line contains a tab character.	467
	'{' is not preceded with whitespace.	467
	Line contains a tab character.	468
	'{' is not preceded with whitespace.	468
	Line contains a tab character.	469
	Line contains a tab character.	470
	Line contains a tab character.	471
	Line contains a tab character.	472
	Line contains a tab character.	473
	Line contains a tab character.	474
	Line contains a tab character.	475
	'{' is not preceded with whitespace.	475
	Line contains a tab character.	476
	Line contains a tab character.	477
	'if' construct must use '{}'s.	478
	Line contains a tab character.	478
	Line is longer than 80 characters (found 92).	479
	Line contains a tab character.	479
	Line contains a tab character.	480
	'if' construct must use '{}'s.	482
	Line is longer than 80 characters (found 96).	482
	Line contains a tab character.	482
	Line contains a tab character.	483
	Line is longer than 80 characters (found 88).	486
	Missing a Javadoc comment.	486
	Parameter cofactors should be final.	486
	Parameter enzymeId should be final.	486
	Parameter orderIn should be final.	486
	Parameter status should be final.	486
	Line is longer than 80 characters (found 90).	487
	Line contains a tab character.	487
	Parameter operatorGroup should be final.	487
	Parameter currentGroup should be final.	487
	Parameter insertStatement should be final.	487
	'{' is not preceded with whitespace.	488
	Line contains a tab character.	489
	Line contains a tab character.	490
	'{' is not preceded with whitespace.	490
	Line contains a tab character.	491
	Line is longer than 80 characters (found 94).	492
	Line contains a tab character.	492
	Line contains a tab character.	493
	Line contains a tab character.	494
	Line contains a tab character.	495
	Line contains a tab character.	496
	Line contains a tab character.	497
	Line contains a tab character.	498
	Line is longer than 80 characters (found 115).	499
	Line contains a tab character.	499
	'+' is not preceded with whitespace.	499
	'+' is not followed by whitespace.	499
	Line contains a tab character.	500
	Line contains a tab character.	501
	Line contains a tab character.	502
	Line is longer than 80 characters (found 85).	514
	Parameter cofactor should be final.	514
	Parameter enzymeId should be final.	514
	Parameter orderIn should be final.	514
	Parameter status should be final.	514
	Expected @param tag for 'status'.	514
	Line is longer than 80 characters (found 97).	515
	Parameter operator should be final.	515
	Expected @param tag for 'operator'.	515
	Parameter operatorGroup should be final.	515
	Expected @param tag for 'operatorGroup'.	515
	Parameter insertStatement should be final.	515
	Expected @throws tag for 'SQLException'.	516
	Line is longer than 80 characters (found 85).	521
	Line is longer than 80 characters (found 104).	522
	'3' is a magic number.	526
	'4' is a magic number.	527
	'5' is a magic number.	528
	'6' is a magic number.	529
	'{' is not preceded with whitespace.	530
	'7' is a magic number.	531
	'7' is a magic number.	534
	'{' is not preceded with whitespace.	536
	Line contains a tab character.	537
	'8' is a magic number.	537
	Line contains a tab character.	538
	'9' is a magic number.	538
	Line contains a tab character.	540
	'8' is a magic number.	540
	Line contains a tab character.	541
	'9' is a magic number.	541

uk/ac/ebi/intenz/mapper/EnzymeCommentMapper.java

Violation	Message	Line
	Line is longer than 80 characters (found 102).	26
	Missing a Javadoc comment.	26
	Missing a Javadoc comment.	28
	Line contains a tab character.	29
	Missing a Javadoc comment.	31
	Missing a Javadoc comment.	34
	'+' should be on a new line.	35
	'+' should be on a new line.	36
	Missing a Javadoc comment.	40
	'+' should be on a new line.	41
	'+' should be on a new line.	42
	Line is longer than 80 characters (found 82).	43
	'+' should be on a new line.	43
	Missing a Javadoc comment.	47
	Line is longer than 80 characters (found 122).	48
	Missing a Javadoc comment.	51
	Line is longer than 80 characters (found 122).	52
	Missing a Javadoc comment.	55
	Line is longer than 80 characters (found 86).	67
	Method 'find' is not designed for extension - needs to be abstract, final or empty.	67
	Parameter enzymeId should be final.	67
	Parameter con should be final.	67
	Expected @throws tag for 'SQLException'.	67
	'if' construct must use '{}'s.	68
	Line is longer than 80 characters (found 99).	68
	'if' construct must use '{}'s.	69
	Line is longer than 80 characters (found 89).	69
	'if' construct must use '{}'s.	86
	Line contains a tab character.	86
	'if' construct must use '{}'s.	87
	Line is longer than 80 characters (found 106).	105
	Line is longer than 80 characters (found 83).	107
	Unused @throws tag for 'NullPointerException'.	107
	Line is longer than 80 characters (found 99).	109
	Method 'exportSibComments' is not designed for extension - needs to be abstract, final or empty.	109
	Parameter enzymeId should be final.	109
	Parameter con should be final.	109
	'if' construct must use '{}'s.	110
	Line is longer than 80 characters (found 99).	110
	'if' construct must use '{}'s.	111
	Line is longer than 80 characters (found 89).	111
	'3' is a magic number.	122
	'4' is a magic number.	123
	'5' is a magic number.	124
	'if' construct must use '{}'s.	132
	Line contains a tab character.	132
	'if' construct must use '{}'s.	133
	'if' construct must use '{}'s.	136
	Line is longer than 80 characters (found 96).	140
	Method 'reload' is not designed for extension - needs to be abstract, final or empty.	140
	Missing a Javadoc comment.	140
	Parameter comments should be final.	140
	Parameter enzymeId should be final.	140
	Parameter status should be final.	140
	Parameter con should be final.	140
	Unused @throws tag for 'NullPointerException'.	152
	Method 'deleteAll' is not designed for extension - needs to be abstract, final or empty.	154
	Parameter enzymeId should be final.	154
	Parameter con should be final.	154
	'if' construct must use '{}'s.	155
	Line is longer than 80 characters (found 99).	155
	'if' construct must use '{}'s.	156
	Line is longer than 80 characters (found 89).	156
	'if' construct must use '{}'s.	165
	Line is longer than 80 characters (found 96).	178
	Method 'insert' is not designed for extension - needs to be abstract, final or empty.	178
	Parameter comments should be final.	178
	Parameter enzymeId should be final.	178
	Parameter status should be final.	178
	Parameter con should be final.	178
	Expected @throws tag for 'SQLException'.	179
	'if' construct must use '{}'s.	180
	Line is longer than 80 characters (found 99).	180
	'if' construct must use '{}'s.	181
	Line is longer than 80 characters (found 99).	181
	'if' construct must use '{}'s.	182
	Line is longer than 80 characters (found 95).	182
	'if' construct must use '{}'s.	183
	Line is longer than 80 characters (found 89).	183
	'+' is not preceded with whitespace.	190
	'+' is not followed by whitespace.	190
	'if' construct must use '{}'s.	194
	Line is longer than 80 characters (found 124).	198
	Method 'update' is not designed for extension - needs to be abstract, final or empty.	198
	Missing a Javadoc comment.	198
	Parameter comment should be final.	198
	Parameter enzymeId should be final.	198
	Parameter status should be final.	198
	Parameter orderIn should be final.	198
	Parameter con should be final.	198
	'if' construct must use '{}'s.	199
	Line is longer than 80 characters (found 97).	199
	'if' construct must use '{}'s.	200
	Line is longer than 80 characters (found 99).	200
	'if' construct must use '{}'s.	201
	Line is longer than 80 characters (found 95).	201
	'if' construct must use '{}'s.	202
	Line is longer than 80 characters (found 96).	202
	'if' construct must use '{}'s.	203
	Line is longer than 80 characters (found 89).	203
	'if' construct must use '{}'s.	211
	Parameter rs should be final.	224
	Expected @throws tag for 'SQLException'.	224
	'if' construct must use '{}'s.	230
	Line is longer than 80 characters (found 85).	230
	'if' construct must use '{}'s.	231
	'if' construct must use '{}'s.	232
	Line is longer than 80 characters (found 98).	234
	Line is longer than 80 characters (found 89).	235
	Line is longer than 80 characters (found 89).	249
	Parameter comment should be final.	249
	Parameter enzymeId should be final.	249
	Parameter orderIn should be final.	249
	Expected @param tag for 'orderIn'.	249
	Parameter status should be final.	249
	Parameter insertStatement should be final.	250
	Expected @throws tag for 'SQLException'.	251
	Line is longer than 80 characters (found 85).	255
	'3' is a magic number.	259
	'4' is a magic number.	260
	'5' is a magic number.	261
	'6' is a magic number.	262
	Line is longer than 80 characters (found 89).	265
	Missing a Javadoc comment.	265
	Parameter comment should be final.	265
	Parameter enzymeId should be final.	265
	Parameter status should be final.	265
	Parameter orderIn should be final.	265
	Parameter updateStatement should be final.	266
	Line is longer than 80 characters (found 85).	272
	'3' is a magic number.	276
	'4' is a magic number.	277
	'5' is a magic number.	278
	'6' is a magic number.	279

uk/ac/ebi/intenz/mapper/EnzymeEntryMapper.java

Violation	Message	Line
	Line has trailing spaces.	45
	Line contains a tab character.	45
	Line is longer than 80 characters (found 81).	46
	Missing a Javadoc comment.	46
	Line is longer than 80 characters (found 84).	53
	Line contains a tab character.	53
	'+' should be on a new line.	53
	Missing a Javadoc comment.	56
	Line is longer than 80 characters (found 81).	57
	Line contains a tab character.	57
	Missing a Javadoc comment.	59
	Missing a Javadoc comment.	61
	Line contains a tab character.	62
	Missing a Javadoc comment.	65
	Parameter enzymeReactionMapper should be final.	65
	'enzymeReactionMapper' hides a field.	65
	'{' is not preceded with whitespace.	65
	Line has trailing spaces.	66
	Line contains a tab character.	66
	Line has trailing spaces.	68
	Method 'finalize' is not designed for extension - needs to be abstract, final or empty.	69
	Line contains a tab character.	70
	Line contains a tab character.	71
	Line contains a tab character.	72
	Line contains a tab character.	74
	Method 'close' is not designed for extension - needs to be abstract, final or empty.	74
	Missing a Javadoc comment.	74
	Line contains a tab character.	75
	'{' is not preceded with whitespace.	75
	Line contains a tab character.	76
	Line contains a tab character.	77
	Line contains a tab character.	78
	Line contains a tab character.	79
	Line contains a tab character.	80
	Line contains a tab character.	81
	Line contains a tab character.	82
	Line contains a tab character.	92
	Line contains a tab character.	93
	Line contains a tab character.	94
	Line contains a tab character.	95
	Line is longer than 80 characters (found 83).	96
	Line contains a tab character.	97
	Line is longer than 80 characters (found 87).	109
	Line has trailing spaces.	112
	Line is longer than 80 characters (found 83).	115
	Line contains a tab character.	115
	Line contains a tab character.	116
	Expected an @return tag.	119
	Parameter preliminary should be final.	119
	'{' is not preceded with whitespace.	119
	Line contains a tab character.	120
	Line is longer than 80 characters (found 86).	121
	Line contains a tab character.	121
	Line is longer than 80 characters (found 84).	122
	Line contains a tab character.	122
	Line contains a tab character.	123
	Line contains a tab character.	124
	Line contains a tab character.	125
	'{' is not preceded with whitespace.	125
	Line is longer than 80 characters (found 92).	126
	Line contains a tab character.	126
	'?' is not preceded with whitespace.	126
	Avoid inline conditionals.	126
	Line contains a tab character.	127
	Line contains a tab character.	128
	Line is longer than 80 characters (found 85).	139
	Line is longer than 80 characters (found 83).	155
	Line is longer than 80 characters (found 117).	163
	Line is longer than 80 characters (found 87).	171
	Line contains a tab character.	171
	Line contains a tab character.	172
	Line is longer than 80 characters (found 82).	187
	Missing a Javadoc comment.	194
	Line is longer than 80 characters (found 86).	199
	Missing a Javadoc comment.	225
	Line contains a tab character.	226
	Line is longer than 80 characters (found 83).	228
	Missing a Javadoc comment.	232
	Missing a Javadoc comment.	236
	Missing a Javadoc comment.	240
	Line is longer than 80 characters (found 105).	250
	'+' should be on a new line.	250
	Line contains a tab character.	251
	Line is longer than 80 characters (found 81).	260
	'+' should be on a new line.	260
	Line is longer than 80 characters (found 85).	261
	Line contains a tab character.	261
	Line is longer than 80 characters (found 87).	270
	Line contains a tab character.	307
	Line has trailing spaces.	311
	Method 'findByEc' is not designed for extension - needs to be abstract, final or empty.	315
	Parameter ec1 should be final.	315
	Parameter ec2 should be final.	315
	Parameter ec3 should be final.	315
	Parameter ec4 should be final.	315
	Parameter status should be final.	315
	Line contains a tab character.	316
	Parameter con should be final.	316
	Expected @throws tag for 'DomainException'.	317
	'3' is a magic number.	326
	'4' is a magic number.	327
	'5' is a magic number.	328
	'6' is a magic number.	329
	'7' is a magic number.	330
	'8' is a magic number.	331
	'9' is a magic number.	332
	'10' is a magic number.	333
	'11' is a magic number.	334
	'?' is not preceded with whitespace.	334
	Avoid inline conditionals.	334
	'if' construct must use '{}'s.	341
	Line contains a tab character.	341
	'if' construct must use '{}'s.	342
	Line has trailing spaces.	347
	Method 'findByEc' is not designed for extension - needs to be abstract, final or empty.	359
	Parameter ecString should be final.	359
	Parameter status should be final.	359
	Parameter con should be final.	359
	Expected @throws tag for 'NumberFormatException'.	360
	Redundant throws: 'NumberFormatException' is unchecked exception.	360
	Expected @throws tag for 'SQLException'.	360
	Expected @throws tag for 'DomainException'.	360
	Expected @throws tag for 'MapperException'.	360
	'{' is not preceded with whitespace.	360
	Line contains a tab character.	361
	Line contains a tab character.	362
	'{' is not preceded with whitespace.	362
	Line contains a tab character.	363
	Line contains a tab character.	364
	Line contains a tab character.	365
	Line contains a tab character.	366
	Line has trailing spaces.	368
	Method 'findAllByEc' is not designed for extension - needs to be abstract, final or empty.	369
	Missing a Javadoc comment.	369
	Parameter ec1 should be final.	369
	Parameter ec2 should be final.	369
	Parameter ec3 should be final.	369
	Parameter ec4 should be final.	369
	Line contains a tab character.	370
	Parameter preliminary should be final.	370
	Parameter con should be final.	370
	'if' construct must use '{}'s.	372
	Line is longer than 80 characters (found 97).	372
	Line contains a tab character.	372
	Line contains a tab character.	373
	Line contains a tab character.	374
	Line contains a tab character.	375
	Line contains a tab character.	377
	Line contains a tab character.	378
	Line is longer than 80 characters (found 93).	379
	Line contains a tab character.	379
	Line contains a tab character.	380
	Line contains a tab character.	381
	Line contains a tab character.	382
	'3' is a magic number.	382
	Line contains a tab character.	383
	'4' is a magic number.	383
	Line contains a tab character.	384
	'5' is a magic number.	384
	Line contains a tab character.	385
	'6' is a magic number.	385
	Line contains a tab character.	386
	'7' is a magic number.	386
	Line contains a tab character.	387
	'8' is a magic number.	387
	Line contains a tab character.	388
	'9' is a magic number.	388
	Line contains a tab character.	389
	'10' is a magic number.	389
	Line contains a tab character.	390
	Line contains a tab character.	391
	Line contains a tab character.	392
	Line contains a tab character.	394
	Line contains a tab character.	395
	Line contains a tab character.	397
	Line contains a tab character.	398
	Line is longer than 80 characters (found 100).	399
	Line contains a tab character.	399
	'if' construct must use '{}'s.	400
	Line is longer than 80 characters (found 81).	400
	Line contains a tab character.	400
	Line contains a tab character.	402
	Line contains a tab character.	403
	Line contains a tab character.	404
	'if' construct must use '{}'s.	405
	Line contains a tab character.	405
	'if' construct must use '{}'s.	406
	Line contains a tab character.	406
	Line contains a tab character.	407
	'if' construct must use '{}'s.	409
	Line contains a tab character.	409
	Line contains a tab character.	410
	Line has trailing spaces.	411
	Line contains a tab character.	411
	Line has trailing spaces.	412
	Line contains a tab character.	412
	Line is longer than 80 characters (found 81).	416
	Line contains a tab character.	424
	Line is longer than 80 characters (found 85).	425
	Unused @throws tag for 'NullPointerException'.	425
	Line is longer than 80 characters (found 90).	429
	Method 'findAllByEc' is not designed for extension - needs to be abstract, final or empty.	429
	Parameter ec1 should be final.	429
	Parameter ec2 should be final.	429
	Parameter ec3 should be final.	429
	Parameter ec4 should be final.	429
	Parameter con should be final.	429
	Line contains a tab character.	431
	Line is longer than 80 characters (found 85).	434
	Line contains a tab character.	434
	Missing a Javadoc comment.	434
	Parameter con should be final.	434
	Parameter enzymeEntry should be final.	434
	Line contains a tab character.	435
	Line contains a tab character.	436
	Line contains a tab character.	437
	'{' is not preceded with whitespace.	437
	Line contains a tab character.	438
	Line contains a tab character.	439
	'{' is not preceded with whitespace.	439
	Line is longer than 80 characters (found 88).	440
	Line contains a tab character.	440
	Line is longer than 80 characters (found 93).	441
	Line contains a tab character.	441
	Line is longer than 80 characters (found 85).	442
	Line contains a tab character.	442
	Line contains a tab character.	443
	Line contains a tab character.	444
	Line is longer than 80 characters (found 85).	445
	Line contains a tab character.	445
	Line contains a tab character.	446
	Line is longer than 80 characters (found 88).	447
	Line contains a tab character.	447
	Line contains a tab character.	448
	Line contains a tab character.	449
	Line contains a tab character.	450
	Line is longer than 80 characters (found 85).	451
	Line contains a tab character.	451
	Line contains a tab character.	452
	Line contains a tab character.	453
	Line contains a tab character.	454
	Line contains a tab character.	455
	Line is longer than 80 characters (found 99).	457
	Method 'findAllSubSubclassEntriesByEc' is not designed for extension - needs to be abstract, final or empty.	457
	Missing a Javadoc comment.	457
	Parameter ec1 should be final.	457
	Parameter ec2 should be final.	457
	Parameter ec3 should be final.	457
	Parameter con should be final.	457
	'if' construct must use '{}'s.	459
	Line is longer than 80 characters (found 89).	459
	Line contains a tab character.	463
	Line is longer than 80 characters (found 92).	467
	'3' is a magic number.	470
	'4' is a magic number.	471
	'5' is a magic number.	472
	'6' is a magic number.	473
	'7' is a magic number.	474
	'8' is a magic number.	475
	'9' is a magic number.	476
	'{' is not preceded with whitespace.	480
	Line is longer than 80 characters (found 82).	481
	Line contains a tab character.	481
	Line contains a tab character.	482
	Line contains a tab character.	483
	'if' construct must use '{}'s.	484
	Line is longer than 80 characters (found 83).	484
	Line contains a tab character.	484
	Line contains a tab character.	485
	Line is longer than 80 characters (found 92).	492
	'if' construct must use '{}'s.	493
	'if' construct must use '{}'s.	498
	Line contains a tab character.	498
	'if' construct must use '{}'s.	499
	'?' is not preceded with whitespace.	502
	Avoid inline conditionals.	502
	Line contains a tab character.	511
	Line has trailing spaces.	513
	Line contains a tab character.	515
	Method 'findById' is not designed for extension - needs to be abstract, final or empty.	517
	Parameter id should be final.	517
	Parameter con should be final.	517
	Parameter ghost should be final.	517
	Expected @throws tag for 'SQLException'.	518
	'if' construct must use '{}'s.	530
	'else' construct must use '{}'s.	532
	'if' construct must use '{}'s.	534
	'else' construct must use '{}'s.	536
	'if' construct must use '{}'s.	538
	'else' construct must use '{}'s.	540
	'else' construct must use '{}'s.	542
	'if' construct must use '{}'s.	545
	'3' is a magic number.	551
	'4' is a magic number.	552
	'5' is a magic number.	553
	'6' is a magic number.	554
	'7' is a magic number.	555
	Line contains a tab character.	558
	'{' is not preceded with whitespace.	558
	Line contains a tab character.	559
	Line contains a tab character.	560
	Line contains a tab character.	561
	Line contains a tab character.	562
	Line contains a tab character.	563
	'if' construct must use '{}'s.	566
	Line contains a tab character.	566
	'if' construct must use '{}'s.	567
	Line contains a tab character.	567
	'if' construct must use '{}'s.	568
	Line contains a tab character.	568
	Line has trailing spaces.	573
	Line contains a tab character.	579
	Method 'findById' is not designed for extension - needs to be abstract, final or empty.	584
	Parameter id should be final.	584
	Expected @param tag for 'id'.	584
	Parameter con should be final.	584
	Expected @param tag for 'con'.	584
	Expected @throws tag for 'SQLException'.	585
	Expected @throws tag for 'DomainException'.	585
	'{' is not preceded with whitespace.	585
	Line contains a tab character.	586
	Line is longer than 80 characters (found 97).	594
	Method 'findGhostById' is not designed for extension - needs to be abstract, final or empty.	598
	Parameter id should be final.	598
	Parameter con should be final.	598
	Expected @throws tag for 'SQLException'.	599
	Expected @throws tag for 'DomainException'.	599
	Line contains a tab character.	600
	Line contains a tab character.	601
	Line contains a tab character.	602
	Line contains a tab character.	603
	Must have at least one statement.	603
	Line contains a tab character.	604
	Line contains a tab character.	605
	Line contains a tab character.	606
	Method 'findIDInMappingTable' is not designed for extension - needs to be abstract, final or empty.	609
	Missing a Javadoc comment.	609
	Parameter ec should be final.	609
	Parameter status should be final.	609
	Parameter con should be final.	609
	'if' construct must use '{}'s.	611
	'if' construct must use '{}'s.	625
	Line contains a tab character.	625
	'if' construct must use '{}'s.	626
	Line contains a tab character.	635
	Line has trailing spaces.	637
	Line is longer than 80 characters (found 89).	639
	Method 'findAll' is not designed for extension - needs to be abstract, final or empty.	639
	Parameter con should be final.	639
	Expected @throws tag for 'SQLException'.	639
	Line is longer than 80 characters (found 92).	655
	'if' construct must use '{}'s.	656
	'if' construct must use '{}'s.	660
	Line contains a tab character.	660
	'if' construct must use '{}'s.	661
	'if' construct must use '{}'s.	664
	Line is longer than 80 characters (found 91).	675
	Line has trailing spaces.	678
	Method 'findList' is not designed for extension - needs to be abstract, final or empty.	680
	Parameter ec1 should be final.	680
	Parameter ec2 should be final.	680
	Parameter ec3 should be final.	680
	Line contains a tab character.	681
	Parameter con should be final.	681
	Expected @throws tag for 'SQLException'.	682
	'3' is a magic number.	692
	Line is longer than 80 characters (found 92).	704
	'if' construct must use '{}'s.	705
	'if' construct must use '{}'s.	709
	Line contains a tab character.	709
	'if' construct must use '{}'s.	710
	'if' construct must use '{}'s.	713
	Method 'findByStatus' is not designed for extension - needs to be abstract, final or empty.	725
	Parameter con should be final.	725
	Expected @param tag for 'con'.	725
	Parameter status should be final.	725
	Expected @param tag for 'status'.	725
	Expected @throws tag for 'SQLException'.	726
	Expected @throws tag for 'DomainException'.	726
	'{' is not preceded with whitespace.	726
	Line contains a tab character.	727
	Line contains a tab character.	728
	Line contains a tab character.	729
	Line contains a tab character.	730
	Line contains a tab character.	731
	Line contains a tab character.	732
	Line contains a tab character.	733
	Line contains a tab character.	735
	Line contains a tab character.	736
	Line contains a tab character.	737
	Line contains a tab character.	738
	Line contains a tab character.	739
	Line contains a tab character.	740
	Line is longer than 80 characters (found 100).	741
	Line contains a tab character.	741
	'if' construct must use '{}'s.	742
	Line is longer than 80 characters (found 81).	742
	Line contains a tab character.	742
	Line contains a tab character.	743
	Line contains a tab character.	744
	Line contains a tab character.	745
	'if' construct must use '{}'s.	746
	Line contains a tab character.	746
	'if' construct must use '{}'s.	747
	Line contains a tab character.	747
	Line contains a tab character.	748
	Line contains a tab character.	749
	Line has trailing spaces.	751
	Line contains a tab character.	757
	Method 'findProposedList' is not designed for extension - needs to be abstract, final or empty.	761
	Parameter con should be final.	761
	Line contains a tab character.	771
	Line has trailing spaces.	773
	Method 'findSuggestedList' is not designed for extension - needs to be abstract, final or empty.	775
	Parameter con should be final.	775
	Expected @throws tag for 'SQLException'.	776
	Method 'findPreliminaryEcsList' is not designed for extension - needs to be abstract, final or empty.	787
	Parameter con should be final.	787
	Expected @param tag for 'con'.	787
	Expected @throws tag for 'SQLException'.	788
	Expected @throws tag for 'DomainException'.	788
	'{' is not preceded with whitespace.	788
	Line has trailing spaces.	791
	Line has trailing spaces.	796
	Line has trailing spaces.	797
	Method 'exportAllEntries' is not designed for extension - needs to be abstract, final or empty.	800
	Parameter con should be final.	800
	Expected @param tag for 'con'.	800
	'{' is not preceded with whitespace.	801
	Line contains a tab character.	802
	Line contains a tab character.	803
	Line contains a tab character.	804
	Line contains a tab character.	805
	Line contains a tab character.	806
	Line contains a tab character.	807
	Line contains a tab character.	808
	'{' is not preceded with whitespace.	808
	Line contains a tab character.	809
	Line contains a tab character.	810
	Line contains a tab character.	811
	Line contains a tab character.	812
	Line contains a tab character.	813
	'if' construct must use '{}'s.	814
	Line contains a tab character.	814
	'if' construct must use '{}'s.	815
	Line contains a tab character.	815
	Line contains a tab character.	816
	Line contains a tab character.	817
	'?' is not preceded with whitespace.	817
	Avoid inline conditionals.	817
	Line is longer than 80 characters (found 86).	821
	Line is longer than 80 characters (found 97).	826
	Line contains a tab character.	827
	Line has trailing spaces.	829
	Line has trailing spaces.	832
	Method 'exportApprovedSibEntries' is not designed for extension - needs to be abstract, final or empty.	832
	Parameter con should be final.	832
	Expected @throws tag for 'SQLException'.	833
	'if' construct must use '{}'s.	846
	Line contains a tab character.	846
	'if' construct must use '{}'s.	847
	'?' is not preceded with whitespace.	849
	Avoid inline conditionals.	849
	':' is not preceded with whitespace.	849
	Line is longer than 80 characters (found 93).	858
	Line contains a tab character.	859
	Line has trailing spaces.	861
	Method 'findFullProposedList' is not designed for extension - needs to be abstract, final or empty.	864
	Parameter con should be final.	864
	Expected @throws tag for 'SQLException'.	865
	'if' construct must use '{}'s.	883
	Line contains a tab character.	883
	'if' construct must use '{}'s.	884
	'if' construct must use '{}'s.	887
	Line is longer than 80 characters (found 93).	897
	Line contains a tab character.	898
	Line has trailing spaces.	900
	Method 'findFullSuggestedList' is not designed for extension - needs to be abstract, final or empty.	903
	Parameter con should be final.	903
	Expected @throws tag for 'SQLException'.	904
	'if' construct must use '{}'s.	922
	Line contains a tab character.	922
	'if' construct must use '{}'s.	923
	'if' construct must use '{}'s.	926
	Line has trailing spaces.	937
	Method 'findEC' is not designed for extension - needs to be abstract, final or empty.	939
	Parameter id should be final.	939
	Parameter con should be final.	939
	Expected @throws tag for 'SQLException'.	940
	'if' construct must use '{}'s.	958
	Line contains a tab character.	958
	'if' construct must use '{}'s.	959
	Line contains a tab character.	963
	Unused @throws tag for 'NullPointerException'.	973
	Parameter ec should be final.	975
	Parameter con should be final.	975
	'if' construct must use '{}'s.	977
	Line is longer than 80 characters (found 87).	977
	'if' construct must use '{}'s.	978
	Line is longer than 80 characters (found 89).	978
	switch without "default" clause.	983
	Line is longer than 80 characters (found 88).	985
	'+' should be on a new line.	989
	Line contains a tab character.	990
	'+' should be on a new line.	995
	Line contains a tab character.	996
	'3' is a magic number.	999
	'+' should be on a new line.	1002
	Line is longer than 80 characters (found 96).	1003
	Line contains a tab character.	1003
	'3' is a magic number.	1006
	'4' is a magic number.	1007
	'+' should be on a new line.	1010
	Line is longer than 80 characters (found 95).	1011
	Line contains a tab character.	1011
	Line contains a tab character.	1012
	Line contains a tab character.	1013
	Line contains a tab character.	1014
	'3' is a magic number.	1014
	Line contains a tab character.	1015
	'4' is a magic number.	1015
	'if' construct must use '{}'s.	1021
	Line contains a tab character.	1021
	'if' construct must use '{}'s.	1022
	Method 'findHistoryLine' is not designed for extension - needs to be abstract, final or empty.	1034
	Parameter id should be final.	1034
	Parameter con should be final.	1034
	Expected @throws tag for 'SQLException'.	1034
	Line is longer than 80 characters (found 82).	1039
	'if' construct must use '{}'s.	1044
	Line is longer than 80 characters (found 83).	1044
	'if' construct must use '{}'s.	1047
	Line contains a tab character.	1047
	'if' construct must use '{}'s.	1048
	Method 'findNote' is not designed for extension - needs to be abstract, final or empty.	1062
	Parameter id should be final.	1062
	Parameter con should be final.	1062
	Expected @throws tag for 'SQLException'.	1062
	'if' construct must use '{}'s.	1073
	'if' construct must use '{}'s.	1076
	Line contains a tab character.	1076
	'if' construct must use '{}'s.	1077
	Expected an @return tag.	1088
	Method 'findStats' is not designed for extension - needs to be abstract, final or empty.	1088
	Parameter con should be final.	1088
	Expected @throws tag for 'SQLException'.	1088
	Line contains a tab character.	1090
	'if' construct must use '{}'s.	1109
	'if' construct must use '{}'s.	1113
	'if' construct must use '{}'s.	1117
	'if' construct must use '{}'s.	1148
	Line contains a tab character.	1148
	Line has trailing spaces.	1165
	Line has trailing spaces.	1166
	Line has trailing spaces.	1167
	Line has trailing spaces.	1170
	Line has trailing spaces.	1171
	Line has trailing spaces.	1173
	Method 'insert' is not designed for extension - needs to be abstract, final or empty.	1175
	More than 7 parameters (found 8).	1175
	Parameter enzymeId should be final.	1175
	Parameter ec should be final.	1175
	Parameter status should be final.	1175
	Line is longer than 80 characters (found 82).	1176
	Parameter source should be final.	1176
	Expected @param tag for 'source'.	1176
	Parameter note should be final.	1176
	Parameter historyLine should be final.	1176
	Parameter isActive should be final.	1177
	Expected @param tag for 'isActive'.	1177
	Parameter con should be final.	1177
	Expected @param tag for 'con'.	1177
	'3' is a magic number.	1184
	'4' is a magic number.	1185
	'5' is a magic number.	1186
	'6' is a magic number.	1187
	'7' is a magic number.	1188
	'8' is a magic number.	1189
	'9' is a magic number.	1190
	'10' is a magic number.	1191
	Avoid inline conditionals.	1191
	Line is longer than 80 characters (found 88).	1202
	Line is longer than 80 characters (found 90).	1204
	Line has trailing spaces.	1216
	Method 'update' is not designed for extension - needs to be abstract, final or empty.	1218
	More than 7 parameters (found 8).	1218
	Parameter enzymeId should be final.	1218
	Parameter ec should be final.	1218
	Parameter status should be final.	1218
	Line contains a tab character.	1219
	Parameter source should be final.	1219
	Parameter note should be final.	1219
	Parameter historyLine should be final.	1219
	Line contains a tab character.	1220
	Parameter active should be final.	1220
	Parameter con should be final.	1220
	'if' construct must use '{}'s.	1222
	Line is longer than 80 characters (found 99).	1222
	'if' construct must use '{}'s.	1223
	Line is longer than 80 characters (found 87).	1223
	'if' construct must use '{}'s.	1224
	Line is longer than 80 characters (found 95).	1224
	'if' construct must use '{}'s.	1225
	Line is longer than 80 characters (found 95).	1225
	'if' construct must use '{}'s.	1226
	Line is longer than 80 characters (found 91).	1226
	'if' construct must use '{}'s.	1227
	Line is longer than 80 characters (found 105).	1227
	'if' construct must use '{}'s.	1228
	Line is longer than 80 characters (found 89).	1228
	'3' is a magic number.	1235
	'4' is a magic number.	1236
	'5' is a magic number.	1237
	'6' is a magic number.	1238
	'7' is a magic number.	1239
	'8' is a magic number.	1240
	'9' is a magic number.	1241
	'?' is not preceded with whitespace.	1241
	Avoid inline conditionals.	1241
	'10' is a magic number.	1242
	Line is longer than 80 characters (found 105).	1257
	Method 'updateEc' is not designed for extension - needs to be abstract, final or empty.	1257
	Parameter enzymeId should be final.	1257
	Parameter newEc should be final.	1257
	Parameter con should be final.	1257
	Expected @throws tag for 'SQLException'.	1257
	'3' is a magic number.	1264
	'4' is a magic number.	1265
	'5' is a magic number.	1266
	Line is longer than 80 characters (found 90).	1281
	Method 'updateNote' is not designed for extension - needs to be abstract, final or empty.	1281
	Parameter enzymeId should be final.	1281
	Parameter note should be final.	1281
	Parameter con should be final.	1281
	Expected @throws tag for 'SQLException'.	1281
	Line is longer than 80 characters (found 94).	1302
	Method 'updateStatus' is not designed for extension - needs to be abstract, final or empty.	1302
	Parameter enzymeId should be final.	1302
	Parameter status should be final.	1302
	Parameter con should be final.	1302
	Expected @throws tag for 'SQLException'.	1302
	Line is longer than 80 characters (found 104).	1323
	Method 'updateHistoryLine' is not designed for extension - needs to be abstract, final or empty.	1323
	Parameter enzymeId should be final.	1323
	Parameter historyLine should be final.	1323
	Parameter con should be final.	1323
	Expected @throws tag for 'SQLException'.	1323
	Line is longer than 80 characters (found 86).	1327
	Method 'cloneExists' is not designed for extension - needs to be abstract, final or empty.	1344
	Parameter id should be final.	1344
	Parameter con should be final.	1344
	Expected @throws tag for 'SQLException'.	1344
	Line is longer than 80 characters (found 95).	1354
	Line is longer than 80 characters (found 87).	1357
	Parameter rs should be final.	1360
	Expected @throws tag for 'EcException'.	1360
	'if' construct must use '{}'s.	1375
	'if' construct must use '{}'s.	1376
	'if' construct must use '{}'s.	1377
	'3' is a magic number.	1377
	'3' is a magic number.	1377
	'if' construct must use '{}'s.	1378
	'4' is a magic number.	1378
	'4' is a magic number.	1378
	'if' construct must use '{}'s.	1379
	'5' is a magic number.	1379
	'5' is a magic number.	1379
	'if' construct must use '{}'s.	1380
	'6' is a magic number.	1380
	'6' is a magic number.	1380
	'if' construct must use '{}'s.	1381
	'7' is a magic number.	1381
	'7' is a magic number.	1381
	'if' construct must use '{}'s.	1382
	'8' is a magic number.	1382
	'8' is a magic number.	1382
	'if' construct must use '{}'s.	1383
	'9' is a magic number.	1383
	'9' is a magic number.	1383
	'if' construct must use '{}'s.	1384
	'10' is a magic number.	1384
	'10' is a magic number.	1384
	'if' construct must use '{}'s.	1385
	'11' is a magic number.	1385
	'11' is a magic number.	1385
	'if' construct must use '{}'s.	1386
	'12' is a magic number.	1386
	'12' is a magic number.	1386
	'if' construct must use '{}'s.	1387
	'13' is a magic number.	1387
	'13' is a magic number.	1387
	Line contains a tab character.	1393
	Line contains a tab character.	1397
	Line is longer than 80 characters (found 85).	1415
	Parameter rs should be final.	1415
	Expected @throws tag for 'SQLException'.	1415
	Expected @throws tag for 'DomainException'.	1415
	'if' construct must use '{}'s.	1427
	'if' construct must use '{}'s.	1428
	'if' construct must use '{}'s.	1429
	'3' is a magic number.	1429
	'3' is a magic number.	1429
	'if' construct must use '{}'s.	1430
	'4' is a magic number.	1430
	'4' is a magic number.	1430
	'if' construct must use '{}'s.	1431
	'5' is a magic number.	1431
	'5' is a magic number.	1431
	'if' construct must use '{}'s.	1432
	'6' is a magic number.	1432
	'6' is a magic number.	1432
	'if' construct must use '{}'s.	1433
	'7' is a magic number.	1433
	'7' is a magic number.	1433
	'if' construct must use '{}'s.	1434
	'8' is a magic number.	1434
	'8' is a magic number.	1434
	'if' construct must use '{}'s.	1435
	'9' is a magic number.	1435
	'9' is a magic number.	1435
	'if' construct must use '{}'s.	1436
	'10' is a magic number.	1436
	'10' is a magic number.	1436
	Line contains a tab character.	1442
	Line contains a tab character.	1446
	Line is longer than 80 characters (found 93).	1454
	Line is longer than 80 characters (found 94).	1460
	Parameter entry should be final.	1460
	Parameter names should be final.	1460
	Expected @throws tag for 'DomainException'.	1460
	Line is longer than 80 characters (found 96).	1476
	Line is longer than 80 characters (found 86).	1482
	Parameter rs should be final.	1482
	Expected @throws tag for 'SQLException'.	1482
	Expected @throws tag for 'DomainException'.	1482
	'if' construct must use '{}'s.	1493
	Line is longer than 80 characters (found 81).	1493
	'if' construct must use '{}'s.	1494
	'if' construct must use '{}'s.	1495
	'if' construct must use '{}'s.	1496
	'if' construct must use '{}'s.	1497
	'if' construct must use '{}'s.	1498
	'if' construct must use '{}'s.	1499
	'if' construct must use '{}'s.	1500
	'if' construct must use '{}'s.	1501
	Line contains a tab character.	1504
	Line contains a tab character.	1507
	Line contains a tab character.	1510
	'if' construct must use '{}'s.	1511
	Line is longer than 80 characters (found 88).	1511
	'if' construct must use '{}'s.	1512
	Line is longer than 80 characters (found 93).	1518
	Line is longer than 80 characters (found 82).	1523
	Parameter enzymeEntry should be final.	1525
	Parameter con should be final.	1525
	Expected @throws tag for 'DomainException'.	1526
	Expected @throws tag for 'EnzymeReactionException'.	1526
	Redundant throws: 'EnzymeReactionException' is subclass of 'DomainException'.	1526
	Line contains a tab character.	1527
	Expected @throws tag for 'EnzymeReferenceException'.	1527
	Redundant throws: 'EnzymeReferenceException' is subclass of 'DomainException'.	1527
	'if' construct must use '{}'s.	1533
	Line contains a tab character.	1537
	'if' construct must use '{}'s.	1538
	'if' construct must use '{}'s.	1544
	Line contains a tab character.	1550
	Line contains a tab character.	1551
	'if' construct must use '{}'s.	1556
	'if' construct must use '{}'s.	1561
	Line is longer than 80 characters (found 94).	1573
	Parameter enzymeEntry should be final.	1576
	Parameter con should be final.	1576
	Redundant throws: 'EnzymeReactionException' is subclass of 'DomainException'.	1578
	Line has trailing spaces.	1583
	Line is longer than 80 characters (found 81).	1586
	'if' construct must use '{}'s.	1587
	Line is longer than 80 characters (found 82).	1591
	Line contains a tab character.	1591
	'if' construct must use '{}'s.	1592
	Line is longer than 80 characters (found 88).	1596
	'if' construct must use '{}'s.	1598
	Line is longer than 80 characters (found 81).	1602
	'if' construct must use '{}'s.	1603
	Line is longer than 80 characters (found 93).	1608
	'if' construct must use '{}'s.	1609
	Method 'findNextEnzymeId' is not designed for extension - needs to be abstract, final or empty.	1619
	Parameter con should be final.	1619
	Expected @throws tag for 'SQLException'.	1619
	'if' construct must use '{}'s.	1620
	Line is longer than 80 characters (found 89).	1620
	Line contains a tab character.	1637
	Missing a Javadoc comment.	1637
	Parameter enzymeEntry should be final.	1637
	Parameter con should be final.	1637
	Line contains a tab character.	1639
	'if' construct must use '{}'s.	1640
	Line contains a tab character.	1640
	Line contains a tab character.	1641

uk/ac/ebi/intenz/mapper/EnzymeFutureMapper.java

Violation	Message	Line
	Line is longer than 80 characters (found 107).	28
	Missing a Javadoc comment.	28
	'+' should be on a new line.	28
	'+' should be on a new line.	29
	Missing a Javadoc comment.	32
	Missing a Javadoc comment.	36
	'+' should be on a new line.	37
	'+' should be on a new line.	38
	Line is longer than 80 characters (found 85).	39
	Method 'find' is not designed for extension - needs to be abstract, final or empty.	42
	Parameter enzymeEntry should be final.	43
	Parameter con should be final.	43
	'if' construct must use '{}'s.	45
	'if' construct must use '{}'s.	47
	Line is longer than 80 characters (found 81).	54
	Line is longer than 80 characters (found 96).	58
	Line is longer than 80 characters (found 87).	61
	Method 'futureEventExists' is not designed for extension - needs to be abstract, final or empty.	61
	Parameter enzymeId should be final.	61
	Parameter con should be final.	61
	Expected @throws tag for 'SQLException'.	61
	'if' construct must use '{}'s.	73
	Line contains a tab character.	73
	Missing a Javadoc comment.	83
	Parameter currentEntry should be final.	83
	Parameter isRoot should be final.	83
	Line contains a tab character.	84
	Parameter con should be final.	84
	Line is longer than 80 characters (found 89).	91
	Line is longer than 80 characters (found 86).	94
	Missing a Javadoc comment.	106
	Parameter currentNode should be final.	106
	Parameter con should be final.	106
	Line is longer than 80 characters (found 81).	114
	Line is longer than 80 characters (found 81).	115
	'if' construct must use '{}'s.	121
	Line contains a tab character.	121
	'if' construct must use '{}'s.	122
	Line contains a tab character.	122
	Parameter rs should be final.	135
	Parameter currentNode should be final.	135
	Expected @param tag for 'currentNode'.	135
	Line contains a tab character.	136
	Parameter con should be final.	136
	Expected @param tag for 'con'.	136
	Expected @throws tag for 'SQLException'.	137
	Expected @throws tag for 'DomainException'.	137
	'if' construct must use '{}'s.	151
	'if' construct must use '{}'s.	152
	'if' construct must use '{}'s.	153
	'3' is a magic number.	153
	'3' is a magic number.	153
	'if' construct must use '{}'s.	154
	'4' is a magic number.	154
	'4' is a magic number.	154
	'if' construct must use '{}'s.	155
	'5' is a magic number.	155
	'5' is a magic number.	155
	'if' construct must use '{}'s.	156
	'6' is a magic number.	156
	'6' is a magic number.	156
	'if' construct must use '{}'s.	157
	'7' is a magic number.	157
	'7' is a magic number.	157
	'if' construct must use '{}'s.	158
	'8' is a magic number.	158
	'8' is a magic number.	158
	'if' construct must use '{}'s.	159
	'9' is a magic number.	159
	'9' is a magic number.	159
	'if' construct must use '{}'s.	160
	'10' is a magic number.	160
	'10' is a magic number.	160
	'if' construct must use '{}'s.	161
	'11' is a magic number.	161
	'11' is a magic number.	161
	'if' construct must use '{}'s.	162
	'12' is a magic number.	162
	'12' is a magic number.	162
	Line is longer than 80 characters (found 112).	164
	Line has trailing spaces.	204

uk/ac/ebi/intenz/mapper/EnzymeHistoryMapper.java

Violation	Message	Line
	Missing a Javadoc comment.	30
	Name 'LOGGER' must match pattern '^[a-z][a-zA-Z0-9]*$'.	30
	Missing a Javadoc comment.	32
	Variable 'visitedNodes' must be private and have accessor methods.	32
	Line is longer than 80 characters (found 119).	34
	Missing a Javadoc comment.	34
	Missing a Javadoc comment.	36
	Missing a Javadoc comment.	40
	'+' should be on a new line.	41
	Method 'find' is not designed for extension - needs to be abstract, final or empty.	45
	Missing a Javadoc comment.	45
	Parameter enzymeEntry should be final.	45
	Parameter con should be final.	45
	'if' construct must use '{}'s.	47
	'if' construct must use '{}'s.	49
	Missing a Javadoc comment.	56
	Parameter currentEntry should be final.	56
	Parameter isRoot should be final.	56
	Line contains a tab character.	57
	Parameter con should be final.	57
	Line is longer than 80 characters (found 89).	64
	'if' construct must use '{}'s.	66
	Line is longer than 80 characters (found 86).	67
	Missing a Javadoc comment.	78
	Parameter currentNode should be final.	78
	Parameter con should be final.	78
	Line is longer than 80 characters (found 81).	86
	Line is longer than 80 characters (found 81).	87
	'if' construct must use '{}'s.	93
	Line contains a tab character.	93
	'if' construct must use '{}'s.	94
	Line is longer than 80 characters (found 85).	102
	Line is longer than 80 characters (found 81).	104
	Parameter rs should be final.	110
	Parameter currentNode should be final.	110
	Expected @param tag for 'currentNode'.	110
	Line contains a tab character.	111
	Parameter con should be final.	111
	Expected @param tag for 'con'.	111
	Expected @throws tag for 'SQLException'.	112
	Expected @throws tag for 'DomainException'.	112
	'if' construct must use '{}'s.	121
	'if' construct must use '{}'s.	122
	'if' construct must use '{}'s.	123
	'if' construct must use '{}'s.	124
	'{' is not preceded with whitespace.	125
	'if' construct must use '{}'s.	129
	Line is longer than 80 characters (found 83).	129
	'if' construct must use '{}'s.	130
	Line is longer than 80 characters (found 86).	130
	Line is longer than 80 characters (found 112).	132
	Line has trailing spaces.	162
	Line has trailing spaces.	164

uk/ac/ebi/intenz/mapper/EnzymeLinkMapper.java

Violation	Message	Line
	Missing a Javadoc comment.	26
	Missing a Javadoc comment.	28
	Missing a Javadoc comment.	30
	Line is longer than 80 characters (found 90).	31
	Missing a Javadoc comment.	32
	Line is longer than 80 characters (found 82).	34
	Missing a Javadoc comment.	36
	Missing a Javadoc comment.	39
	'+' should be on a new line.	40
	'+' should be on a new line.	41
	'+' should be on a new line.	42
	Missing a Javadoc comment.	46
	'+' should be on a new line.	47
	'+' should be on a new line.	48
	Line is longer than 80 characters (found 132).	49
	'+' should be on a new line.	49
	Missing a Javadoc comment.	53
	'+' should be on a new line.	54
	'+' should be on a new line.	55
	'+' should be on a new line.	56
	Missing a Javadoc comment.	60
	'+' should be on a new line.	61
	'+' should be on a new line.	62
	Line is longer than 80 characters (found 132).	63
	'+' should be on a new line.	63
	Missing a Javadoc comment.	67
	Line is longer than 80 characters (found 131).	68
	Missing a Javadoc comment.	71
	Line is longer than 80 characters (found 149).	72
	Missing a Javadoc comment.	75
	Line is longer than 80 characters (found 91).	76
	Missing a Javadoc comment.	79
	Missing a Javadoc comment.	83
	Missing a Javadoc comment.	87
	Line is longer than 80 characters (found 101).	88
	Missing a Javadoc comment.	91
	Missing a Javadoc comment.	95
	Missing a Javadoc comment.	99
	Line is longer than 80 characters (found 126).	108
	Line is longer than 80 characters (found 100).	111
	Method 'find' is not designed for extension - needs to be abstract, final or empty.	111
	Parameter enzymeId should be final.	111
	Parameter con should be final.	111
	Expected @throws tag for 'SQLException'.	111
	Expected @throws tag for 'DomainException'.	111
	'if' construct must use '{}'s.	112
	Line is longer than 80 characters (found 99).	112
	'if' construct must use '{}'s.	113
	Line is longer than 80 characters (found 89).	113
	'if' construct must use '{}'s.	125
	'if' construct must use '{}'s.	129
	'if' construct must use '{}'s.	131
	Line contains a tab character.	131
	'if' construct must use '{}'s.	132
	'if' construct must use '{}'s.	135
	Line is longer than 80 characters (found 100).	146
	Line is longer than 80 characters (found 83).	148
	Unused @throws tag for 'NullPointerException'.	148
	Line is longer than 80 characters (found 110).	150
	Method 'exportSibLinks' is not designed for extension - needs to be abstract, final or empty.	150
	Parameter enzymeId should be final.	150
	Parameter con should be final.	150
	Expected @throws tag for 'DomainException'.	150
	'if' construct must use '{}'s.	151
	Line is longer than 80 characters (found 99).	151
	'if' construct must use '{}'s.	152
	Line is longer than 80 characters (found 89).	152
	'3' is a magic number.	162
	'4' is a magic number.	163
	'5' is a magic number.	164
	'if' construct must use '{}'s.	168
	'if' construct must use '{}'s.	172
	'if' construct must use '{}'s.	174
	Line contains a tab character.	174
	'if' construct must use '{}'s.	175
	'if' construct must use '{}'s.	178
	Line is longer than 80 characters (found 126).	187
	Line is longer than 80 characters (found 105).	190
	Method 'findXrefs' is not designed for extension - needs to be abstract, final or empty.	190
	Parameter enzymeId should be final.	190
	Parameter con should be final.	190
	Expected @throws tag for 'SQLException'.	190
	Expected @throws tag for 'DomainException'.	190
	'if' construct must use '{}'s.	191
	Line is longer than 80 characters (found 99).	191
	'if' construct must use '{}'s.	192
	Line is longer than 80 characters (found 89).	192
	'if' construct must use '{}'s.	207
	'if' construct must use '{}'s.	211
	Line contains a tab character.	211
	'if' construct must use '{}'s.	212
	'if' construct must use '{}'s.	215
	Line is longer than 80 characters (found 100).	224
	Line is longer than 80 characters (found 83).	226
	Unused @throws tag for 'NullPointerException'.	226
	Line is longer than 80 characters (found 108).	228
	Method 'findSibXrefs' is not designed for extension - needs to be abstract, final or empty.	228
	Parameter enzymeId should be final.	228
	Parameter con should be final.	228
	Expected @throws tag for 'DomainException'.	228
	'if' construct must use '{}'s.	229
	Line is longer than 80 characters (found 99).	229
	'if' construct must use '{}'s.	230
	Line is longer than 80 characters (found 89).	230
	'3' is a magic number.	242
	'4' is a magic number.	243
	'5' is a magic number.	244
	'if' construct must use '{}'s.	249
	'if' construct must use '{}'s.	253
	Line contains a tab character.	253
	'if' construct must use '{}'s.	254
	'if' construct must use '{}'s.	257
	Line is longer than 80 characters (found 90).	270
	Method 'insert' is not designed for extension - needs to be abstract, final or empty.	270
	Parameter links should be final.	270
	Parameter enzymeId should be final.	270
	Parameter status should be final.	270
	Parameter con should be final.	270
	Expected @throws tag for 'SQLException'.	271
	'if' construct must use '{}'s.	272
	Line is longer than 80 characters (found 93).	272
	'if' construct must use '{}'s.	273
	Line is longer than 80 characters (found 99).	273
	'if' construct must use '{}'s.	274
	Line is longer than 80 characters (found 95).	274
	'if' construct must use '{}'s.	275
	Line is longer than 80 characters (found 89).	275
	'if' construct must use '{}'s.	293
	'if' construct must use '{}'s.	294
	Line is longer than 80 characters (found 109).	298
	Method 'insertLink' is not designed for extension - needs to be abstract, final or empty.	298
	Missing a Javadoc comment.	298
	Parameter link should be final.	298
	Parameter enzymeId should be final.	298
	Parameter status should be final.	298
	Parameter con should be final.	298
	'if' construct must use '{}'s.	299
	Line is longer than 80 characters (found 91).	299
	'if' construct must use '{}'s.	300
	Line is longer than 80 characters (found 99).	300
	'if' construct must use '{}'s.	301
	Line is longer than 80 characters (found 95).	301
	'if' construct must use '{}'s.	302
	Line is longer than 80 characters (found 89).	302
	'if' construct must use '{}'s.	310
	Line is longer than 80 characters (found 112).	314
	Method 'updateLinkUrl' is not designed for extension - needs to be abstract, final or empty.	314
	Missing a Javadoc comment.	314
	Parameter link should be final.	314
	Parameter enzymeId should be final.	314
	Parameter status should be final.	314
	Parameter con should be final.	314
	'if' construct must use '{}'s.	315
	Line is longer than 80 characters (found 91).	315
	'if' construct must use '{}'s.	316
	Line is longer than 80 characters (found 99).	316
	'if' construct must use '{}'s.	317
	Line is longer than 80 characters (found 95).	317
	'if' construct must use '{}'s.	318
	Line is longer than 80 characters (found 89).	318
	'3' is a magic number.	325
	'if' construct must use '{}'s.	326
	Comment matches to-do format 'TODO:'.	327
	Line is longer than 80 characters (found 83).	327
	'4' is a magic number.	327
	'else' construct must use '{}'s.	328
	'4' is a magic number.	329
	'if' construct must use '{}'s.	332
	Line is longer than 80 characters (found 117).	336
	Method 'reloadLinks' is not designed for extension - needs to be abstract, final or empty.	336
	Missing a Javadoc comment.	336
	Parameter links should be final.	336
	Parameter enzymeId should be final.	336
	Parameter status should be final.	336
	Parameter con should be final.	336
	'if' construct must use '{}'s.	337
	Line is longer than 80 characters (found 93).	337
	'if' construct must use '{}'s.	338
	Line is longer than 80 characters (found 99).	338
	'if' construct must use '{}'s.	339
	Line is longer than 80 characters (found 95).	339
	'if' construct must use '{}'s.	340
	Line is longer than 80 characters (found 89).	340
	Line is longer than 80 characters (found 90).	346
	Method 'delete' is not designed for extension - needs to be abstract, final or empty.	346
	Missing a Javadoc comment.	346
	Parameter enzymeId should be final.	346
	Parameter link should be final.	346
	Parameter con should be final.	346
	'if' construct must use '{}'s.	347
	Line is longer than 80 characters (found 99).	347
	'if' construct must use '{}'s.	348
	Line is longer than 80 characters (found 91).	348
	'if' construct must use '{}'s.	349
	Line is longer than 80 characters (found 89).	349
	'if' construct must use '{}'s.	355
	'else' construct must use '{}'s.	357
	'3' is a magic number.	359
	'if' construct must use '{}'s.	366
	Method 'deleteAll' is not designed for extension - needs to be abstract, final or empty.	370
	Missing a Javadoc comment.	370
	Parameter enzymeId should be final.	370
	Parameter con should be final.	370
	'if' construct must use '{}'s.	371
	Line is longer than 80 characters (found 99).	371
	'if' construct must use '{}'s.	372
	Line is longer than 80 characters (found 89).	372
	'if' construct must use '{}'s.	384
	Line is longer than 80 characters (found 94).	388
	Method 'deleteXref' is not designed for extension - needs to be abstract, final or empty.	388
	Missing a Javadoc comment.	388
	Parameter enzymeId should be final.	388
	Parameter xref should be final.	388
	Parameter con should be final.	388
	'if' construct must use '{}'s.	389
	Line is longer than 80 characters (found 99).	389
	'if' construct must use '{}'s.	390
	Line is longer than 80 characters (found 91).	390
	'if' construct must use '{}'s.	391
	Line is longer than 80 characters (found 89).	391
	'if' construct must use '{}'s.	396
	'if' construct must use '{}'s.	397
	'3' is a magic number.	403
	'4' is a magic number.	404
	'if' construct must use '{}'s.	411
	Method 'deleteAllXref' is not designed for extension - needs to be abstract, final or empty.	415
	Missing a Javadoc comment.	415
	Parameter enzymeId should be final.	415
	Parameter con should be final.	415
	'if' construct must use '{}'s.	416
	Line is longer than 80 characters (found 99).	416
	'if' construct must use '{}'s.	417
	Line is longer than 80 characters (found 89).	417
	'if' construct must use '{}'s.	429
	Line is longer than 80 characters (found 99).	433
	Method 'deleteByName' is not designed for extension - needs to be abstract, final or empty.	433
	Missing a Javadoc comment.	433
	Parameter enzymeId should be final.	433
	Parameter displayName should be final.	433
	Parameter con should be final.	433
	'if' construct must use '{}'s.	434
	Line is longer than 80 characters (found 99).	434
	'if' construct must use '{}'s.	435
	Line is longer than 80 characters (found 105).	435
	'if' construct must use '{}'s.	436
	Line is longer than 80 characters (found 89).	436
	'if' construct must use '{}'s.	449
	Line is longer than 80 characters (found 101).	453
	Method 'deleteByCodeXref' is not designed for extension - needs to be abstract, final or empty.	453
	Missing a Javadoc comment.	453
	Parameter enzymeId should be final.	453
	Parameter xrefCode should be final.	453
	Parameter con should be final.	453
	'if' construct must use '{}'s.	454
	Line is longer than 80 characters (found 102).	454
	'if' construct must use '{}'s.	455
	Line is longer than 80 characters (found 102).	455
	'if' construct must use '{}'s.	456
	Line is longer than 80 characters (found 92).	456
	'if' construct must use '{}'s.	459
	Line is longer than 80 characters (found 93).	459
	'if' construct must use '{}'s.	460
	Line is longer than 80 characters (found 91).	460
	Line is longer than 80 characters (found 83).	463
	'if' construct must use '{}'s.	472
	Line is longer than 80 characters (found 107).	477
	Method 'deleteOtherLinks' is not designed for extension - needs to be abstract, final or empty.	477
	Missing a Javadoc comment.	477
	Parameter links should be final.	477
	Parameter enzymeId should be final.	477
	Parameter con should be final.	477
	'if' construct must use '{}'s.	478
	Line is longer than 80 characters (found 93).	478
	'if' construct must use '{}'s.	479
	Line is longer than 80 characters (found 99).	479
	'if' construct must use '{}'s.	480
	Line is longer than 80 characters (found 89).	480
	Parameter rs should be final.	498
	Expected @throws tag for 'SQLException'.	498
	Expected @throws tag for 'DomainException'.	498
	'if' construct must use '{}'s.	509
	Line is longer than 80 characters (found 89).	509
	'if' construct must use '{}'s.	510
	'if' construct must use '{}'s.	511
	'if' construct must use '{}'s.	512
	'if' construct must use '{}'s.	513
	Line is longer than 80 characters (found 89).	513
	'if' construct must use '{}'s.	515
	'if' construct must use '{}'s.	516
	Line is longer than 80 characters (found 91).	519
	'{' is not preceded with whitespace.	519
	Line is longer than 80 characters (found 96).	521
	'{' is not preceded with whitespace.	521
	Line is longer than 80 characters (found 98).	523
	'{' is not preceded with whitespace.	523
	Line is longer than 80 characters (found 89).	524
	';' is not followed by whitespace.	524
	Line is longer than 80 characters (found 94).	525
	'{' is not preceded with whitespace.	525
	Line is longer than 80 characters (found 98).	527
	'\|\|' should be on a new line.	527
	'{' is not preceded with whitespace.	528
	Line is longer than 80 characters (found 97).	530
	'\|\|' should be on a new line.	530
	Line is longer than 80 characters (found 93).	531
	'if' construct must use '{}'s.	534
	'if' is not followed by whitespace.	534
	Line is longer than 80 characters (found 112).	536
	Line contains a tab character.	536
	'{' is not preceded with whitespace.	539
	Line is longer than 80 characters (found 91).	540
	Line has trailing spaces.	541
	Line is longer than 80 characters (found 108).	541
	'{' is not preceded with whitespace.	542
	Line is longer than 80 characters (found 103).	543
	Line is longer than 80 characters (found 108).	544
	Line is longer than 80 characters (found 84).	558
	Parameter rs should be final.	558
	Expected @throws tag for 'SQLException'.	558
	Expected @throws tag for 'DomainException'.	558
	'if' construct must use '{}'s.	568
	Line is longer than 80 characters (found 92).	568
	'if' construct must use '{}'s.	569
	Line is longer than 80 characters (found 85).	569
	'if' construct must use '{}'s.	570
	'if' construct must use '{}'s.	571
	'if' construct must use '{}'s.	572
	'if' construct must use '{}'s.	573
	Line is longer than 80 characters (found 89).	573
	'if' construct must use '{}'s.	575
	'if' construct must use '{}'s.	576
	Line is longer than 80 characters (found 82).	579
	Line is longer than 80 characters (found 144).	580
	Line contains a tab character.	580
	Line is longer than 80 characters (found 94).	583
	Line is longer than 80 characters (found 96).	584
	Parameter link should be final.	596
	Parameter enzymeId should be final.	596
	Parameter status should be final.	596
	Parameter insertStatement should be final.	597
	Expected @throws tag for 'SQLException'.	597
	Line is longer than 80 characters (found 85).	601
	'if' construct must use '{}'s.	609
	Comment matches to-do format 'TODO:'.	609
	Line is longer than 80 characters (found 95).	609
	'3' is a magic number.	610
	'else' construct must use '{}'s.	611
	'3' is a magic number.	612
	'4' is a magic number.	613
	'5' is a magic number.	614
	'6' is a magic number.	615
	'{' is not preceded with whitespace.	616
	'7' is a magic number.	617
	'7' is a magic number.	619
	Missing a Javadoc comment.	623
	Parameter xref should be final.	623
	Parameter enzymeId should be final.	623
	Parameter status should be final.	623
	Line is longer than 80 characters (found 88).	624
	Parameter insertXrefStatement should be final.	624
	Line is longer than 80 characters (found 93).	628
	Line has trailing spaces.	629
	'if' construct must use '{}'s.	631
	'if' construct must use '{}'s.	632
	'if' construct must use '{}'s.	636
	'3' is a magic number.	637
	'else' construct must use '{}'s.	638
	'3' is a magic number.	639
	'4' is a magic number.	640
	'5' is a magic number.	641
	'6' is a magic number.	642
	'7' is a magic number.	643
	'{' is not preceded with whitespace.	644
	'8' is a magic number.	645
	'8' is a magic number.	647

uk/ac/ebi/intenz/mapper/EnzymeNameMapper.java

Violation	Message	Line
	Missing a Javadoc comment.	28
	Line contains a tab character.	29
	Line is longer than 80 characters (found 121).	31
	Missing a Javadoc comment.	31
	Missing a Javadoc comment.	33
	Missing a Javadoc comment.	36
	'+' should be on a new line.	37
	'+' should be on a new line.	38
	Line is longer than 80 characters (found 82).	39
	'+' should be on a new line.	39
	Missing a Javadoc comment.	43
	'+' should be on a new line.	44
	'+' should be on a new line.	45
	'+' should be on a new line.	46
	Missing a Javadoc comment.	50
	'+' should be on a new line.	51
	'+' should be on a new line.	52
	'+' should be on a new line.	53
	Missing a Javadoc comment.	57
	Line is longer than 80 characters (found 147).	58
	Missing a Javadoc comment.	61
	Line is longer than 80 characters (found 92).	62
	'+' should be on a new line.	62
	Missing a Javadoc comment.	66
	Line is longer than 80 characters (found 126).	75
	Line is longer than 80 characters (found 83).	78
	Method 'find' is not designed for extension - needs to be abstract, final or empty.	78
	Parameter enzymeId should be final.	78
	Parameter con should be final.	78
	Expected @throws tag for 'SQLException'.	78
	'if' construct must use '{}'s.	79
	Line is longer than 80 characters (found 99).	79
	'if' construct must use '{}'s.	80
	Line is longer than 80 characters (found 89).	80
	'if' construct must use '{}'s.	100
	Line contains a tab character.	100
	'if' construct must use '{}'s.	101
	'if' construct must use '{}'s.	104
	Line is longer than 80 characters (found 100).	115
	Line is longer than 80 characters (found 83).	117
	Unused @throws tag for 'NullPointerException'.	117
	Line is longer than 80 characters (found 93).	119
	Method 'exportSibNames' is not designed for extension - needs to be abstract, final or empty.	119
	Parameter enzymeId should be final.	119
	Parameter con should be final.	119
	'if' construct must use '{}'s.	120
	Line is longer than 80 characters (found 99).	120
	'if' construct must use '{}'s.	121
	Line is longer than 80 characters (found 89).	121
	'3' is a magic number.	133
	'4' is a magic number.	134
	'5' is a magic number.	135
	'if' construct must use '{}'s.	145
	Line contains a tab character.	145
	'if' construct must use '{}'s.	146
	'if' construct must use '{}'s.	149
	Line is longer than 80 characters (found 94).	163
	Method 'findCommonNames' is not designed for extension - needs to be abstract, final or empty.	163
	Parameter enzymeId should be final.	163
	Parameter con should be final.	163
	Expected @throws tag for 'SQLException'.	163
	'if' construct must use '{}'s.	164
	Line is longer than 80 characters (found 99).	164
	'if' construct must use '{}'s.	165
	Line is longer than 80 characters (found 89).	165
	'if' construct must use '{}'s.	187
	Line contains a tab character.	187
	'if' construct must use '{}'s.	188
	'if' construct must use '{}'s.	191
	Line is longer than 80 characters (found 91).	203
	Method 'findSystematicName' is not designed for extension - needs to be abstract, final or empty.	203
	Parameter enzymeId should be final.	203
	Parameter con should be final.	203
	Expected @throws tag for 'SQLException'.	203
	'if' construct must use '{}'s.	204
	Line is longer than 80 characters (found 99).	204
	'if' construct must use '{}'s.	205
	Line is longer than 80 characters (found 89).	205
	Line is longer than 80 characters (found 84).	214
	'if' construct must use '{}'s.	220
	Line contains a tab character.	220
	'if' construct must use '{}'s.	221
	Line is longer than 80 characters (found 96).	227
	Method 'update' is not designed for extension - needs to be abstract, final or empty.	227
	Missing a Javadoc comment.	227
	Parameter name should be final.	227
	Parameter enzymeId should be final.	227
	Parameter status should be final.	227
	Parameter orderIn should be final.	227
	Parameter con should be final.	227
	'if' construct must use '{}'s.	229
	Line is longer than 80 characters (found 91).	229
	'if' construct must use '{}'s.	230
	Line is longer than 80 characters (found 99).	230
	'if' construct must use '{}'s.	231
	Line is longer than 80 characters (found 95).	231
	'if' construct must use '{}'s.	232
	Line is longer than 80 characters (found 96).	232
	'if' construct must use '{}'s.	233
	Line is longer than 80 characters (found 89).	233
	'if' construct must use '{}'s.	245
	Line is longer than 80 characters (found 95).	249
	Method 'insertNames' is not designed for extension - needs to be abstract, final or empty.	249
	Missing a Javadoc comment.	249
	Parameter names should be final.	249
	Parameter enzymeId should be final.	249
	Parameter status should be final.	249
	Parameter con should be final.	249
	'if' construct must use '{}'s.	251
	Line is longer than 80 characters (found 93).	251
	'if' construct must use '{}'s.	252
	Line is longer than 80 characters (found 99).	252
	'if' construct must use '{}'s.	253
	Line is longer than 80 characters (found 95).	253
	'if' construct must use '{}'s.	254
	Line is longer than 80 characters (found 89).	254
	'+' is not preceded with whitespace.	256
	'+' is not followed by whitespace.	256
	Line is longer than 80 characters (found 102).	260
	Method 'insert' is not designed for extension - needs to be abstract, final or empty.	260
	Missing a Javadoc comment.	260
	Parameter enzymeName should be final.	260
	Parameter enzymeId should be final.	260
	Parameter status should be final.	260
	Parameter orderIn should be final.	260
	Parameter con should be final.	260
	'if' construct must use '{}'s.	262
	Line is longer than 80 characters (found 103).	262
	'if' construct must use '{}'s.	263
	Line is longer than 80 characters (found 99).	263
	'if' construct must use '{}'s.	264
	Line is longer than 80 characters (found 95).	264
	'if' construct must use '{}'s.	265
	Line is longer than 80 characters (found 89).	265
	'if' construct must use '{}'s.	277
	Line is longer than 80 characters (found 103).	281
	Method 'reload' is not designed for extension - needs to be abstract, final or empty.	281
	Missing a Javadoc comment.	281
	Parameter names should be final.	281
	Parameter enzymeId should be final.	281
	Parameter type should be final.	281
	Parameter status should be final.	281
	Parameter con should be final.	282
	Line is longer than 80 characters (found 111).	288
	Method 'deleteNames' is not designed for extension - needs to be abstract, final or empty.	288
	Missing a Javadoc comment.	288
	Parameter enzymeId should be final.	288
	Parameter nameType should be final.	288
	Parameter con should be final.	288
	'if' construct must use '{}'s.	289
	Line is longer than 80 characters (found 99).	289
	'if' construct must use '{}'s.	290
	Line is longer than 80 characters (found 89).	290
	'if' construct must use '{}'s.	303
	Parameter rs should be final.	318
	Expected @throws tag for 'SQLException'.	318
	'if' construct must use '{}'s.	327
	'if' construct must use '{}'s.	328
	Line is longer than 80 characters (found 83).	328
	'if' construct must use '{}'s.	329
	'if' construct must use '{}'s.	330
	'if' construct must use '{}'s.	331
	Line is longer than 80 characters (found 92).	333
	Line is longer than 80 characters (found 89).	334
	Line is longer than 80 characters (found 105).	335
	First sentence should end with a period.	338
	Line is longer than 80 characters (found 83).	347
	Parameter name should be final.	347
	Parameter enzymeId should be final.	347
	Parameter status should be final.	347
	Parameter orderIn should be final.	347
	Expected @param tag for 'orderIn'.	347
	Parameter insertStatement should be final.	348
	Expected @throws tag for 'SQLException'.	348
	Line is longer than 80 characters (found 85).	353
	'3' is a magic number.	357
	'if' construct must use '{}'s.	358
	'4' is a magic number.	359
	'else' construct must use '{}'s.	360
	'4' is a magic number.	361
	'5' is a magic number.	362
	'6' is a magic number.	363
	'7' is a magic number.	364
	'8' is a magic number.	365
	'9' is a magic number.	366
	Line is longer than 80 characters (found 83).	369
	Missing a Javadoc comment.	369
	Parameter name should be final.	369
	Parameter enzymeId should be final.	369
	Parameter status should be final.	369
	Parameter orderIn should be final.	369
	Parameter updateStatement should be final.	370
	Line is longer than 80 characters (found 85).	375
	'if' construct must use '{}'s.	378
	'else' construct must use '{}'s.	380
	'3' is a magic number.	382
	'4' is a magic number.	383
	'5' is a magic number.	384
	'6' is a magic number.	385
	'7' is a magic number.	386

uk/ac/ebi/intenz/mapper/EnzymeReactionMapper.java

Violation	Message	Line
	Line contains a tab character.	27
	Line contains a tab character.	32
	Missing a Javadoc comment.	32
	Line contains a tab character.	33
	Line has trailing spaces.	34
	Line contains a tab character.	34
	Line contains a tab character.	35
	Missing a Javadoc comment.	35
	Variable 'rheaReader' must be private and have accessor methods.	35
	Line has trailing spaces.	36
	Line contains a tab character.	36
	Missing a Javadoc comment.	37
	'{' is not preceded with whitespace.	37
	Line contains a tab character.	38
	Line contains a tab character.	39
	Line contains a tab character.	40
	Line contains a tab character.	41
	Line contains a tab character.	42
	Line contains a tab character.	43
	Missing a Javadoc comment.	46
	Line contains a tab character.	47
	'+' should be on a new line.	47
	Line contains a tab character.	48
	'+' should be on a new line.	48
	Line contains a tab character.	49
	Missing a Javadoc comment.	51
	Line contains a tab character.	52
	'+' should be on a new line.	52
	Line contains a tab character.	53
	'+' should be on a new line.	53
	Line contains a tab character.	54
	Missing a Javadoc comment.	56
	Line contains a tab character.	57
	'+' should be on a new line.	57
	Line contains a tab character.	58
	'+' should be on a new line.	58
	Line contains a tab character.	59
	'+' should be on a new line.	59
	Line contains a tab character.	60
	Missing a Javadoc comment.	62
	Line is longer than 80 characters (found 81).	63
	Line contains a tab character.	63
	'+' should be on a new line.	63
	Line contains a tab character.	64
	Missing a Javadoc comment.	66
	Line contains a tab character.	67
	Line has trailing spaces.	70
	Line contains a tab character.	71
	Missing a Javadoc comment.	71
	Line is longer than 80 characters (found 82).	72
	Line contains a tab character.	72
	'+' should be on a new line.	72
	Line contains a tab character.	73
	Line contains a tab character.	75
	Missing a Javadoc comment.	75
	Line contains a tab character.	76
	'+' should be on a new line.	76
	Line contains a tab character.	77
	Line contains a tab character.	79
	Missing a Javadoc comment.	79
	Line contains a tab character.	80
	'+' should be on a new line.	80
	Line is longer than 80 characters (found 84).	81
	Line contains a tab character.	81
	Line contains a tab character.	83
	Missing a Javadoc comment.	83
	Line is longer than 80 characters (found 89).	84
	Line contains a tab character.	84
	'+' should be on a new line.	84
	Line contains a tab character.	85
	Missing a Javadoc comment.	87
	Line contains a tab character.	88
	Line is longer than 80 characters (found 86).	96
	Line contains a tab character.	96
	Method 'find' is not designed for extension - needs to be abstract, final or empty.	100
	Parameter enzymeId should be final.	100
	Parameter con should be final.	100
	Line is longer than 80 characters (found 85).	103
	Line contains a tab character.	110
	Line contains a tab character.	111
	'if' construct must use '{}'s.	115
	Line contains a tab character.	115
	Line contains a tab character.	128
	Line is longer than 80 characters (found 83).	131
	Unused @throws tag for 'NullPointerException'.	131
	Method 'exportSibReactions' is not designed for extension - needs to be abstract, final or empty.	133
	Parameter enzymeId should be final.	133
	Parameter con should be final.	133
	'if' construct must use '{}'s.	135
	Line is longer than 80 characters (found 99).	135
	'if' construct must use '{}'s.	136
	Line is longer than 80 characters (found 89).	136
	'if' construct must use '{}'s.	139
	Line contains a tab character.	140
	'else' construct must use '{}'s.	141
	Line has trailing spaces.	145
	Missing a Javadoc comment.	146
	Parameter enzymeId should be final.	146
	Parameter con should be final.	146
	Line contains a tab character.	147
	Parameter findQuery should be final.	147
	Line contains a tab character.	149
	Line contains a tab character.	150
	Line contains a tab character.	151
	Line contains a tab character.	152
	Line contains a tab character.	153
	Line contains a tab character.	154
	Line contains a tab character.	155
	Line contains a tab character.	156
	'if' construct must use '{}'s.	157
	Line contains a tab character.	157
	Line contains a tab character.	159
	Line contains a tab character.	160
	Line contains a tab character.	161
	'if' construct must use '{}'s.	162
	Line contains a tab character.	162
	'if' construct must use '{}'s.	163
	Line contains a tab character.	163
	Line contains a tab character.	164
	Line contains a tab character.	165
	Line is longer than 80 characters (found 81).	176
	Method 'insert' is not designed for extension - needs to be abstract, final or empty.	176
	Parameter reactions should be final.	176
	Parameter enzymeId should be final.	176
	Parameter con should be final.	176
	Expected @throws tag for 'SQLException'.	177
	'if' construct must use '{}'s.	178
	Line is longer than 80 characters (found 101).	178
	'if' construct must use '{}'s.	179
	Line is longer than 80 characters (found 99).	179
	'if' construct must use '{}'s.	180
	Line is longer than 80 characters (found 89).	180
	Line contains a tab character.	183
	Line contains a tab character.	184
	Line contains a tab character.	185
	Line contains a tab character.	186
	'{' is not preceded with whitespace.	186
	Line contains a tab character.	187
	'+' is not preceded with whitespace.	187
	'+' is not followed by whitespace.	187
	Line contains a tab character.	188
	Line is longer than 80 characters (found 81).	189
	Line contains a tab character.	189
	'+' is not preceded with whitespace.	189
	'+' is not followed by whitespace.	189
	Line contains a tab character.	190
	Line has trailing spaces.	193
	Parameter enzymeId should be final.	204
	Expected @param tag for 'enzymeId'.	204
	Parameter reaction should be final.	204
	Expected @param tag for 'reaction'.	204
	Line is longer than 80 characters (found 86).	205
	Line contains a tab character.	205
	Parameter view should be final.	205
	Expected @param tag for 'view'.	205
	Parameter iubmb should be final.	205
	Expected @param tag for 'iubmb'.	205
	Parameter orderIn should be final.	205
	Expected @param tag for 'orderIn'.	205
	Parameter con should be final.	205
	Expected @param tag for 'con'.	205
	Expected @throws tag for 'SQLException'.	206
	Line contains a tab character.	207
	Line contains a tab character.	208
	Line contains a tab character.	209
	Line contains a tab character.	210
	Line contains a tab character.	211
	Line contains a tab character.	212
	'3' is a magic number.	212
	Line is longer than 80 characters (found 81).	213
	Line contains a tab character.	213
	'4' is a magic number.	213
	Line contains a tab character.	214
	'5' is a magic number.	214
	Line contains a tab character.	215
	'6' is a magic number.	215
	Line contains a tab character.	216
	Line contains a tab character.	217
	'if' construct must use '{}'s.	218
	Line contains a tab character.	218
	Line contains a tab character.	219
	Line has trailing spaces.	221
	Method 'insertMapping' is not designed for extension - needs to be abstract, final or empty.	232
	Parameter enzymeId should be final.	232
	Expected @param tag for 'enzymeId'.	232
	Parameter reactionId should be final.	232
	Expected @param tag for 'reactionId'.	232
	Line contains a tab character.	233
	Parameter view should be final.	233
	Expected @param tag for 'view'.	233
	Parameter iubmb should be final.	233
	Expected @param tag for 'iubmb'.	233
	Line contains a tab character.	234
	Parameter orderIn should be final.	234
	Expected @param tag for 'orderIn'.	234
	Parameter con should be final.	234
	Expected @param tag for 'con'.	234
	Expected @throws tag for 'SQLException'.	234
	'{' is not preceded with whitespace.	234
	Line contains a tab character.	235
	Line contains a tab character.	236
	Line contains a tab character.	237
	Line contains a tab character.	238
	Line contains a tab character.	239
	Line contains a tab character.	240
	'3' is a magic number.	240
	Line contains a tab character.	241
	'4' is a magic number.	241
	'?' is not preceded with whitespace.	241
	Avoid inline conditionals.	241
	Line contains a tab character.	242
	'5' is a magic number.	242
	Line contains a tab character.	243
	Line is longer than 80 characters (found 98).	244
	Line contains a tab character.	244
	Line contains a tab character.	245
	'if' construct must use '{}'s.	246
	Line contains a tab character.	246
	Line contains a tab character.	247
	Line is longer than 80 characters (found 81).	259
	Method 'update' is not designed for extension - needs to be abstract, final or empty.	259
	Parameter enzymeId should be final.	259
	Parameter reactions should be final.	259
	Parameter con should be final.	259
	Expected @param tag for 'con'.	259
	Expected @throws tag for 'SQLException'.	260
	Line is longer than 80 characters (found 90).	266
	Method 'deleteAll' is not designed for extension - needs to be abstract, final or empty.	272
	Parameter enzymeId should be final.	272
	Parameter con should be final.	272
	Expected @throws tag for 'SQLException'.	272
	'if' construct must use '{}'s.	273
	Line is longer than 80 characters (found 99).	273
	'if' construct must use '{}'s.	274
	Line is longer than 80 characters (found 89).	274
	'if' construct must use '{}'s.	286
	Expected an @return tag.	301
	Parameter reactionId should be final.	301
	Expected @param tag for 'reactionId'.	301
	Parameter equation should be final.	301
	Expected @param tag for 'equation'.	301
	Parameter source should be final.	302
	Parameter status should be final.	302
	Expected @param tag for 'status'.	302
	Expected @throws tag for 'SQLException'.	303
	Line is longer than 80 characters (found 90).	304
	Line is longer than 80 characters (found 84).	317
	Parameter rs should be final.	317
	Line contains a tab character.	324
	'if' construct must use '{}'s.	325
	Line contains a tab character.	325
	'{' is not preceded with whitespace.	327
	Line contains a tab character.	337
	Line contains a tab character.	343
	Method 'close' is not designed for extension - needs to be abstract, final or empty.	343
	Missing a Javadoc comment.	343
	Line contains a tab character.	344
	Line contains a tab character.	345
	Line contains a tab character.	347
	Method 'finalize' is not designed for extension - needs to be abstract, final or empty.	347
	Line contains a tab character.	348
	Line contains a tab character.	349
	Line contains a tab character.	350

uk/ac/ebi/intenz/mapper/EnzymeReferenceMapper.java

Violation	Message	Line
	Line is longer than 80 characters (found 103).	26
	Missing a Javadoc comment.	26
	'+' should be on a new line.	26
	Line is longer than 80 characters (found 118).	27
	'+' should be on a new line.	27
	Line is longer than 80 characters (found 112).	28
	Line is longer than 80 characters (found 87).	30
	Missing a Javadoc comment.	32
	Missing a Javadoc comment.	35
	'+' should be on a new line.	36
	'+' should be on a new line.	37
	Missing a Javadoc comment.	41
	Missing a Javadoc comment.	45
	Missing a Javadoc comment.	49
	Missing a Javadoc comment.	53
	'+' should be on a new line.	54
	Line is longer than 80 characters (found 145).	55
	'+' should be on a new line.	55
	Missing a Javadoc comment.	59
	'+' should be on a new line.	60
	Line is longer than 80 characters (found 119).	61
	'+' should be on a new line.	61
	Line is longer than 80 characters (found 83).	62
	'+' should be on a new line.	62
	Missing a Javadoc comment.	66
	'+' should be on a new line.	67
	Line is longer than 80 characters (found 163).	68
	'+' should be on a new line.	68
	Missing a Javadoc comment.	72
	'+' should be on a new line.	73
	Line is longer than 80 characters (found 116).	74
	'+' should be on a new line.	74
	Line is longer than 80 characters (found 112).	75
	'+' should be on a new line.	75
	Missing a Javadoc comment.	79
	'+' should be on a new line.	80
	Line is longer than 80 characters (found 91).	81
	'+' should be on a new line.	81
	Missing a Javadoc comment.	85
	'+' should be on a new line.	86
	Line is longer than 80 characters (found 113).	87
	'+' should be on a new line.	87
	Missing a Javadoc comment.	91
	Line is longer than 80 characters (found 104).	92
	Missing a Javadoc comment.	95
	Missing a Javadoc comment.	99
	Missing a Javadoc comment.	103
	Missing a Javadoc comment.	107
	Line is longer than 80 characters (found 125).	116
	Line is longer than 80 characters (found 82).	119
	Method 'find' is not designed for extension - needs to be abstract, final or empty.	119
	Parameter enzymeId should be final.	119
	Parameter con should be final.	119
	Expected @throws tag for 'SQLException'.	119
	'if' construct must use '{}'s.	120
	Line is longer than 80 characters (found 99).	120
	'if' construct must use '{}'s.	121
	Line is longer than 80 characters (found 89).	121
	'if' construct must use '{}'s.	135
	'if' construct must use '{}'s.	139
	Line contains a tab character.	139
	'if' construct must use '{}'s.	140
	'if' construct must use '{}'s.	143
	Line is longer than 80 characters (found 83).	147
	Method 'findPubIds' is not designed for extension - needs to be abstract, final or empty.	147
	Missing a Javadoc comment.	147
	Parameter enzymeId should be final.	147
	Parameter con should be final.	147
	'if' construct must use '{}'s.	148
	Line is longer than 80 characters (found 99).	148
	'if' construct must use '{}'s.	149
	Line is longer than 80 characters (found 89).	149
	'if' construct must use '{}'s.	163
	Line contains a tab character.	163
	'if' construct must use '{}'s.	164
	Line is longer than 80 characters (found 109).	170
	Method 'insert' is not designed for extension - needs to be abstract, final or empty.	170
	Missing a Javadoc comment.	170
	Parameter reference should be final.	170
	Parameter enzymeId should be final.	170
	Parameter status should be final.	170
	Parameter con should be final.	170
	'if' construct must use '{}'s.	171
	Line is longer than 80 characters (found 101).	171
	'if' construct must use '{}'s.	172
	Line is longer than 80 characters (found 99).	172
	'if' construct must use '{}'s.	173
	Line is longer than 80 characters (found 95).	173
	'if' construct must use '{}'s.	174
	Line is longer than 80 characters (found 89).	174
	Line contains a tab character.	177
	Line contains a tab character.	178
	'?' is not preceded with whitespace.	190
	Avoid inline conditionals.	190
	Line is longer than 80 characters (found 108).	192
	'if' construct must use '{}'s.	219
	'if' construct must use '{}'s.	220
	'if' construct must use '{}'s.	221
	'if' construct must use '{}'s.	222
	'if' construct must use '{}'s.	223
	Line is longer than 80 characters (found 94).	236
	Method 'insert' is not designed for extension - needs to be abstract, final or empty.	236
	Parameter references should be final.	236
	Parameter enzymeId should be final.	236
	Parameter status should be final.	236
	Parameter con should be final.	236
	Expected @throws tag for 'SQLException'.	237
	'if' construct must use '{}'s.	238
	Line is longer than 80 characters (found 103).	238
	'if' construct must use '{}'s.	239
	Line is longer than 80 characters (found 99).	239
	'if' construct must use '{}'s.	240
	Line is longer than 80 characters (found 95).	240
	'if' construct must use '{}'s.	241
	Line is longer than 80 characters (found 89).	241
	Line is longer than 80 characters (found 94).	249
	Method 'reload' is not designed for extension - needs to be abstract, final or empty.	249
	Missing a Javadoc comment.	249
	Parameter references should be final.	249
	Parameter enzymeId should be final.	249
	Parameter status should be final.	249
	Parameter con should be final.	249
	Line is longer than 80 characters (found 109).	255
	Method 'update' is not designed for extension - needs to be abstract, final or empty.	255
	Missing a Javadoc comment.	255
	Parameter reference should be final.	255
	Parameter enzymeId should be final.	255
	Parameter status should be final.	255
	Parameter con should be final.	255
	'if' construct must use '{}'s.	256
	Line is longer than 80 characters (found 101).	256
	'if' construct must use '{}'s.	257
	Line is longer than 80 characters (found 99).	257
	'if' construct must use '{}'s.	258
	Line is longer than 80 characters (found 95).	258
	'if' construct must use '{}'s.	259
	Line is longer than 80 characters (found 89).	259
	Line contains a tab character.	262
	'if' construct must use '{}'s.	290
	'if' construct must use '{}'s.	291
	'if' construct must use '{}'s.	292
	Line is longer than 80 characters (found 94).	296
	Method 'update' is not designed for extension - needs to be abstract, final or empty.	296
	Missing a Javadoc comment.	296
	Parameter references should be final.	296
	Parameter enzymeId should be final.	296
	Parameter status should be final.	296
	Parameter con should be final.	296
	'if' construct must use '{}'s.	298
	Line is longer than 80 characters (found 103).	298
	'if' construct must use '{}'s.	299
	Line is longer than 80 characters (found 99).	299
	'if' construct must use '{}'s.	300
	Line is longer than 80 characters (found 95).	300
	'if' construct must use '{}'s.	301
	Line is longer than 80 characters (found 89).	301
	Method 'deleteAll' is not designed for extension - needs to be abstract, final or empty.	309
	Missing a Javadoc comment.	309
	Parameter enzymeId should be final.	309
	Parameter con should be final.	309
	'if' construct must use '{}'s.	310
	Line is longer than 80 characters (found 99).	310
	'if' construct must use '{}'s.	311
	Line is longer than 80 characters (found 89).	311
	Line is longer than 80 characters (found 117).	313
	Line is longer than 80 characters (found 82).	322
	Method 'deleteCitations' is not designed for extension - needs to be abstract, final or empty.	322
	Missing a Javadoc comment.	322
	Parameter enzymeId should be final.	322
	Parameter con should be final.	322
	'if' construct must use '{}'s.	323
	Line is longer than 80 characters (found 99).	323
	'if' construct must use '{}'s.	324
	Line is longer than 80 characters (found 89).	324
	Line is longer than 80 characters (found 82).	328
	'if' construct must use '{}'s.	336
	Line is longer than 80 characters (found 84).	347
	Unused @throws tag for 'NullPointerException'.	347
	Unused @throws tag for 'IllegalArgumentException'.	348
	Line is longer than 80 characters (found 101).	350
	Method 'deleteCitations' is not designed for extension - needs to be abstract, final or empty.	350
	Parameter pubIds should be final.	350
	Parameter enzymeId should be final.	350
	Parameter con should be final.	350
	'if' construct must use '{}'s.	351
	Line is longer than 80 characters (found 95).	351
	'if' construct must use '{}'s.	352
	Line is longer than 80 characters (found 99).	352
	'if' construct must use '{}'s.	353
	Line is longer than 80 characters (found 89).	353
	Line is longer than 80 characters (found 89).	359
	'if' construct must use '{}'s.	369
	Line is longer than 80 characters (found 81).	373
	Method 'deletePublication' is not designed for extension - needs to be abstract, final or empty.	373
	Missing a Javadoc comment.	373
	Parameter pubId should be final.	373
	Parameter con should be final.	373
	'if' construct must use '{}'s.	374
	Line is longer than 80 characters (found 93).	374
	'if' construct must use '{}'s.	375
	Line is longer than 80 characters (found 89).	375
	Line is longer than 80 characters (found 86).	379
	'if' construct must use '{}'s.	387
	Line is longer than 80 characters (found 81).	387
	Parameter rs should be final.	401
	Expected @throws tag for 'SQLException'.	401
	'if' construct must use '{}'s.	422
	'if' construct must use '{}'s.	423
	Line is longer than 80 characters (found 83).	423
	'if' construct must use '{}'s.	424
	'if' construct must use '{}'s.	425
	'if' construct must use '{}'s.	426
	'if' construct must use '{}'s.	427
	'if' construct must use '{}'s.	428
	'if' construct must use '{}'s.	429
	Line is longer than 80 characters (found 85).	429
	'if' construct must use '{}'s.	430
	'if' construct must use '{}'s.	431
	Line is longer than 80 characters (found 83).	431
	'if' construct must use '{}'s.	432
	'if' construct must use '{}'s.	433
	'if' construct must use '{}'s.	434
	'if' construct must use '{}'s.	435
	Line is longer than 80 characters (found 85).	435
	'if' construct must use '{}'s.	436
	'if' construct must use '{}'s.	437
	'if' construct must use '{}'s.	438
	'if' construct must use '{}'s.	440
	Line is longer than 80 characters (found 83).	441
	Line is longer than 80 characters (found 104).	442
	'if' construct must use '{}'s.	445
	Line is longer than 80 characters (found 115).	446
	Line is longer than 80 characters (found 100).	447
	'if' construct must use '{}'s.	449
	Line is longer than 80 characters (found 101).	450
	Line is longer than 80 characters (found 131).	451
	Parameter con should be final.	463
	Expected @throws tag for 'SQLException'.	463
	'if' construct must use '{}'s.	476
	Line contains a tab character.	476
	'if' construct must use '{}'s.	477
	Line is longer than 80 characters (found 82).	483
	Missing a Javadoc comment.	483
	Parameter enzymeId should be final.	483
	Parameter con should be final.	483
	'if' construct must use '{}'s.	498
	Line contains a tab character.	498
	'if' construct must use '{}'s.	499
	Line is longer than 80 characters (found 115).	516
	Parameter enzymeId should be final.	516
	Parameter pubId should be final.	516
	Parameter orderIn should be final.	516
	Parameter status should be final.	516
	Parameter source should be final.	516
	Line is longer than 80 characters (found 96).	517
	Parameter insertCitationStatement should be final.	517
	Expected @throws tag for 'SQLException'.	517
	'3' is a magic number.	520
	'4' is a magic number.	521
	'5' is a magic number.	522
	Line is longer than 80 characters (found 126).	525
	Missing a Javadoc comment.	525
	Parameter newPubId should be final.	525
	Parameter journal should be final.	525
	Parameter insertJournalStatement should be final.	525
	Line is longer than 80 characters (found 99).	528
	'3' is a magic number.	532
	'4' is a magic number.	533
	'5' is a magic number.	534
	'6' is a magic number.	535
	'7' is a magic number.	536
	'8' is a magic number.	537
	'9' is a magic number.	538
	'10' is a magic number.	539
	'11' is a magic number.	540
	'12' is a magic number.	541
	'13' is a magic number.	542
	Line is longer than 80 characters (found 111).	545
	Missing a Javadoc comment.	545
	Parameter journal should be final.	545
	Parameter updateJournalStatement should be final.	545
	Line is longer than 80 characters (found 99).	547
	'3' is a magic number.	551
	'4' is a magic number.	552
	'5' is a magic number.	553
	'6' is a magic number.	554
	'7' is a magic number.	555
	'8' is a magic number.	556
	'9' is a magic number.	557
	'10' is a magic number.	558
	'11' is a magic number.	559
	'12' is a magic number.	560
	'13' is a magic number.	561
	Line is longer than 80 characters (found 114).	564
	Missing a Javadoc comment.	564
	Parameter newPubId should be final.	564
	Parameter book should be final.	564
	Parameter insertBookStatement should be final.	564
	Line is longer than 80 characters (found 93).	567
	'3' is a magic number.	571
	'4' is a magic number.	572
	'5' is a magic number.	573
	'6' is a magic number.	574
	'7' is a magic number.	575
	'8' is a magic number.	576
	'9' is a magic number.	577
	'10' is a magic number.	578
	'11' is a magic number.	579
	'12' is a magic number.	580
	'13' is a magic number.	581
	'14' is a magic number.	582
	'15' is a magic number.	583
	Line is longer than 80 characters (found 99).	586
	Missing a Javadoc comment.	586
	Parameter book should be final.	586
	Parameter updateBookStatement should be final.	586
	Line is longer than 80 characters (found 93).	588
	'3' is a magic number.	592
	'4' is a magic number.	593
	'5' is a magic number.	594
	'6' is a magic number.	595
	'7' is a magic number.	596
	'8' is a magic number.	597
	'9' is a magic number.	598
	'10' is a magic number.	599
	'11' is a magic number.	600
	'12' is a magic number.	601
	'13' is a magic number.	602
	'14' is a magic number.	603
	'15' is a magic number.	604
	Line is longer than 80 characters (found 122).	607
	Missing a Javadoc comment.	607
	Parameter newPubId should be final.	607
	Parameter patent should be final.	607
	Parameter insertPatentStatement should be final.	607
	Line is longer than 80 characters (found 97).	610
	'3' is a magic number.	614
	'4' is a magic number.	615
	'5' is a magic number.	616
	'6' is a magic number.	617
	'7' is a magic number.	618
	'8' is a magic number.	619
	Line is longer than 80 characters (found 107).	622
	Missing a Javadoc comment.	622
	Parameter patent should be final.	622
	Parameter updatePatentStatement should be final.	622
	Line is longer than 80 characters (found 97).	624
	'3' is a magic number.	628
	'4' is a magic number.	629
	'5' is a magic number.	630
	'6' is a magic number.	631
	'7' is a magic number.	632
	'8' is a magic number.	633

uk/ac/ebi/intenz/mapper/EnzymeSubSubclassMapper.java

Violation	Message	Line
	Line is longer than 80 characters (found 108).	24
	Missing a Javadoc comment.	24
	Missing a Javadoc comment.	26
	Line has trailing spaces.	28
	Missing a Javadoc comment.	29
	Missing a Javadoc comment.	32
	'+' should be on a new line.	33
	Line is longer than 80 characters (found 156).	34
	'+' should be on a new line.	34
	Missing a Javadoc comment.	38
	'+' should be on a new line.	39
	Line is longer than 80 characters (found 141).	40
	'+' should be on a new line.	40
	Missing a Javadoc comment.	44
	Line is longer than 80 characters (found 81).	45
	Missing a Javadoc comment.	48
	Line is longer than 80 characters (found 109).	49
	Line is longer than 80 characters (found 97).	59
	Unused @throws tag for 'NullPointerException'.	60
	Line is longer than 80 characters (found 84).	62
	Method 'find' is not designed for extension - needs to be abstract, final or empty.	64
	Parameter ec1 should be final.	64
	Parameter ec2 should be final.	64
	Parameter ec3 should be final.	64
	Parameter con should be final.	64
	'if' construct must use '{}'s.	66
	Line is longer than 80 characters (found 89).	66
	Line is longer than 80 characters (found 82).	75
	'if' construct must use '{}'s.	76
	'if' is not followed by whitespace.	76
	'3' is a magic number.	82
	'4' is a magic number.	83
	'5' is a magic number.	84
	'6' is a magic number.	85
	Line contains a tab character.	91
	'if' construct must use '{}'s.	92
	Line contains a tab character.	92
	'if' construct must use '{}'s.	93
	Line is longer than 80 characters (found 120).	105
	Line is longer than 80 characters (found 81).	108
	Method 'findList' is not designed for extension - needs to be abstract, final or empty.	108
	Parameter ec1 should be final.	108
	Parameter ec2 should be final.	108
	Parameter con should be final.	108
	Expected @throws tag for 'SQLException'.	109
	Expected @throws tag for 'DomainException'.	109
	'3' is a magic number.	119
	'4' is a magic number.	120
	'5' is a magic number.	121
	'if' construct must use '{}'s.	129
	Line contains a tab character.	129
	'if' construct must use '{}'s.	130
	'if' construct must use '{}'s.	133
	Line has trailing spaces.	136
	Line is longer than 80 characters (found 94).	137
	Method 'findAll' is not designed for extension - needs to be abstract, final or empty.	137
	Missing a Javadoc comment.	137
	Parameter con should be final.	137
	'{' is not preceded with whitespace.	137
	'{' is not preceded with whitespace.	144
	'if' construct must use '{}'s.	148
	Line contains a tab character.	148
	'if' construct must use '{}'s.	149
	Unused @throws tag for 'NullPointerException'.	162
	Line is longer than 80 characters (found 142).	164
	Method 'insertSubSubclass' is not designed for extension - needs to be abstract, final or empty.	164
	Parameter ec should be final.	164
	Parameter name should be final.	164
	Parameter description should be final.	164
	Parameter con should be final.	164
	'if' construct must use '{}'s.	165
	Line is longer than 80 characters (found 87).	165
	'if' construct must use '{}'s.	166
	Line is longer than 80 characters (found 91).	166
	'if' construct must use '{}'s.	167
	Line is longer than 80 characters (found 105).	167
	'if' construct must use '{}'s.	168
	Line is longer than 80 characters (found 89).	168
	'if' construct must use '{}'s.	180
	Line is longer than 80 characters (found 108).	194
	Method 'subSubclassExists' is not designed for extension - needs to be abstract, final or empty.	194
	Parameter ec1 should be final.	194
	Parameter ec2 should be final.	194
	Parameter ec3 should be final.	194
	Parameter con should be final.	194
	Expected @throws tag for 'SQLException'.	194
	'3' is a magic number.	202
	'if' construct must use '{}'s.	208
	Line contains a tab character.	208
	'if' construct must use '{}'s.	209
	Line has trailing spaces.	215
	Line is longer than 80 characters (found 81).	219
	Parameter rs should be final.	225
	Parameter entries should be final.	225
	Expected @param tag for 'entries'.	225
	Expected @throws tag for 'SQLException'.	226
	Expected @throws tag for 'DomainException'.	226
	'if' construct must use '{}'s.	235
	'if' construct must use '{}'s.	236
	'if' construct must use '{}'s.	237
	'3' is a magic number.	237
	'3' is a magic number.	237
	'if' construct must use '{}'s.	238
	'4' is a magic number.	238
	'4' is a magic number.	238
	'if' construct must use '{}'s.	239
	'5' is a magic number.	239
	'5' is a magic number.	239
	'if' construct must use '{}'s.	240
	'6' is a magic number.	240
	'6' is a magic number.	240
	'if' construct must use '{}'s.	241
	'7' is a magic number.	241
	'7' is a magic number.	241
	Line is longer than 80 characters (found 86).	244
	Line is longer than 80 characters (found 140).	247
	Missing a Javadoc comment.	247
	Parameter ec should be final.	247
	Parameter name should be final.	247
	Parameter description should be final.	247
	Parameter insertStatement should be final.	247
	Line is longer than 80 characters (found 85).	251
	'3' is a magic number.	255
	'4' is a magic number.	256
	'5' is a magic number.	257
	'6' is a magic number.	258

uk/ac/ebi/intenz/mapper/EnzymeSubclassMapper.java

Violation	Message	Line
	Line is longer than 80 characters (found 86).	24
	Missing a Javadoc comment.	24
	Line is longer than 80 characters (found 97).	26
	Missing a Javadoc comment.	26
	Line has trailing spaces.	27
	Missing a Javadoc comment.	28
	Missing a Javadoc comment.	31
	Line is longer than 80 characters (found 131).	32
	Missing a Javadoc comment.	35
	Line is longer than 80 characters (found 117).	36
	Missing a Javadoc comment.	39
	Line is longer than 80 characters (found 97).	49
	Unused @throws tag for 'NullPointerException'.	50
	Line is longer than 80 characters (found 84).	52
	Line is longer than 80 characters (found 107).	54
	Method 'find' is not designed for extension - needs to be abstract, final or empty.	54
	Parameter ec1 should be final.	54
	Parameter ec2 should be final.	54
	Parameter con should be final.	54
	'if' construct must use '{}'s.	55
	Line is longer than 80 characters (found 89).	55
	'if' construct must use '{}'s.	56
	Line is longer than 80 characters (found 89).	56
	'if' construct must use '{}'s.	57
	Line is longer than 80 characters (found 89).	57
	'3' is a magic number.	72
	'if' construct must use '{}'s.	78
	Line contains a tab character.	78
	'if' construct must use '{}'s.	79
	Line is longer than 80 characters (found 120).	90
	Line is longer than 80 characters (found 105).	93
	Method 'findList' is not designed for extension - needs to be abstract, final or empty.	93
	Parameter ec1 should be final.	93
	Parameter con should be final.	93
	Expected @throws tag for 'SQLException'.	93
	Expected @throws tag for 'DomainException'.	93
	'if' construct must use '{}'s.	109
	Line contains a tab character.	109
	'if' construct must use '{}'s.	110
	'if' construct must use '{}'s.	113
	Line has trailing spaces.	116
	Line has trailing spaces.	118
	Line has trailing spaces.	122
	Line has trailing spaces.	123
	Line is longer than 80 characters (found 91).	125
	Method 'findAll' is not designed for extension - needs to be abstract, final or empty.	125
	Parameter con should be final.	125
	Expected @param tag for 'con'.	125
	'{' is not preceded with whitespace.	125
	'{' is not preceded with whitespace.	132
	'if' construct must use '{}'s.	136
	Line contains a tab character.	136
	'if' construct must use '{}'s.	137
	Line is longer than 80 characters (found 93).	151
	Method 'subclassExists' is not designed for extension - needs to be abstract, final or empty.	151
	Parameter ec1 should be final.	151
	Parameter ec2 should be final.	151
	Parameter con should be final.	151
	Expected @throws tag for 'SQLException'.	151
	'if' construct must use '{}'s.	163
	Line contains a tab character.	163
	'if' construct must use '{}'s.	164
	Line is longer than 80 characters (found 84).	180
	Parameter rs should be final.	180
	Parameter subSubclasses should be final.	180
	Expected @param tag for 'subSubclasses'.	180
	Expected @throws tag for 'SQLException'.	181
	Expected @throws tag for 'DomainException'.	181
	'if' construct must use '{}'s.	188
	'if' construct must use '{}'s.	189
	'if' construct must use '{}'s.	190
	'3' is a magic number.	190
	'3' is a magic number.	190
	'if' construct must use '{}'s.	191
	'4' is a magic number.	191
	'4' is a magic number.	191
	'if' construct must use '{}'s.	192
	'5' is a magic number.	192
	'5' is a magic number.	192
	Line is longer than 80 characters (found 117).	194

uk/ac/ebi/intenz/mapper/EventPackageMapper.java

Violation	Message	Line
	Missing a Javadoc comment.	19
	Missing a Javadoc comment.	22
	Missing a Javadoc comment.	26
	Missing a Javadoc comment.	30
	Missing a Javadoc comment.	34
	Missing a Javadoc comment.	38
	Missing a Javadoc comment.	42
	Missing a Javadoc comment.	46
	Missing a Javadoc comment.	50
	Line is longer than 80 characters (found 83).	55
	Line is longer than 80 characters (found 92).	61
	Method 'insertFutureCreationEvent' is not designed for extension - needs to be abstract, final or empty.	61
	Parameter enzymeId should be final.	61
	Parameter con should be final.	61
	Expected @throws tag for 'SQLException'.	61
	'if' construct must use '{}'s.	74
	Line is longer than 80 characters (found 81).	79
	Line is longer than 80 characters (found 121).	87
	Method 'updateFutureCreationEvent' is not designed for extension - needs to be abstract, final or empty.	87
	Parameter groupId should be final.	87
	Parameter eventId should be final.	87
	Parameter newStatus should be final.	87
	Parameter con should be final.	87
	Expected @throws tag for 'SQLException'.	87
	'3' is a magic number.	94
	'if' construct must use '{}'s.	101
	Line contains a tab character.	101
	Line is longer than 80 characters (found 83).	106
	Line is longer than 80 characters (found 110).	113
	Method 'insertFutureModificationEvent' is not designed for extension - needs to be abstract, final or empty.	113
	Parameter beforeId should be final.	113
	Parameter afterId should be final.	113
	Parameter con should be final.	113
	Expected @throws tag for 'SQLException'.	113
	'3' is a magic number.	120
	'if' construct must use '{}'s.	127
	Line contains a tab character.	127
	Line is longer than 80 characters (found 81).	132
	Line is longer than 80 characters (found 125).	140
	Method 'updateFutureModificationEvent' is not designed for extension - needs to be abstract, final or empty.	140
	Parameter groupId should be final.	140
	Parameter eventId should be final.	140
	Parameter newStatus should be final.	140
	Parameter con should be final.	140
	Expected @throws tag for 'SQLException'.	140
	'3' is a magic number.	147
	'if' construct must use '{}'s.	154
	Line contains a tab character.	154
	Line is longer than 80 characters (found 122).	167
	Method 'insertFutureTransferEvent' is not designed for extension - needs to be abstract, final or empty.	167
	Parameter beforeId should be final.	167
	Parameter afterId should be final.	167
	Parameter comment should be final.	167
	Parameter con should be final.	167
	Expected @throws tag for 'SQLException'.	167
	'3' is a magic number.	176
	'4' is a magic number.	177
	'5' is a magic number.	178
	'if' construct must use '{}'s.	185
	Line contains a tab character.	185
	Line is longer than 80 characters (found 100).	190
	Line is longer than 80 characters (found 181).	199
	Method 'updateFutureTransferEvent' is not designed for extension - needs to be abstract, final or empty.	199
	Parameter groupId should be final.	199
	Parameter eventId should be final.	199
	Parameter newHistoryComment should be final.	199
	Parameter newStatus should be final.	199
	Parameter historyLineOfDeletedEntry should be final.	199
	Expected @param tag for 'historyLineOfDeletedEntry'.	199
	Parameter con should be final.	199
	Expected @throws tag for 'SQLException'.	199
	'3' is a magic number.	206
	'4' is a magic number.	207
	'5' is a magic number.	208
	'if' construct must use '{}'s.	215
	Line contains a tab character.	215
	Line is longer than 80 characters (found 122).	228
	Method 'insertFutureDeletionEvent' is not designed for extension - needs to be abstract, final or empty.	228
	Parameter beforeId should be final.	228
	Parameter afterId should be final.	228
	Parameter comment should be final.	228
	Parameter con should be final.	228
	Expected @throws tag for 'SQLException'.	228
	'3' is a magic number.	235
	'4' is a magic number.	236
	'5' is a magic number.	237
	'if' construct must use '{}'s.	244
	Line contains a tab character.	244
	Line is longer than 80 characters (found 137).	258
	Method 'updateFutureDeletionEvent' is not designed for extension - needs to be abstract, final or empty.	258
	Parameter groupId should be final.	258
	Parameter eventId should be final.	258
	Parameter comment should be final.	258
	Parameter newStatus should be final.	258
	Parameter con should be final.	258
	Expected @throws tag for 'SQLException'.	258
	'3' is a magic number.	265
	'4' is a magic number.	266
	'if' construct must use '{}'s.	273
	Line contains a tab character.	273

uk/ac/ebi/intenz/mapper/HistoryEventMapper.java

Violation	Message	Line
	Missing a Javadoc comment.	11
	Line contains a tab character.	13
	Missing a Javadoc comment.	13
	Line contains a tab character.	14
	'+' should be on a new line.	14
	Line is longer than 80 characters (found 99).	15
	Line contains a tab character.	15
	'+' should be on a new line.	15
	Line is longer than 80 characters (found 98).	16
	Line contains a tab character.	16
	Line has trailing spaces.	17
	Line contains a tab character.	17
	Line contains a tab character.	18
	Line contains a tab character.	19
	Missing a Javadoc comment.	19
	Line contains a tab character.	20
	'+' should be on a new line.	20
	Line contains a tab character.	21
	'+' should be on a new line.	21
	Line contains a tab character.	22
	Line contains a tab character.	24
	Missing a Javadoc comment.	24
	Line contains a tab character.	25
	'+' should be on a new line.	25
	Line contains a tab character.	26
	'+' should be on a new line.	26
	Line contains a tab character.	27
	Line contains a tab character.	29
	Missing a Javadoc comment.	29
	Line contains a tab character.	30
	'+' should be on a new line.	30
	Line contains a tab character.	31
	Method 'insertEvent' is not designed for extension - needs to be abstract, final or empty.	33
	Missing a Javadoc comment.	33
	Parameter event should be final.	33
	Parameter beforeId should be final.	33
	Parameter afterId should be final.	33
	Line contains a tab character.	34
	Parameter note should be final.	34
	Parameter con should be final.	34
	'{' is not preceded with whitespace.	34
	Line contains a tab character.	35
	Line contains a tab character.	36
	Line contains a tab character.	37
	Line contains a tab character.	38
	Line contains a tab character.	39
	Line contains a tab character.	40
	Line contains a tab character.	41
	Line contains a tab character.	42
	'3' is a magic number.	42
	Line contains a tab character.	43
	Line contains a tab character.	44
	Line contains a tab character.	45
	Line contains a tab character.	46
	'3' is a magic number.	46
	Line contains a tab character.	47
	Line contains a tab character.	48
	Line contains a tab character.	49
	Line contains a tab character.	50
	'3' is a magic number.	50
	Line contains a tab character.	51
	Line contains a tab character.	52
	Line is longer than 80 characters (found 100).	53
	Line contains a tab character.	53
	Line contains a tab character.	54
	Line contains a tab character.	55
	'{' is not preceded with whitespace.	55
	Line contains a tab character.	56
	'4' is a magic number.	56
	Line contains a tab character.	57
	Line contains a tab character.	58
	'4' is a magic number.	58
	Line contains a tab character.	59
	Line is longer than 80 characters (found 87).	60
	Line contains a tab character.	60
	'5' is a magic number.	60
	Line contains a tab character.	61
	Line contains a tab character.	62
	'if' construct must use '{}'s.	63
	Line contains a tab character.	63
	Line contains a tab character.	64
	Line contains a tab character.	65
	Line has trailing spaces.	66
	Method 'updateEventNote' is not designed for extension - needs to be abstract, final or empty.	75
	Parameter eventId should be final.	75
	Parameter groupId should be final.	75
	Parameter newNote should be final.	75
	Line contains a tab character.	76
	Parameter con should be final.	76
	Expected @throws tag for 'SQLException'.	76
	'{' is not preceded with whitespace.	76
	Line contains a tab character.	77
	Line contains a tab character.	78
	Line contains a tab character.	79
	Line contains a tab character.	80
	Line contains a tab character.	81
	Line contains a tab character.	82
	Line contains a tab character.	83
	Line contains a tab character.	84
	Line contains a tab character.	85
	'if' construct must use '{}'s.	86
	Line contains a tab character.	86
	Line contains a tab character.	87
	Line has trailing spaces.	89
	Method 'updateEvent' is not designed for extension - needs to be abstract, final or empty.	100
	Parameter eventId should be final.	100
	Parameter groupId should be final.	100
	Parameter newNote should be final.	100
	Line contains a tab character.	101
	Parameter beforeId should be final.	101
	Parameter afterId should be final.	101
	Parameter con should be final.	101
	Line contains a tab character.	102
	Expected @throws tag for 'SQLException'.	102
	'{' is not preceded with whitespace.	102
	Line contains a tab character.	103
	Line contains a tab character.	104
	Line contains a tab character.	105
	Line contains a tab character.	106
	Line contains a tab character.	107
	'{' is not preceded with whitespace.	107
	Line contains a tab character.	108
	Line contains a tab character.	109
	Line contains a tab character.	110
	Line contains a tab character.	111
	Line contains a tab character.	112
	'{' is not preceded with whitespace.	112
	Line contains a tab character.	113
	Line contains a tab character.	114
	Line contains a tab character.	115
	Line contains a tab character.	116
	Line contains a tab character.	117
	Line contains a tab character.	118
	Line contains a tab character.	119
	Line contains a tab character.	120
	Line contains a tab character.	121
	'if' construct must use '{}'s.	122
	Line contains a tab character.	122
	Line contains a tab character.	123

Parent Project

IntEnz mapper module

Project Documentation

Checkstyle Results

Summary

Files

Rules

Details

uk/ac/ebi/intenz/mapper/AuditPackageMapper.java

uk/ac/ebi/intenz/mapper/CommonProceduresMapper.java

uk/ac/ebi/intenz/mapper/EnzymeClassMapper.java

uk/ac/ebi/intenz/mapper/EnzymeCofactorMapper.java

uk/ac/ebi/intenz/mapper/EnzymeCommentMapper.java

uk/ac/ebi/intenz/mapper/EnzymeEntryMapper.java

uk/ac/ebi/intenz/mapper/EnzymeFutureMapper.java

uk/ac/ebi/intenz/mapper/EnzymeHistoryMapper.java

uk/ac/ebi/intenz/mapper/EnzymeLinkMapper.java

uk/ac/ebi/intenz/mapper/EnzymeNameMapper.java

uk/ac/ebi/intenz/mapper/EnzymeReactionMapper.java

uk/ac/ebi/intenz/mapper/EnzymeReferenceMapper.java

uk/ac/ebi/intenz/mapper/EnzymeSubSubclassMapper.java

uk/ac/ebi/intenz/mapper/EnzymeSubclassMapper.java

uk/ac/ebi/intenz/mapper/EventPackageMapper.java

uk/ac/ebi/intenz/mapper/HistoryEventMapper.java