The following document contains the results of Checkstyle. 
| Rules | Violations | Severity |
|---|---|---|
JavadocPackage
| 1 |  Error |
| NewlineAtEndOfFile | 0 | Error |
| Translation | 0 | Error |
| FileLength | 0 | Error |
FileTabCharacter
| 358 | Error |
RegexpSingleline
| 27 | Error |
| JavadocMethod | 72 | Error |
| JavadocType | 4 | Error |
| JavadocVariable | 26 | Error |
| JavadocStyle | 2 | Error |
| ConstantName | 0 | Error |
| LocalFinalVariableName | 1 | Error |
| LocalVariableName | 1 | Error |
| MemberName | 5 | Error |
| MethodName | 0 | Error |
| PackageName | 0 | Error |
| ParameterName | 0 | Error |
| StaticVariableName | 0 | Error |
| TypeName | 0 | Error |
| AvoidStarImport | 3 | Error |
| IllegalImport | 0 | Error |
| RedundantImport | 0 | Error |
| UnusedImports | 0 | Error |
| LineLength | 116 | Error |
| MethodLength | 0 | Error |
| ParameterNumber | 0 | Error |
| EmptyForIteratorPad | 0 | Error |
| MethodParamPad | 0 | Error |
| NoWhitespaceAfter | 0 | Error |
| NoWhitespaceBefore | 0 | Error |
| OperatorWrap | 1 | Error |
| ParenPad | 0 | Error |
| TypecastParenPad | 0 | Error |
| WhitespaceAfter | 18 | Error |
| WhitespaceAround | 89 | Error |
| ModifierOrder | 2 | Error |
| RedundantModifier | 0 | Error |
| AvoidNestedBlocks | 0 | Error |
| EmptyBlock | 0 | Error |
| LeftCurly | 0 | Error |
| NeedBraces | 31 | Error |
| RightCurly | 0 | Error |
| AvoidInlineConditionals | 1 | Error |
| EmptyStatement | 0 | Error |
| EqualsHashCode | 0 | Error |
| HiddenField | 13 | Error |
| IllegalInstantiation | 0 | Error |
| InnerAssignment | 0 | Error |
| MagicNumber | 2 | Error |
| MissingSwitchDefault | 2 | Error |
| RedundantThrows | 0 | Error |
| SimplifyBooleanExpression | 0 | Error |
| SimplifyBooleanReturn | 0 | Error |
| DesignForExtension | 24 | Error |
| FinalClass | 0 | Error |
| HideUtilityClassConstructor | 1 | Error |
| InterfaceIsType | 0 | Error |
| VisibilityModifier | 0 | Error |
| ArrayTypeStyle | 0 | Error |
| FinalParameters | 106 | Error |
| TodoComment | 0 | Error |
| UpperEll | 0 | Error |
| Violation | Message | Line |
|---|---|---|
| Missing package-info.java file. | 0 |
| Using the '.*' form of import should be avoided - java.util.*. | 11 |
| Using the '.*' form of import should be avoided - org.apache.commons.cli.*. | 15 |
| Using the '.*' form of import should be avoided - uk.ac.ebi.intenz.domain.enzyme.*. | 22 |
| Missing a Javadoc comment. | 33 |
| Missing a Javadoc comment. | 35 |
| Line contains a tab character. | 36 |
| Missing a Javadoc comment. | 36 |
| Line contains a tab character. | 37 |
| Missing a Javadoc comment. | 37 |
| Line contains a tab character. | 38 |
| Missing a Javadoc comment. | 38 |
| Line contains a tab character. | 39 |
| Missing a Javadoc comment. | 39 |
| Line contains a tab character. | 40 |
| Missing a Javadoc comment. | 40 |
| Line contains a tab character. | 41 |
| Missing a Javadoc comment. | 41 |
| Parameter cliOption should be final. | 41 |
| 'cliOption' hides a field. | 41 |
| '{' is not preceded with whitespace. | 41 |
| Line contains a tab character. | 42 |
| Line contains a tab character. | 43 |
| Line contains a tab character. | 44 |
| Line has trailing spaces. | 45 |
| Missing a Javadoc comment. | 46 |
| Line has trailing spaces. | 47 |
| Line contains a tab character. | 48 |
| Missing a Javadoc comment. | 48 |
| Line contains a tab character. | 50 |
| Missing a Javadoc comment. | 50 |
| Missing a Javadoc comment. | 52 |
| Line contains a tab character. | 57 |
| Line is longer than 80 characters (found 85). | 58 |
| Line contains a tab character. | 58 |
| Line contains a tab character. | 60 |
| Line is longer than 80 characters (found 82). | 61 |
| Line contains a tab character. | 61 |
| Line is longer than 80 characters (found 83). | 62 |
| Line contains a tab character. | 62 |
| Line is longer than 80 characters (found 85). | 63 |
| Line contains a tab character. | 63 |
| Line contains a tab character. | 64 |
| Line contains a tab character. | 66 |
| Line contains a tab character. | 67 |
| Line is longer than 80 characters (found 82). | 71 |
| Line contains a tab character. | 71 |
| Line contains a tab character. | 72 |
| Line is longer than 80 characters (found 88). | 73 |
| Line contains a tab character. | 73 |
| Line contains a tab character. | 74 |
| Line contains a tab character. | 75 |
| Line contains a tab character. | 76 |
| Line contains a tab character. | 77 |
| Line is longer than 80 characters (found 84). | 78 |
| Line contains a tab character. | 78 |
| Line contains a tab character. | 79 |
| Line contains a tab character. | 80 |
| Line is longer than 80 characters (found 88). | 81 |
| Line contains a tab character. | 81 |
| Parameter args should be final. | 90 |
| Line is longer than 80 characters (found 96). | 91 |
| Expected @throws tag for 'ClassNotFoundException'. | 91 |
| Expected @throws tag for 'SQLException'. | 91 |
| Expected @throws tag for 'MapperException'. | 91 |
| Expected @throws tag for 'IOException'. | 91 |
| Expected @throws tag for 'DomainException'. | 91 |
| Line contains a tab character. | 92 |
| Line contains a tab character. | 93 |
| Line contains a tab character. | 94 |
| Line is longer than 80 characters (found 81). | 95 |
| Line contains a tab character. | 95 |
| Line contains a tab character. | 96 |
| Line contains a tab character. | 97 |
| Line contains a tab character. | 98 |
| Line is longer than 80 characters (found 86). | 99 |
| Line contains a tab character. | 99 |
| Line contains a tab character. | 100 |
| Line contains a tab character. | 101 |
| Line contains a tab character. | 102 |
| Line is longer than 80 characters (found 89). | 103 |
| 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 is longer than 80 characters (found 91). | 107 |
| Line contains a tab character. | 107 |
| Line contains a tab character. | 108 |
| Line contains a tab character. | 109 |
| Line contains a tab character. | 110 |
| Line is longer than 80 characters (found 87). | 111 |
| Line contains a tab character. | 111 |
| Line contains a tab character. | 112 |
| Line contains a tab character. | 113 |
| Line contains a tab character. | 114 |
| Line is longer than 80 characters (found 84). | 115 |
| 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 |
| '{' is not preceded with whitespace. | 120 |
| Line is longer than 80 characters (found 92). | 121 |
| Line contains a tab character. | 121 |
| Line contains a tab character. | 122 |
| Line contains a tab character. | 123 |
| Line has trailing spaces. | 124 |
| Line contains a tab character. | 124 |
| Line contains a tab character. | 127 |
| Line contains a tab character. | 129 |
| Line contains a tab character. | 131 |
| Line is longer than 80 characters (found 92). | 132 |
| Line contains a tab character. | 132 |
| Line is longer than 80 characters (found 98). | 133 |
| Line contains a tab character. | 133 |
| Line is longer than 80 characters (found 97). | 134 |
| Line contains a tab character. | 134 |
| Line is longer than 80 characters (found 106). | 135 |
| Line contains a tab character. | 135 |
| Line is longer than 80 characters (found 115). | 136 |
| Line contains a tab character. | 136 |
| Line contains a tab character. | 137 |
| Line is longer than 80 characters (found 81). | 138 |
| '{' is not preceded with whitespace. | 139 |
| Line contains a tab character. | 141 |
| '{' is not preceded with whitespace. | 147 |
| Line is longer than 80 characters (found 81). | 149 |
| Line contains a tab character. | 149 |
| '{' is not preceded with whitespace. | 155 |
| Line contains a tab character. | 157 |
| '{' is not preceded with whitespace. | 163 |
| Line contains a tab character. | 164 |
| Line is longer than 80 characters (found 90). | 165 |
| Line contains a tab character. | 165 |
| Line contains a tab character. | 166 |
| Line contains a tab character. | 169 |
| Missing a Javadoc comment. | 173 |
| Parameter dbConfig should be final. | 173 |
| Line contains a tab character. | 176 |
| Method 'finalize' is not designed for extension - needs to be abstract, final or empty. | 180 |
| Line contains a tab character. | 181 |
| 'if' construct must use '{}'s. | 182 |
| Line contains a tab character. | 182 |
| Line contains a tab character. | 183 |
| Line contains a tab character. | 185 |
| Expected an @return tag. | 192 |
| Method 'getEnzymeList' is not designed for extension - needs to be abstract, final or empty. | 192 |
| Parameter ecString should be final. | 192 |
| Expected @throws tag for 'SQLException'. | 193 |
| Expected @throws tag for 'MapperException'. | 193 |
| Expected @throws tag for 'DomainException'. | 193 |
| '{' is not preceded with whitespace. | 193 |
| Line contains a tab character. | 196 |
| '{' is not preceded with whitespace. | 196 |
| Line is longer than 80 characters (found 85). | 197 |
| Line contains a tab character. | 197 |
| Line contains a tab character. | 198 |
| '?' is not preceded with whitespace. | 198 |
| '?' should be on a new line. | 198 |
| Avoid inline conditionals. | 198 |
| Line contains a tab character. | 199 |
| Line contains a tab character. | 200 |
| Line is longer than 80 characters (found 86). | 201 |
| Line contains a tab character. | 201 |
| Line is longer than 80 characters (found 88). | 202 |
| Line contains a tab character. | 202 |
| Line contains a tab character. | 205 |
| Line contains a tab character. | 208 |
| Line contains a tab character. | 217 |
| Line contains a tab character. | 218 |
| Parameter con should be final. | 222 |
| Expected @throws tag for 'SQLException'. | 223 |
| Expected @throws tag for 'DomainException'. | 223 |
| '{' is not preceded with whitespace. | 223 |
| Line is longer than 80 characters (found 82). | 228 |
| Line is longer than 80 characters (found 86). | 239 |
| Line has trailing spaces. | 247 |
| Line has trailing spaces. | 248 |
| Method 'exportXML' is not designed for extension - needs to be abstract, final or empty. | 252 |
| Parameter enzymeList should be final. | 252 |
| Line is longer than 80 characters (found 82). | 253 |
| Line contains a tab character. | 253 |
| Parameter descriptions should be final. | 253 |
| Parameter toDir should be final. | 253 |
| Expected @throws tag for 'Exception'. | 253 |
| '{' is not preceded with whitespace. | 263 |
| Line is longer than 80 characters (found 82). | 268 |
| Line is longer than 80 characters (found 84). | 271 |
| Line is longer than 80 characters (found 95). | 272 |
| Line is longer than 80 characters (found 101). | 273 |
| Line is longer than 80 characters (found 86). | 274 |
| Line is longer than 80 characters (found 106). | 277 |
| 'if' construct must use '{}'s. | 286 |
| 'if' construct must use '{}'s. | 300 |
| Method 'exportSitemap' is not designed for extension - needs to be abstract, final or empty. | 305 |
| Missing a Javadoc comment. | 305 |
| Parameter enzymeList should be final. | 305 |
| Line contains a tab character. | 306 |
| Parameter descriptions should be final. | 306 |
| Parameter sitemapFile should be final. | 306 |
| '{' is not preceded with whitespace. | 307 |
| Line is longer than 80 characters (found 84). | 308 |
| Line contains a tab character. | 308 |
| Line is longer than 80 characters (found 84). | 309 |
| Line contains a tab character. | 309 |
| Line contains a tab character. | 310 |
| 'if' construct must use '{}'s. | 312 |
| Line contains a tab character. | 312 |
| Line contains a tab character. | 313 |
| Line contains a tab character. | 314 |
| Line contains a tab character. | 315 |
| Line contains a tab character. | 316 |
| Line contains a tab character. | 317 |
| Line contains a tab character. | 318 |
| Line contains a tab character. | 319 |
| Line contains a tab character. | 320 |
| Line contains a tab character. | 321 |
| Line contains a tab character. | 322 |
| Line contains a tab character. | 323 |
| Line contains a tab character. | 324 |
| Line contains a tab character. | 326 |
| Line contains a tab character. | 327 |
| '{' is not preceded with whitespace. | 327 |
| Line contains a tab character. | 328 |
| Line contains a tab character. | 329 |
| Line contains a tab character. | 330 |
| Line contains a tab character. | 331 |
| Line contains a tab character. | 332 |
| Line contains a tab character. | 333 |
| '{' is not preceded with whitespace. | 333 |
| Line contains a tab character. | 334 |
| Line contains a tab character. | 335 |
| Line contains a tab character. | 336 |
| Line contains a tab character. | 337 |
| Line contains a tab character. | 338 |
| Line contains a tab character. | 339 |
| Line contains a tab character. | 340 |
| Line contains a tab character. | 341 |
| Line contains a tab character. | 342 |
| Line contains a tab character. | 343 |
| 'if' construct must use '{}'s. | 344 |
| Line contains a tab character. | 345 |
| Line is longer than 80 characters (found 86). | 348 |
| Method 'exportBiopax' is not designed for extension - needs to be abstract, final or empty. | 348 |
| Missing a Javadoc comment. | 348 |
| Parameter enzymeList should be final. | 348 |
| Parameter biopaxFile should be final. | 348 |
| '{' is not preceded with whitespace. | 349 |
| 'if' construct must use '{}'s. | 355 |
| 'if' construct must use '{}'s. | 359 |
| Method 'exportKegg' is not designed for extension - needs to be abstract, final or empty. | 363 |
| Missing a Javadoc comment. | 363 |
| Parameter enzymes should be final. | 363 |
| Parameter keggFile should be final. | 363 |
| Line contains a tab character. | 365 |
| Line contains a tab character. | 366 |
| Line contains a tab character. | 367 |
| 'if' construct must use '{}'s. | 369 |
| Line is longer than 80 characters (found 85). | 369 |
| Line contains a tab character. | 369 |
| Line contains a tab character. | 370 |
| Line contains a tab character. | 371 |
| Line contains a tab character. | 372 |
| 'if' construct must use '{}'s. | 374 |
| Line contains a tab character. | 375 |
| Line has trailing spaces. | 376 |
| Line contains a tab character. | 376 |
| Line contains a tab character. | 377 |
| Line contains a tab character. | 379 |
| Missing a Javadoc comment. | 379 |
| Parameter toDir should be final. | 379 |
| '{' is not preceded with whitespace. | 379 |
| '{' is not preceded with whitespace. | 381 |
| '{' is not preceded with whitespace. | 382 |
| Line contains a tab character. | 383 |
| '{' is not preceded with whitespace. | 387 |
| Line contains a tab character. | 388 |
| Violation | Message | Line |
|---|---|---|
| Line has trailing spaces. | 21 |
| Utility classes should not have a public or default constructor. | 25 |
| Missing a Javadoc comment. | 27 |
| Missing a Javadoc comment. | 28 |
| Line is longer than 80 characters (found 88). | 30 |
| Missing a Javadoc comment. | 30 |
| Parameter className should be final. | 30 |
| Parameter errorMessage should be final. | 30 |
| Parameter userName should be final. | 30 |
| Line is longer than 80 characters (found 92). | 38 |
| Line is longer than 80 characters (found 136). | 55 |
| Missing a Javadoc comment. | 55 |
| Parameter from should be final. | 55 |
| Parameter to should be final. | 55 |
| Parameter subject should be final. | 55 |
| Parameter messageText should be final. | 55 |
| Parameter singleAttachment should be final. | 55 |
| Line is longer than 80 characters (found 88). | 63 |
| Name 'file_part' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 71 |
| Violation | Message | Line |
|---|---|---|
| Expected @throws tag for 'IOException'. | 23 |
| Expected @throws tag for 'IOException'. | 31 |
| Violation | Message | Line |
|---|---|---|
| Method 'export' is not designed for extension - needs to be abstract, final or empty. | 30 |
| Missing a Javadoc comment. | 30 |
| Parameter enzymes should be final. | 30 |
| Parameter os should be final. | 30 |
| Method 'export' is not designed for extension - needs to be abstract, final or empty. | 41 |
| Missing a Javadoc comment. | 41 |
| Parameter enzyme should be final. | 41 |
| Parameter os should be final. | 41 |
| Method 'export' is not designed for extension - needs to be abstract, final or empty. | 53 |
| Parameter essc should be final. | 53 |
| Parameter os should be final. | 53 |
| '{' is not preceded with whitespace. | 53 |
| Method 'export' is not designed for extension - needs to be abstract, final or empty. | 64 |
| Parameter essc should be final. | 64 |
| Parameter os should be final. | 64 |
| Parameter onlyActive should be final. | 65 |
| '{' is not preceded with whitespace. | 65 |
| Method 'export' is not designed for extension - needs to be abstract, final or empty. | 76 |
| Parameter esc should be final. | 76 |
| Parameter os should be final. | 76 |
| '{' is not preceded with whitespace. | 76 |
| Method 'export' is not designed for extension - needs to be abstract, final or empty. | 87 |
| Parameter ec should be final. | 87 |
| Parameter os should be final. | 87 |
| '{' is not preceded with whitespace. | 87 |
| Method 'export' is not designed for extension - needs to be abstract, final or empty. | 98 |
| Parameter ecs should be final. | 98 |
| Parameter os should be final. | 98 |
| '{' is not preceded with whitespace. | 98 |
| Parameter enzyme should be final. | 118 |
| Expected @param tag for 'enzyme'. | 118 |
| '{' is not preceded with whitespace. | 124 |
| Parameter essc should be final. | 146 |
| Parameter onlyActive should be final. | 147 |
| '{' is not preceded with whitespace. | 147 |
| 'if' construct must use '{}'s. | 156 |
| Parameter esc should be final. | 175 |
| '{' is not preceded with whitespace. | 175 |
| Parameter ec should be final. | 207 |
| '{' is not preceded with whitespace. | 207 |
| Violation | Message | Line |
|---|---|---|
| Missing a Javadoc comment. | 21 |
| Line is longer than 80 characters (found 82). | 23 |
| Line contains a tab character. | 23 |
| Missing a Javadoc comment. | 23 |
| Line contains a tab character. | 25 |
| Missing a Javadoc comment. | 25 |
| Line contains a tab character. | 26 |
| Line contains a tab character. | 27 |
| Line contains a tab character. | 28 |
| Line contains a tab character. | 30 |
| Line has trailing spaces. | 31 |
| Line contains a tab character. | 31 |
| Line contains a tab character. | 32 |
| Method 'export' is not designed for extension - needs to be abstract, final or empty. | 32 |
| Missing a Javadoc comment. | 32 |
| Parameter enzymes should be final. | 32 |
| Parameter os should be final. | 32 |
| Line contains a tab character. | 33 |
| '{' is not preceded with whitespace. | 33 |
| Line has trailing spaces. | 40 |
| Line is longer than 80 characters (found 83). | 43 |
| Line contains a tab character. | 43 |
| Line contains a tab character. | 44 |
| Line contains a tab character. | 45 |
| Line contains a tab character. | 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 |
| 'if' construct must use '{}'s. | 51 |
| Line contains a tab character. | 51 |
| 'if' construct must use '{}'s. | 60 |
| Line contains a tab character. | 62 |
| Method 'export' is not designed for extension - needs to be abstract, final or empty. | 64 |
| Missing a Javadoc comment. | 64 |
| Parameter enzyme should be final. | 64 |
| Parameter os should be final. | 64 |
| Violation | Message | Line |
|---|---|---|
| First sentence should end with a period. | 21 |
| Line contains a tab character. | 29 |
| Missing a Javadoc comment. | 29 |
| Missing a Javadoc comment. | 30 |
| Missing a Javadoc comment. | 31 |
| Name 'INTENZ_URL' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 31 |
| Missing a Javadoc comment. | 33 |
| '{' is not preceded with whitespace. | 33 |
| Line is longer than 80 characters (found 97). | 37 |
| Line contains a tab character. | 37 |
| Line is longer than 80 characters (found 102). | 38 |
| Line contains a tab character. | 38 |
| Line contains a tab character. | 39 |
| Line contains a tab character. | 41 |
| First sentence should end with a period. | 43 |
| Line is longer than 80 characters (found 91). | 49 |
| Line contains a tab character. | 49 |
| Method 'export' is not designed for extension - needs to be abstract, final or empty. | 49 |
| Parameter urls should be final. | 49 |
| Parameter os should be final. | 49 |
| Expected @param tag for 'os'. | 49 |
| Line contains a tab character. | 50 |
| Name 'CHANGE_FREQ' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 50 |
| Line contains a tab character. | 51 |
| Line contains a tab character. | 52 |
| Line contains a tab character. | 53 |
| Line is longer than 80 characters (found 92). | 54 |
| Line contains a tab character. | 54 |
| Line contains a tab character. | 55 |
| Line is longer than 80 characters (found 93). | 56 |
| Line contains a tab character. | 56 |
| '0.8' is a magic number. | 56 |
| ',' is not followed by whitespace. | 56 |
| Line contains a tab character. | 57 |
| Line contains a tab character. | 58 |
| Line contains a tab character. | 59 |
| Line contains a tab character. | 60 |
| Line contains a tab character. | 61 |
| Line contains a tab character. | 62 |
| Line contains a tab character. | 63 |
| Line contains a tab character. | 64 |
| Line contains a tab character. | 65 |
| Violation | Message | Line |
|---|---|---|
| Line contains a tab character. | 87 |
| Line contains a tab character. | 88 |
| Line is longer than 80 characters (found 87). | 89 |
| Line contains a tab character. | 89 |
| Line contains a tab character. | 90 |
| Line is longer than 80 characters (found 84). | 93 |
| Line is longer than 80 characters (found 88). | 95 |
| Missing a Javadoc comment. | 101 |
| Missing a Javadoc comment. | 102 |
| Missing a Javadoc comment. | 104 |
| Missing a Javadoc comment. | 104 |
| Missing a Javadoc comment. | 104 |
| Line has trailing spaces. | 105 |
| Line has trailing spaces. | 124 |
| 'static' modifier out of order with the JLS suggestions. | 128 |
| Line contains a tab character. | 129 |
| 'static' modifier out of order with the JLS suggestions. | 133 |
| Line contains a tab character. | 134 |
| Line contains a tab character. | 136 |
| Line contains a tab character. | 137 |
| Line is longer than 80 characters (found 85). | 138 |
| Line contains a tab character. | 138 |
| Line contains a tab character. | 139 |
| Line is longer than 80 characters (found 86). | 142 |
| Missing a Javadoc comment. | 142 |
| Name 'NAME_QUALIFIERS' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 142 |
| Missing a Javadoc comment. | 143 |
| Name 'VIEWS' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 143 |
| Missing a Javadoc comment. | 144 |
| Name 'DATABASES' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 144 |
| Missing a Javadoc comment. | 145 |
| Name 'DESCRIPTIONS' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 145 |
| Missing a Javadoc comment. | 146 |
| Missing a Javadoc comment. | 147 |
| Line contains a tab character. | 148 |
| Missing a Javadoc comment. | 148 |
| Line has trailing spaces. | 149 |
| Missing a Javadoc comment. | 150 |
| '{' is not preceded with whitespace. | 150 |
| Line contains a tab character. | 151 |
| Line contains a tab character. | 152 |
| Line contains a tab character. | 158 |
| Line is longer than 80 characters (found 86). | 159 |
| Line contains a tab character. | 159 |
| Line contains a tab character. | 163 |
| Line contains a tab character. | 164 |
| Line is longer than 80 characters (found 85). | 165 |
| Line contains a tab character. | 165 |
| Line contains a tab character. | 167 |
| '{' is not preceded with whitespace. | 167 |
| Line contains a tab character. | 168 |
| Line is longer than 80 characters (found 114). | 169 |
| Line contains a tab character. | 169 |
| Parameter arg0 should be final. | 169 |
| Parameter arg1 should be final. | 169 |
| Parameter arg2 should be final. | 169 |
| Line contains a tab character. | 170 |
| Line contains a tab character. | 171 |
| Line contains a tab character. | 172 |
| Line is longer than 80 characters (found 87). | 173 |
| Line contains a tab character. | 173 |
| Line is longer than 80 characters (found 84). | 174 |
| Line contains a tab character. | 174 |
| Line is longer than 80 characters (found 96). | 175 |
| Line contains a tab character. | 175 |
| Line contains a tab character. | 176 |
| Line contains a tab character. | 177 |
| Line contains a tab character. | 178 |
| Line is longer than 80 characters (found 93). | 179 |
| Line contains a tab character. | 179 |
| Line contains a tab character. | 180 |
| Line is longer than 80 characters (found 93). | 181 |
| Line contains a tab character. | 181 |
| Line contains a tab character. | 182 |
| Line contains a tab character. | 183 |
| Method 'setReleaseNumber' is not designed for extension - needs to be abstract, final or empty. | 186 |
| Missing a Javadoc comment. | 186 |
| Parameter releaseNumber should be final. | 186 |
| 'releaseNumber' hides a field. | 186 |
| Method 'setReleaseDate' is not designed for extension - needs to be abstract, final or empty. | 190 |
| Missing a Javadoc comment. | 190 |
| Parameter releaseDate should be final. | 190 |
| 'releaseDate' hides a field. | 190 |
| Missing a Javadoc comment. | 194 |
| '{' is not preceded with whitespace. | 194 |
| Line contains a tab character. | 196 |
| Line contains a tab character. | 198 |
| Line contains a tab character. | 200 |
| Line contains a tab character. | 202 |
| Line contains a tab character. | 204 |
| Line contains a tab character. | 206 |
| Line has trailing spaces. | 208 |
| Missing a Javadoc comment. | 209 |
| '{' is not preceded with whitespace. | 209 |
| Line has trailing spaces. | 218 |
| Missing a Javadoc comment. | 219 |
| '{' is not preceded with whitespace. | 219 |
| ',' is not followed by whitespace. | 221 |
| ',' is not followed by whitespace. | 222 |
| ',' is not followed by whitespace. | 223 |
| ',' is not followed by whitespace. | 224 |
| ',' is not followed by whitespace. | 225 |
| ',' is not followed by whitespace. | 226 |
| ',' is not followed by whitespace. | 227 |
| ',' is not followed by whitespace. | 228 |
| ',' is not followed by whitespace. | 229 |
| ',' is not followed by whitespace. | 230 |
| ',' is not followed by whitespace. | 231 |
| ',' is not followed by whitespace. | 232 |
| ',' is not followed by whitespace. | 233 |
| ',' is not followed by whitespace. | 234 |
| Line contains a tab character. | 235 |
| Method 'setDescriptions' is not designed for extension - needs to be abstract, final or empty. | 238 |
| Missing a Javadoc comment. | 238 |
| Parameter descriptions should be final. | 238 |
| '{' is not preceded with whitespace. | 238 |
| Line contains a tab character. | 239 |
| Line contains a tab character. | 240 |
| Line contains a tab character. | 242 |
| Method 'setFlavour' is not designed for extension - needs to be abstract, final or empty. | 242 |
| Missing a Javadoc comment. | 242 |
| Parameter flavour should be final. | 242 |
| 'flavour' hides a field. | 242 |
| '{' is not preceded with whitespace. | 242 |
| Line contains a tab character. | 243 |
| Line contains a tab character. | 244 |
| Method 'export' is not designed for extension - needs to be abstract, final or empty. | 246 |
| Missing a Javadoc comment. | 246 |
| Parameter enzymes should be final. | 246 |
| Parameter os should be final. | 246 |
| Line is longer than 80 characters (found 88). | 260 |
| Method 'export' is not designed for extension - needs to be abstract, final or empty. | 274 |
| Missing a Javadoc comment. | 274 |
| Parameter enzyme should be final. | 274 |
| Parameter os should be final. | 274 |
| Line contains a tab character. | 278 |
| Line contains a tab character. | 279 |
| Line contains a tab character. | 280 |
| Line is longer than 80 characters (found 83). | 281 |
| Line contains a tab character. | 281 |
| Line is longer than 80 characters (found 81). | 282 |
| Line contains a tab character. | 282 |
| Line contains a tab character. | 283 |
| Line contains a tab character. | 284 |
| Line contains a tab character. | 289 |
| Method 'export' is not designed for extension - needs to be abstract, final or empty. | 290 |
| Parameter entry should be final. | 290 |
| Parameter release should be final. | 290 |
| Parameter relDate should be final. | 291 |
| Parameter os should be final. | 291 |
| Expected @throws tag for 'Exception'. | 291 |
| Line has trailing spaces. | 294 |
| Line is longer than 80 characters (found 83). | 298 |
| Line contains a tab character. | 298 |
| Line is longer than 80 characters (found 81). | 299 |
| Line contains a tab character. | 299 |
| Line contains a tab character. | 300 |
| Method 'export' is not designed for extension - needs to be abstract, final or empty. | 306 |
| Parameter entries should be final. | 306 |
| Parameter release should be final. | 306 |
| Parameter relDate should be final. | 307 |
| Parameter os should be final. | 307 |
| Expected @throws tag for 'Exception'. | 307 |
| '{' is not preceded with whitespace. | 307 |
| Line is longer than 80 characters (found 87). | 310 |
| Line has trailing spaces. | 315 |
| Line is longer than 80 characters (found 84). | 318 |
| Line has trailing spaces. | 319 |
| Line has trailing spaces. | 326 |
| Missing a Javadoc comment. | 327 |
| Parameter intenz should be final. | 327 |
| Parameter ec1 should be final. | 327 |
| 'if' construct must use '{}'s. | 329 |
| '{' is not preceded with whitespace. | 334 |
| '{' is not preceded with whitespace. | 336 |
| Line is longer than 80 characters (found 81). | 338 |
| Line contains a tab character. | 338 |
| '{' is not preceded with whitespace. | 341 |
| Line is longer than 80 characters (found 103). | 343 |
| Line contains a tab character. | 343 |
| Line has trailing spaces. | 350 |
| Missing a Javadoc comment. | 351 |
| Parameter clazz should be final. | 351 |
| Parameter ec1 should be final. | 351 |
| Parameter ec2 should be final. | 351 |
| '{' is not preceded with whitespace. | 351 |
| '{' is not preceded with whitespace. | 352 |
| 'if' construct must use '{}'s. | 353 |
| '{' is not preceded with whitespace. | 358 |
| '+' is not preceded with whitespace. | 359 |
| '+' is not followed by whitespace. | 359 |
| '+' is not preceded with whitespace. | 359 |
| '+' is not followed by whitespace. | 359 |
| '{' is not preceded with whitespace. | 360 |
| Line is longer than 80 characters (found 81). | 365 |
| '{' is not preceded with whitespace. | 365 |
| Line is longer than 80 characters (found 89). | 367 |
| Line has trailing spaces. | 374 |
| Line is longer than 80 characters (found 97). | 375 |
| Missing a Javadoc comment. | 375 |
| Parameter subClazz should be final. | 375 |
| Parameter ec1 should be final. | 375 |
| Parameter ec2 should be final. | 375 |
| Parameter ec3 should be final. | 375 |
| '{' is not preceded with whitespace. | 375 |
| '{' is not preceded with whitespace. | 376 |
| 'if' construct must use '{}'s. | 377 |
| '{' is not preceded with whitespace. | 382 |
| Line is longer than 80 characters (found 94). | 383 |
| '+' is not preceded with whitespace. | 383 |
| '+' is not followed by whitespace. | 383 |
| '+' is not preceded with whitespace. | 383 |
| '+' is not followed by whitespace. | 383 |
| '+' is not preceded with whitespace. | 383 |
| '+' is not followed by whitespace. | 383 |
| '+' is not preceded with whitespace. | 383 |
| '+' is not followed by whitespace. | 383 |
| '{' is not preceded with whitespace. | 384 |
| Line is longer than 80 characters (found 83). | 389 |
| '{' is not preceded with whitespace. | 389 |
| Line is longer than 80 characters (found 91). | 391 |
| Line has trailing spaces. | 398 |
| Line contains a tab character. | 398 |
| Line contains a tab character. | 400 |
| Line contains a tab character. | 401 |
| Line contains a tab character. | 402 |
| Line contains a tab character. | 403 |
| Line contains a tab character. | 404 |
| Line contains a tab character. | 405 |
| Line contains a tab character. | 406 |
| Line contains a tab character. | 407 |
| Parameter s should be final. | 407 |
| '{' is not preceded with whitespace. | 407 |
| Line contains a tab character. | 408 |
| Line contains a tab character. | 409 |
| switch without "default" clause. | 409 |
| '{' is not preceded with whitespace. | 409 |
| Line contains a tab character. | 410 |
| Line is longer than 80 characters (found 95). | 411 |
| Line contains a tab character. | 411 |
| Line contains a tab character. | 412 |
| Line contains a tab character. | 413 |
| '{' is not preceded with whitespace. | 417 |
| Line contains a tab character. | 418 |
| Line is longer than 80 characters (found 87). | 419 |
| Line contains a tab character. | 419 |
| ',' is not followed by whitespace. | 419 |
| ',' is not followed by whitespace. | 419 |
| Line contains a tab character. | 420 |
| Line contains a tab character. | 422 |
| Line is longer than 80 characters (found 82). | 423 |
| Line contains a tab character. | 423 |
| ',' is not followed by whitespace. | 423 |
| Line contains a tab character. | 424 |
| Line contains a tab character. | 425 |
| Line contains a tab character. | 426 |
| Line contains a tab character. | 427 |
| Missing a Javadoc comment. | 429 |
| Parameter os should be final. | 429 |
| Line contains a tab character. | 431 |
| switch without "default" clause. | 431 |
| '{' is not preceded with whitespace. | 431 |
| Line contains a tab character. | 432 |
| Line contains a tab character. | 433 |
| Line contains a tab character. | 434 |
| Line contains a tab character. | 435 |
| Line contains a tab character. | 436 |
| Line contains a tab character. | 437 |
| Line contains a tab character. | 438 |
| Line contains a tab character. | 439 |
| Line contains a tab character. | 440 |
| Line contains a tab character. | 441 |
| Line contains a tab character. | 444 |
| Line has trailing spaces. | 445 |
| Line has trailing spaces. | 449 |
| Missing a Javadoc comment. | 453 |
| Parameter entry should be final. | 453 |
| Line contains a tab character. | 460 |
| Line has trailing spaces. | 461 |
| '{' is not preceded with whitespace. | 462 |
| 'if' construct must use '{}'s. | 465 |
| '{' is not preceded with whitespace. | 467 |
| 'if' construct must use '{}'s. | 470 |
| Line has trailing spaces. | 480 |
| Line has trailing spaces. | 483 |
| Line is longer than 80 characters (found 130). | 493 |
| Parameter entry should be final. | 493 |
| Expected @param tag for 'entry'. | 493 |
| Parameter jaxbEnzyme should be final. | 493 |
| Expected @param tag for 'jaxbEnzyme'. | 493 |
| Parameter of should be final. | 493 |
| 'of' hides a field. | 493 |
| Expected @param tag for 'of'. | 493 |
| Expected @throws tag for 'DatatypeConfigurationException'. | 493 |
| 'if' construct must use '{}'s. | 496 |
| '{' is not preceded with whitespace. | 500 |
| '{' is not preceded with whitespace. | 514 |
| 'if' construct must use '{}'s. | 521 |
| Line is longer than 80 characters (found 90). | 521 |
| 'if' construct must use '{}'s. | 523 |
| Line is longer than 80 characters (found 88). | 523 |
| '{' is not preceded with whitespace. | 526 |
| Line is longer than 80 characters (found 98). | 534 |
| Line is longer than 80 characters (found 87). | 545 |
| Parameter entry should be final. | 545 |
| Expected @param tag for 'entry'. | 545 |
| Parameter jaxbEnzyme should be final. | 545 |
| Expected @param tag for 'jaxbEnzyme'. | 545 |
| Parameter of should be final. | 545 |
| 'of' hides a field. | 545 |
| Expected @param tag for 'of'. | 545 |
| 'if' construct must use '{}'s. | 549 |
| 'if' construct must use '{}'s. | 551 |
| Line is longer than 80 characters (found 85). | 555 |
| '{' is not preceded with whitespace. | 555 |
| Line contains a tab character. | 556 |
| Line is longer than 80 characters (found 91). | 557 |
| '{' is not preceded with whitespace. | 557 |
| Line is longer than 80 characters (found 106). | 558 |
| '+' is not preceded with whitespace. | 558 |
| '+' is not followed by whitespace. | 558 |
| '3' is a magic number. | 558 |
| Line contains a tab character. | 560 |
| '{' is not preceded with whitespace. | 563 |
| Line is longer than 80 characters (found 98). | 564 |
| '+' is not preceded with whitespace. | 564 |
| '+' is not followed by whitespace. | 564 |
| 'if' construct must use '{}'s. | 567 |
| Line contains a tab character. | 570 |
| '{' is not preceded with whitespace. | 576 |
| Line contains a tab character. | 580 |
| '{' is not preceded with whitespace. | 580 |
| Line contains a tab character. | 581 |
| 'if' construct must use '{}'s. | 583 |
| Line is longer than 80 characters (found 89). | 590 |
| Line is longer than 80 characters (found 93). | 591 |
| Line is longer than 80 characters (found 90). | 602 |
| Parameter entry should be final. | 602 |
| Expected @param tag for 'entry'. | 602 |
| Parameter jaxbEnzyme should be final. | 602 |
| Expected @param tag for 'jaxbEnzyme'. | 602 |
| Parameter of should be final. | 602 |
| 'of' hides a field. | 602 |
| Expected @param tag for 'of'. | 602 |
| 'if' construct must use '{}'s. | 605 |
| Line is longer than 80 characters (found 81). | 609 |
| Line is longer than 80 characters (found 91). | 620 |
| Parameter entry should be final. | 620 |
| Expected @param tag for 'entry'. | 620 |
| Parameter jaxbEnzyme should be final. | 620 |
| Expected @param tag for 'jaxbEnzyme'. | 620 |
| Parameter of should be final. | 620 |
| 'of' hides a field. | 620 |
| Expected @param tag for 'of'. | 620 |
| Line has trailing spaces. | 622 |
| Line contains a tab character. | 622 |
| '{' is not preceded with whitespace. | 623 |
| Line contains a tab character. | 624 |
| 'if' construct must use '{}'s. | 625 |
| Line contains a tab character. | 627 |
| '{' is not preceded with whitespace. | 627 |
| Line contains a tab character. | 628 |
| Line is longer than 80 characters (found 87). | 629 |
| Line contains a tab character. | 629 |
| Line contains a tab character. | 630 |
| Line contains a tab character. | 631 |
| Line contains a tab character. | 632 |
| Line contains a tab character. | 633 |
| Line contains a tab character. | 634 |
| Line contains a tab character. | 635 |
| Line contains a tab character. | 636 |
| '{' is not preceded with whitespace. | 636 |
| Line is longer than 80 characters (found 84). | 637 |
| Line contains a tab character. | 637 |
| Line contains a tab character. | 638 |
| Line contains a tab character. | 642 |
| Line contains a tab character. | 643 |
| Line contains a tab character. | 644 |
| Line contains a tab character. | 645 |
| Line contains a tab character. | 646 |
| Line contains a tab character. | 647 |
| Line is longer than 80 characters (found 94). | 648 |
| Line contains a tab character. | 648 |
| Parameter of should be final. | 648 |
| 'of' hides a field. | 648 |
| Parameter cofactor should be final. | 648 |
| Line contains a tab character. | 649 |
| Line contains a tab character. | 650 |
| Line is longer than 80 characters (found 85). | 651 |
| Line contains a tab character. | 651 |
| Line contains a tab character. | 652 |
| Line is longer than 80 characters (found 87). | 653 |
| Line contains a tab character. | 653 |
| Line is longer than 80 characters (found 81). | 654 |
| Line contains a tab character. | 654 |
| Line contains a tab character. | 655 |
| Line contains a tab character. | 656 |
| Line is longer than 80 characters (found 87). | 658 |
| Missing a Javadoc comment. | 658 |
| Parameter of should be final. | 658 |
| 'of' hides a field. | 658 |
| Parameter os should be final. | 658 |
| Line contains a tab character. | 659 |
| Line contains a tab character. | 660 |
| Line contains a tab character. | 661 |
| Line contains a tab character. | 662 |
| '{' is not preceded with whitespace. | 662 |
| Line contains a tab character. | 663 |
| Line contains a tab character. | 664 |
| '{' is not preceded with whitespace. | 664 |
| Line contains a tab character. | 665 |
| Line contains a tab character. | 666 |
| Line contains a tab character. | 667 |
| Line is longer than 80 characters (found 90). | 668 |
| Line contains a tab character. | 668 |
| Line contains a tab character. | 669 |
| 'if' construct must use '{}'s. | 670 |
| Line contains a tab character. | 670 |
| Line is longer than 80 characters (found 94). | 671 |
| Line contains a tab character. | 671 |
| Line contains a tab character. | 672 |
| Line contains a tab character. | 673 |
| Line contains a tab character. | 674 |
| Line contains a tab character. | 675 |
| Line contains a tab character. | 676 |
| Line contains a tab character. | 678 |
| Line is longer than 80 characters (found 91). | 683 |
| Parameter entry should be final. | 683 |
| Expected @param tag for 'entry'. | 683 |
| Parameter jaxbEnzyme should be final. | 683 |
| Expected @param tag for 'jaxbEnzyme'. | 683 |
| Parameter of should be final. | 683 |
| 'of' hides a field. | 683 |
| Expected @param tag for 'of'. | 683 |
| Line contains a tab character. | 689 |
| '{' is not preceded with whitespace. | 689 |
| Line contains a tab character. | 690 |
| 'if' construct must use '{}'s. | 691 |
| Line contains a tab character. | 691 |
| Line is longer than 80 characters (found 84). | 692 |
| Line contains a tab character. | 692 |
| Line is longer than 80 characters (found 90). | 693 |
| Line contains a tab character. | 693 |
| Line is longer than 80 characters (found 96). | 694 |
| Line contains a tab character. | 694 |
| Line contains a tab character. | 695 |
| Line contains a tab character. | 696 |
| Line contains a tab character. | 697 |
| Line contains a tab character. | 698 |
| Line is longer than 80 characters (found 91). | 699 |
| Line contains a tab character. | 699 |
| Line contains a tab character. | 700 |
| Line contains a tab character. | 701 |
| Line contains a tab character. | 702 |
| Line contains a tab character. | 703 |
| Line contains a tab character. | 704 |
| Line is longer than 80 characters (found 101). | 705 |
| Line contains a tab character. | 705 |
| Line contains a tab character. | 706 |
| Line contains a tab character. | 707 |
| Line contains a tab character. | 708 |
| Line contains a tab character. | 709 |
| 'if' construct must use '{}'s. | 710 |
| Line is longer than 80 characters (found 87). | 722 |
| Parameter entry should be final. | 722 |
| Expected @param tag for 'entry'. | 722 |
| Parameter jaxbEnzyme should be final. | 722 |
| Expected @param tag for 'jaxbEnzyme'. | 722 |
| Parameter of should be final. | 722 |
| 'of' hides a field. | 722 |
| Expected @param tag for 'of'. | 722 |
| '{' is not preceded with whitespace. | 730 |
| '{' is not preceded with whitespace. | 734 |
| 'if' construct must use '{}'s. | 735 |
| Expected an @return tag. | 747 |
| Parameter entry should be final. | 747 |
| Expected @param tag for 'entry'. | 747 |
| Line is longer than 80 characters (found 84). | 749 |
| Line is longer than 80 characters (found 88). | 750 |
| 'if' construct must use '{}'s. | 752 |
| Line is longer than 80 characters (found 82). | 752 |
| Expected an @return tag. | 762 |
| Line is longer than 80 characters (found 81). | 762 |
| Parameter of should be final. | 762 |
| 'of' hides a field. | 762 |
| Expected @param tag for 'of'. | 762 |
| Parameter name should be final. | 762 |
| Expected @param tag for 'name'. | 762 |
