The following document contains the results of Checkstyle. 
| Rules | Violations | Severity |
|---|---|---|
JavadocPackage
| 0 |  Error |
| NewlineAtEndOfFile | 0 | Error |
| Translation | 0 | Error |
| FileLength | 0 | Error |
FileTabCharacter
| 27 | Error |
RegexpSingleline
| 8 | Error |
| JavadocMethod | 32 | Error |
| JavadocType | 0 | Error |
| JavadocVariable | 34 | Error |
| JavadocStyle | 2 | Error |
| ConstantName | 0 | Error |
| LocalFinalVariableName | 0 | Error |
| LocalVariableName | 2 | Error |
| MemberName | 9 | Error |
| MethodName | 0 | Error |
| PackageName | 0 | Error |
| ParameterName | 0 | Error |
| StaticVariableName | 3 | Error |
| TypeName | 0 | Error |
| AvoidStarImport | 4 | Error |
| IllegalImport | 0 | Error |
| RedundantImport | 0 | Error |
| UnusedImports | 4 | Error |
| LineLength | 104 | Error |
| MethodLength | 0 | Error |
| ParameterNumber | 0 | Error |
| EmptyForIteratorPad | 0 | Error |
| MethodParamPad | 4 | Error |
| NoWhitespaceAfter | 0 | Error |
| NoWhitespaceBefore | 0 | Error |
| OperatorWrap | 12 | Error |
| ParenPad | 3 | Error |
| TypecastParenPad | 0 | Error |
| WhitespaceAfter | 12 | Error |
| WhitespaceAround | 18 | Error |
| ModifierOrder | 0 | Error |
| RedundantModifier | 2 | Error |
| AvoidNestedBlocks | 0 | Error |
| EmptyBlock | 2 | Error |
| LeftCurly | 0 | Error |
| NeedBraces | 41 | Error |
| RightCurly | 0 | Error |
| AvoidInlineConditionals | 0 | Error |
| EmptyStatement | 0 | Error |
| EqualsHashCode | 0 | Error |
| HiddenField | 4 | Error |
| IllegalInstantiation | 0 | Error |
| InnerAssignment | 0 | Error |
| MagicNumber | 8 | Error |
| MissingSwitchDefault | 2 | Error |
| RedundantThrows | 0 | Error |
| SimplifyBooleanExpression | 0 | Error |
| SimplifyBooleanReturn | 0 | Error |
| DesignForExtension | 3 | Error |
| FinalClass | 7 | Error |
| HideUtilityClassConstructor | 0 | Error |
| InterfaceIsType | 0 | Error |
| VisibilityModifier | 1 | Error |
| ArrayTypeStyle | 0 | Error |
| FinalParameters | 64 | Error |
| TodoComment | 1 | Error |
| UpperEll | 0 | Error |
| Violation | Message | Line |
|---|---|---|
| Unused import - java.util.Vector. | 5 |
| Missing a Javadoc comment. | 18 |
| Missing a Javadoc comment. | 20 |
| Missing a Javadoc comment. | 22 |
| Missing a Javadoc comment. | 24 |
| Missing a Javadoc comment. | 26 |
| Parameter dir should be final. | 43 |
| Expected @param tag for 'dir'. | 43 |
| Parameter ec should be final. | 43 |
| Parameter dir should be final. | 66 |
| Parameter type should be final. | 66 |
| Parameter enzymeLogFormat should be final. | 66 |
| 'enzymeLogFormat' hides a field. | 66 |
| Expected @param tag for 'enzymeLogFormat'. | 66 |
| 'if' construct must use '{}'s. | 68 |
| 'if' construct must use '{}'s. | 69 |
| 'else' construct must use '{}'s. | 71 |
| Missing a Javadoc comment. | 75 |
| Parameter type should be final. | 75 |
| Parameter dir should be final. | 75 |
| switch without "default" clause. | 78 |
| '3' is a magic number. | 97 |
| Missing a Javadoc comment. | 109 |
| Parameter type should be final. | 109 |
| Parameter dir should be final. | 109 |
| switch without "default" clause. | 111 |
| Line is longer than 80 characters (found 93). | 115 |
| Line is longer than 80 characters (found 122). | 118 |
| Line is longer than 80 characters (found 90). | 123 |
| Line is longer than 80 characters (found 122). | 126 |
| Line is longer than 80 characters (found 93). | 131 |
| Line is longer than 80 characters (found 174). | 134 |
| '3' is a magic number. | 136 |
| Line is longer than 80 characters (found 90). | 139 |
| Line is longer than 80 characters (found 122). | 142 |
| Method 'add' is not designed for extension - needs to be abstract, final or empty. | 171 |
| Parameter before should be final. | 171 |
| Parameter after should be final. | 171 |
| Parameter ec should be final. | 171 |
| 'if' construct must use '{}'s. | 180 |
| 'if' construct must use '{}'s. | 182 |
| Line is longer than 80 characters (found 88). | 186 |
| 'if' construct must use '{}'s. | 190 |
| '4' is a magic number. | 190 |
| 'if' construct must use '{}'s. | 191 |
| '4' is a magic number. | 191 |
| Line is longer than 80 characters (found 82). | 201 |
| Line is longer than 80 characters (found 256). | 205 |
| '+' should be on a new line. | 205 |
| Line is longer than 80 characters (found 164). | 206 |
| '+' should be on a new line. | 206 |
| '+' should be on a new line. | 207 |
| Line is longer than 80 characters (found 177). | 208 |
| Line is longer than 80 characters (found 89). | 211 |
| 'if' construct must use '{}'s. | 214 |
| '4' is a magic number. | 214 |
| Line is longer than 80 characters (found 256). | 227 |
| '+' should be on a new line. | 227 |
| Line is longer than 80 characters (found 131). | 228 |
| '+' should be on a new line. | 228 |
| Line is longer than 80 characters (found 177). | 229 |
| Line is longer than 80 characters (found 89). | 232 |
| 'if' construct must use '{}'s. | 235 |
| '4' is a magic number. | 235 |
| Line is longer than 80 characters (found 82). | 244 |
| Line is longer than 80 characters (found 256). | 248 |
| '+' should be on a new line. | 248 |
| Line is longer than 80 characters (found 164). | 249 |
| '+' should be on a new line. | 249 |
| '+' should be on a new line. | 250 |
| Line is longer than 80 characters (found 100). | 251 |
| Line is longer than 80 characters (found 90). | 254 |
| Line is longer than 80 characters (found 256). | 267 |
| '+' should be on a new line. | 267 |
| Line is longer than 80 characters (found 131). | 268 |
| '+' should be on a new line. | 268 |
| Line is longer than 80 characters (found 100). | 269 |
| Missing a Javadoc comment. | 277 |
| Parameter text should be final. | 277 |
| Method 'addOtherNameLog' is not designed for extension - needs to be abstract, final or empty. | 281 |
| Missing a Javadoc comment. | 281 |
| Parameter nameNotMatching should be final. | 281 |
| Parameter set should be final. | 281 |
| Parameter ec should be final. | 281 |
| Must have at least one statement. | 287 |
| 'else' construct must use '{}'s. | 289 |
| Line is longer than 80 characters (found 212). | 290 |
| '+' should be on a new line. | 290 |
| Line is longer than 80 characters (found 106). | 334 |
| Line is longer than 80 characters (found 81). | 345 |
| Method 'close' is not designed for extension - needs to be abstract, final or empty. | 361 |
| 'if' construct must use '{}'s. | 363 |
| 'if' is not followed by whitespace. | 363 |
| Missing a Javadoc comment. | 370 |
| Parameter text should be final. | 370 |
| Missing a Javadoc comment. | 382 |
| Parameter before should be final. | 382 |
| Parameter after should be final. | 382 |
| Line contains a tab character. | 384 |
| Line is longer than 80 characters (found 92). | 385 |
| Line contains a tab character. | 385 |
| Line contains a tab character. | 386 |
| Line is longer than 80 characters (found 89). | 387 |
| Line contains a tab character. | 387 |
| 'if' construct must use '{}'s. | 393 |
| 'else' construct must use '{}'s. | 395 |
| 'if' construct must use '{}'s. | 397 |
| 'else' construct must use '{}'s. | 399 |
| 'if' construct must use '{}'s. | 401 |
| Violation | Message | Line |
|---|---|---|
| Using the '.*' form of import should be avoided - uk.ac.ebi.intenz.tools.sib.translator.rules.*. | 3 |
| Unused import - java.util.PropertyResourceBundle. | 8 |
| Unused import - java.io.FileInputStream. | 9 |
| Unused import - java.io.IOException. | 10 |
| Line is longer than 80 characters (found 101). | 15 |
| Line is longer than 80 characters (found 142). | 17 |
| Class XCharsASCIITranslator should be declared as final. | 22 |
| Line is longer than 80 characters (found 86). | 24 |
| Missing a Javadoc comment. | 24 |
| Line is longer than 80 characters (found 84). | 35 |
| Line is longer than 80 characters (found 88). | 68 |
| Unused @throws tag for 'NullPointerException'. | 70 |
| Parameter text should be final. | 72 |
| Parameter useReactionRules should be final. | 72 |
| 'if' construct must use '{}'s. | 73 |
| Line is longer than 80 characters (found 91). | 73 |
| 'if' construct must use '{}'s. | 75 |
| 'if' construct must use '{}'s. | 78 |
| 'if' is not followed by whitespace. | 78 |
| '(' is followed by whitespace. | 78 |
| ')' is preceded with whitespace. | 78 |
| Line is longer than 80 characters (found 100). | 85 |
| Line is longer than 80 characters (found 88). | 88 |
| Unused @throws tag for 'NullPointerException'. | 90 |
| Parameter texts should be final. | 92 |
| Parameter useReactionRules should be final. | 92 |
| 'if' construct must use '{}'s. | 93 |
| Line is longer than 80 characters (found 93). | 93 |
| Line is longer than 80 characters (found 90). | 96 |
| Line is longer than 80 characters (found 91). | 104 |
| Line is longer than 80 characters (found 120). | 106 |
| Unused @throws tag for 'NullPointerException'. | 108 |
| Parameter text should be final. | 110 |
| Parameter useReactionRules should be final. | 110 |
| 'if' construct must use '{}'s. | 111 |
| Line is longer than 80 characters (found 91). | 111 |
| 'if' construct must use '{}'s. | 119 |
| 'if' construct must use '{}'s. | 121 |
| Line is longer than 80 characters (found 120). | 133 |
| Unused @throws tag for 'NullPointerException'. | 135 |
| Parameter text should be final. | 137 |
| Parameter useReactionRules should be final. | 137 |
| Line contains a tab character. | 138 |
| Parameter useDeLineRules should be final. | 138 |
| Expected @param tag for 'useDeLineRules'. | 138 |
| Line contains a tab character. | 142 |
| Line contains a tab character. | 143 |
| Line contains a tab character. | 144 |
| Line contains a tab character. | 145 |
| Line contains a tab character. | 146 |
| Line contains a tab character. | 147 |
| Line contains a tab character. | 148 |
| Line contains a tab character. | 149 |
| Expected an @return tag. | 150 |
| Line contains a tab character. | 150 |
| Parameter text should be final. | 150 |
| Parameter useReactionRules should be final. | 150 |
| Line contains a tab character. | 151 |
| Parameter useDeLineRules should be final. | 151 |
| Parameter useGrammarRules should be final. | 151 |
| Line contains a tab character. | 152 |
| Line contains a tab character. | 153 |
| 'if' construct must use '{}'s. | 154 |
| Line is longer than 80 characters (found 84). | 154 |
| Line contains a tab character. | 154 |
| Line contains a tab character. | 155 |
| 'if' construct must use '{}'s. | 156 |
| Line is longer than 80 characters (found 89). | 156 |
| Line contains a tab character. | 156 |
| Line contains a tab character. | 157 |
| 'if' construct must use '{}'s. | 158 |
| Line is longer than 80 characters (found 82). | 158 |
| Line contains a tab character. | 158 |
| Line contains a tab character. | 159 |
| Line contains a tab character. | 160 |
| Line contains a tab character. | 161 |
| Line contains a tab character. | 162 |
| Line contains a tab character. | 163 |
| Expected an @return tag. | 169 |
| '(' is preceded with whitespace. | 169 |
| Violation | Message | Line |
|---|---|---|
| Using the '.*' form of import should be avoided - java.util.*. | 10 |
| Class DescriptionLineRules should be declared as final. | 29 |
| Missing a Javadoc comment. | 31 |
| Line is longer than 80 characters (found 82). | 33 |
| Missing a Javadoc comment. | 33 |
| Missing a Javadoc comment. | 35 |
| 'try' is not followed by whitespace. | 45 |
| '{' is not preceded with whitespace. | 45 |
| Line is longer than 80 characters (found 99). | 46 |
| 'if' construct must use '{}'s. | 58 |
| '!=' is not preceded with whitespace. | 58 |
| '!=' is not followed by whitespace. | 58 |
| First sentence should end with a period. | 77 |
| Unused @throws tag for 'NullPointerException'. | 82 |
| Parameter text should be final. | 84 |
| 'if' construct must use '{}'s. | 85 |
| Line is longer than 80 characters (found 92). | 85 |
| Unused @throws tag for 'NullPointerException'. | 94 |
| Parameter text should be final. | 96 |
| 'if' construct must use '{}'s. | 97 |
| Line is longer than 80 characters (found 91). | 97 |
| Parameter text should be final. | 109 |
| Parameter rules should be final. | 109 |
| Violation | Message | Line |
|---|---|---|
| First sentence should end with a period. | 19 |
| Line is longer than 80 characters (found 82). | 28 |
| Class GrammarRules should be declared as final. | 31 |
| Missing a Javadoc comment. | 33 |
| Missing a Javadoc comment. | 35 |
| Name 'INSTANCE' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 35 |
| Missing a Javadoc comment. | 37 |
| Name 'CAPITILISATION_RULES_REVERSED' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 37 |
| Missing a Javadoc comment. | 63 |
| Name 'CAPITILISATION_EXCLUSIONS' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 63 |
| Missing a Javadoc comment. | 106 |
| Name 'SNEAKY_CAPIT_PATTERNS' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 106 |
| Line is longer than 80 characters (found 83). | 111 |
| Missing a Javadoc comment. | 111 |
| Name 'SNEAKY_CAPIT_PATTERN' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 111 |
| Missing a Javadoc comment. | 113 |
| Name 'DECAPITALIZATION_PATTERNS' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 113 |
| Missing a Javadoc comment. | 115 |
| '(' is preceded with whitespace. | 115 |
| Line is longer than 80 characters (found 115). | 116 |
| '{' is not preceded with whitespace. | 121 |
| '{' is not preceded with whitespace. | 131 |
| Must have at least one statement. | 131 |
| '{' is not followed by whitespace. | 131 |
| '}' is not preceded with whitespace. | 131 |
| Missing a Javadoc comment. | 147 |
| '(' is preceded with whitespace. | 147 |
| Parameter text should be final. | 147 |
| Missing a Javadoc comment. | 151 |
| Parameter text should be final. | 151 |
| 'if' construct must use '{}'s. | 152 |
| Line is longer than 80 characters (found 81). | 153 |
| 'if' construct must use '{}'s. | 154 |
| 'if' construct must use '{}'s. | 166 |
| Missing a Javadoc comment. | 173 |
| '(' is preceded with whitespace. | 173 |
| Parameter text should be final. | 173 |
| '{' is not preceded with whitespace. | 174 |
| '{' is not preceded with whitespace. | 176 |
| Line is longer than 80 characters (found 110). | 177 |
| '3' is a magic number. | 177 |
| ',' is not followed by whitespace. | 180 |
| Missing a Javadoc comment. | 185 |
| Parameter text should be final. | 185 |
| '{' is not preceded with whitespace. | 186 |
| Line is longer than 80 characters (found 83). | 188 |
| '{' is not preceded with whitespace. | 190 |
| Line is longer than 80 characters (found 114). | 191 |
| '3' is a magic number. | 191 |
| Parameter text should be final. | 205 |
| Parameter rules should be final. | 205 |
| Violation | Message | Line |
|---|---|---|
| Line is longer than 80 characters (found 85). | 9 |
| Line is longer than 80 characters (found 111). | 11 |
| Class OrderedRules should be declared as final. | 19 |
| Missing a Javadoc comment. | 21 |
| Missing a Javadoc comment. | 23 |
| Name 'INSTANCE' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 23 |
| Missing a Javadoc comment. | 25 |
| Name 'RULES' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 25 |
| Line is longer than 80 characters (found 88). | 28 |
| Line is longer than 80 characters (found 103). | 29 |
| Line is longer than 80 characters (found 87). | 30 |
| Line is longer than 80 characters (found 83). | 41 |
| Line is longer than 80 characters (found 84). | 48 |
| ',' is not followed by whitespace. | 112 |
| Missing a Javadoc comment. | 115 |
| Name 'RULES_REVERSED' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 115 |
| Line is longer than 80 characters (found 137). | 117 |
| Line is longer than 80 characters (found 84). | 119 |
| '+' should be on a new line. | 119 |
| Line is longer than 80 characters (found 88). | 122 |
| Line is longer than 80 characters (found 99). | 131 |
| Line is longer than 80 characters (found 83). | 134 |
| ',' is not followed by whitespace. | 141 |
| ',' is not followed by whitespace. | 142 |
| Comment matches to-do format 'TODO:'. | 143 |
| Line is longer than 80 characters (found 395). | 144 |
| ',' is not followed by whitespace. | 144 |
| Line is longer than 80 characters (found 91). | 145 |
| ',' is not followed by whitespace. | 145 |
| ',' is not followed by whitespace. | 146 |
| Line is longer than 80 characters (found 140). | 150 |
| Missing a Javadoc comment. | 150 |
| Name 'STEREO_TERMS' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 150 |
| Line is longer than 80 characters (found 113). | 151 |
| Unused @throws tag for 'NullPointerException'. | 176 |
| Parameter text should be final. | 178 |
| 'if' construct must use '{}'s. | 179 |
| Line is longer than 80 characters (found 91). | 179 |
| Unused @throws tag for 'NullPointerException'. | 191 |
| Parameter text should be final. | 193 |
| 'if' construct must use '{}'s. | 194 |
| Line is longer than 80 characters (found 91). | 194 |
| Parameter text should be final. | 208 |
| Parameter rules should be final. | 208 |
| Line is longer than 80 characters (found 118). | 217 |
| Parameter text should be final. | 223 |
| Line is longer than 80 characters (found 84). | 224 |
| Name 'RSZEPattern' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 234 |
| Name 'RSZEMatcher' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 235 |
| 'if' construct must use '{}'s. | 241 |
| Line is longer than 80 characters (found 83). | 246 |
| Parameter text should be final. | 251 |
| Parameter text should be final. | 261 |
| Line is longer than 80 characters (found 89). | 265 |
| Parameter text should be final. | 276 |
| Line is longer than 80 characters (found 117). | 279 |
| Line is longer than 80 characters (found 100). | 280 |
| Violation | Message | Line |
|---|---|---|
| Using the '.*' form of import should be avoided - java.util.*. | 8 |
| Line is longer than 80 characters (found 85). | 11 |
| Line is longer than 80 characters (found 111). | 13 |
| Class ReactionRules should be declared as final. | 21 |
| Missing a Javadoc comment. | 23 |
| Missing a Javadoc comment. | 25 |
| Missing a Javadoc comment. | 27 |
| Missing a Javadoc comment. | 29 |
| Line has trailing spaces. | 33 |
| Line is longer than 80 characters (found 111). | 35 |
| Line is longer than 80 characters (found 105). | 53 |
| Line has trailing spaces. | 74 |
| Line has trailing spaces. | 76 |
| Line has trailing spaces. | 78 |
| Line has trailing spaces. | 85 |
| Unused @throws tag for 'NullPointerException'. | 88 |
| Line has trailing spaces. | 89 |
| Parameter text should be final. | 90 |
| 'if' construct must use '{}'s. | 91 |
| Line is longer than 80 characters (found 91). | 91 |
| Line has trailing spaces. | 98 |
| Unused @throws tag for 'NullPointerException'. | 101 |
| Parameter text should be final. | 103 |
| 'if' construct must use '{}'s. | 104 |
| Line is longer than 80 characters (found 91). | 104 |
| Parameter text should be final. | 116 |
| Parameter rules should be final. | 116 |
| 'rules' hides a field. | 116 |
| Violation | Message | Line |
|---|---|---|
| Line is longer than 80 characters (found 94). | 4 |
| Line is longer than 80 characters (found 99). | 13 |
| Redundant 'public' modifier. | 18 |
| Line is longer than 80 characters (found 114). | 21 |
| Redundant 'public' modifier. | 26 |
| Violation | Message | Line |
|---|---|---|
| Line is longer than 80 characters (found 85). | 9 |
| Line is longer than 80 characters (found 111). | 11 |
| Class TagRules should be declared as final. | 17 |
| Missing a Javadoc comment. | 19 |
| Missing a Javadoc comment. | 21 |
| Name 'INSTANCE' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 21 |
| Missing a Javadoc comment. | 22 |
| Variable 'encoding' must be private and have accessor methods. | 22 |
| Missing a Javadoc comment. | 24 |
| Name 'RULES' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 24 |
| ',' is not followed by whitespace. | 27 |
| ',' is not followed by whitespace. | 28 |
| ',' is not followed by whitespace. | 29 |
| ',' is not followed by whitespace. | 30 |
| ',' is not followed by whitespace. | 31 |
| Parameter encoding should be final. | 37 |
| 'encoding' hides a field. | 37 |
| Expected @param tag for 'encoding'. | 37 |
| Parameter encoding should be final. | 49 |
| Expected @param tag for 'encoding'. | 49 |
| 'if' is not followed by whitespace. | 50 |
| '(' is followed by whitespace. | 50 |
| '{' is not preceded with whitespace. | 50 |
| '{' is not preceded with whitespace. | 51 |
| 'if' construct must use '{}'s. | 52 |
| 'if' is not followed by whitespace. | 52 |
| Unused @throws tag for 'NullPointerException'. | 64 |
| Parameter text should be final. | 66 |
| 'if' construct must use '{}'s. | 67 |
| Line is longer than 80 characters (found 91). | 67 |
| Unused @throws tag for 'NullPointerException'. | 76 |
| Parameter text should be final. | 78 |
| Line is longer than 80 characters (found 93). | 79 |
| Parameter text should be final. | 90 |
| Parameter rules should be final. | 90 |
| Line has trailing spaces. | 96 |
| Violation | Message | Line |
|---|---|---|
| Using the '.*' form of import should be avoided - java.util.*. | 8 |
| Line is longer than 80 characters (found 85). | 11 |
| Line is longer than 80 characters (found 111). | 13 |
| Class UnorderedRules should be declared as final. | 19 |
| Missing a Javadoc comment. | 21 |
| Missing a Javadoc comment. | 23 |
| Missing a Javadoc comment. | 25 |
| Missing a Javadoc comment. | 27 |
| Missing a Javadoc comment. | 29 |
| Line is longer than 80 characters (found 112). | 35 |
| Line is longer than 80 characters (found 106). | 54 |
| Line is longer than 80 characters (found 101). | 63 |
| Unused @throws tag for 'NullPointerException'. | 99 |
| Parameter text should be final. | 101 |
| 'if' construct must use '{}'s. | 102 |
| Line is longer than 80 characters (found 91). | 102 |
| Line is longer than 80 characters (found 90). | 110 |
| Unused @throws tag for 'NullPointerException'. | 115 |
| Parameter text should be final. | 117 |
| 'if' construct must use '{}'s. | 118 |
| Line is longer than 80 characters (found 91). | 118 |
| Parameter text should be final. | 132 |
| Parameter rules should be final. | 132 |
| 'rules' hides a field. | 132 |
