Checkstyle Results
The following document contains the results of Checkstyle. 
Files
Rules
| Rules | Violations | Severity |
|---|---|---|
JavadocPackage
| 4 |  Error |
| NewlineAtEndOfFile | 0 | Error |
| Translation | 0 | Error |
| FileLength | 0 | Error |
FileTabCharacter
| 102 | Error |
RegexpSingleline
| 17 | Error |
| JavadocMethod | 218 | Error |
| JavadocType | 3 | Error |
| JavadocVariable | 63 | Error |
| JavadocStyle | 3 | Error |
| ConstantName | 2 | Error |
| LocalFinalVariableName | 0 | Error |
| LocalVariableName | 29 | Error |
| MemberName | 0 | Error |
| MethodName | 0 | Error |
| PackageName | 0 | Error |
| ParameterName | 4 | Error |
| StaticVariableName | 1 | Error |
| TypeName | 1 | Error |
| AvoidStarImport | 7 | Error |
| IllegalImport | 0 | Error |
| RedundantImport | 0 | Error |
| UnusedImports | 3 | Error |
| LineLength | 584 | Error |
| MethodLength | 0 | Error |
| ParameterNumber | 0 | Error |
| EmptyForIteratorPad | 0 | Error |
| MethodParamPad | 25 | Error |
| NoWhitespaceAfter | 1 | Error |
| NoWhitespaceBefore | 0 | Error |
| OperatorWrap | 35 | Error |
| ParenPad | 105 | Error |
| TypecastParenPad | 0 | Error |
| WhitespaceAfter | 5 | Error |
| WhitespaceAround | 68 | Error |
| ModifierOrder | 0 | Error |
| RedundantModifier | 1 | Error |
| AvoidNestedBlocks | 0 | Error |
| EmptyBlock | 4 | Error |
| LeftCurly | 0 | Error |
| NeedBraces | 119 | Error |
| RightCurly | 0 | Error |
| AvoidInlineConditionals | 5 | Error |
| EmptyStatement | 0 | Error |
| EqualsHashCode | 0 | Error |
| HiddenField | 7 | Error |
| IllegalInstantiation | 0 | Error |
| InnerAssignment | 1 | Error |
| MagicNumber | 13 | Error |
| MissingSwitchDefault | 0 | Error |
| RedundantThrows | 21 | Error |
| SimplifyBooleanExpression | 0 | Error |
| SimplifyBooleanReturn | 0 | Error |
| DesignForExtension | 134 | Error |
| FinalClass | 3 | Error |
| HideUtilityClassConstructor | 8 | Error |
| InterfaceIsType | 0 | Error |
| VisibilityModifier | 1 | Error |
| ArrayTypeStyle | 0 | Error |
| FinalParameters | 225 | Error |
| TodoComment | 0 | Error |
| UpperEll | 0 | Error |
Details
uk/ac/ebi/intenz/tools/sib/ApplicationResources.java
| Violation | Message | Line |
|---|---|---|
| Unused import - java.io.FileInputStream. | 13 |
| Line is longer than 80 characters (found 82). | 33 |
| Class ApplicationResources should be declared as final. | 36 |
| Missing a Javadoc comment. | 38 |
| Name 'LOGGER' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 38 |
| Line contains a tab character. | 39 |
| Missing a Javadoc comment. | 41 |
| Variable 'resources' must be private and have accessor methods. | 41 |
| '(' is preceded with whitespace. | 48 |
| Parameter stream should be final. | 48 |
| Expected @throws tag for 'IOException'. | 48 |
| Line is longer than 80 characters (found 85). | 55 |
| Expected an @return tag. | 58 |
| '(' is preceded with whitespace. | 58 |
| '(' is followed by whitespace. | 59 |
| ')' is preceded with whitespace. | 59 |
| '(' is followed by whitespace. | 60 |
| ')' is preceded with whitespace. | 60 |
| '(' is followed by whitespace. | 61 |
| ')' is preceded with whitespace. | 61 |
| Line contains a tab character. | 63 |
| Line is longer than 80 characters (found 119). | 64 |
| Line is longer than 80 characters (found 95). | 65 |
| Line contains a tab character. | 65 |
| Line is longer than 80 characters (found 90). | 66 |
| Line contains a tab character. | 66 |
| '(' is followed by whitespace. | 68 |
| ')' is preceded with whitespace. | 68 |
| Line is longer than 80 characters (found 86). | 69 |
| Missing a Javadoc comment. | 80 |
| '{' is not preceded with whitespace. | 80 |
| Missing a Javadoc comment. | 84 |
| '{' is not preceded with whitespace. | 84 |
| Missing a Javadoc comment. | 88 |
| '{' is not preceded with whitespace. | 88 |
| Missing a Javadoc comment. | 92 |
| '{' is not preceded with whitespace. | 92 |
| Missing a Javadoc comment. | 96 |
| '{' is not preceded with whitespace. | 96 |
| Missing a Javadoc comment. | 100 |
| '{' is not preceded with whitespace. | 100 |
| Missing a Javadoc comment. | 104 |
| '{' is not preceded with whitespace. | 104 |
uk/ac/ebi/intenz/tools/sib/EnzymeFlatFileComparatorApp.java
| Violation | Message | Line |
|---|---|---|
| Unused import - uk.ac.ebi.intenz.tools.sib.writer.EnzymeFlatFileWriter. | 4 |
| Unused import - java.util.PropertyResourceBundle. | 7 |
| Line is longer than 80 characters (found 90). | 12 |
| Utility classes should not have a public or default constructor. | 17 |
| Missing a Javadoc comment. | 19 |
| Line contains a tab character. | 20 |
| Line is longer than 80 characters (found 90). | 25 |
| Parameter args should be final. | 27 |
| Line is longer than 80 characters (found 89). | 33 |
| Line is longer than 80 characters (found 90). | 34 |
| Line is longer than 80 characters (found 111). | 35 |
| '+' is not preceded with whitespace. | 35 |
| '+' is not followed by whitespace. | 35 |
| Line is longer than 80 characters (found 97). | 41 |
| Parameter args should be final. | 51 |
| Line is longer than 80 characters (found 119). | 53 |
| Line is longer than 80 characters (found 89). | 64 |
uk/ac/ebi/intenz/tools/sib/EnzymeFlatFileWriterApp.java
| Violation | Message | Line |
|---|---|---|
| Line is longer than 80 characters (found 90). | 29 |
| Utility classes should not have a public or default constructor. | 34 |
| Missing a Javadoc comment. | 36 |
| Line contains a tab character. | 37 |
| Missing a Javadoc comment. | 40 |
| Missing a Javadoc comment. | 41 |
| '=' is not followed by whitespace. | 41 |
| Line is longer than 80 characters (found 83). | 43 |
| Line is longer than 80 characters (found 98). | 45 |
| Line contains a tab character. | 49 |
| Parameter args should be final. | 53 |
| Line contains a tab character. | 55 |
| Line contains a tab character. | 57 |
| Line contains a tab character. | 58 |
| Line is longer than 80 characters (found 86). | 59 |
| Line contains a tab character. | 59 |
| Line contains a tab character. | 60 |
| Line contains a tab character. | 61 |
| Line contains a tab character. | 63 |
| Line is longer than 80 characters (found 114). | 64 |
| Line contains a tab character. | 64 |
| Line is longer than 80 characters (found 123). | 65 |
| Line contains a tab character. | 65 |
| Line is longer than 80 characters (found 105). | 66 |
| Line contains a tab character. | 66 |
| Line is longer than 80 characters (found 110). | 67 |
| Line contains a tab character. | 67 |
| '1000' is a magic number. | 67 |
| Line contains a tab character. | 68 |
| Line contains a tab character. | 69 |
| Line contains a tab character. | 70 |
| Line is longer than 80 characters (found 98). | 76 |
| Line is longer than 80 characters (found 83). | 78 |
| '(' is preceded with whitespace. | 81 |
| 'try' is not followed by whitespace. | 82 |
| '{' is not preceded with whitespace. | 82 |
| Line is longer than 80 characters (found 119). | 83 |
| 'catch' is not preceded with whitespace. | 84 |
| '}' is not followed by whitespace. | 84 |
| '{' is not preceded with whitespace. | 84 |
| Line contains a tab character. | 95 |
| Parameter args should be final. | 101 |
| '{' is not preceded with whitespace. | 115 |
| Line contains a tab character. | 116 |
| Line contains a tab character. | 118 |
| Line contains a tab character. | 119 |
| Line contains a tab character. | 121 |
| Line is longer than 80 characters (found 102). | 122 |
| Line contains a tab character. | 122 |
| '?' is not preceded with whitespace. | 122 |
| Avoid inline conditionals. | 122 |
| Line contains a tab character. | 123 |
| Line contains a tab character. | 124 |
| Line is longer than 80 characters (found 128). | 133 |
| Line is longer than 80 characters (found 108). | 150 |
| Line is longer than 80 characters (found 100). | 169 |
| Parameter args should be final. | 174 |
| '+' is not preceded with whitespace. | 180 |
| '+' is not followed by whitespace. | 180 |
| Line is longer than 80 characters (found 89). | 182 |
| Line is longer than 80 characters (found 82). | 198 |
| Line is longer than 80 characters (found 144). | 199 |
uk/ac/ebi/intenz/tools/sib/comparator/FlatFileComparator.java
| Violation | Message | Line |
|---|---|---|
| Missing package-info.java file. | 0 |
| Using the '.*' form of import should be avoided - java.io.*. | 10 |
| Utility classes should not have a public or default constructor. | 22 |
| Missing a Javadoc comment. | 24 |
| Line contains a tab character. | 25 |
| Missing a Javadoc comment. | 26 |
| Missing a Javadoc comment. | 27 |
| Missing a Javadoc comment. | 28 |
| Missing a Javadoc comment. | 29 |
| Missing a Javadoc comment. | 30 |
| Missing a Javadoc comment. | 31 |
| Missing a Javadoc comment. | 32 |
| Missing a Javadoc comment. | 33 |
| Missing a Javadoc comment. | 34 |
| Line is longer than 80 characters (found 87). | 37 |
| Missing a Javadoc comment. | 40 |
| Missing a Javadoc comment. | 42 |
| Line is longer than 80 characters (found 89). | 44 |
| Missing a Javadoc comment. | 44 |
| Line is longer than 80 characters (found 89). | 45 |
| Missing a Javadoc comment. | 45 |
| Missing a Javadoc comment. | 47 |
| Missing a Javadoc comment. | 48 |
| Missing a Javadoc comment. | 49 |
| Missing a Javadoc comment. | 50 |
| Missing a Javadoc comment. | 51 |
| Missing a Javadoc comment. | 52 |
| Missing a Javadoc comment. | 53 |
| Missing a Javadoc comment. | 54 |
| Missing a Javadoc comment. | 55 |
| Missing a Javadoc comment. | 57 |
| '(' is preceded with whitespace. | 57 |
| Parameter flatFile1 should be final. | 57 |
| Parameter flatFile2 should be final. | 57 |
| Line is longer than 80 characters (found 98). | 74 |
| '(' is followed by whitespace. | 75 |
| ')' is preceded with whitespace. | 75 |
| '(' is followed by whitespace. | 77 |
| ')' is preceded with whitespace. | 77 |
| 'if' construct must use '{}'s. | 78 |
| Line is longer than 80 characters (found 124). | 78 |
| 'if' construct must use '{}'s. | 79 |
| Line is longer than 80 characters (found 127). | 79 |
| Line is longer than 80 characters (found 112). | 82 |
| Line is longer than 80 characters (found 95). | 83 |
| '(' is followed by whitespace. | 84 |
| ')' is preceded with whitespace. | 84 |
| Line is longer than 80 characters (found 104). | 85 |
| 'if' construct must use '{}'s. | 86 |
| Line is longer than 80 characters (found 84). | 87 |
| Line is longer than 80 characters (found 96). | 89 |
| '(' is followed by whitespace. | 90 |
| ')' is preceded with whitespace. | 90 |
| '{' is not preceded with whitespace. | 90 |
| 'if' construct must use '{}'s. | 96 |
| Line is longer than 80 characters (found 97). | 96 |
| 'if' construct must use '{}'s. | 97 |
| Line is longer than 80 characters (found 97). | 97 |
| Line is longer than 80 characters (found 104). | 99 |
| '(' is followed by whitespace. | 101 |
| ')' is preceded with whitespace. | 101 |
| 'if' construct must use '{}'s. | 102 |
| Line is longer than 80 characters (found 81). | 103 |
| Line is longer than 80 characters (found 96). | 105 |
| '(' is followed by whitespace. | 106 |
| ')' is preceded with whitespace. | 106 |
| '{' is not preceded with whitespace. | 106 |
| 'if' construct must use '{}'s. | 112 |
| Line is longer than 80 characters (found 97). | 112 |
| 'if' construct must use '{}'s. | 113 |
| Line is longer than 80 characters (found 97). | 113 |
| '(' is followed by whitespace. | 115 |
| ')' is preceded with whitespace. | 115 |
| 'if' construct must use '{}'s. | 122 |
| Line is longer than 80 characters (found 97). | 122 |
| 'if' construct must use '{}'s. | 123 |
| Line is longer than 80 characters (found 100). | 123 |
| 'if' construct must use '{}'s. | 124 |
| Line is longer than 80 characters (found 106). | 124 |
| '(' is followed by whitespace. | 124 |
| ')' is preceded with whitespace. | 124 |
| '(' is followed by whitespace. | 130 |
| ')' is preceded with whitespace. | 130 |
| 'if' construct must use '{}'s. | 134 |
| '(' is followed by whitespace. | 134 |
| ')' is preceded with whitespace. | 134 |
| 'if' construct must use '{}'s. | 135 |
| '(' is followed by whitespace. | 135 |
| ')' is preceded with whitespace. | 135 |
| '(' is followed by whitespace. | 136 |
| ')' is preceded with whitespace. | 136 |
| Line has trailing spaces. | 141 |
| Line is longer than 80 characters (found 90). | 145 |
| Parameter outputResult should be final. | 148 |
| Expected @param tag for 'outputResult'. | 148 |
| '{' is not preceded with whitespace. | 150 |
| '{' is not preceded with whitespace. | 152 |
| Missing a Javadoc comment. | 158 |
| Parameter reader should be final. | 158 |
| Line is longer than 80 characters (found 95). | 170 |
| Line is longer than 80 characters (found 109). | 172 |
| '(' is preceded with whitespace. | 172 |
| Parameter entryA should be final. | 172 |
| Parameter entryB should be final. | 172 |
| 'if' construct must use '{}'s. | 173 |
| Line is longer than 80 characters (found 99). | 173 |
| '(' is followed by whitespace. | 173 |
| ')' is preceded with whitespace. | 173 |
| 'if' construct must use '{}'s. | 174 |
| Line is longer than 80 characters (found 99). | 174 |
| '(' is followed by whitespace. | 174 |
| ')' is preceded with whitespace. | 174 |
| Line is longer than 80 characters (found 81). | 180 |
| '(' is followed by whitespace. | 183 |
| ')' is preceded with whitespace. | 183 |
| Line contains a tab character. | 185 |
| Line is longer than 80 characters (found 110). | 186 |
| Line contains a tab character. | 186 |
| '?' is not preceded with whitespace. | 186 |
| Avoid inline conditionals. | 186 |
| '(' is followed by whitespace. | 190 |
| ')' is preceded with whitespace. | 190 |
| Line contains a tab character. | 192 |
| Line is longer than 80 characters (found 110). | 193 |
| Line contains a tab character. | 193 |
| '?' is not preceded with whitespace. | 193 |
| Avoid inline conditionals. | 193 |
| 'if' construct must use '{}'s. | 199 |
| '(' is followed by whitespace. | 199 |
| ')' is preceded with whitespace. | 199 |
| '(' is followed by whitespace. | 202 |
| ')' is preceded with whitespace. | 202 |
| Line is longer than 80 characters (found 84). | 209 |
| Line is longer than 80 characters (found 84). | 212 |
| '{' is not preceded with whitespace. | 214 |
| '{' is not preceded with whitespace. | 215 |
| '{' is not preceded with whitespace. | 220 |
| Line is longer than 80 characters (found 85). | 231 |
| Line is longer than 80 characters (found 93). | 233 |
| '(' is followed by whitespace. | 239 |
| ')' is preceded with whitespace. | 239 |
| Line is longer than 80 characters (found 90). | 240 |
| '(' is followed by whitespace. | 241 |
| ')' is preceded with whitespace. | 241 |
| '(' is followed by whitespace. | 248 |
| ')' is preceded with whitespace. | 248 |
| Line is longer than 80 characters (found 101). | 249 |
| '(' is followed by whitespace. | 250 |
| ')' is preceded with whitespace. | 250 |
| '(' is followed by whitespace. | 257 |
| ')' is preceded with whitespace. | 257 |
| Line is longer than 80 characters (found 101). | 258 |
| '(' is followed by whitespace. | 259 |
| ')' is preceded with whitespace. | 259 |
| '(' is followed by whitespace. | 266 |
| ')' is preceded with whitespace. | 266 |
| Line is longer than 80 characters (found 101). | 267 |
| '(' is followed by whitespace. | 268 |
| ')' is preceded with whitespace. | 268 |
| '(' is followed by whitespace. | 275 |
| ')' is preceded with whitespace. | 275 |
| Line is longer than 80 characters (found 101). | 276 |
| '(' is followed by whitespace. | 277 |
| ')' is preceded with whitespace. | 277 |
| '(' is followed by whitespace. | 284 |
| ')' is preceded with whitespace. | 284 |
| Line is longer than 80 characters (found 101). | 285 |
| '(' is followed by whitespace. | 286 |
| ')' is preceded with whitespace. | 286 |
| '(' is followed by whitespace. | 293 |
| ')' is preceded with whitespace. | 293 |
| Line is longer than 80 characters (found 101). | 294 |
| '(' is followed by whitespace. | 295 |
| ')' is preceded with whitespace. | 295 |
| Line is longer than 80 characters (found 91). | 299 |
| '(' is followed by whitespace. | 303 |
| ')' is preceded with whitespace. | 303 |
| Line is longer than 80 characters (found 101). | 304 |
| '(' is followed by whitespace. | 305 |
| ')' is preceded with whitespace. | 305 |
| Line is longer than 80 characters (found 92). | 309 |
| '(' is followed by whitespace. | 312 |
| ')' is preceded with whitespace. | 312 |
| Must have at least one statement. | 312 |
| Line is longer than 80 characters (found 81). | 323 |
| Line is longer than 80 characters (found 81). | 324 |
| Line is longer than 80 characters (found 81). | 325 |
| Expected an @return tag. | 330 |
| '(' is preceded with whitespace. | 330 |
| Parameter entry should be final. | 330 |
| Expected @param tag for 'entry'. | 330 |
| Line is longer than 80 characters (found 84). | 334 |
| '(' is followed by whitespace. | 338 |
| ')' is preceded with whitespace. | 338 |
| '(' is followed by whitespace. | 347 |
| ')' is preceded with whitespace. | 347 |
| '{' is not preceded with whitespace. | 351 |
| Line is longer than 80 characters (found 93). | 361 |
| Line is longer than 80 characters (found 100). | 362 |
| Line has trailing spaces. | 363 |
| Line has trailing spaces. | 365 |
| Line has trailing spaces. | 367 |
| Line has trailing spaces. | 372 |
| First sentence should end with a period. | 373 |
| Parameter text should be final. | 380 |
| Expected @param tag for 'text'. | 380 |
| Parameter regex should be final. | 380 |
| Line is longer than 80 characters (found 93). | 402 |
| '(' is preceded with whitespace. | 402 |
| Parameter lineOfLoadedFF should be final. | 402 |
| Expected @param tag for 'lineOfLoadedFF'. | 402 |
| Parameter flatFile1Reader should be final. | 402 |
| Expected @param tag for 'flatFile1Reader'. | 402 |
| Parameter entryA should be final. | 403 |
| Expected @param tag for 'entryA'. | 403 |
| Expected @throws tag for 'IOException'. | 403 |
| '(' is followed by whitespace. | 404 |
| ')' is preceded with whitespace. | 404 |
| '(' is followed by whitespace. | 406 |
| ')' is preceded with whitespace. | 406 |
| Missing a Javadoc comment. | 412 |
| '(' is preceded with whitespace. | 412 |
| Parameter line should be final. | 412 |
| Line is longer than 80 characters (found 98). | 417 |
| Line is longer than 80 characters (found 117). | 425 |
| '(' is preceded with whitespace. | 425 |
| Parameter flatFile2Reader should be final. | 425 |
| Expected @param tag for 'flatFile2Reader'. | 425 |
| Parameter entryB should be final. | 425 |
| Expected @param tag for 'entryB'. | 425 |
| Expected @throws tag for 'IOException'. | 425 |
| '(' is preceded with whitespace. | 439 |
| Parameter entryA should be final. | 439 |
| Expected @param tag for 'entryA'. | 439 |
| Parameter entryB should be final. | 439 |
| Expected @param tag for 'entryB'. | 439 |
| '(' is preceded with whitespace. | 447 |
| Line is longer than 80 characters (found 82). | 448 |
| Expected an @return tag. | 470 |
| '(' is preceded with whitespace. | 470 |
| Parameter lineToAdd should be final. | 470 |
| Expected @param tag for 'lineToAdd'. | 470 |
| Inner assignments should be avoided. | 471 |
| Line is longer than 80 characters (found 82). | 475 |
| Line is longer than 80 characters (found 105). | 480 |
| Line is longer than 80 characters (found 93). | 482 |
| '(' is preceded with whitespace. | 482 |
| Parameter entryA should be final. | 482 |
| Parameter entryB should be final. | 482 |
| Parameter lineType should be final. | 482 |
| Line is longer than 80 characters (found 82). | 492 |
| Line is longer than 80 characters (found 118). | 497 |
| Line is longer than 80 characters (found 91). | 500 |
| '(' is preceded with whitespace. | 500 |
| Parameter entryA should be final. | 500 |
| Parameter entryB should be final. | 500 |
| Parameter lineType should be final. | 500 |
| '(' is followed by whitespace. | 506 |
| ')' is preceded with whitespace. | 506 |
| 'if' construct must use '{}'s. | 508 |
| '(' is followed by whitespace. | 508 |
| ')' is preceded with whitespace. | 508 |
| 'if' construct must use '{}'s. | 511 |
| '(' is followed by whitespace. | 511 |
| ')' is preceded with whitespace. | 511 |
| Line is longer than 80 characters (found 86). | 520 |
| Line is longer than 80 characters (found 112). | 526 |
| '(' is preceded with whitespace. | 526 |
| Parameter lineType should be final. | 526 |
| Parameter entryA should be final. | 526 |
| Parameter entryB should be final. | 526 |
| Parameter logger should be final. | 526 |
| Expected @param tag for 'logger'. | 526 |
| Line is longer than 80 characters (found 98). | 536 |
| Line is longer than 80 characters (found 98). | 539 |
| Line is longer than 80 characters (found 109). | 548 |
| Line is longer than 80 characters (found 87). | 550 |
| Line is longer than 80 characters (found 127). | 556 |
| '(' is preceded with whitespace. | 556 |
| Parameter lineType should be final. | 556 |
| Parameter entryA should be final. | 556 |
| Parameter entryB should be final. | 556 |
| Expected @param tag for 'entryB'. | 556 |
| Parameter lineIndex should be final. | 556 |
| Parameter logger should be final. | 556 |
| Expected @param tag for 'logger'. | 556 |
| Line is longer than 80 characters (found 120). | 567 |
| Line is longer than 80 characters (found 120). | 570 |
| '(' is preceded with whitespace. | 582 |
| Parameter entryA should be final. | 582 |
| Line is longer than 80 characters (found 88). | 584 |
| Name 'IDLinePattern' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 584 |
| Name 'IDLinePatternMatcher' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 585 |
| 'if' construct must use '{}'s. | 586 |
| '(' is followed by whitespace. | 586 |
| ')' is preceded with whitespace. | 586 |
| '(' is preceded with whitespace. | 597 |
| Parameter entry should be final. | 597 |
| Parameter lineType should be final. | 597 |
| Line is longer than 80 characters (found 85). | 599 |
| 'if' construct must use '{}'s. | 601 |
| '(' is followed by whitespace. | 601 |
| ')' is preceded with whitespace. | 601 |
| '(' is preceded with whitespace. | 612 |
| Parameter entry should be final. | 612 |
| Parameter lineType should be final. | 612 |
| Line is longer than 80 characters (found 85). | 615 |
| 'while' construct must use '{}'s. | 618 |
| Line is longer than 80 characters (found 81). | 618 |
| '(' is followed by whitespace. | 618 |
| ')' is preceded with whitespace. | 618 |
| Line is longer than 80 characters (found 91). | 629 |
| Unused @throws tag for 'IndexOutOfBoundsException'. | 629 |
| Expected an @return tag. | 632 |
| Line is longer than 80 characters (found 94). | 632 |
| '(' is preceded with whitespace. | 632 |
| Parameter entry should be final. | 632 |
| Expected @param tag for 'entry'. | 632 |
| Parameter lineType should be final. | 632 |
| Expected @param tag for 'lineType'. | 632 |
| Parameter lineIndex should be final. | 632 |
| Expected @param tag for 'lineIndex'. | 632 |
| 'if' construct must use '{}'s. | 635 |
| '(' is followed by whitespace. | 635 |
| ')' is preceded with whitespace. | 635 |
| 'if' construct must use '{}'s. | 637 |
| '(' is followed by whitespace. | 637 |
| ')' is preceded with whitespace. | 637 |
| 'else' construct must use '{}'s. | 639 |
uk/ac/ebi/intenz/tools/sib/exceptions/EnzymeEntryValidationException.java
| Violation | Message | Line |
|---|---|---|
| Missing package-info.java file. | 0 |
| Missing a Javadoc comment. | 11 |
| Parameter message should be final. | 11 |
uk/ac/ebi/intenz/tools/sib/helper/EnzymeHelper.java
| Violation | Message | Line |
|---|---|---|
| Missing package-info.java file. | 0 |
| Utility classes should not have a public or default constructor. | 36 |
| Missing a Javadoc comment. | 38 |
| Line contains a tab character. | 39 |
| Expected an @return tag. | 50 |
| Parameter enzymeEntry should be final. | 50 |
| Expected @param tag for 'enzymeEntry'. | 50 |
| Line is longer than 80 characters (found 104). | 51 |
| Parameter encoding should be final. | 51 |
| Expected @param tag for 'encoding'. | 51 |
| Parameter encodingType should be final. | 51 |
| Expected @param tag for 'encodingType'. | 51 |
| Line is longer than 80 characters (found 91). | 52 |
| Parameter translate should be final. | 52 |
| Expected @param tag for 'translate'. | 52 |
| Expected @throws tag for 'SPTRException'. | 52 |
| Line is longer than 80 characters (found 81). | 53 |
| 'if' construct must use '{}'s. | 58 |
| Line is longer than 80 characters (found 107). | 58 |
| 'if' construct must use '{}'s. | 71 |
| Line is longer than 80 characters (found 139). | 72 |
| 'else' construct must use '{}'s. | 73 |
| Line is longer than 80 characters (found 117). | 74 |
| 'if' is not followed by whitespace. | 78 |
| Line is longer than 80 characters (found 95). | 79 |
| '+' is not preceded with whitespace. | 79 |
| '+' is not followed by whitespace. | 79 |
| '+' is not preceded with whitespace. | 79 |
| '+' is not followed by whitespace. | 79 |
| 'if' construct must use '{}'s. | 88 |
| Line is longer than 80 characters (found 134). | 89 |
| 'else' construct must use '{}'s. | 90 |
| Line is longer than 80 characters (found 100). | 91 |
| Line is longer than 80 characters (found 88). | 99 |
| 'if' construct must use '{}'s. | 100 |
| Line is longer than 80 characters (found 152). | 101 |
| 'else' construct must use '{}'s. | 102 |
| Line is longer than 80 characters (found 119). | 103 |
| Line contains a tab character. | 111 |
| Line contains a tab character. | 113 |
| '?' is not preceded with whitespace. | 113 |
| '?' should be on a new line. | 113 |
| Avoid inline conditionals. | 113 |
| Line contains a tab character. | 114 |
| ':' should be on a new line. | 114 |
| Line contains a tab character. | 115 |
| Line is longer than 80 characters (found 107). | 116 |
| 'if' construct must use '{}'s. | 117 |
| Line is longer than 80 characters (found 134). | 129 |
| '&&' should be on a new line. | 139 |
| Name 'DICrossReference' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 141 |
| Line is longer than 80 characters (found 83). | 144 |
| '&&' should be on a new line. | 144 |
| Name 'PRCrossReference' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 146 |
| Line is longer than 80 characters (found 85). | 149 |
| '&&' should be on a new line. | 149 |
| Name 'DRCrossReference' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 151 |
| Line has trailing spaces. | 162 |
| Line is longer than 80 characters (found 111). | 164 |
| Missing a Javadoc comment. | 164 |
| Parameter enzymeEntry should be final. | 164 |
| '+' should be on a new line. | 172 |
| Line is longer than 80 characters (found 142). | 173 |
| Line is longer than 80 characters (found 101). | 178 |
| Missing a Javadoc comment. | 178 |
| Parameter enzymeLink should be final. | 178 |
| Line is longer than 80 characters (found 93). | 181 |
| Line is longer than 80 characters (found 99). | 183 |
| Line is longer than 80 characters (found 101). | 190 |
| Missing a Javadoc comment. | 190 |
| Parameter enzymeLink should be final. | 190 |
| Line is longer than 80 characters (found 97). | 193 |
| Line is longer than 80 characters (found 101). | 201 |
| Missing a Javadoc comment. | 201 |
| Parameter enzymeLink should be final. | 201 |
| Line is longer than 80 characters (found 99). | 204 |
| Line is longer than 80 characters (found 99). | 206 |
uk/ac/ebi/intenz/tools/sib/helper/FFWriterHelper.java
| Violation | Message | Line |
|---|---|---|
| Line is longer than 80 characters (found 118). | 7 |
| Line is longer than 80 characters (found 94). | 11 |
| Utility classes should not have a public or default constructor. | 13 |
| Unused @throws tag for 'NullPointerException'. | 22 |
| Parameter flatFile should be final. | 24 |
| 'if' construct must use '{}'s. | 25 |
| Line is longer than 80 characters (found 99). | 25 |
| Line is longer than 80 characters (found 157). | 27 |
| Line is longer than 80 characters (found 174). | 29 |
| Name 'DRLinePattern' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 31 |
| Name 'DRLinePatternMatcher' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 32 |
| Name 'DRLineContents' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 35 |
| Line is longer than 80 characters (found 150). | 37 |
| Line is longer than 80 characters (found 97). | 38 |
uk/ac/ebi/intenz/tools/sib/helper/SibEntryHelper.java
| Violation | Message | Line |
|---|---|---|
| Utility classes should not have a public or default constructor. | 38 |
| Line is longer than 80 characters (found 83). | 40 |
| Line is longer than 80 characters (found 105). | 42 |
| Missing a Javadoc comment. | 42 |
| Parameter enzymeEntry should be final. | 42 |
| Line is longer than 80 characters (found 127). | 43 |
| Parameter encoding should be final. | 43 |
| Parameter encodingType should be final. | 43 |
| Line is longer than 80 characters (found 81). | 44 |
| 'if' construct must use '{}'s. | 49 |
| Line is longer than 80 characters (found 107). | 49 |
| Line has trailing spaces. | 51 |
| Line is longer than 80 characters (found 137). | 60 |
| Line is longer than 80 characters (found 91). | 66 |
| Line is longer than 80 characters (found 135). | 76 |
| Line is longer than 80 characters (found 96). | 80 |
| Line is longer than 80 characters (found 108). | 81 |
| 'if' construct must use '{}'s. | 88 |
| Line is longer than 80 characters (found 82). | 89 |
| Line contains a tab character. | 89 |
| Line contains a tab character. | 90 |
| Line contains a tab character. | 91 |
| Line is longer than 80 characters (found 88). | 92 |
| Line contains a tab character. | 93 |
| Line contains a tab character. | 94 |
| ',' is not followed by whitespace. | 94 |
| ',' is not followed by whitespace. | 94 |
| Line contains a tab character. | 95 |
| ',' is not followed by whitespace. | 95 |
| ',' is not followed by whitespace. | 95 |
| Line is longer than 80 characters (found 111). | 96 |
| Line contains a tab character. | 105 |
| '{' is not preceded with whitespace. | 105 |
| Line is longer than 80 characters (found 110). | 123 |
| Line has trailing spaces. | 124 |
| Line contains a tab character. | 124 |
| Line is longer than 80 characters (found 85). | 126 |
| '{' is not preceded with whitespace. | 127 |
| 'if' construct must use '{}'s. | 129 |
| '-' is not preceded with whitespace. | 129 |
| '-' is not followed by whitespace. | 129 |
| Line is longer than 80 characters (found 135). | 140 |
| ')' is preceded with whitespace. | 140 |
| '&&' should be on a new line. | 150 |
| Name 'DICrossReference' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 152 |
| Line is longer than 80 characters (found 83). | 155 |
| '&&' should be on a new line. | 155 |
| Name 'PRCrossReference' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 157 |
| Line is longer than 80 characters (found 85). | 160 |
| '&&' should be on a new line. | 160 |
| Name 'DRCrossReference' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 162 |
| Expected an @return tag. | 178 |
| Line is longer than 80 characters (found 83). | 178 |
| Parameter constant should be final. | 178 |
| Expected @param tag for 'constant'. | 178 |
| '{' is not preceded with whitespace. | 178 |
| Line has trailing spaces. | 180 |
| 'if' is not followed by whitespace. | 180 |
| '!=' is not preceded with whitespace. | 180 |
| '!=' is not followed by whitespace. | 180 |
| '{' is not preceded with whitespace. | 180 |
| 'if' is not followed by whitespace. | 182 |
| '(' is followed by whitespace. | 182 |
| ')' is preceded with whitespace. | 182 |
| '{' is not preceded with whitespace. | 182 |
| Line is longer than 80 characters (found 142). | 191 |
| Missing a Javadoc comment. | 191 |
| Parameter enzymeEntry should be final. | 191 |
| Line contains a tab character. | 199 |
| Line is longer than 80 characters (found 107). | 200 |
| Line contains a tab character. | 200 |
| Line contains a tab character. | 201 |
| Line contains a tab character. | 202 |
| Line is longer than 80 characters (found 103). | 203 |
| Line contains a tab character. | 203 |
| Line contains a tab character. | 204 |
| '{' is not preceded with whitespace. | 204 |
| Line contains a tab character. | 205 |
| Line contains a tab character. | 206 |
| Must have at least one statement. | 206 |
| Line has trailing spaces. | 207 |
| Line contains a tab character. | 208 |
| Line contains a tab character. | 209 |
| '{' is not preceded with whitespace. | 209 |
| Must have at least one statement. | 209 |
| '{' is not followed by whitespace. | 209 |
| '}' is not preceded with whitespace. | 209 |
| Line is longer than 80 characters (found 101). | 210 |
| Line is longer than 80 characters (found 107). | 211 |
| Line contains a tab character. | 211 |
| Line is longer than 80 characters (found 144). | 213 |
| Line is longer than 80 characters (found 101). | 218 |
| Missing a Javadoc comment. | 218 |
| Parameter enzymeLink should be final. | 218 |
| Line is longer than 80 characters (found 93). | 221 |
| Line is longer than 80 characters (found 106). | 223 |
| Line is longer than 80 characters (found 101). | 230 |
| Missing a Javadoc comment. | 230 |
| Parameter enzymeLink should be final. | 230 |
| Line is longer than 80 characters (found 97). | 233 |
| Line is longer than 80 characters (found 101). | 241 |
| Missing a Javadoc comment. | 241 |
| Parameter enzymeLink should be final. | 241 |
| Line is longer than 80 characters (found 99). | 244 |
| Line is longer than 80 characters (found 106). | 246 |
uk/ac/ebi/intenz/tools/sib/sptr_enzyme/EnzymeCrossReference.java
| Violation | Message | Line |
|---|---|---|
| Line has trailing spaces. | 8 |
| Line is longer than 80 characters (found 111). | 9 |
| Missing a Javadoc comment. | 25 |
| Missing a Javadoc comment. | 27 |
| Missing a Javadoc comment. | 29 |
| Line is longer than 80 characters (found 81). | 32 |
| Line is longer than 80 characters (found 103). | 36 |
| Line is longer than 80 characters (found 99). | 37 |
| Line is longer than 80 characters (found 108). | 38 |
| Parameter databaseName should be final. | 43 |
| 'databaseName' hides a field. | 43 |
| Line is longer than 80 characters (found 84). | 55 |
| Line is longer than 80 characters (found 83). | 56 |
| Line is longer than 80 characters (found 88). | 57 |
| Line is longer than 80 characters (found 139). | 61 |
| Line is longer than 80 characters (found 112). | 63 |
| Method 'setAccessionNumber' is not designed for extension - needs to be abstract, final or empty. | 69 |
| Parameter accessionNumber should be final. | 69 |
| 'accessionNumber' hides a field. | 69 |
| Line is longer than 80 characters (found 84). | 79 |
| Line is longer than 80 characters (found 83). | 80 |
| Line is longer than 80 characters (found 88). | 81 |
| Line is longer than 80 characters (found 139). | 85 |
| Line is longer than 80 characters (found 112). | 87 |
| Method 'getAccessionNumber' is not designed for extension - needs to be abstract, final or empty. | 93 |
| Line is longer than 80 characters (found 107). | 103 |
| Line is longer than 80 characters (found 91). | 107 |
| Unused @throws tag for 'IllegalArgumentException'. | 107 |
| Method 'setPropertyValue' is not designed for extension - needs to be abstract, final or empty. | 109 |
| Parameter property should be final. | 109 |
| Parameter value should be final. | 109 |
| 'if' construct must use '{}'s. | 110 |
| Line is longer than 80 characters (found 137). | 110 |
| 'if' is not followed by whitespace. | 110 |
| Method 'hasProperty' is not designed for extension - needs to be abstract, final or empty. | 122 |
| Parameter property should be final. | 122 |
| Method 'getPropertyValue' is not designed for extension - needs to be abstract, final or empty. | 134 |
| Parameter property should be final. | 134 |
| Method 'getDatabaseName' is not designed for extension - needs to be abstract, final or empty. | 145 |
uk/ac/ebi/intenz/tools/sib/sptr_enzyme/EnzymeCrossReferenceException.java
| Violation | Message | Line |
|---|---|---|
| Line has trailing spaces. | 5 |
| Missing a Javadoc comment. | 14 |
| Parameter message should be final. | 14 |
| Missing a Javadoc comment. | 18 |
| Parameter originalException should be final. | 18 |
| Line is longer than 80 characters (found 85). | 22 |
| Missing a Javadoc comment. | 22 |
| Parameter message should be final. | 22 |
| Parameter originalException should be final. | 22 |
uk/ac/ebi/intenz/tools/sib/sptr_enzyme/EnzymeEntryImpl.java
| Violation | Message | Line |
|---|---|---|
| Line is longer than 80 characters (found 90). | 11 |
| Missing a Javadoc comment. | 17 |
| Missing a Javadoc comment. | 18 |
| Missing a Javadoc comment. | 19 |
| Missing a Javadoc comment. | 20 |
| Missing a Javadoc comment. | 22 |
| Method 'getId' is not designed for extension - needs to be abstract, final or empty. | 34 |
| Missing a Javadoc comment. | 34 |
| Method 'setId' is not designed for extension - needs to be abstract, final or empty. | 38 |
| Missing a Javadoc comment. | 38 |
| Parameter id should be final. | 38 |
| 'id' hides a field. | 38 |
| Line is longer than 80 characters (found 83). | 42 |
| Method 'setEC' is not designed for extension - needs to be abstract, final or empty. | 42 |
| Missing a Javadoc comment. | 42 |
| Parameter s should be final. | 42 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 42 |
| Method 'getEC' is not designed for extension - needs to be abstract, final or empty. | 46 |
| Missing a Javadoc comment. | 46 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 46 |
| Line is longer than 80 characters (found 91). | 50 |
| Method 'setCommonName' is not designed for extension - needs to be abstract, final or empty. | 50 |
| Missing a Javadoc comment. | 50 |
| Parameter s should be final. | 50 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 50 |
| Line is longer than 80 characters (found 85). | 54 |
| Method 'getCommonName' is not designed for extension - needs to be abstract, final or empty. | 54 |
| Missing a Javadoc comment. | 54 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 54 |
| Line is longer than 80 characters (found 88). | 58 |
| Method 'addSynonym' is not designed for extension - needs to be abstract, final or empty. | 58 |
| Missing a Javadoc comment. | 58 |
| Parameter s should be final. | 58 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 58 |
| Line is longer than 80 characters (found 94). | 62 |
| Method 'removeSynonym' is not designed for extension - needs to be abstract, final or empty. | 62 |
| Missing a Javadoc comment. | 62 |
| Parameter s should be final. | 62 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 62 |
| Line is longer than 80 characters (found 85). | 66 |
| Method 'getSynonyms' is not designed for extension - needs to be abstract, final or empty. | 66 |
| Missing a Javadoc comment. | 66 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 66 |
| Line is longer than 80 characters (found 98). | 74 |
| Method 'setSynonyms' is not designed for extension - needs to be abstract, final or empty. | 74 |
| Missing a Javadoc comment. | 74 |
| Parameter synonyms should be final. | 74 |
| 'synonyms' hides a field. | 74 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 74 |
| Line is longer than 80 characters (found 89). | 80 |
| Method 'addReaction' is not designed for extension - needs to be abstract, final or empty. | 80 |
| Missing a Javadoc comment. | 80 |
| Parameter s should be final. | 80 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 80 |
| Line is longer than 80 characters (found 95). | 84 |
| Method 'removeReaction' is not designed for extension - needs to be abstract, final or empty. | 84 |
| Missing a Javadoc comment. | 84 |
| Parameter s should be final. | 84 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 84 |
| Line is longer than 80 characters (found 86). | 88 |
| Method 'getReactions' is not designed for extension - needs to be abstract, final or empty. | 88 |
| Missing a Javadoc comment. | 88 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 88 |
| Line is longer than 80 characters (found 100). | 96 |
| Method 'setReactions' is not designed for extension - needs to be abstract, final or empty. | 96 |
| Missing a Javadoc comment. | 96 |
| Parameter reactions should be final. | 96 |
| 'reactions' hides a field. | 96 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 96 |
| Line is longer than 80 characters (found 90). | 102 |
| Method 'setCofactors' is not designed for extension - needs to be abstract, final or empty. | 102 |
| Missing a Javadoc comment. | 102 |
| Parameter s should be final. | 102 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 102 |
| Line is longer than 80 characters (found 84). | 106 |
| Method 'getCofactors' is not designed for extension - needs to be abstract, final or empty. | 106 |
| Missing a Javadoc comment. | 106 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 106 |
| Line is longer than 80 characters (found 88). | 110 |
| Method 'setComment' is not designed for extension - needs to be abstract, final or empty. | 110 |
| Missing a Javadoc comment. | 110 |
| Parameter s should be final. | 110 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 110 |
| Line is longer than 80 characters (found 82). | 114 |
| Method 'getComment' is not designed for extension - needs to be abstract, final or empty. | 114 |
| Missing a Javadoc comment. | 114 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 114 |
| Line is longer than 80 characters (found 124). | 118 |
| Method 'addCrossReference' is not designed for extension - needs to be abstract, final or empty. | 118 |
| Missing a Javadoc comment. | 118 |
| Parameter sptrCrossReference should be final. | 118 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 118 |
| Line is longer than 80 characters (found 127). | 122 |
| Method 'addCrossReferences' is not designed for extension - needs to be abstract, final or empty. | 122 |
| Missing a Javadoc comment. | 122 |
| Parameter sptrCrossReference should be final. | 122 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 122 |
| Line is longer than 80 characters (found 130). | 128 |
| Method 'removeCrossReference' is not designed for extension - needs to be abstract, final or empty. | 128 |
| Missing a Javadoc comment. | 128 |
| Parameter sptrCrossReference should be final. | 128 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 128 |
| Line is longer than 80 characters (found 104). | 132 |
| Method 'getCrossReferences' is not designed for extension - needs to be abstract, final or empty. | 132 |
| Missing a Javadoc comment. | 132 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 132 |
| Line is longer than 80 characters (found 114). | 140 |
| Method 'setCrossReferences' is not designed for extension - needs to be abstract, final or empty. | 140 |
| Missing a Javadoc comment. | 140 |
| Parameter xrefs should be final. | 140 |
| 'xrefs' hides a field. | 140 |
| Redundant throws: 'UnsupportedOperationException' is unchecked exception. | 140 |
| Method 'isTransferredOrDeleted' is not designed for extension - needs to be abstract, final or empty. | 146 |
| Missing a Javadoc comment. | 146 |
| Method 'setTransferredOrDeleted' is not designed for extension - needs to be abstract, final or empty. | 150 |
| Missing a Javadoc comment. | 150 |
| Parameter transferredOrDeleted should be final. | 150 |
uk/ac/ebi/intenz/tools/sib/sptr_enzyme/EnzymeXrefFactory.java
| Violation | Message | Line |
|---|---|---|
| Using the '.*' form of import should be avoided - uk.ac.ebi.interfaces.uniref.*. | 4 |
| Using the '.*' form of import should be avoided - uk.ac.ebi.interfaces.go.*. | 11 |
| Using the '.*' form of import should be avoided - uk.ac.ebi.interfaces.interpro.*. | 12 |
| Using the '.*' form of import should be avoided - uk.ac.ebi.interfaces.integr8.*. | 16 |
| Using the '.*' form of import should be avoided - uk.ac.ebi.interfaces.citation.*. | 17 |
| Using the '.*' form of import should be avoided - uk.ac.ebi.interfaces.sptr.*. | 22 |
| Line is longer than 80 characters (found 97). | 28 |
| Line is longer than 80 characters (found 130). | 29 |
| Method 'newSPTREntryInstance' is not designed for extension - needs to be abstract, final or empty. | 36 |
| Missing a Javadoc comment. | 36 |
| Parameter entryType should be final. | 36 |
| Method 'newSPTREntryInstance' is not designed for extension - needs to be abstract, final or empty. | 40 |
| Missing a Javadoc comment. | 40 |
| Method 'copySPTREntryInstance' is not designed for extension - needs to be abstract, final or empty. | 44 |
| Missing a Javadoc comment. | 44 |
| Parameter entry should be final. | 44 |
| Method 'newEnzymeEntryInstance' is not designed for extension - needs to be abstract, final or empty. | 48 |
| Missing a Javadoc comment. | 48 |
| Line is longer than 80 characters (found 86). | 52 |
| Method 'copyEnzymeEntryInstance' is not designed for extension - needs to be abstract, final or empty. | 52 |
| Missing a Javadoc comment. | 52 |
| Parameter entry should be final. | 52 |
| Line is longer than 80 characters (found 81). | 56 |
| Method 'newFeatureInstance' is not designed for extension - needs to be abstract, final or empty. | 56 |
| Missing a Javadoc comment. | 56 |
| Parameter featureType should be final. | 56 |
| Method 'copyFeatureInstance' is not designed for extension - needs to be abstract, final or empty. | 60 |
| Missing a Javadoc comment. | 60 |
| Parameter feature should be final. | 60 |
| Method 'newFeatureLocationInstance' is not designed for extension - needs to be abstract, final or empty. | 64 |
| Missing a Javadoc comment. | 64 |
| Line is longer than 80 characters (found 104). | 68 |
| Method 'copyFeatureLocationInstance' is not designed for extension - needs to be abstract, final or empty. | 68 |
| Missing a Javadoc comment. | 68 |
| Parameter location should be final. | 68 |
| Method 'newAuthorInstance' is not designed for extension - needs to be abstract, final or empty. | 72 |
| Missing a Javadoc comment. | 72 |
| Method 'copyAuthorInstance' is not designed for extension - needs to be abstract, final or empty. | 76 |
| Missing a Javadoc comment. | 76 |
| Parameter author should be final. | 76 |
| Method 'newBookInstance' is not designed for extension - needs to be abstract, final or empty. | 80 |
| Missing a Javadoc comment. | 80 |
| Method 'copyBookInstance' is not designed for extension - needs to be abstract, final or empty. | 84 |
| Missing a Javadoc comment. | 84 |
| Parameter book should be final. | 84 |
| Line is longer than 80 characters (found 84). | 88 |
| Method 'newElectronicArticleInstance' is not designed for extension - needs to be abstract, final or empty. | 88 |
| Missing a Javadoc comment. | 88 |
| Line is longer than 80 characters (found 120). | 92 |
| Method 'copyElectronicArticleInstance' is not designed for extension - needs to be abstract, final or empty. | 92 |
| Missing a Javadoc comment. | 92 |
| Parameter electronicArticle should be final. | 92 |
| Method 'newJournalArticleInstance' is not designed for extension - needs to be abstract, final or empty. | 96 |
| Missing a Javadoc comment. | 96 |
| Line is longer than 80 characters (found 108). | 100 |
| Method 'copyJournalArticleInstance' is not designed for extension - needs to be abstract, final or empty. | 100 |
| Missing a Javadoc comment. | 100 |
| Parameter journalArticle should be final. | 100 |
| Method 'newPatentInstance' is not designed for extension - needs to be abstract, final or empty. | 104 |
| Missing a Javadoc comment. | 104 |
| Method 'copyPatentInstance' is not designed for extension - needs to be abstract, final or empty. | 108 |
| Missing a Javadoc comment. | 108 |
| Parameter patent should be final. | 108 |
| Method 'newSubmissionInstance' is not designed for extension - needs to be abstract, final or empty. | 112 |
| Missing a Javadoc comment. | 112 |
| Line is longer than 80 characters (found 92). | 116 |
| Method 'copySubmissionInstance' is not designed for extension - needs to be abstract, final or empty. | 116 |
| Missing a Javadoc comment. | 116 |
| Parameter submission should be final. | 116 |
| Method 'newThesisInstance' is not designed for extension - needs to be abstract, final or empty. | 120 |
| Missing a Javadoc comment. | 120 |
| Method 'copyThesisInstance' is not designed for extension - needs to be abstract, final or empty. | 124 |
| Missing a Javadoc comment. | 124 |
| Parameter thesis should be final. | 124 |
| Line is longer than 80 characters (found 96). | 128 |
| Method 'newUnpublishedObservationsInstance' is not designed for extension - needs to be abstract, final or empty. | 128 |
| Missing a Javadoc comment. | 128 |
| Line is longer than 80 characters (found 144). | 132 |
| Method 'copyUnpublishedObservationsInstance' is not designed for extension - needs to be abstract, final or empty. | 132 |
| Missing a Javadoc comment. | 132 |
| Parameter unpublishedObservations should be final. | 132 |
| Line is longer than 80 characters (found 86). | 136 |
| Method 'newUnpublishedResultsInstance' is not designed for extension - needs to be abstract, final or empty. | 136 |
| Missing a Javadoc comment. | 136 |
| Line is longer than 80 characters (found 124). | 140 |
| Method 'copyUnpublishedResultsInstance' is not designed for extension - needs to be abstract, final or empty. | 140 |
| Missing a Javadoc comment. | 140 |
| Parameter unpublishedResults should be final. | 140 |
| Method 'newSPTRCommentInstance' is not designed for extension - needs to be abstract, final or empty. | 144 |
| Missing a Javadoc comment. | 144 |
| Parameter type should be final. | 144 |
| Line is longer than 80 characters (found 92). | 148 |
| Method 'copySPTRCommentInstance' is not designed for extension - needs to be abstract, final or empty. | 148 |
| Missing a Javadoc comment. | 148 |
| Parameter sptrComment should be final. | 148 |
| Method 'newIsoformInstance' is not designed for extension - needs to be abstract, final or empty. | 152 |
| Missing a Javadoc comment. | 152 |
| Method 'copyIsoformInstance' is not designed for extension - needs to be abstract, final or empty. | 156 |
| Missing a Javadoc comment. | 156 |
| Parameter isoform should be final. | 156 |
| Line is longer than 80 characters (found 103). | 165 |
| Line is longer than 80 characters (found 87). | 167 |
| Method 'newEnzymeCrossReference' is not designed for extension - needs to be abstract, final or empty. | 167 |
| Parameter type should be final. | 167 |
| Expected @param tag for 'type'. | 167 |
| 'if' construct must use '{}'s. | 169 |
| 'if' is not followed by whitespace. | 169 |
| '&&' should be on a new line. | 169 |
| '&&' should be on a new line. | 170 |
| Line is longer than 80 characters (found 132). | 171 |
| Line is longer than 80 characters (found 85). | 176 |
| Method 'newSPTRCrossReference' is not designed for extension - needs to be abstract, final or empty. | 176 |
| Missing a Javadoc comment. | 176 |
| Parameter type should be final. | 176 |
| Line is longer than 80 characters (found 112). | 180 |
| Method 'copySPTRCrossReference' is not designed for extension - needs to be abstract, final or empty. | 180 |
| Missing a Javadoc comment. | 180 |
| Parameter sptrCrossReference should be final. | 180 |
| Line is longer than 80 characters (found 103). | 184 |
| Method 'copyProteomeEntryInstance' is not designed for extension - needs to be abstract, final or empty. | 184 |
| Missing a Javadoc comment. | 184 |
| Parameter proteomeEntry should be final. | 184 |
| Line is longer than 80 characters (found 95). | 185 |
| Method 'newSPINSubmissionInstance' is not designed for extension - needs to be abstract, final or empty. | 188 |
| Missing a Javadoc comment. | 188 |
| Line is longer than 80 characters (found 95). | 189 |
| Line is longer than 80 characters (found 108). | 192 |
| Method 'copySPINSubmissionInstance' is not designed for extension - needs to be abstract, final or empty. | 192 |
| Missing a Javadoc comment. | 192 |
| Parameter spinSubmission should be final. | 192 |
| Line is longer than 80 characters (found 95). | 193 |
| Line is longer than 80 characters (found 90). | 196 |
| Method 'newSPTRCrossReferenceInstance' is not designed for extension - needs to be abstract, final or empty. | 196 |
| Missing a Javadoc comment. | 196 |
| Parameter s should be final. | 196 |
| Line is longer than 80 characters (found 95). | 197 |
| Line is longer than 80 characters (found 120). | 200 |
| Method 'copySPTRCrossReferenceInstance' is not designed for extension - needs to be abstract, final or empty. | 200 |
| Missing a Javadoc comment. | 200 |
| Parameter sptrCrossReference should be final. | 200 |
| Line is longer than 80 characters (found 95). | 201 |
| Method 'newPythiaEntryInstance' is not designed for extension - needs to be abstract, final or empty. | 204 |
| Missing a Javadoc comment. | 204 |
| Parameter i should be final. | 204 |
| Line is longer than 80 characters (found 95). | 205 |
| Line is longer than 80 characters (found 94). | 208 |
| Method 'copyPythiaEntryInstance' is not designed for extension - needs to be abstract, final or empty. | 208 |
| Missing a Javadoc comment. | 208 |
| Parameter pythiaEntry should be final. | 208 |
| Line is longer than 80 characters (found 95). | 209 |
| Line is longer than 80 characters (found 84). | 212 |
| Method 'newPredictiveInstance' is not designed for extension - needs to be abstract, final or empty. | 212 |
| Missing a Javadoc comment. | 212 |
| Parameter s should be final. | 212 |
| Line is longer than 80 characters (found 95). | 213 |
| Line is longer than 80 characters (found 114). | 216 |
| Method 'copyPredictiveInstance' is not designed for extension - needs to be abstract, final or empty. | 216 |
| Missing a Javadoc comment. | 216 |
| Parameter predictiveInstance should be final. | 216 |
| Line is longer than 80 characters (found 95). | 217 |
| Line is longer than 80 characters (found 99). | 220 |
| Method 'newInterProProteinData' is not designed for extension - needs to be abstract, final or empty. | 220 |
| Missing a Javadoc comment. | 220 |
| Parameter sptrEntry should be final. | 220 |
| Line is longer than 80 characters (found 95). | 221 |
| Line is longer than 80 characters (found 120). | 224 |
| Method 'copyInterProProteinData' is not designed for extension - needs to be abstract, final or empty. | 224 |
| Missing a Javadoc comment. | 224 |
| Parameter interProProteinData should be final. | 224 |
| Line is longer than 80 characters (found 95). | 225 |
| Line is longer than 80 characters (found 103). | 228 |
| Method 'newInterProStructure' is not designed for extension - needs to be abstract, final or empty. | 228 |
| Missing a Javadoc comment. | 228 |
| Parameter interProEntry should be final. | 228 |
| Line is longer than 80 characters (found 95). | 229 |
| Line is longer than 80 characters (found 112). | 232 |
| Method 'copyInterProStructure' is not designed for extension - needs to be abstract, final or empty. | 232 |
| Missing a Javadoc comment. | 232 |
| Parameter interProStructure should be final. | 232 |
| Line is longer than 80 characters (found 95). | 233 |
| Method 'newInterProEntry' is not designed for extension - needs to be abstract, final or empty. | 236 |
| Missing a Javadoc comment. | 236 |
| Line is longer than 80 characters (found 95). | 237 |
| Line is longer than 80 characters (found 96). | 240 |
| Method 'copyInterProEntry' is not designed for extension - needs to be abstract, final or empty. | 240 |
| Missing a Javadoc comment. | 240 |
| Parameter interProEntry should be final. | 240 |
| Line is longer than 80 characters (found 95). | 241 |
| Method 'newSignatureDBHit' is not designed for extension - needs to be abstract, final or empty. | 244 |
| Missing a Javadoc comment. | 244 |
| Line is longer than 80 characters (found 95). | 245 |
| Line is longer than 80 characters (found 99). | 248 |
| Method 'copySignaturDBHit' is not designed for extension - needs to be abstract, final or empty. | 248 |
| Missing a Javadoc comment. | 248 |
| Parameter signatureDBHit should be final. | 248 |
| Line is longer than 80 characters (found 95). | 249 |
| Method 'newSignatureDBEntry' is not designed for extension - needs to be abstract, final or empty. | 252 |
| Missing a Javadoc comment. | 252 |
| Parameter i should be final. | 252 |
| Line is longer than 80 characters (found 95). | 253 |
| Line is longer than 80 characters (found 108). | 256 |
| Method 'copySignatureDBEntry' is not designed for extension - needs to be abstract, final or empty. | 256 |
| Missing a Javadoc comment. | 256 |
| Parameter signatureDBEntry should be final. | 256 |
| Line is longer than 80 characters (found 95). | 257 |
| Method 'newAnnotationInstance' is not designed for extension - needs to be abstract, final or empty. | 260 |
| Missing a Javadoc comment. | 260 |
| '(' is preceded with whitespace. | 260 |
| Line is longer than 80 characters (found 97). | 261 |
| Line is longer than 80 characters (found 94). | 264 |
| Method 'copyAnnotationInstance' is not designed for extension - needs to be abstract, final or empty. | 264 |
| Missing a Javadoc comment. | 264 |
| '(' is preceded with whitespace. | 264 |
| Parameter annotation should be final. | 264 |
| Line is longer than 80 characters (found 97). | 265 |
| Line is longer than 80 characters (found 104). | 268 |
| Method 'newInterProCrossReferenceInstance' is not designed for extension - needs to be abstract, final or empty. | 268 |
| Missing a Javadoc comment. | 268 |
| '(' is preceded with whitespace. | 268 |
| Parameter s should be final. | 268 |
| Line is longer than 80 characters (found 97). | 269 |
| Line is longer than 80 characters (found 142). | 272 |
| Method 'copyInterProCrossReferenceInstance' is not designed for extension - needs to be abstract, final or empty. | 272 |
| Missing a Javadoc comment. | 272 |
| '(' is preceded with whitespace. | 272 |
| Parameter interProCrossReference should be final. | 272 |
| Line is longer than 80 characters (found 97). | 273 |
| Method 'newGOTerm' is not designed for extension - needs to be abstract, final or empty. | 276 |
| Missing a Javadoc comment. | 276 |
| Line is longer than 80 characters (found 95). | 277 |
| Method 'copyGOTerm' is not designed for extension - needs to be abstract, final or empty. | 280 |
| Missing a Javadoc comment. | 280 |
| Parameter goTerm should be final. | 280 |
| Line is longer than 80 characters (found 95). | 281 |
| Method 'newGOEvidence' is not designed for extension - needs to be abstract, final or empty. | 284 |
| Missing a Javadoc comment. | 284 |
| Line is longer than 80 characters (found 95). | 285 |
| Method 'copyGOEvidence' is not designed for extension - needs to be abstract, final or empty. | 288 |
| Missing a Javadoc comment. | 288 |
| Parameter goEvidence should be final. | 288 |
| Line is longer than 80 characters (found 95). | 289 |
| Line is longer than 80 characters (found 81). | 292 |
| Method 'newGOProteinData' is not designed for extension - needs to be abstract, final or empty. | 292 |
| Missing a Javadoc comment. | 292 |
| Parameter sptrEntry should be final. | 292 |
| Line is longer than 80 characters (found 95). | 293 |
| Line is longer than 80 characters (found 90). | 296 |
| Method 'copyGOProteinData' is not designed for extension - needs to be abstract, final or empty. | 296 |
| Missing a Javadoc comment. | 296 |
| Parameter goProteinData should be final. | 296 |
| Line is longer than 80 characters (found 95). | 297 |
| Method 'newGOStructure' is not designed for extension - needs to be abstract, final or empty. | 300 |
| Missing a Javadoc comment. | 300 |
| Line is longer than 80 characters (found 95). | 301 |
| Line is longer than 80 characters (found 82). | 304 |
| Method 'copyGOStructure' is not designed for extension - needs to be abstract, final or empty. | 304 |
| Missing a Javadoc comment. | 304 |
| Parameter goStructure should be final. | 304 |
| Line is longer than 80 characters (found 95). | 305 |
| Method 'newCluSTrEntry' is not designed for extension - needs to be abstract, final or empty. | 308 |
| Missing a Javadoc comment. | 308 |
| Line is longer than 80 characters (found 95). | 309 |
| Line is longer than 80 characters (found 86). | 312 |
| Method 'copyCluSTrEntry' is not designed for extension - needs to be abstract, final or empty. | 312 |
| Missing a Javadoc comment. | 312 |
| Parameter cluSTrEntry should be final. | 312 |
| Line is longer than 80 characters (found 95). | 313 |
| Method 'newUniParcEntry' is not designed for extension - needs to be abstract, final or empty. | 316 |
| Missing a Javadoc comment. | 316 |
| Line is longer than 80 characters (found 95). | 317 |
| Method 'newUniParcEntry' is not designed for extension - needs to be abstract, final or empty. | 320 |
| Missing a Javadoc comment. | 320 |
| Parameter sptrEntry should be final. | 320 |
| Parameter s should be final. | 320 |
| Line is longer than 80 characters (found 124). | 321 |
| Parameter uniParcCrossReferenceMetaData should be final. | 321 |
| Line is longer than 80 characters (found 95). | 322 |
| Line is longer than 80 characters (found 91). | 325 |
| Method 'copyUniParcEntry' is not designed for extension - needs to be abstract, final or empty. | 325 |
| Missing a Javadoc comment. | 325 |
| Parameter uniParcEntry should be final. | 325 |
| Line is longer than 80 characters (found 95). | 326 |
| Line is longer than 80 characters (found 91). | 329 |
| Method 'newUniParcCrossReference' is not designed for extension - needs to be abstract, final or empty. | 329 |
| Missing a Javadoc comment. | 329 |
| Parameter s should be final. | 329 |
| Line is longer than 80 characters (found 95). | 330 |
| Line is longer than 80 characters (found 127). | 333 |
| Method 'copyUniParcCrossReference' is not designed for extension - needs to be abstract, final or empty. | 333 |
| Missing a Javadoc comment. | 333 |
| Parameter uniParcCrossReference should be final. | 333 |
| Line is longer than 80 characters (found 95). | 334 |
| Line is longer than 80 characters (found 99). | 337 |
| Method 'newUniParcCrossReferenceMetaData' is not designed for extension - needs to be abstract, final or empty. | 337 |
| Missing a Javadoc comment. | 337 |
| Line is longer than 80 characters (found 95). | 338 |
| Method 'copyUniParcCrossReferenceMetaData' is not designed for extension - needs to be abstract, final or empty. | 341 |
| Missing a Javadoc comment. | 341 |
| Line is longer than 80 characters (found 96). | 342 |
| Parameter uniParcCrossReferenceMetaData should be final. | 342 |
| Line is longer than 80 characters (found 95). | 343 |
| Method 'newUniRef100Entry' is not designed for extension - needs to be abstract, final or empty. | 346 |
| Missing a Javadoc comment. | 346 |
| Line is longer than 80 characters (found 95). | 347 |
| Line is longer than 80 characters (found 87). | 350 |
| Method 'newUniRef100Entry' is not designed for extension - needs to be abstract, final or empty. | 350 |
| Missing a Javadoc comment. | 350 |
| Parameter sptrEntry should be final. | 350 |
| Line is longer than 80 characters (found 95). | 351 |
| Method 'newUniRef90Entry' is not designed for extension - needs to be abstract, final or empty. | 354 |
| Missing a Javadoc comment. | 354 |
| Line is longer than 80 characters (found 95). | 355 |
| Line is longer than 80 characters (found 85). | 358 |
| Method 'newUniRef90Entry' is not designed for extension - needs to be abstract, final or empty. | 358 |
| Missing a Javadoc comment. | 358 |
| Parameter sptrEntry should be final. | 358 |
| Line is longer than 80 characters (found 95). | 359 |
| Method 'newUniRef50Entry' is not designed for extension - needs to be abstract, final or empty. | 362 |
| Missing a Javadoc comment. | 362 |
| Line is longer than 80 characters (found 95). | 363 |
| Line is longer than 80 characters (found 85). | 366 |
| Method 'newUniRef50Entry' is not designed for extension - needs to be abstract, final or empty. | 366 |
| Missing a Javadoc comment. | 366 |
| Parameter sptrEntry should be final. | 366 |
| Line is longer than 80 characters (found 95). | 367 |
| Method 'newClusterMember' is not designed for extension - needs to be abstract, final or empty. | 370 |
| Missing a Javadoc comment. | 370 |
| Parameter s should be final. | 370 |
| Line is longer than 80 characters (found 95). | 371 |
| Method 'newGeneInstance' is not designed for extension - needs to be abstract, final or empty. | 374 |
| Missing a Javadoc comment. | 374 |
| Line is longer than 80 characters (found 95). | 375 |
| Method 'copyGeneInstance' is not designed for extension - needs to be abstract, final or empty. | 378 |
| Missing a Javadoc comment. | 378 |
| Parameter gene should be final. | 378 |
| Line is longer than 80 characters (found 95). | 379 |
| Line is longer than 80 characters (found 108). | 382 |
| Method 'newIntegr8SPTREntryInstance' is not designed for extension - needs to be abstract, final or empty. | 382 |
| Missing a Javadoc comment. | 382 |
| Parameter i should be final. | 382 |
| Line is longer than 80 characters (found 95). | 383 |
| Line is longer than 80 characters (found 122). | 386 |
| Method 'newIntegr8SPTREntryInstance' is not designed for extension - needs to be abstract, final or empty. | 386 |
| Missing a Javadoc comment. | 386 |
| Parameter sptrEntry should be final. | 386 |
| Line is longer than 80 characters (found 95). | 387 |
| Line is longer than 80 characters (found 152). | 390 |
| Method 'copyIntegr8SPTREntryInstance' is not designed for extension - needs to be abstract, final or empty. | 390 |
| Missing a Javadoc comment. | 390 |
| Parameter sptrEntry should be final. | 390 |
| Line is longer than 80 characters (found 95). | 391 |
| Line is longer than 80 characters (found 93). | 394 |
| Method 'newIntegr8GeneInstance' is not designed for extension - needs to be abstract, final or empty. | 394 |
| Missing a Javadoc comment. | 394 |
| Line is longer than 80 characters (found 95). | 395 |
| Line is longer than 80 characters (found 103). | 398 |
| Method 'copyIntegr8GeneInstance' is not designed for extension - needs to be abstract, final or empty. | 398 |
| Missing a Javadoc comment. | 398 |
| Parameter gene should be final. | 398 |
| Line is longer than 80 characters (found 95). | 399 |
| Line is longer than 80 characters (found 132). | 402 |
| Method 'copyIntegr8GeneInstance' is not designed for extension - needs to be abstract, final or empty. | 402 |
| Missing a Javadoc comment. | 402 |
| Parameter gene should be final. | 402 |
| Line is longer than 80 characters (found 95). | 403 |
| Method 'newProteomeEntryInstance' is not designed for extension - needs to be abstract, final or empty. | 406 |
| Missing a Javadoc comment. | 406 |
| Line is longer than 80 characters (found 95). | 407 |
| Method 'newAbsorptionInstance' is not designed for extension - needs to be abstract, final or empty. | 410 |
| Missing a Javadoc comment. | 410 |
| Line is longer than 80 characters (found 95). | 411 |
| Line is longer than 80 characters (found 88). | 414 |
| Method 'copyAbsorptionInstance' is not designed for extension - needs to be abstract, final or empty. | 414 |
| Missing a Javadoc comment. | 414 |
| Parameter absorption should be final. | 414 |
| Line is longer than 80 characters (found 95). | 415 |
| Method 'newKineticParameterInstance' is not designed for extension - needs to be abstract, final or empty. | 418 |
| Missing a Javadoc comment. | 418 |
| Line is longer than 80 characters (found 95). | 419 |
| Line is longer than 80 characters (found 112). | 422 |
| Method 'copyKineticParameterInstance' is not designed for extension - needs to be abstract, final or empty. | 422 |
| Missing a Javadoc comment. | 422 |
| Parameter kineticParameter should be final. | 422 |
| Line is longer than 80 characters (found 95). | 423 |
| Method 'newMaximumVelocityInstance' is not designed for extension - needs to be abstract, final or empty. | 426 |
| Missing a Javadoc comment. | 426 |
| Line is longer than 80 characters (found 95). | 427 |
| Line is longer than 80 characters (found 108). | 430 |
| Method 'copyMaximumVelocityInstance' is not designed for extension - needs to be abstract, final or empty. | 430 |
| Missing a Javadoc comment. | 430 |
| Parameter maximumVelocity should be final. | 430 |
| Line is longer than 80 characters (found 95). | 431 |
| Method 'newMichaelisConstantInstance' is not designed for extension - needs to be abstract, final or empty. | 434 |
| Missing a Javadoc comment. | 434 |
| Line is longer than 80 characters (found 95). | 435 |
| Line is longer than 80 characters (found 116). | 438 |
| Method 'copyMichaelisConstantInstance' is not designed for extension - needs to be abstract, final or empty. | 438 |
| Missing a Javadoc comment. | 438 |
| Parameter michaelisConstant should be final. | 438 |
| Line is longer than 80 characters (found 95). | 439 |
| Line is longer than 80 characters (found 88). | 442 |
| Method 'newMassSpectrometryRangeInstance' is not designed for extension - needs to be abstract, final or empty. | 442 |
| Missing a Javadoc comment. | 442 |
| Line is longer than 80 characters (found 95). | 443 |
| Line is longer than 80 characters (found 132). | 446 |
| Method 'copyMassSpectrometryRangeInstance' is not designed for extension - needs to be abstract, final or empty. | 446 |
| Missing a Javadoc comment. | 446 |
| Parameter massSpectrometryRange should be final. | 446 |
| Line is longer than 80 characters (found 95). | 447 |
uk/ac/ebi/intenz/tools/sib/validator/EnzymeEntryValidator.java
| Violation | Message | Line |
|---|---|---|
| Missing package-info.java file. | 0 |
| Utility classes should not have a public or default constructor. | 20 |
| Missing a Javadoc comment. | 22 |
| Line contains a tab character. | 23 |
| Line is longer than 80 characters (found 89). | 25 |
| Missing a Javadoc comment. | 25 |
| Missing a Javadoc comment. | 26 |
| Missing a Javadoc comment. | 27 |
| Missing a Javadoc comment. | 28 |
| Line is longer than 80 characters (found 112). | 29 |
| Missing a Javadoc comment. | 29 |
| Line is longer than 80 characters (found 85). | 30 |
| Missing a Javadoc comment. | 30 |
| '+' should be on a new line. | 30 |
| Line is longer than 80 characters (found 103). | 31 |
| Line is longer than 80 characters (found 85). | 32 |
| Missing a Javadoc comment. | 32 |
| '+' should be on a new line. | 32 |
| Line is longer than 80 characters (found 85). | 33 |
| '+' should be on a new line. | 33 |
| Line is longer than 80 characters (found 105). | 34 |
| Line is longer than 80 characters (found 81). | 35 |
| Missing a Javadoc comment. | 35 |
| Line is longer than 80 characters (found 83). | 36 |
| Missing a Javadoc comment. | 36 |
| Line is longer than 80 characters (found 107). | 37 |
| Missing a Javadoc comment. | 37 |
| Line is longer than 80 characters (found 107). | 38 |
| Missing a Javadoc comment. | 38 |
| Line is longer than 80 characters (found 107). | 39 |
| Missing a Javadoc comment. | 39 |
| Line is longer than 80 characters (found 86). | 41 |
| Missing a Javadoc comment. | 41 |
| Parameter entry should be final. | 41 |
| 'if' construct must use '{}'s. | 42 |
| Line is longer than 80 characters (found 93). | 42 |
| 'if' construct must use '{}'s. | 43 |
| Line is longer than 80 characters (found 96). | 43 |
| Name 'CCLineStringBuffer' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 47 |
| Name 'CCLinesProcessed' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 48 |
| 'if' construct must use '{}'s. | 51 |
| Line is longer than 80 characters (found 92). | 52 |
| 'if' construct must use '{}'s. | 57 |
| '&&' should be on a new line. | 57 |
| Line is longer than 80 characters (found 104). | 59 |
| 'if' construct must use '{}'s. | 61 |
| '&&' should be on a new line. | 61 |
| Line is longer than 80 characters (found 85). | 62 |
| Line is longer than 80 characters (found 100). | 63 |
| 'if' construct must use '{}'s. | 65 |
| '&&' should be on a new line. | 65 |
| Line is longer than 80 characters (found 85). | 66 |
| Line is longer than 80 characters (found 100). | 67 |
| 'if' construct must use '{}'s. | 70 |
| '&&' should be on a new line. | 70 |
| Line is longer than 80 characters (found 86). | 71 |
| Line is longer than 80 characters (found 102). | 72 |
| 'if' construct must use '{}'s. | 74 |
| '&&' should be on a new line. | 74 |
| Line is longer than 80 characters (found 81). | 75 |
| Line is longer than 80 characters (found 102). | 76 |
| 'if' construct must use '{}'s. | 79 |
| '&&' should be on a new line. | 79 |
| Line is longer than 80 characters (found 85). | 80 |
| Line is longer than 80 characters (found 100). | 81 |
| 'if' construct must use '{}'s. | 87 |
| Line is longer than 80 characters (found 91). | 89 |
| Line is longer than 80 characters (found 113). | 90 |
| 'if' construct must use '{}'s. | 91 |
| Line is longer than 80 characters (found 92). | 91 |
| '&&' should be on a new line. | 91 |
| Line is longer than 80 characters (found 89). | 92 |
| '&&' should be on a new line. | 92 |
| Line is longer than 80 characters (found 145). | 93 |
| Line is longer than 80 characters (found 120). | 94 |
| Line is longer than 80 characters (found 96). | 95 |
| Line is longer than 80 characters (found 110). | 96 |
| 'if' construct must use '{}'s. | 99 |
| Line is longer than 80 characters (found 90). | 99 |
| '&&' should be on a new line. | 99 |
| Line is longer than 80 characters (found 87). | 100 |
| '&&' should be on a new line. | 100 |
| Line is longer than 80 characters (found 87). | 101 |
| Line is longer than 80 characters (found 118). | 102 |
| 'if' construct must use '{}'s. | 108 |
| '&&' should be on a new line. | 108 |
| Line is longer than 80 characters (found 100). | 110 |
| 'if' construct must use '{}'s. | 112 |
| '&&' should be on a new line. | 112 |
| Line is longer than 80 characters (found 100). | 114 |
| 'if' construct must use '{}'s. | 119 |
| Line is longer than 80 characters (found 89). | 119 |
| Line is longer than 80 characters (found 106). | 120 |
| 'if' construct must use '{}'s. | 123 |
| Line is longer than 80 characters (found 89). | 123 |
| Line is longer than 80 characters (found 106). | 124 |
| '3' is a magic number. | 126 |
| 'if' construct must use '{}'s. | 127 |
| Line is longer than 80 characters (found 89). | 127 |
| Line is longer than 80 characters (found 106). | 128 |
| Line is longer than 80 characters (found 104). | 131 |
| 'if' construct must use '{}'s. | 140 |
| Line is longer than 80 characters (found 86). | 160 |
| Parameter line should be final. | 162 |
| Parameter entry should be final. | 162 |
| Name 'CALinePattern' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 165 |
| Name 'CALinePatternMatcher' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 166 |
| 'if' construct must use '{}'s. | 169 |
| 'if' construct must use '{}'s. | 170 |
| Parameter DRLineContent should be final. | 181 |
| Name 'DRLineContent' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 181 |
| Line is longer than 80 characters (found 81). | 182 |
| Name 'DRXrefPattern' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 183 |
| Name 'DRXrefPatternMatcher' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 184 |
uk/ac/ebi/intenz/tools/sib/writer/CC_LineFormatter.java
| Violation | Message | Line |
|---|---|---|
| Line is longer than 80 characters (found 85). | 9 |
| Line is longer than 80 characters (found 113). | 11 |
| Line is longer than 80 characters (found 116). | 12 |
| Name 'CC_LineFormatter' must match pattern '^[A-Z][a-zA-Z0-9]*$'. | 22 |
| Line is longer than 80 characters (found 105). | 24 |
| Line is longer than 80 characters (found 82). | 29 |
| Unused @throws tag for 'NullPointerException'. | 30 |
| Line is longer than 80 characters (found 102). | 31 |
| Unused @throws tag for 'IllegalArgumentException'. | 31 |
| Line is longer than 80 characters (found 97). | 33 |
| Method 'formatLines' is not designed for extension - needs to be abstract, final or empty. | 33 |
| Parameter text should be final. | 33 |
| Parameter lineType should be final. | 33 |
| 'if' construct must use '{}'s. | 34 |
| 'if' construct must use '{}'s. | 35 |
| Line is longer than 80 characters (found 93). | 37 |
| Name 'CCContent' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 39 |
| Line is longer than 80 characters (found 89). | 40 |
| 'if' construct must use '{}'s. | 48 |
| Line is longer than 80 characters (found 101). | 49 |
| Line is longer than 80 characters (found 117). | 60 |
| Line is longer than 80 characters (found 96). | 62 |
| Line is longer than 80 characters (found 97). | 64 |
| Parameter text should be final. | 64 |
| Parameter addIndent should be final. | 64 |
| Line is longer than 80 characters (found 84). | 68 |
| '4' is a magic number. | 68 |
| Line is longer than 80 characters (found 82). | 85 |
| 'if' construct must use '{}'s. | 88 |
| Line is longer than 80 characters (found 92). | 89 |
| Line is longer than 80 characters (found 95). | 92 |
| Line is longer than 80 characters (found 113). | 95 |
| Line is longer than 80 characters (found 93). | 99 |
| Line is longer than 80 characters (found 84). | 103 |
| 'if' construct must use '{}'s. | 106 |
| Line is longer than 80 characters (found 83). | 106 |
| 'if' construct must use '{}'s. | 107 |
| Line is longer than 80 characters (found 87). | 121 |
| Method 'getCommentSentences' is not designed for extension - needs to be abstract, final or empty. | 138 |
| Parameter commentText should be final. | 138 |
| Line is longer than 80 characters (found 86). | 142 |
| Line is longer than 80 characters (found 99). | 166 |
| '{' is followed by whitespace. | 178 |
| Line is longer than 80 characters (found 120). | 192 |
| Line is longer than 80 characters (found 105). | 200 |
| Line is longer than 80 characters (found 84). | 212 |
| 'if' construct must use '{}'s. | 213 |
| Line is longer than 80 characters (found 85). | 213 |
| 'if' construct must use '{}'s. | 215 |
| 'else' construct must use '{}'s. | 217 |
| Line is longer than 80 characters (found 95). | 218 |
| 'if' construct must use '{}'s. | 231 |
| Line is longer than 80 characters (found 101). | 231 |
| Line is longer than 80 characters (found 106). | 240 |
| Parameter sentences should be final. | 242 |
| 'else' construct must use '{}'s. | 255 |
| Parameter line should be final. | 268 |
| Line is longer than 80 characters (found 103). | 273 |
uk/ac/ebi/intenz/tools/sib/writer/DefaultLineFormatter.java
| Violation | Message | Line |
|---|---|---|
| Line is longer than 80 characters (found 94). | 6 |
| Line is longer than 80 characters (found 111). | 13 |
| Line is longer than 80 characters (found 92). | 19 |
| Unused @throws tag for 'NullPointerException'. | 20 |
| Line is longer than 80 characters (found 97). | 22 |
| Method 'formatLines' is not designed for extension - needs to be abstract, final or empty. | 22 |
| Parameter text should be final. | 22 |
| Parameter lineType should be final. | 22 |
| 'if' construct must use '{}'s. | 23 |
| 'if' construct must use '{}'s. | 28 |
| 'if' is not followed by whitespace. | 28 |
| '&&' should be on a new line. | 28 |
| Line has trailing spaces. | 29 |
| Line is longer than 80 characters (found 94). | 29 |
| '||' should be on a new line. | 29 |
| '&&' should be on a new line. | 30 |
| Line is longer than 80 characters (found 95). | 46 |
| Line is longer than 80 characters (found 116). | 47 |
| 'if' construct must use '{}'s. | 48 |
| Line is longer than 80 characters (found 112). | 48 |
| Line is longer than 80 characters (found 104). | 49 |
| Line is longer than 80 characters (found 121). | 50 |
| 'for' construct must use '{}'s. | 51 |
| Line is longer than 80 characters (found 105). | 51 |
| Line is longer than 80 characters (found 103). | 53 |
| 'if' construct must use '{}'s. | 59 |
| Line is longer than 80 characters (found 110). | 59 |
| 'for' construct must use '{}'s. | 60 |
uk/ac/ebi/intenz/tools/sib/writer/EnzymeFlatFileWriteException.java
| Violation | Message | Line |
|---|---|---|
| Line is longer than 80 characters (found 97). | 6 |
| Parameter e should be final. | 17 |
| Line is longer than 80 characters (found 93). | 22 |
| Parameter message should be final. | 27 |
| Parameter e should be final. | 27 |
| Parameter message should be final. | 36 |
uk/ac/ebi/intenz/tools/sib/writer/EnzymeFlatFileWriter.java
| Violation | Message | Line |
|---|---|---|
| Line is longer than 80 characters (found 98). | 29 |
| Line is longer than 80 characters (found 82). | 32 |
| Line is longer than 80 characters (found 84). | 38 |
| Line is longer than 80 characters (found 84). | 42 |
| Line is longer than 80 characters (found 84). | 58 |
| Line is longer than 80 characters (found 83). | 59 |
| Line is longer than 80 characters (found 83). | 60 |
| Line is longer than 80 characters (found 84). | 62 |
| Line is longer than 80 characters (found 85). | 78 |
| Class EnzymeFlatFileWriter should be declared as final. | 98 |
| Missing a Javadoc comment. | 100 |
| Line contains a tab character. | 101 |
| Line has trailing spaces. | 102 |
| Line contains a tab character. | 110 |
| Line is longer than 80 characters (found 119). | 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 contains a tab character. | 115 |
| Line contains a tab character. | 116 |
| Line contains a tab character. | 117 |
| 'if' construct must use '{}'s. | 118 |
| Line contains a tab character. | 118 |
| Line contains a tab character. | 119 |
| '{' is not preceded with whitespace. | 119 |
| Must have at least one statement. | 119 |
| '{' is not followed by whitespace. | 119 |
| '}' is not preceded with whitespace. | 119 |
| Line contains a tab character. | 120 |
| Expected an @return tag. | 140 |
| Parameter enzyme should be final. | 140 |
| Expected @param tag for 'enzyme'. | 140 |
| Expected @throws tag for 'SPTRException'. | 140 |
| 'if' construct must use '{}'s. | 141 |
| Line is longer than 80 characters (found 95). | 141 |
| Line is longer than 80 characters (found 99). | 152 |
| Line is longer than 80 characters (found 83). | 154 |
| Line is longer than 80 characters (found 89). | 158 |
| Unused @throws tag for 'NullPointerException'. | 158 |
| Line is longer than 80 characters (found 118). | 159 |
| Unused @throws tag for 'IllegalArgumentException'. | 159 |
| Line is longer than 80 characters (found 84). | 161 |
| Line is longer than 80 characters (found 103). | 163 |
| Parameter enzymes should be final. | 163 |
| Parameter version should be final. | 163 |
| Parameter outputFile should be final. | 163 |
| 'if' construct must use '{}'s. | 164 |
| Line is longer than 80 characters (found 103). | 164 |
| 'if' construct must use '{}'s. | 165 |
| Line is longer than 80 characters (found 103). | 165 |
| Line is longer than 80 characters (found 86). | 166 |
| Line is longer than 80 characters (found 121). | 168 |
| 'if' construct must use '{}'s. | 169 |
| Line is longer than 80 characters (found 109). | 169 |
| 'if' construct must use '{}'s. | 190 |
| Parameter enzymeEntry should be final. | 205 |
| Expected @param tag for 'enzymeEntry'. | 205 |
| Parameter writer should be final. | 205 |
| Expected @param tag for 'writer'. | 205 |
| Expected @throws tag for 'SPTRException'. | 206 |
| Expected @throws tag for 'IOException'. | 206 |
| Line has trailing spaces. | 207 |
| Line is longer than 80 characters (found 110). | 207 |
| Line is longer than 80 characters (found 103). | 222 |
| Line is longer than 80 characters (found 107). | 224 |
| Line is longer than 80 characters (found 109). | 226 |
| Line is longer than 80 characters (found 84). | 229 |
| Line is longer than 80 characters (found 109). | 230 |
| Line is longer than 80 characters (found 81). | 232 |
| '?' is not preceded with whitespace. | 232 |
| '?' should be on a new line. | 232 |
| Avoid inline conditionals. | 232 |
| Line contains a tab character. | 233 |
| ':' is not preceded with whitespace. | 233 |
| ':' should be on a new line. | 233 |
| Line contains a tab character. | 234 |
| Line is longer than 80 characters (found 117). | 242 |
| Line is longer than 80 characters (found 81). | 245 |
| Line is longer than 80 characters (found 131). | 247 |
| Line is longer than 80 characters (found 119). | 249 |
| Line is longer than 80 characters (found 107). | 252 |
| Unused @throws tag for 'NullPointerException'. | 252 |
| Line is longer than 80 characters (found 118). | 253 |
| Unused @throws tag for 'IllegalArgumentException'. | 253 |
| Line is longer than 80 characters (found 113). | 254 |
| Line is longer than 80 characters (found 84). | 255 |
| Line is longer than 80 characters (found 115). | 257 |
| Parameter enzymes should be final. | 257 |
| Parameter version should be final. | 257 |
| Parameter dir should be final. | 257 |
| Parameter fileName should be final. | 257 |
| 'if' construct must use '{}'s. | 258 |
| Line is longer than 80 characters (found 103). | 258 |
| 'if' construct must use '{}'s. | 259 |
| Line is longer than 80 characters (found 103). | 259 |
| Line is longer than 80 characters (found 121). | 261 |
| 'if' construct must use '{}'s. | 267 |
| Line is longer than 80 characters (found 110). | 267 |
| 'if' construct must use '{}'s. | 269 |
| Line is longer than 80 characters (found 85). | 269 |
| 'if' construct must use '{}'s. | 271 |
| 'else' construct must use '{}'s. | 273 |
| First sentence should end with a period. | 283 |
| Expected an @return tag. | 289 |
| '(' is preceded with whitespace. | 289 |
| Parameter synonyms should be final. | 289 |
| Expected @param tag for 'synonyms'. | 289 |
| Expected @throws tag for 'SPTRException'. | 289 |
| Line is longer than 80 characters (found 114). | 298 |
| Parameter ec should be final. | 305 |
| 'if' construct must use '{}'s. | 307 |
| Line is longer than 80 characters (found 91). | 307 |
| Line is longer than 80 characters (found 92). | 308 |
| Line contains a tab character. | 308 |
| Name 'IDContent' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 312 |
| Line is longer than 80 characters (found 113). | 323 |
| Line is longer than 80 characters (found 116). | 326 |
| Line is longer than 80 characters (found 97). | 332 |
| Parameter commonName should be final. | 332 |
| Parameter wrapLines should be final. | 332 |
| Expected @param tag for 'wrapLines'. | 332 |
| Line is longer than 80 characters (found 121). | 335 |
| Name 'DEContent' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 337 |
| 'if' construct must use '{}'s. | 338 |
| Line is longer than 80 characters (found 110). | 352 |
| Line is longer than 80 characters (found 98). | 355 |
| Parameter synonyms should be final. | 355 |
| Parameter wrapLines should be final. | 355 |
| Expected @param tag for 'wrapLines'. | 355 |
| Name 'ANContent' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 358 |
| 'if' construct must use '{}'s. | 361 |
| 'if' construct must use '{}'s. | 362 |
| Line is longer than 80 characters (found 111). | 375 |
| Line is longer than 80 characters (found 99). | 378 |
| Parameter reactions should be final. | 378 |
| Parameter wrapLines should be final. | 378 |
| Expected @param tag for 'wrapLines'. | 378 |
| Name 'CAContent' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 381 |
| 'if' construct must use '{}'s. | 383 |
| 'if' construct must use '{}'s. | 386 |
| Line is longer than 80 characters (found 94). | 387 |
| 'else' construct must use '{}'s. | 388 |
| 'if' construct must use '{}'s. | 396 |
| 'else' construct must use '{}'s. | 398 |
| Line is longer than 80 characters (found 108). | 411 |
| Line is longer than 80 characters (found 97). | 414 |
| Parameter cofactors should be final. | 414 |
| Parameter wrapLines should be final. | 414 |
| Expected @param tag for 'wrapLines'. | 414 |
| 'if' construct must use '{}'s. | 417 |
| Name 'CFContent' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 419 |
| 'if' construct must use '{}'s. | 420 |
| Line is longer than 80 characters (found 109). | 434 |
| Line is longer than 80 characters (found 95). | 437 |
| Parameter comment should be final. | 437 |
| Parameter wrapLines should be final. | 437 |
| Expected @param tag for 'wrapLines'. | 437 |
| 'if' construct must use '{}'s. | 439 |
| 'if' construct must use '{}'s. | 440 |
| Line is longer than 80 characters (found 93). | 447 |
| Line is longer than 80 characters (found 119). | 448 |
| Parameter DICrossReferences should be final. | 450 |
| Name 'DICrossReferences' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 450 |
| Name 'DIContent' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 453 |
| Line is longer than 80 characters (found 100). | 455 |
| Line is longer than 80 characters (found 105). | 457 |
| Line is longer than 80 characters (found 81). | 467 |
| Line is longer than 80 characters (found 97). | 469 |
| Line is longer than 80 characters (found 119). | 470 |
| Parameter PRCrossReferences should be final. | 472 |
| Name 'PRCrossReferences' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 472 |
| Name 'PRContent' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 475 |
| Line is longer than 80 characters (found 100). | 477 |
| Line is longer than 80 characters (found 99). | 493 |
| Line is longer than 80 characters (found 119). | 494 |
| Parameter DRCrossReferences should be final. | 496 |
| Name 'DRCrossReferences' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 496 |
| Name 'DRContent' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 499 |
| Line is longer than 80 characters (found 100). | 502 |
| '{' is not preceded with whitespace. | 503 |
| '10' is a magic number. | 508 |
| '11' is a magic number. | 511 |
| Line is longer than 80 characters (found 108). | 515 |
| 'if' construct must use '{}'s. | 524 |
| Line is longer than 80 characters (found 108). | 525 |
| 'if' construct must use '{}'s. | 526 |
| '3' is a magic number. | 526 |
| Line is longer than 80 characters (found 119). | 534 |
| Line is longer than 80 characters (found 82). | 539 |
| Line is longer than 80 characters (found 95). | 542 |
| Parameter allCrossReferences should be final. | 542 |
| Expected @param tag for 'allCrossReferences'. | 542 |
| Name 'DICrossReferences' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 545 |
| Name 'PRCrossReferences' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 546 |
| Name 'DRCrossReferences' must match pattern '^[a-z][a-zA-Z0-9]*$'. | 547 |
| Line is longer than 80 characters (found 91). | 550 |
| Line is longer than 80 characters (found 82). | 554 |
| Line is longer than 80 characters (found 84). | 557 |
| Line is longer than 80 characters (found 82). | 564 |
| Line has trailing spaces. | 568 |
| Parameter s should be final. | 575 |
| Parameter length should be final. | 575 |
| '{' is not preceded with whitespace. | 575 |
| 'if' construct must use '{}'s. | 576 |
| '{' is not preceded with whitespace. | 578 |
| Line is longer than 80 characters (found 103). | 585 |
| Line is longer than 80 characters (found 95). | 587 |
| Parameter version should be final. | 591 |
| Expected @param tag for 'version'. | 591 |
| Line is longer than 80 characters (found 105). | 599 |
| Line contains a tab character. | 599 |
| Line contains a tab character. | 600 |
| Line contains a tab character. | 601 |
| Line contains a tab character. | 602 |
| Line is longer than 80 characters (found 113). | 603 |
| Line contains a tab character. | 603 |
| Line contains a tab character. | 604 |
| Line contains a tab character. | 605 |
| Line contains a tab character. | 606 |
| Line is longer than 80 characters (found 113). | 607 |
| Line contains a tab character. | 607 |
| Line contains a tab character. | 608 |
| Line contains a tab character. | 609 |
| Line contains a tab character. | 610 |
| Line contains a tab character. | 611 |
| Line contains a tab character. | 612 |
| Line contains a tab character. | 613 |
| Line contains a tab character. | 614 |
| Line contains a tab character. | 615 |
| Line contains a tab character. | 616 |
| Line contains a tab character. | 617 |
| Line contains a tab character. | 618 |
| Line contains a tab character. | 619 |
| Line is longer than 80 characters (found 113). | 620 |
| Line contains a tab character. | 620 |
| Line is longer than 80 characters (found 100). | 621 |
| Line contains a tab character. | 621 |
| Line is longer than 80 characters (found 109). | 622 |
| Line contains a tab character. | 622 |
| Line contains a tab character. | 623 |
| Line is longer than 80 characters (found 113). | 624 |
| Line contains a tab character. | 624 |
| Line contains a tab character. | 625 |
| Line is longer than 80 characters (found 81). | 633 |
| Line is longer than 80 characters (found 88). | 639 |
| Unused @throws tag for 'NullPointerException'. | 640 |
| Line is longer than 80 characters (found 104). | 642 |
| Parameter nonWrappedText should be final. | 642 |
| Parameter lineType should be final. | 642 |
| 'if' construct must use '{}'s. | 643 |
| Line is longer than 80 characters (found 117). | 643 |
| 'if' construct must use '{}'s. | 644 |
| Line is longer than 80 characters (found 105). | 644 |
uk/ac/ebi/intenz/tools/sib/writer/LineFormatter.java
| Violation | Message | Line |
|---|---|---|
| Line is longer than 80 characters (found 111). | 4 |
| Line is longer than 80 characters (found 106). | 6 |
| Line is longer than 80 characters (found 110). | 8 |
| Line is longer than 80 characters (found 99). | 9 |
| Line is longer than 80 characters (found 96). | 10 |
| Line is longer than 80 characters (found 118). | 13 |
| Line is longer than 80 characters (found 118). | 14 |
| Line is longer than 80 characters (found 113). | 17 |
| Line is longer than 80 characters (found 119). | 20 |
| Line is longer than 80 characters (found 119). | 21 |
| Redundant 'static' modifier. | 34 |
| Line is longer than 80 characters (found 111). | 37 |
| Line is longer than 80 characters (found 92). | 43 |
| Line is longer than 80 characters (found 89). | 45 |
uk/ac/ebi/intenz/tools/sib/writer/LineType.java
| Violation | Message | Line |
|---|---|---|
| Class LineType should be declared as final. | 16 |
| Missing a Javadoc comment. | 22 |
| Missing a Javadoc comment. | 23 |
| Missing a Javadoc comment. | 24 |
| Missing a Javadoc comment. | 25 |
| Missing a Javadoc comment. | 26 |
| Missing a Javadoc comment. | 27 |
| Missing a Javadoc comment. | 28 |
| Missing a Javadoc comment. | 29 |
| Missing a Javadoc comment. | 30 |
| Line is longer than 80 characters (found 92). | 35 |
| Line is longer than 80 characters (found 104). | 40 |
| Parameter lineTypeCode should be final. | 47 |
| 'lineTypeCode' hides a field. | 47 |
uk/ac/ebi/intenz/tools/sib/writer/LineWrapper.java
| Violation | Message | Line |
|---|---|---|
| Line is longer than 80 characters (found 98). | 6 |
| Extra HTML tag found: </center> | 8 |
| Line is longer than 80 characters (found 118). | 11 |
| Line is longer than 80 characters (found 139). | 15 |
| Line is longer than 80 characters (found 82). | 23 |
| Line is longer than 80 characters (found 102). | 25 |
| Line has trailing spaces. | 27 |
| Line is longer than 80 characters (found 82). | 31 |
| Line is longer than 80 characters (found 86). | 33 |
uk/ac/ebi/intenz/tools/sib/writer/LineWrapperFactory.java
| Violation | Message | Line |
|---|---|---|
| Line is longer than 80 characters (found 105). | 10 |
| Utility classes should not have a public or default constructor. | 15 |
| Line is longer than 80 characters (found 107). | 18 |
| Name 'lineBreakPatterns' must match pattern '^[A-Z][A-Z0-9]*(_[A-Z0-9]+)*$'. | 20 |
| Missing a Javadoc comment. | 37 |
| Name 'enforcedLineBreakPatterns' must match pattern '^[A-Z][A-Z0-9]*(_[A-Z0-9]+)*$'. | 37 |
| Line is longer than 80 characters (found 116). | 42 |
| Unused @throws tag for 'NullPointerException'. | 48 |
| Parameter wholeText should be final. | 50 |
| Parameter lineType should be final. | 50 |
| 'if' construct must use '{}'s. | 51 |
| Line is longer than 80 characters (found 100). | 54 |
| Line is longer than 80 characters (found 112). | 55 |
| Line is longer than 80 characters (found 92). | 57 |
| '3' is a magic number. | 62 |
| '4' is a magic number. | 63 |
| 'if' construct must use '{}'s. | 64 |
| '3' is a magic number. | 64 |
| '3' is a magic number. | 64 |
| '||' should be on a new line. | 64 |
| '3' is a magic number. | 65 |
| '3' is a magic number. | 65 |
| 'else' construct must use '{}'s. | 72 |
| Missing a Javadoc comment. | 76 |
| Missing a Javadoc comment. | 77 |
| Missing a Javadoc comment. | 78 |
| Line is longer than 80 characters (found 96). | 80 |
| Missing a Javadoc comment. | 80 |
| Parameter text should be final. | 80 |
| Parameter netLineWidth should be final. | 80 |
| Line is longer than 80 characters (found 95). | 81 |
| 'if' construct must use '{}'s. | 82 |
| Line is longer than 80 characters (found 118). | 82 |
| Line is longer than 80 characters (found 89). | 83 |
| Line is longer than 80 characters (found 90). | 87 |
| Line is longer than 80 characters (found 120). | 91 |
| Line is longer than 80 characters (found 83). | 94 |
| Parameter text should be final. | 94 |
| Parameter lineWidth should be final. | 94 |
| Expected @param tag for 'lineWidth'. | 94 |
| Line is longer than 80 characters (found 96). | 108 |
| 'if' construct must use '{}'s. | 109 |
| Line is longer than 80 characters (found 104). | 109 |
| '{' is not preceded with whitespace. | 110 |
| Line contains a tab character. | 111 |
| Line is longer than 80 characters (found 116). | 132 |
| Parameter possibleLineBreakPositions should be final. | 132 |
| Parameter netLineWidth should be final. | 132 |
| Parameter text should be final. | 132 |
| Expected @param tag for 'text'. | 132 |
| 'if' construct must use '{}'s. | 145 |
| Line is longer than 80 characters (found 128). | 145 |
| Line is longer than 80 characters (found 111). | 152 |
| '5' is a magic number. | 153 |
| '&&' should be on a new line. | 153 |
| '||' should be on a new line. | 154 |
| '||' should be on a new line. | 155 |
| Line is longer than 80 characters (found 113). | 157 |
| Line is longer than 80 characters (found 109). | 158 |
| 'if' construct must use '{}'s. | 167 |
| 'if' is not followed by whitespace. | 167 |
| '==' is not preceded with whitespace. | 167 |
| '==' is not followed by whitespace. | 167 |
| 'if' construct must use '{}'s. | 168 |
| 'if' is not followed by whitespace. | 168 |
| '!=' is not preceded with whitespace. | 168 |
| '!=' is not followed by whitespace. | 168 |
| Line is longer than 80 characters (found 98). | 169 |
| Line is longer than 80 characters (found 84). | 175 |
| Missing a Javadoc comment. | 175 |
| Parameter index should be final. | 175 |
| Parameter lastSpace should be final. | 175 |
| Parameter text should be final. | 175 |
| Line is longer than 80 characters (found 89). | 179 |
| Line is longer than 80 characters (found 116). | 184 |
| Line is longer than 80 characters (found 99). | 185 |
| Line is longer than 80 characters (found 90). | 187 |
| Line is longer than 80 characters (found 88). | 192 |
| Line is longer than 80 characters (found 99). | 193 |
| 'if' construct must use '{}'s. | 196 |
| Line is longer than 80 characters (found 83). | 196 |
| 'if' construct must use '{}'s. | 197 |
| Line is longer than 80 characters (found 122). | 197 |
| Missing a Javadoc comment. | 205 |
| Line is longer than 80 characters (found 83). | 206 |
| Missing a Javadoc comment. | 206 |
| Parameter text should be final. | 206 |
| Parameter lineWidth should be final. | 206 |
| 'if' construct must use '{}'s. | 211 |
| 'if' construct must use '{}'s. | 218 |
| Missing a Javadoc comment. | 228 |
| Line is longer than 80 characters (found 83). | 230 |
| Missing a Javadoc comment. | 230 |
| Parameter text should be final. | 230 |
| Parameter lineWidth should be final. | 230 |
| Line is longer than 80 characters (found 98). | 231 |
| 'if' construct must use '{}'s. | 239 |
| Missing a Javadoc comment. | 249 |
| Parameter text should be final. | 249 |
| 'while' construct must use '{}'s. | 253 |