jalview-jalopy.xml

   1 <!------------------------------------------------------------------------------
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
   4  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18 -->
  19   Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
  20   Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  21
  22   This program is free software; you can redistribute it and/or
  23   modify it under the terms of the GNU General Public License
  24   as published by the Free Software Foundation; either version 2
  25   of the License, or (at your option) any later version.
  26
  27   This program is distributed in the hope that it will be useful,
  28   but WITHOUT ANY WARRANTY; without even the implied warranty of
  29   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  30   GNU General Public License for more details.
  31
  32   You should have received a copy of the GNU General Public License
  33   along with this program; if not, write to the Free Software
  34   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  35 ------------------------------------------------------------------------------->
  36 <?xml version="1.0" encoding="UTF-8"?>
  37 <jalopy>
  38     <general>
  39         <compliance>
  40             <version>14</version>
  41         </compliance>
  42         <style>
  43             <description>Sun Java Coding Convention</description>
  44             <name>Sun</name>
  45         </style>
  46     </general>
  47     <inspector>
  48         <enable>true</enable>
  49         <naming>
  50             <classes>
  51                 <abstract>[A-Z][a-zA-Z0-9]+</abstract>
  52                 <general>[A-Z][a-zA-Z0-9]+</general>
  53             </classes>
  54             <fields>
  55                 <default>[a-z][\w]+</default>
  56                 <defaultStatic>[a-z][\w]+</defaultStatic>
  57                 <defaultStaticFinal>[a-zA-Z][\w]+</defaultStaticFinal>
  58                 <private>[a-z][\w]+</private>
  59                 <privateStatic>[a-z][\w]+</privateStatic>
  60                 <privateStaticFinal>[a-zA-Z][\w]+</privateStaticFinal>
  61                 <protected>[a-z][\w]+</protected>
  62                 <protectedStatic>[a-z][\w]+</protectedStatic>
  63                 <protectedStaticFinal>[a-zA-Z][\w]+</protectedStaticFinal>
  64                 <public>[a-z][\w]+</public>
  65                 <publicStatic>[a-z][\w]+</publicStatic>
  66                 <publicStaticFinal>[a-zA-Z][\w]+</publicStaticFinal>
  67             </fields>
  68             <interfaces>[A-Z][a-zA-Z0-9]+</interfaces>
  69             <labels>\w+</labels>
  70             <methods>
  71                 <default>[a-z][\w]+</default>
  72                 <defaultStatic>[a-z][\w]+</defaultStatic>
  73                 <defaultStaticFinal>[a-z][\w]+</defaultStaticFinal>
  74                 <private>[a-z][\w]+</private>
  75                 <privateStatic>[a-z][\w]+</privateStatic>
  76                 <privateStaticFinal>[a-z][\w]+</privateStaticFinal>
  77                 <protected>[a-z][\w]+</protected>
  78                 <protectedStatic>[a-z][\w]+</protectedStatic>
  79                 <protectedStaticFinal>[a-z][\w]+</protectedStaticFinal>
  80                 <public>[a-z][\w]+</public>
  81                 <publicStatic>[a-z][\w]+</publicStatic>
  82                 <publicStaticFinal>[a-z][\w]+</publicStaticFinal>
  83             </methods>
  84             <packages>[a-z]+(?:\.[a-z]+)*</packages>
  85             <parameters>
  86                 <default>[a-z][\w]+</default>
  87                 <final>[a-z][\w]+</final>
  88             </parameters>
  89             <variables>[a-z][\w]*</variables>
  90         </naming>
  91         <tips>
  92             <adhereToNamingConvention>false</adhereToNamingConvention>
  93             <alwaysOverrideHashCode>false</alwaysOverrideHashCode>
  94             <avoidThreadGroups>false</avoidThreadGroups>
  95             <declareCollectionComment>false</declareCollectionComment>
  96             <dontIgnoreExceptions>false</dontIgnoreExceptions>
  97             <dontSubstituteObjectEquals>false</dontSubstituteObjectEquals>
  98             <neverDeclareException>false</neverDeclareException>
  99             <neverDeclareThrowable>false</neverDeclareThrowable>
 100             <neverInvokeWaitOutsideLoop>false</neverInvokeWaitOutsideLoop>
 101             <neverReturnZeroArrays>false</neverReturnZeroArrays>
 102             <neverUseEmptyFinally>false</neverUseEmptyFinally>
 103             <obeyContractEquals>false</obeyContractEquals>
 104             <overrideToString>false</overrideToString>
 105             <referToObjectsByInterface>false</referToObjectsByInterface>
 106             <replaceStructureWithClass>false</replaceStructureWithClass>
 107             <stringLiterallI18n>false</stringLiterallI18n>
 108             <useInterfaceOnlyForTypes>false</useInterfaceOnlyForTypes>
 109             <wrongCollectionComment>false</wrongCollectionComment>
 110         </tips>
 111     </inspector>
 112     <internal>
 113         <version>6</version>
 114     </internal>
 115     <messages>
 116         <priority>
 117             <general>30000</general>
 118             <parser>30000</parser>
 119             <parserJavadoc>30000</parserJavadoc>
 120             <printer>30000</printer>
 121             <printerJavadoc>30000</printerJavadoc>
 122             <transform>30000</transform>
 123         </priority>
 124         <showErrorStackTrace>true</showErrorStackTrace>
 125     </messages>
 126     <misc>
 127         <threadCount>1</threadCount>
 128     </misc>
 129     <printer>
 130         <alignment>
 131             <methodCallChain>true</methodCallChain>
 132             <parameterMethodDeclaration>false</parameterMethodDeclaration>
 133             <ternaryOperator>true</ternaryOperator>
 134             <variableAssignment>false</variableAssignment>
 135             <variableIdentifier>false</variableIdentifier>
 136         </alignment>
 137         <backup>
 138             <directory>bak</directory>
 139             <level>1</level>
 140         </backup>
 141         <blanklines>
 142             <after>
 143                 <block>1</block>
 144                 <braceLeft>0</braceLeft>
 145                 <class>1</class>
 146                 <declaration>0</declaration>
 147                 <footer>1</footer>
 148                 <header>0</header>
 149                 <interface>1</interface>
 150                 <lastImport>2</lastImport>
 151                 <method>1</method>
 152                 <package>1</package>
 153             </after>
 154             <before>
 155                 <block>1</block>
 156                 <braceRight>0</braceRight>
 157                 <caseBlock>1</caseBlock>
 158                 <comment>
 159                     <javadoc>1</javadoc>
 160                     <multiline>1</multiline>
 161                     <singleline>1</singleline>
 162                 </comment>
 163                 <controlStatement>1</controlStatement>
 164                 <declaration>1</declaration>
 165                 <footer>0</footer>
 166                 <header>0</header>
 167             </before>
 168             <keepUpTo>1</keepUpTo>
 169         </blanklines>
 170         <braces>
 171             <empty>
 172                 <cuddle>false</cuddle>
 173                 <insertStatement>false</insertStatement>
 174             </empty>
 175             <insert>
 176                 <dowhile>false</dowhile>
 177                 <for>false</for>
 178                 <ifelse>true</ifelse>
 179                 <while>false</while>
 180             </insert>
 181             <remove>
 182                 <block>true</block>
 183                 <dowhile>false</dowhile>
 184                 <for>false</for>
 185                 <ifelse>false</ifelse>
 186                 <while>false</while>
 187             </remove>
 188             <treatDifferent>
 189                 <methodClass>false</methodClass>
 190                 <methodClassIfWrapped>false</methodClassIfWrapped>
 191             </treatDifferent>
 192         </braces>
 193         <chunks>
 194             <blanklines>true</blanklines>
 195             <comments>true</comments>
 196         </chunks>
 197         <comments>
 198             <format>
 199                 <multiline>false</multiline>
 200             </format>
 201             <javadoc>
 202                 <check>
 203                     <innerclass>true</innerclass>
 204                     <tags>true</tags>
 205                     <throwsTags>true</throwsTags>
 206                 </check>
 207                 <fieldsShort>true</fieldsShort>
 208                 <generate>
 209                     <class>5</class>
 210                     <constructor>5</constructor>
 211                     <field>5</field>
 212                     <method>5</method>
 213                 </generate>
 214                 <parseComments>false</parseComments>
 215                 <tags>
 216                     <in-line />
 217                     <standard />
 218                 </tags>
 219                 <templates>
 220                     <method>
 221                         <bottom> */</bottom>
 222                         <exception> * @throws $exceptionType$ TODO: DOCUMENT ME!</exception>
 223                         <param> * @param $paramType$ TODO: DOCUMENT ME!</param>
 224                         <return> * @return TODO: DOCUMENT ME!</return>
 225                         <top>/**| * TODO: DOCUMENT ME!</top>
 226                     </method>
 227                 </templates>
 228             </javadoc>
 229             <remove>
 230                 <javadoc>false</javadoc>
 231                 <multiline>false</multiline>
 232                 <singleline>false</singleline>
 233             </remove>
 234             <separator>
 235                 <fillCharacter>-</fillCharacter>
 236                 <insert>false</insert>
 237                 <insertRecursive>false</insertRecursive>
 238                 <text>
 239                     <class>Inner Classes</class>
 240                     <constructor>Constructors</constructor>
 241                     <field>Instance fields</field>
 242                     <initializer>Instance initializers</initializer>
 243                     <interface>Inner Interfaces</interface>
 244                     <method>Methods</method>
 245                     <static>Static fields/initializers</static>
 246                 </text>
 247             </separator>
 248         </comments>
 249         <environment />
 250         <footer>
 251             <keys />
 252             <smartMode>0</smartMode>
 253             <use>false</use>
 254         </footer>
 255         <header>
 256             <keys />
 257             <smartMode>0</smartMode>
 258             <use>false</use>
 259         </header>
 260         <history>
 261             <policy>disabled</policy>
 262         </history>
 263         <imports>
 264             <grouping>
 265                 <defaultDepth>3</defaultDepth>
 266                 <packages>*:0|gnu:2|java:2|javax:2</packages>
 267             </grouping>
 268             <policy>disabled</policy>
 269             <sort>true</sort>
 270         </imports>
 271         <indentation>
 272             <caseFromSwitch>true</caseFromSwitch>
 273             <continuation>
 274                 <block>true</block>
 275                 <operator>false</operator>
 276             </continuation>
 277             <firstColumnComments>true</firstColumnComments>
 278             <label>false</label>
 279             <policy>
 280                 <deep>false</deep>
 281             </policy>
 282             <sizes>
 283                 <braceCuddled>1</braceCuddled>
 284                 <braceLeft>1</braceLeft>
 285                 <braceRight>0</braceRight>
 286                 <braceRightAfter>1</braceRightAfter>
 287                 <continuation>4</continuation>
 288                 <deep>55</deep>
 289                 <extends>-1</extends>
 290                 <general>4</general>
 291                 <implements>-1</implements>
 292                 <leading>0</leading>
 293                 <tabs>8</tabs>
 294                 <throws>-1</throws>
 295                 <trailingComment>1</trailingComment>
 296             </sizes>
 297             <tabs>
 298                 <enable>false</enable>
 299                 <onlyLeading>false</onlyLeading>
 300             </tabs>
 301         </indentation>
 302         <misc>
 303             <arrayBracketsAfterIdent>false</arrayBracketsAfterIdent>
 304             <forceFormatting>false</forceFormatting>
 305             <insertExpressionParentheses>true</insertExpressionParentheses>
 306             <insertLoggingConditional>false</insertLoggingConditional>
 307             <insertTrailingNewline>true</insertTrailingNewline>
 308             <insertUID>false</insertUID>
 309         </misc>
 310         <sorting>
 311             <declaration>
 312                 <class>false</class>
 313                 <constructor>false</constructor>
 314                 <enable>false</enable>
 315                 <interface>false</interface>
 316                 <method>false</method>
 317                 <order>static|field|initializer|constructor|method|interface|class</order>
 318                 <variable>false</variable>
 319             </declaration>
 320             <modifier>
 321                 <enable>false</enable>
 322                 <order>public|protected|private|abstract|static|final|synchronized|transient|volatile|native|strictfp</order>
 323             </modifier>
 324         </sorting>
 325         <whitespace>
 326             <after>
 327                 <comma>true</comma>
 328                 <semicolon>true</semicolon>
 329                 <typeCast>true</typeCast>
 330             </after>
 331             <before>
 332                 <braces>true</braces>
 333                 <brackets>false</brackets>
 334                 <bracketsTypes>false</bracketsTypes>
 335                 <caseColon>false</caseColon>
 336                 <operator>
 337                     <not>false</not>
 338                 </operator>
 339                 <parentheses>
 340                     <methodCall>false</methodCall>
 341                     <methodDeclaration>false</methodDeclaration>
 342                     <statement>true</statement>
 343                 </parentheses>
 344             </before>
 345             <padding>
 346                 <braces>true</braces>
 347                 <brackets>false</brackets>
 348                 <operator>
 349                     <assignment>true</assignment>
 350                     <bitwise>true</bitwise>
 351                     <logical>true</logical>
 352                     <mathematical>true</mathematical>
 353                     <relational>true</relational>
 354                     <shift>true</shift>
 355                 </operator>
 356                 <parenthesis>false</parenthesis>
 357                 <typeCast>false</typeCast>
 358             </padding>
 359         </whitespace>
 360         <wrapping>
 361             <always>
 362                 <after>
 363                     <arrayElement>0</arrayElement>
 364                     <braceRight>false</braceRight>
 365                     <extendsTypes>false</extendsTypes>
 366                     <implementsTypes>false</implementsTypes>
 367                     <label>true</label>
 368                     <methodCallChained>false</methodCallChained>
 369                     <ternaryOperator>
 370                         <first>false</first>
 371                         <second>false</second>
 372                     </ternaryOperator>
 373                     <throwsTypes>false</throwsTypes>
 374                 </after>
 375                 <before>
 376                     <braceLeft>false</braceLeft>
 377                     <extends>false</extends>
 378                     <implements>false</implements>
 379                     <throws>false</throws>
 380                 </before>
 381                 <parameter>
 382                     <methodCall>false</methodCall>
 383                     <methodCallNested>false</methodCallNested>
 384                     <methodDeclaration>false</methodDeclaration>
 385                 </parameter>
 386             </always>
 387             <general>
 388                 <beforeOperator>true</beforeOperator>
 389                 <enable>true</enable>
 390                 <lineLength>80</lineLength>
 391             </general>
 392             <ondemand>
 393                 <after>
 394                     <assignment>false</assignment>
 395                     <leftParenthesis>false</leftParenthesis>
 396                     <parameter>false</parameter>
 397                     <types>
 398                         <extends>false</extends>
 399                         <implements>false</implements>
 400                         <throws>false</throws>
 401                     </types>
 402                 </after>
 403                 <before>
 404                     <rightParenthesis>false</rightParenthesis>
 405                 </before>
 406                 <groupingParentheses>false</groupingParentheses>
 407             </ondemand>
 408         </wrapping>
 409     </printer>
 410 </jalopy>
 411