1 <!------------------------------------------------------------------------------
3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
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.
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.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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
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.
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.
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"?>
43 <description>Sun Java Coding Convention</description>
51 <abstract>[A-Z][a-zA-Z0-9]+</abstract>
52 <general>[A-Z][a-zA-Z0-9]+</general>
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>
68 <interfaces>[A-Z][a-zA-Z0-9]+</interfaces>
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>
84 <packages>[a-z]+(?:\.[a-z]+)*</packages>
86 <default>[a-z][\w]+</default>
87 <final>[a-z][\w]+</final>
89 <variables>[a-z][\w]*</variables>
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>
117 <general>30000</general>
118 <parser>30000</parser>
119 <parserJavadoc>30000</parserJavadoc>
120 <printer>30000</printer>
121 <printerJavadoc>30000</printerJavadoc>
122 <transform>30000</transform>
124 <showErrorStackTrace>true</showErrorStackTrace>
127 <threadCount>1</threadCount>
131 <methodCallChain>true</methodCallChain>
132 <parameterMethodDeclaration>false</parameterMethodDeclaration>
133 <ternaryOperator>true</ternaryOperator>
134 <variableAssignment>false</variableAssignment>
135 <variableIdentifier>false</variableIdentifier>
138 <directory>bak</directory>
144 <braceLeft>0</braceLeft>
146 <declaration>0</declaration>
149 <interface>1</interface>
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160 <multiline>1</multiline>
161 <singleline>1</singleline>
163 <controlStatement>1</controlStatement>
164 <declaration>1</declaration>
168 <keepUpTo>1</keepUpTo>
172 <cuddle>false</cuddle>
173 <insertStatement>false</insertStatement>
176 <dowhile>false</dowhile>
178 <ifelse>true</ifelse>
183 <dowhile>false</dowhile>
185 <ifelse>false</ifelse>
189 <methodClass>false</methodClass>
190 <methodClassIfWrapped>false</methodClassIfWrapped>
194 <blanklines>true</blanklines>
195 <comments>true</comments>
199 <multiline>false</multiline>
203 <innerclass>true</innerclass>
205 <throwsTags>true</throwsTags>
207 <fieldsShort>true</fieldsShort>
210 <constructor>5</constructor>
214 <parseComments>false</parseComments>
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>
230 <javadoc>false</javadoc>
231 <multiline>false</multiline>
232 <singleline>false</singleline>
235 <fillCharacter>-</fillCharacter>
236 <insert>false</insert>
237 <insertRecursive>false</insertRecursive>
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>
252 <smartMode>0</smartMode>
257 <smartMode>0</smartMode>
261 <policy>disabled</policy>
265 <defaultDepth>3</defaultDepth>
266 <packages>*:0|gnu:2|java:2|javax:2</packages>
268 <policy>disabled</policy>
272 <caseFromSwitch>true</caseFromSwitch>
275 <operator>false</operator>
277 <firstColumnComments>true</firstColumnComments>
283 <braceCuddled>1</braceCuddled>
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286 <braceRightAfter>1</braceRightAfter>
287 <continuation>4</continuation>
289 <extends>-1</extends>
291 <implements>-1</implements>
295 <trailingComment>1</trailingComment>
298 <enable>false</enable>
299 <onlyLeading>false</onlyLeading>
303 <arrayBracketsAfterIdent>false</arrayBracketsAfterIdent>
304 <forceFormatting>false</forceFormatting>
305 <insertExpressionParentheses>true</insertExpressionParentheses>
306 <insertLoggingConditional>false</insertLoggingConditional>
307 <insertTrailingNewline>true</insertTrailingNewline>
308 <insertUID>false</insertUID>
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>
321 <enable>false</enable>
322 <order>public|protected|private|abstract|static|final|synchronized|transient|volatile|native|strictfp</order>
328 <semicolon>true</semicolon>
329 <typeCast>true</typeCast>
332 <braces>true</braces>
333 <brackets>false</brackets>
334 <bracketsTypes>false</bracketsTypes>
335 <caseColon>false</caseColon>
340 <methodCall>false</methodCall>
341 <methodDeclaration>false</methodDeclaration>
342 <statement>true</statement>
346 <braces>true</braces>
347 <brackets>false</brackets>
349 <assignment>true</assignment>
350 <bitwise>true</bitwise>
351 <logical>true</logical>
352 <mathematical>true</mathematical>
353 <relational>true</relational>
356 <parenthesis>false</parenthesis>
357 <typeCast>false</typeCast>
363 <arrayElement>0</arrayElement>
364 <braceRight>false</braceRight>
365 <extendsTypes>false</extendsTypes>
366 <implementsTypes>false</implementsTypes>
368 <methodCallChained>false</methodCallChained>
371 <second>false</second>
373 <throwsTypes>false</throwsTypes>
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388 <beforeOperator>true</beforeOperator>
389 <enable>true</enable>
390 <lineLength>80</lineLength>
394 <assignment>false</assignment>
395 <leftParenthesis>false</leftParenthesis>
396 <parameter>false</parameter>
398 <extends>false</extends>
399 <implements>false</implements>
400 <throws>false</throws>
404 <rightParenthesis>false</rightParenthesis>
406 <groupingParentheses>false</groupingParentheses>