JAL-3858 improved contactInterval computation and added detailed test coverage for...
[jalview.git] / jalview-jalopy.xml
1 <?xml version="1.0" encoding="UTF-8"?>
2 <!--
3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
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  * The Jalview Authors are detailed in the 'AUTHORS' file.
19 -->
20 <jalopy>
21     <general>
22         <compliance>
23             <version>14</version>
24         </compliance>
25         <style>
26             <description>Sun Java Coding Convention</description>
27             <name>Sun</name>
28         </style>
29     </general>
30     <inspector>
31         <enable>true</enable>
32         <naming>
33             <classes>
34                 <abstract>[A-Z][a-zA-Z0-9]+</abstract>
35                 <general>[A-Z][a-zA-Z0-9]+</general>
36             </classes>
37             <fields>
38                 <default>[a-z][\w]+</default>
39                 <defaultStatic>[a-z][\w]+</defaultStatic>
40                 <defaultStaticFinal>[a-zA-Z][\w]+</defaultStaticFinal>
41                 <private>[a-z][\w]+</private>
42                 <privateStatic>[a-z][\w]+</privateStatic>
43                 <privateStaticFinal>[a-zA-Z][\w]+</privateStaticFinal>
44                 <protected>[a-z][\w]+</protected>
45                 <protectedStatic>[a-z][\w]+</protectedStatic>
46                 <protectedStaticFinal>[a-zA-Z][\w]+</protectedStaticFinal>
47                 <public>[a-z][\w]+</public>
48                 <publicStatic>[a-z][\w]+</publicStatic>
49                 <publicStaticFinal>[a-zA-Z][\w]+</publicStaticFinal>
50             </fields>
51             <interfaces>[A-Z][a-zA-Z0-9]+</interfaces>
52             <labels>\w+</labels>
53             <methods>
54                 <default>[a-z][\w]+</default>
55                 <defaultStatic>[a-z][\w]+</defaultStatic>
56                 <defaultStaticFinal>[a-z][\w]+</defaultStaticFinal>
57                 <private>[a-z][\w]+</private>
58                 <privateStatic>[a-z][\w]+</privateStatic>
59                 <privateStaticFinal>[a-z][\w]+</privateStaticFinal>
60                 <protected>[a-z][\w]+</protected>
61                 <protectedStatic>[a-z][\w]+</protectedStatic>
62                 <protectedStaticFinal>[a-z][\w]+</protectedStaticFinal>
63                 <public>[a-z][\w]+</public>
64                 <publicStatic>[a-z][\w]+</publicStatic>
65                 <publicStaticFinal>[a-z][\w]+</publicStaticFinal>
66             </methods>
67             <packages>[a-z]+(?:\.[a-z]+)*</packages>
68             <parameters>
69                 <default>[a-z][\w]+</default>
70                 <final>[a-z][\w]+</final>
71             </parameters>
72             <variables>[a-z][\w]*</variables>
73         </naming>
74         <tips>
75             <adhereToNamingConvention>false</adhereToNamingConvention>
76             <alwaysOverrideHashCode>false</alwaysOverrideHashCode>
77             <avoidThreadGroups>false</avoidThreadGroups>
78             <declareCollectionComment>false</declareCollectionComment>
79             <dontIgnoreExceptions>false</dontIgnoreExceptions>
80             <dontSubstituteObjectEquals>false</dontSubstituteObjectEquals>
81             <neverDeclareException>false</neverDeclareException>
82             <neverDeclareThrowable>false</neverDeclareThrowable>
83             <neverInvokeWaitOutsideLoop>false</neverInvokeWaitOutsideLoop>
84             <neverReturnZeroArrays>false</neverReturnZeroArrays>
85             <neverUseEmptyFinally>false</neverUseEmptyFinally>
86             <obeyContractEquals>false</obeyContractEquals>
87             <overrideToString>false</overrideToString>
88             <referToObjectsByInterface>false</referToObjectsByInterface>
89             <replaceStructureWithClass>false</replaceStructureWithClass>
90             <stringLiterallI18n>false</stringLiterallI18n>
91             <useInterfaceOnlyForTypes>false</useInterfaceOnlyForTypes>
92             <wrongCollectionComment>false</wrongCollectionComment>
93         </tips>
94     </inspector>
95     <internal>
96         <version>6</version>
97     </internal>
98     <messages>
99         <priority>
100             <general>30000</general>
101             <parser>30000</parser>
102             <parserJavadoc>30000</parserJavadoc>
103             <printer>30000</printer>
104             <printerJavadoc>30000</printerJavadoc>
105             <transform>30000</transform>
106         </priority>
107         <showErrorStackTrace>true</showErrorStackTrace>
108     </messages>
109     <misc>
110         <threadCount>1</threadCount>
111     </misc>
112     <printer>
113         <alignment>
114             <methodCallChain>true</methodCallChain>
115             <parameterMethodDeclaration>false</parameterMethodDeclaration>
116             <ternaryOperator>true</ternaryOperator>
117             <variableAssignment>false</variableAssignment>
118             <variableIdentifier>false</variableIdentifier>
119         </alignment>
120         <backup>
121             <directory>bak</directory>
122             <level>1</level>
123         </backup>
124         <blanklines>
125             <after>
126                 <block>1</block>
127                 <braceLeft>0</braceLeft>
128                 <class>1</class>
129                 <declaration>0</declaration>
130                 <footer>1</footer>
131                 <header>0</header>
132                 <interface>1</interface>
133                 <lastImport>2</lastImport>
134                 <method>1</method>
135                 <package>1</package>
136             </after>
137             <before>
138                 <block>1</block>
139                 <braceRight>0</braceRight>
140                 <caseBlock>1</caseBlock>
141                 <comment>
142                     <javadoc>1</javadoc>
143                     <multiline>1</multiline>
144                     <singleline>1</singleline>
145                 </comment>
146                 <controlStatement>1</controlStatement>
147                 <declaration>1</declaration>
148                 <footer>0</footer>
149                 <header>0</header>
150             </before>
151             <keepUpTo>1</keepUpTo>
152         </blanklines>
153         <braces>
154             <empty>
155                 <cuddle>false</cuddle>
156                 <insertStatement>false</insertStatement>
157             </empty>
158             <insert>
159                 <dowhile>false</dowhile>
160                 <for>false</for>
161                 <ifelse>true</ifelse>
162                 <while>false</while>
163             </insert>
164             <remove>
165                 <block>true</block>
166                 <dowhile>false</dowhile>
167                 <for>false</for>
168                 <ifelse>false</ifelse>
169                 <while>false</while>
170             </remove>
171             <treatDifferent>
172                 <methodClass>false</methodClass>
173                 <methodClassIfWrapped>false</methodClassIfWrapped>
174             </treatDifferent>
175         </braces>
176         <chunks>
177             <blanklines>true</blanklines>
178             <comments>true</comments>
179         </chunks>
180         <comments>
181             <format>
182                 <multiline>false</multiline>
183             </format>
184             <javadoc>
185                 <check>
186                     <innerclass>true</innerclass>
187                     <tags>true</tags>
188                     <throwsTags>true</throwsTags>
189                 </check>
190                 <fieldsShort>true</fieldsShort>
191                 <generate>
192                     <class>5</class>
193                     <constructor>5</constructor>
194                     <field>5</field>
195                     <method>5</method>
196                 </generate>
197                 <parseComments>false</parseComments>
198                 <tags>
199                     <in-line />
200                     <standard />
201                 </tags>
202                 <templates>
203                     <method>
204                         <bottom> */</bottom>
205                         <exception> * @throws $exceptionType$ TODO: DOCUMENT ME!</exception>
206                         <param> * @param $paramType$ TODO: DOCUMENT ME!</param>
207                         <return> * @return TODO: DOCUMENT ME!</return>
208                         <top>/**| * TODO: DOCUMENT ME!</top>
209                     </method>
210                 </templates>
211             </javadoc>
212             <remove>
213                 <javadoc>false</javadoc>
214                 <multiline>false</multiline>
215                 <singleline>false</singleline>
216             </remove>
217             <separator>
218                 <fillCharacter>-</fillCharacter>
219                 <insert>false</insert>
220                 <insertRecursive>false</insertRecursive>
221                 <text>
222                     <class>Inner Classes</class>
223                     <constructor>Constructors</constructor>
224                     <field>Instance fields</field>
225                     <initializer>Instance initializers</initializer>
226                     <interface>Inner Interfaces</interface>
227                     <method>Methods</method>
228                     <static>Static fields/initializers</static>
229                 </text>
230             </separator>
231         </comments>
232         <environment />
233         <footer>
234             <keys />
235             <smartMode>0</smartMode>
236             <use>false</use>
237         </footer>
238         <header>
239             <keys />
240             <smartMode>0</smartMode>
241             <use>false</use>
242         </header>
243         <history>
244             <policy>disabled</policy>
245         </history>
246         <imports>
247             <grouping>
248                 <defaultDepth>3</defaultDepth>
249                 <packages>*:0|gnu:2|java:2|javax:2</packages>
250             </grouping>
251             <policy>disabled</policy>
252             <sort>true</sort>
253         </imports>
254         <indentation>
255             <caseFromSwitch>true</caseFromSwitch>
256             <continuation>
257                 <block>true</block>
258                 <operator>false</operator>
259             </continuation>
260             <firstColumnComments>true</firstColumnComments>
261             <label>false</label>
262             <policy>
263                 <deep>false</deep>
264             </policy>
265             <sizes>
266                 <braceCuddled>1</braceCuddled>
267                 <braceLeft>1</braceLeft>
268                 <braceRight>0</braceRight>
269                 <braceRightAfter>1</braceRightAfter>
270                 <continuation>4</continuation>
271                 <deep>55</deep>
272                 <extends>-1</extends>
273                 <general>4</general>
274                 <implements>-1</implements>
275                 <leading>0</leading>
276                 <tabs>8</tabs>
277                 <throws>-1</throws>
278                 <trailingComment>1</trailingComment>
279             </sizes>
280             <tabs>
281                 <enable>false</enable>
282                 <onlyLeading>false</onlyLeading>
283             </tabs>
284         </indentation>
285         <misc>
286             <arrayBracketsAfterIdent>false</arrayBracketsAfterIdent>
287             <forceFormatting>false</forceFormatting>
288             <insertExpressionParentheses>true</insertExpressionParentheses>
289             <insertLoggingConditional>false</insertLoggingConditional>
290             <insertTrailingNewline>true</insertTrailingNewline>
291             <insertUID>false</insertUID>
292         </misc>
293         <sorting>
294             <declaration>
295                 <class>false</class>
296                 <constructor>false</constructor>
297                 <enable>false</enable>
298                 <interface>false</interface>
299                 <method>false</method>
300                 <order>static|field|initializer|constructor|method|interface|class</order>
301                 <variable>false</variable>
302             </declaration>
303             <modifier>
304                 <enable>false</enable>
305                 <order>public|protected|private|abstract|static|final|synchronized|transient|volatile|native|strictfp</order>
306             </modifier>
307         </sorting>
308         <whitespace>
309             <after>
310                 <comma>true</comma>
311                 <semicolon>true</semicolon>
312                 <typeCast>true</typeCast>
313             </after>
314             <before>
315                 <braces>true</braces>
316                 <brackets>false</brackets>
317                 <bracketsTypes>false</bracketsTypes>
318                 <caseColon>false</caseColon>
319                 <operator>
320                     <not>false</not>
321                 </operator>
322                 <parentheses>
323                     <methodCall>false</methodCall>
324                     <methodDeclaration>false</methodDeclaration>
325                     <statement>true</statement>
326                 </parentheses>
327             </before>
328             <padding>
329                 <braces>true</braces>
330                 <brackets>false</brackets>
331                 <operator>
332                     <assignment>true</assignment>
333                     <bitwise>true</bitwise>
334                     <logical>true</logical>
335                     <mathematical>true</mathematical>
336                     <relational>true</relational>
337                     <shift>true</shift>
338                 </operator>
339                 <parenthesis>false</parenthesis>
340                 <typeCast>false</typeCast>
341             </padding>
342         </whitespace>
343         <wrapping>
344             <always>
345                 <after>
346                     <arrayElement>0</arrayElement>
347                     <braceRight>false</braceRight>
348                     <extendsTypes>false</extendsTypes>
349                     <implementsTypes>false</implementsTypes>
350                     <label>true</label>
351                     <methodCallChained>false</methodCallChained>
352                     <ternaryOperator>
353                         <first>false</first>
354                         <second>false</second>
355                     </ternaryOperator>
356                     <throwsTypes>false</throwsTypes>
357                 </after>
358                 <before>
359                     <braceLeft>false</braceLeft>
360                     <extends>false</extends>
361                     <implements>false</implements>
362                     <throws>false</throws>
363                 </before>
364                 <parameter>
365                     <methodCall>false</methodCall>
366                     <methodCallNested>false</methodCallNested>
367                     <methodDeclaration>false</methodDeclaration>
368                 </parameter>
369             </always>
370             <general>
371                 <beforeOperator>true</beforeOperator>
372                 <enable>true</enable>
373                 <lineLength>80</lineLength>
374             </general>
375             <ondemand>
376                 <after>
377                     <assignment>false</assignment>
378                     <leftParenthesis>false</leftParenthesis>
379                     <parameter>false</parameter>
380                     <types>
381                         <extends>false</extends>
382                         <implements>false</implements>
383                         <throws>false</throws>
384                     </types>
385                 </after>
386                 <before>
387                     <rightParenthesis>false</rightParenthesis>
388                 </before>
389                 <groupingParentheses>false</groupingParentheses>
390             </ondemand>
391         </wrapping>
392     </printer>
393 </jalopy>
394