From 4a2b8ad79f767d56fe23a3f44707c951c4878215 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 6 Dec 2018 10:05:57 +0000
Subject: [PATCH] JAL-1854 Checkstyle updated to 8.12

---
 utils/checkstyle/README.txt              |   17 ++++++++++++++---
 utils/checkstyle/checkstyle-suppress.xml |    1 +
 utils/checkstyle/checkstyle.xml          |   24 +++++++++---------------
 utils/checkstyle/import-control.xml      |    4 ++++
 4 files changed, 28 insertions(+), 18 deletions(-)

diff --git a/utils/checkstyle/README.txt b/utils/checkstyle/README.txt
index e38064e..54f4e48 100644
--- a/utils/checkstyle/README.txt
+++ b/utils/checkstyle/README.txt
@@ -1,6 +1,8 @@
 Checkstyle for Jalview
 ----------------------
 
+See
+https://issues.jalview.org/browse/JAL-1854
 http://checkstyle.sourceforge.net/
 GNU LGPL
 
@@ -9,8 +11,16 @@ To get the Eclipse Checkstyle plugin
 	- Help | Eclipse Marketplace
 	- search for checkstyle
 	- install eclipse-cs checkstyle plugin
-The current version is 6.19.1 (August 2016).
 
+Change Log
+----------
+See http://checkstyle.sourceforge.net/releasenotes.html
+Aug 2016	Initial version used is 6.19.1
+Dec 2018	Updated to 8.12.0 (latest on Eclipse Marketplace, 8.15 is latest release)
+			SuppressionCommentFilter relocated (changed in 8.1)
+			FileContentsHolder removed (changed in 8.2)
+			Updates to import-control.xml for code changes (htsjdk, stackoverflowusers)
+			
 Config
 ------
 
@@ -37,6 +47,7 @@ How to use checkstyle
 	Option 2: on demand on selected code
 		- right-click on a class or package and Checkstyle | Check code with checkstyle
 		- (or Clear Checkstyle violations to remove checkstyle warnings)
+		- recommended to use this as a QA step when changing or reviewing code
 
 Checkstyle rules
 ----------------
@@ -64,11 +75,11 @@ Suppressing findings
 Tips
 ----
 	Sometimes checkstyle needs a kick before it will refresh its findings.
-	A whitespace edit in checkstyle.xml usually does this. There may be better ways.
+	Click the 'refresh' icon at top right in Eclipse | Preferences | Checkstyle.
 	
 	Invalid configuration files may result in checkstyle failing with an error reported
 	in the Eclipse log file. 
-	Help | Installation Details | Configuration takes you to a screen with a 
+	Eclipse | About | Installation Details | Configuration takes you to a screen with a 
 	'View Error Log' button.
 	
 	Sometimes checkstyle can fail silently. Try 'touching' (editing) config files, failing
diff --git a/utils/checkstyle/checkstyle-suppress.xml b/utils/checkstyle/checkstyle-suppress.xml
index 122b8d0..29a3047 100644
--- a/utils/checkstyle/checkstyle-suppress.xml
+++ b/utils/checkstyle/checkstyle-suppress.xml
@@ -26,6 +26,7 @@
     <suppress checks="[a-zA-Z0-9]*" files="[\\/]ext[\\/]edu*"/>
     <suppress checks="[a-zA-Z0-9]*" files="[\\/]ext[\\/]vamsas*"/>
     <suppress checks="[a-zA-Z0-9]*" files="[\\/]org[\\/]jibble*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="[\\/]org[\\/]stackoverflowusers*"/>
     <suppress checks="[a-zA-Z0-9]*" files="[\\/]uk[\\/]ac*"/>
     
     <!-- 
diff --git a/utils/checkstyle/checkstyle.xml b/utils/checkstyle/checkstyle.xml
index 85ac8e6..17946f7 100644
--- a/utils/checkstyle/checkstyle.xml
+++ b/utils/checkstyle/checkstyle.xml
@@ -16,18 +16,6 @@
 	</module>
 
 	<!-- 
-		Allow suppression of rules by comments, e.g.:
-		// CHECKSTYLE.OFF: ParameterNumber
-		..method declaration
-		// CHECKSTYLE.ON: ParameterNumber
-	-->
-	<module name="SuppressionCommentFilter">
-		<property name="offCommentFormat" value="CHECKSTYLE.OFF\: ([\w\|]+)"/>
-		<property name="onCommentFormat" value="CHECKSTYLE.ON\: ([\w\|]+)"/>
-		<property name="checkFormat" value="$1"/>
-	</module>
-
-	<!-- 
 		Check language bundles have the same keys and no duplicates
 		(ensure Checkstyle is configured to scan non-source files)
 	 -->
@@ -54,10 +42,16 @@
 		<property name="tabWidth" value="4"/>
 
 		<!-- 
-			Enables parsing of suppressions comments
-			see http://checkstyle.sourceforge.net/config_filters.html#SuppressionCommentFilter 
+			Allow suppression of rules by comments, e.g.:
+			// CHECKSTYLE.OFF: ParameterNumber
+			..method declaration
+			// CHECKSTYLE.ON: ParameterNumber
 		-->
-		<module name="FileContentsHolder"/>
+		<module name="SuppressionCommentFilter">
+			<property name="offCommentFormat" value="CHECKSTYLE.OFF\: ([\w\|]+)"/>
+			<property name="onCommentFormat" value="CHECKSTYLE.ON\: ([\w\|]+)"/>
+			<property name="checkFormat" value="$1"/>
+		</module>
 
 	<!-- ****************************** -->
 	<!--         NAMING STANDARDS       -->
diff --git a/utils/checkstyle/import-control.xml b/utils/checkstyle/import-control.xml
index c47aaec..478966f 100644
--- a/utils/checkstyle/import-control.xml
+++ b/utils/checkstyle/import-control.xml
@@ -94,6 +94,7 @@
 	    	<allow pkg="compbio.metadata" class="jalview.gui.WsJobParameters"/>
 	    	<allow pkg="fr.orsay.lri.varna" class="jalview.gui.AppVarna"/>
 	    	<allow pkg="fr.orsay.lri.varna" class="jalview.gui.AppVarnaBinding"/>
+	    	<allow pkg="org.stackoverflowusers.file" class="jalview.gui.Desktop"/>
 	    	<allow pkg="uk.ac.vamsas" class="jalview.gui.VamsasApplication"/>
 	    </subpackage>
    		
@@ -116,6 +117,9 @@
 	    	<allow pkg="uk.ac.vamsas"/>
 	    	<allow pkg="fr.orsay.lri.varna"/>
 	    	<allow pkg="MCview"/>
+			<subpackage name="vcf">
+		    	<allow pkg="htsjdk\.*" regex="true"/>
+			</subpackage>	    
 		</subpackage>	    
 		   		
 		<subpackage name="javascript">
-- 
1.7.10.2