From 78d4775e4450ba6579c5d9824a78ad99cbccda22 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 29 Aug 2016 11:23:58 +0100
Subject: [PATCH] JAL-1854 checkstyle relocated to /utils, newlines to Unix
 (?)

---
 .checkstyle                                        |    2 +-
 {resources => utils}/checkstyle/README.txt         |    9 +-
 .../checkstyle/checkstyle-suppress.xml             |   90 ++++++++++----------
 {resources => utils}/checkstyle/checkstyle.xml     |    4 +-
 {resources => utils}/checkstyle/import-control.xml |    0
 5 files changed, 53 insertions(+), 52 deletions(-)
 rename {resources => utils}/checkstyle/README.txt (90%)
 rename {resources => utils}/checkstyle/checkstyle-suppress.xml (96%)
 rename {resources => utils}/checkstyle/checkstyle.xml (98%)
 rename {resources => utils}/checkstyle/import-control.xml (100%)

diff --git a/.checkstyle b/.checkstyle
index c2a7260..0329bb7 100644
--- a/.checkstyle
+++ b/.checkstyle
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
 <fileset-config file-format-version="1.2.0" simple-config="false" sync-formatter="false">
-  <local-check-config name="JalviewCheckstyle" location="resources/checkstyle/checkstyle.xml" type="project" description="">
+  <local-check-config name="JalviewCheckstyle" location="utils/checkstyle/checkstyle.xml" type="project" description="">
     <additional-data name="protect-config-file" value="false"/>
   </local-check-config>
   <fileset name="source" enabled="true" check-config-name="JalviewCheckstyle" local="true">
diff --git a/resources/checkstyle/README.txt b/utils/checkstyle/README.txt
similarity index 90%
rename from resources/checkstyle/README.txt
rename to utils/checkstyle/README.txt
index 1c2aced..119c68e 100644
--- a/resources/checkstyle/README.txt
+++ b/utils/checkstyle/README.txt
@@ -18,7 +18,7 @@ Config
 	This includes confining its scope to src/*.java and resources/*.properties.
 	This can be modified interactively through the checkstyle properties editor.
 	
-	Checkstyle config files in resources/checkstyle:
+	Checkstyle config files in utils/checkstyle:
 		checkstyle.xml          : main configuration file with selected checkstyle modules
 		checkstyle-suppress.xml : rules to exclude certain checks / files
 		import-control.xml      : package import rules
@@ -36,6 +36,7 @@ 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)
 
 Checkstyle rules
 ----------------
@@ -49,13 +50,13 @@ Checkstyle rules
 	
 Suppressing findings
 --------------------
-	If there are warnings you judge it ok to suppress, your options are
-	(from most global to most local scope):
+	If there are warnings you judge it ok to suppress (false positives), 
+	your options are (from most global to most local impact):
 	- remove the rule entirely
 	- adjust its properties
 	- add an entry in checkstyle-suppress.xml to skip the file for the rule
 	- add comments around the reported source lines
-		// CHECKSTYLE.OFF: RuleName
+		// CHECKSTYLE.OFF: RuleName 'a comment to justify suppression'
 		source code here
 		// CHECKSTYLE.ON: RuleName
 	The suppression should be as localised as possible, to avoid false negatives.
diff --git a/resources/checkstyle/checkstyle-suppress.xml b/utils/checkstyle/checkstyle-suppress.xml
similarity index 96%
rename from resources/checkstyle/checkstyle-suppress.xml
rename to utils/checkstyle/checkstyle-suppress.xml
index 0c1d2ee..ac9e260 100644
--- a/resources/checkstyle/checkstyle-suppress.xml
+++ b/utils/checkstyle/checkstyle-suppress.xml
@@ -1,46 +1,46 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!DOCTYPE suppressions PUBLIC
-    "-//Puppy Crawl//DTD Suppressions 1.1//EN"
-    "http://www.puppycrawl.com/dtds/suppressions_1_1.dtd">
-
-<suppressions>
-	<!-- 
-		Do not put individual file-level suppressions here.
-		Instead use embedded comments to switch checks on and off.
-    -->
-        
-    <!-- 
-        Suppress check of XML binding generated code packages 
-    --> 
-    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]schemabinding[\\/]*"/>
-    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]binding[\\/]*"/>
-    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]json[\\/]binding[\\/]*"/>
-    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]xml[\\/]binding[\\/]*"/>
-        
-    <!-- 
-    	Suppress check of externally sourced code 
-    --> 
-    <suppress checks="[a-zA-Z0-9]*" files="com[\\/]*"/>
-    <suppress checks="[a-zA-Z0-9]*" files="ext[\\/]*"/>
-    <suppress checks="[a-zA-Z0-9]*" files="org[\\/]*"/>
-    <suppress checks="[a-zA-Z0-9]*" files="uk[\\/]*"/>
-    
-    <!-- 
-    	ImportControl can only handle one top level package
-    -->
-    <suppress checks="ImportControl" files="MCview[\\/]*" />
-    <suppress checks="ImportControl" files="vamsas[\\/]*" />
-    
-    <!--  
-    	Suppress checks by name 
-    -->
-	<suppress checks="FinalLocalVariable" files=".*\.java"/>
-    
-    <!--  
-    	Suppress checks by id 
-    -->
-	<suppress id="InterfaceNaming" files=".*\.java"/>
-	<suppress id="NoStaticInitialization" files=".*\.java"/>
-	  
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!DOCTYPE suppressions PUBLIC
+    "-//Puppy Crawl//DTD Suppressions 1.1//EN"
+    "http://www.puppycrawl.com/dtds/suppressions_1_1.dtd">
+
+<suppressions>
+	<!-- 
+		Do not put individual file-level suppressions here.
+		Instead use embedded comments to switch checks on and off.
+    -->
+        
+    <!-- 
+        Suppress check of XML binding generated code packages 
+    --> 
+    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]schemabinding[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]binding[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]json[\\/]binding[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]xml[\\/]binding[\\/]*"/>
+        
+    <!-- 
+    	Suppress check of externally sourced code 
+    --> 
+    <suppress checks="[a-zA-Z0-9]*" files="com[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="ext[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="org[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="uk[\\/]*"/>
+    
+    <!-- 
+    	ImportControl can only handle one top level package
+    -->
+    <suppress checks="ImportControl" files="MCview[\\/]*" />
+    <suppress checks="ImportControl" files="vamsas[\\/]*" />
+    
+    <!--  
+    	Suppress checks by name 
+    -->
+	<suppress checks="FinalLocalVariable" files=".*\.java"/>
+    
+    <!--  
+    	Suppress checks by id 
+    -->
+	<suppress id="InterfaceNaming" files=".*\.java"/>
+	<suppress id="NoStaticInitialization" files=".*\.java"/>
+	  
 </suppressions>
\ No newline at end of file
diff --git a/resources/checkstyle/checkstyle.xml b/utils/checkstyle/checkstyle.xml
similarity index 98%
rename from resources/checkstyle/checkstyle.xml
rename to utils/checkstyle/checkstyle.xml
index 423f698..7ca2d26 100644
--- a/resources/checkstyle/checkstyle.xml
+++ b/utils/checkstyle/checkstyle.xml
@@ -12,7 +12,7 @@
 		Add any metrics that you wish to suppress to the following file.
 	-->
 	<module name="SuppressionFilter">
-		<property name="file" value="${basedir}/resources/checkstyle/checkstyle-suppress.xml"/>
+		<property name="file" value="${basedir}/utils/checkstyle/checkstyle-suppress.xml"/>
 	</module>
 
 	<!-- 
@@ -327,7 +327,7 @@
 			see http://checkstyle.sourceforge.net/config_imports.html#ImportControl 
 		-->
 		<module name="ImportControl">
-		    <property name="file" value="${basedir}/resources/checkstyle/import-control.xml"/>
+		    <property name="file" value="${basedir}/utils/checkstyle/import-control.xml"/>
 			<property name="severity" value="error"/>
 		</module>
 		
diff --git a/resources/checkstyle/import-control.xml b/utils/checkstyle/import-control.xml
similarity index 100%
rename from resources/checkstyle/import-control.xml
rename to utils/checkstyle/import-control.xml
-- 
1.7.10.2