From 59cd693d999cfeb2df6981c9e26863ef4f3f30ff Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 23 Oct 2017 10:57:54 +0100
Subject: [PATCH] JAL-2737 JAL-1854 corrected package suppressions, updated
 import controls

---
 .checkstyle                              |    1 -
 utils/checkstyle/checkstyle-suppress.xml |   10 +++++----
 utils/checkstyle/import-control.xml      |   36 +++++++++++++++++++++++++-----
 3 files changed, 37 insertions(+), 10 deletions(-)

diff --git a/.checkstyle b/.checkstyle
index 0329bb7..a87fa04 100644
--- a/.checkstyle
+++ b/.checkstyle
@@ -8,5 +8,4 @@
     <file-match-pattern match-pattern="src/.*.java" include-pattern="true"/>
     <file-match-pattern match-pattern="resources/.*.properties" include-pattern="true"/>
   </fileset>
-  <filter name="NonSrcDirs" enabled="false"/>
 </fileset-config>
diff --git a/utils/checkstyle/checkstyle-suppress.xml b/utils/checkstyle/checkstyle-suppress.xml
index ac9e260..122b8d0 100644
--- a/utils/checkstyle/checkstyle-suppress.xml
+++ b/utils/checkstyle/checkstyle-suppress.xml
@@ -21,10 +21,12 @@
     <!-- 
     	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[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="[\\/]com[\\/]github*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="[\\/]com[\\/]stevesoft*"/>
+    <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="[\\/]uk[\\/]ac*"/>
     
     <!-- 
     	ImportControl can only handle one top level package
diff --git a/utils/checkstyle/import-control.xml b/utils/checkstyle/import-control.xml
index 946f71c..c47aaec 100644
--- a/utils/checkstyle/import-control.xml
+++ b/utils/checkstyle/import-control.xml
@@ -37,13 +37,39 @@
 		<subpackage name="datamodel">
 	    	<disallow pkg="jalview.gui"/>
 	    	<allow pkg="fr.orsay.lri.varna"/>
-			<subpackage name="xdb">
-				<subpackage name="embl">
-			    	<allow pkg="org.exolab.castor"/>
-			    </subpackage>
+			<subpackage name="xdb.embl">
+		    	<allow pkg="org.exolab.castor"/>
 		    </subpackage>
 	    </subpackage>
    		
+		<subpackage name="ext">
+			<subpackage name="ensembl">
+		    	<allow pkg="javax.ws"/>
+		    	<allow pkg="org.json"/>
+			</subpackage>
+			<subpackage name="htsjdk">
+		    	<allow pkg="htsjdk"/>
+			</subpackage>
+			<subpackage name="jmol">
+		    	<allow pkg="MCview"/>
+		    	<allow pkg="org.jmol"/>
+			</subpackage>
+			<subpackage name="paradise">
+		    	<allow pkg="org.apache"/>
+		    	<allow pkg="org.json"/>
+			</subpackage>
+			<subpackage name="rbvi">
+		    	<allow pkg="ext.edu.ucsf"/>
+		    	<allow pkg="javax.servlet"/>
+			</subpackage>
+			<subpackage name="so">
+		    	<allow pkg="org.biojava"/>
+			</subpackage>
+			<subpackage name="varna">
+		    	<allow pkg="fr.orsay"/>
+			</subpackage>
+	    </subpackage>
+   		
 		<subpackage name="fts">
 	    	<allow pkg="javax.swing"/>
 	    	<allow pkg="javax.ws"/>
@@ -101,7 +127,7 @@
 		</subpackage>
 
 		<subpackage name="schemes">
-			<allow pkg="org.exolab.castor"/>
+			<allow pkg="org.exolab.castor" class="jalview.schemes.ColourSchemeLoader"/>
 		</subpackage>
 
 		<subpackage name="structure">
-- 
1.7.10.2