JAL-2737 JAL-1854 corrected package suppressions, updated import

controls

diff --git a/.checkstyle b/.checkstyle
index 0329bb7..a87fa04 100644 (file)
--- 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 (file)
--- 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 (file)
--- 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">