Merge branch 'hotfix-1.1.21'

Author: arteymix

pom.xml

@@ -5,7 +5,7 @@
 	<name>baseCode</name>
 	<groupId>baseCode</groupId>
 	<artifactId>baseCode</artifactId>
-	<version>1.1.20</version>
+	<version>1.1.21</version>
 	<inceptionYear>2003</inceptionYear>
 	<description>
 		<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>
@@ -346,6 +346,8 @@
 					<!-- Do not push to remote -->
 					<pushRemote>false</pushRemote>
 					<verbose>true</verbose>
+					<useSnapshotInHotfix>true</useSnapshotInHotfix>
+					<useSnapshotInRelease>true</useSnapshotInRelease>
 					<!-- Branch naming schemes -->
 					<gitFlowConfig>
 						<productionBranch>master</productionBranch>

src/ubic/basecode/math/DescriptiveWithMissing.java

@@ -484,7 +484,7 @@ private DoubleMatrix<String, String> addIntercept( int rows ) {
      * The primary method for actually setting up the design matrix. Redundant or constant columns are dropped (except
      * the intercept, if included)
      *
-     * @param  which        column of the input matrix are we working on.
+     * @param  columnNum        column of the input matrix are we working on.
      * @param  factorValues of doubles or strings.
      * @param  inputDesign
      * @param  start        1 or 2. Set to 1 to get a column for each level (must not have an intercept in the model);

src/ubic/basecode/math/linearmodels/DesignMatrix.java

@@ -35,7 +35,7 @@
  */
 abstract class AbstractOntologyResource implements OntologyResource {
 
-    protected static Logger log = LoggerFactory.getLogger( AbstractOntologyResource.class );
+    protected static final Logger log = LoggerFactory.getLogger( AbstractOntologyResource.class );
 
     private static final Comparator<OntologyResource> comparator = Comparator
             .comparing( OntologyResource::getScore, nullsLast( reverseOrder() ) )
@@ -60,6 +60,12 @@ public String getUri() {
         return res.getURI();
     }
 
+    @Override
+    public String getLocalName() {
+        return res.getLocalName();
+    }
+
+    @Override
     public String getLabel() {
         String label = res.getLabel( "EN" );
         if ( label == null ) {
@@ -68,6 +74,16 @@ public String getLabel() {
         return label;
     }
 
+    @Nullable
+    @Override
+    public String getComment() {
+        String label = res.getComment( "EN" );
+        if ( label == null ) {
+            label = res.getLabel( null );
+        }
+        return label;
+    }
+
     @Override
     public boolean isObsolete() {
         return res.hasLiteral( OWL2.deprecated, true );
@@ -94,9 +110,8 @@ public boolean equals( Object obj ) {
             if ( other.getLabel() != null ) return false;
         } else if ( !getLabel().equals( other.getLabel() ) ) return false;
         if ( getUri() == null ) {
-            if ( other.getUri() != null ) return false;
-        } else if ( !getUri().equals( other.getUri() ) ) return false;
-        return true;
+            return other.getUri() == null;
+        } else return getUri().equals( other.getUri() );
     }
 
     @Override