Add 'qvalueColumn' argument to 'build-table' command.

Refs #416

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/tunables/TableTunables.java

@@ -20,9 +20,12 @@ public class TableTunables {
 	@Tunable(required=true, description="Name of column that contains the list of genes.")
 	public String genesColumn;
 
-	@Tunable(required=true, description="Name of column that contains p values.")
+	@Tunable(description="Name of column that contains p values. At least one of 'pvalueColumn' or 'qvalueColumn' must be provided.")
 	public String pvalueColumn;
 
+	@Tunable(description="Name of column that contains q values. At least one of 'pvalueColumn' or 'qvalueColumn' must be provided.")
+	public String qvalueColumn;
+	
 	@Tunable(description="Name of column that contains the gene set description (optional).")
 	public String descriptionColumn;
 
@@ -51,14 +54,18 @@ private CyTable getTable() {
 	public TableParameters getTableParameters() throws IllegalArgumentException {
 		CyTable table = getTable();
 		if(table == null)
-			throw new IllegalArgumentException("Table '" + table + "' is invalid.");
+			throw new IllegalArgumentException("Table '" + this.table + "' is invalid.");
 
+		if(pvalueColumn == null && qvalueColumn == null)
+			throw new IllegalArgumentException("At least one of 'pvalueColumn' or 'qvalueColumn' must be provided.");
+			
 		validateColumn(table, nameColumn, false, String.class, true);
 		validateColumn(table, genesColumn, true, String.class, true);
-		validateColumn(table, pvalueColumn, false, Double.class, true);
 		validateColumn(table, descriptionColumn, false, String.class, false);
+		validateColumn(table, pvalueColumn, false, Double.class, false);
+		validateColumn(table, qvalueColumn, false, Double.class, false);
 
-		return new TableParameters(table, nameColumn, genesColumn, pvalueColumn, null, descriptionColumn, null);
+		return new TableParameters(table, nameColumn, genesColumn, pvalueColumn, qvalueColumn, descriptionColumn, null);
 	}
 
 
@@ -69,10 +76,8 @@ private static void validateColumn(CyTable table, String name, boolean isList, C
 			return;
 
 		CyColumn column = table.getColumn(name);
-		if(column == null && required)
-			throw new IllegalArgumentException("Column '" + name + "' is invalid.");
 		if(column == null)
-			return;
+			throw new IllegalArgumentException("Column '" + name + "' is invalid.");
 
 		// if the column exists it must still be of the required type
 		if((isList && !column.getListElementType().equals(type)) || (!isList && !column.getType().equals(type)))