From 4f6d92b81a8bedf3d74c81e02e0dbf6600829a60 Mon Sep 17 00:00:00 2001
From: Ben Soares <bsoares@dundee.ac.uk>
Date: Thu, 7 Mar 2019 15:29:38 +0000
Subject: [PATCH] JAL-3130 deprecation change preparation

---
 build-j11.xml                      |    2 ++
 src/jalview/schemes/Consensus.java |    4 +++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/build-j11.xml b/build-j11.xml
index 4bc58b4..35d3926 100755
--- a/build-j11.xml
+++ b/build-j11.xml
@@ -300,7 +300,9 @@
     <echo message="build.classpath is '${echoClasspath}'" />
     -->
     <echo message="javac.target is '${javac.target}'" />
+    <echo message="adding -Xlint:deprecation to javac" if:set="deprecation"/>
     <javac includeantruntime="false" source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
+      <compilerarg value="-Xlint:deprecation" if:set="deprecation" />
       <exclude name="jalview/*applet*" />
       <exclude name="jalview/appletgui/**" />
       <exclude name="com/stevesoft/**" />
diff --git a/src/jalview/schemes/Consensus.java b/src/jalview/schemes/Consensus.java
index f0d1990..9d2c738 100755
--- a/src/jalview/schemes/Consensus.java
+++ b/src/jalview/schemes/Consensus.java
@@ -53,8 +53,10 @@ public class Consensus
   /**
    * @deprecated Use {@link #isConserved(int[][],int,int,boolean)} instead
    */
+  @Deprecated
   public boolean isConserved(int[][] cons2, int col, int size)
   {
+    System.out.println("DEPRECATED!!!!");
     return isConserved(cons2, col, size, true);
   }
 
@@ -71,7 +73,7 @@ public class Consensus
       tot += cons2[col][mask[i]];
     }
 
-    if ((double) tot > ((threshold * size) / 100))
+    if (tot > ((threshold * size) / 100))
     {
       // System.out.println("True conserved "+tot+" from "+threshold+" out of
       // "+size+" : "+maskstr);
-- 
1.7.10.2