From 75d5069a8e8942343a999fe4d474079856fbc5d3 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 18 Nov 2016 08:55:47 +0000
Subject: [PATCH] JAL-98 with the two types missing from last commit
 Profiles[I] !

---
 src/jalview/datamodel/Profiles.java      |   43 ++++++++++++++++++++++++++++++
 src/jalview/datamodel/ProfilesI.java     |   12 +++++++++
 src/jalview/workers/ConsensusThread.java |    3 ++-
 3 files changed, 57 insertions(+), 1 deletion(-)
 create mode 100644 src/jalview/datamodel/Profiles.java
 create mode 100644 src/jalview/datamodel/ProfilesI.java

diff --git a/src/jalview/datamodel/Profiles.java b/src/jalview/datamodel/Profiles.java
new file mode 100644
index 0000000..98a8c6d
--- /dev/null
+++ b/src/jalview/datamodel/Profiles.java
@@ -0,0 +1,43 @@
+package jalview.datamodel;
+
+public class Profiles implements ProfilesI
+{
+
+  private ProfileI[] profiles;
+
+  public Profiles(ProfileI[] p)
+  {
+    profiles = p;
+  }
+
+  /**
+   * Returns the profile for the given column, or null if none found
+   * 
+   * @param col
+   */
+  @Override
+  public ProfileI get(int col)
+  {
+    return profiles != null && col >= 0 && col < profiles.length ? profiles[col]
+            : null;
+  }
+
+  /**
+   * Returns the first column (base 0) covered by the profiles
+   */
+  @Override
+  public int getStartColumn()
+  {
+    return 0;
+  }
+
+  /**
+   * Returns the last column (base 0) covered by the profiles
+   */
+  @Override
+  public int getEndColumn()
+  {
+    return profiles == null ? 0 : profiles.length - 1;
+  }
+
+}
diff --git a/src/jalview/datamodel/ProfilesI.java b/src/jalview/datamodel/ProfilesI.java
new file mode 100644
index 0000000..6719de6
--- /dev/null
+++ b/src/jalview/datamodel/ProfilesI.java
@@ -0,0 +1,12 @@
+package jalview.datamodel;
+
+public interface ProfilesI
+{
+
+  ProfileI get(int i);
+
+  int getStartColumn();
+
+  int getEndColumn();
+
+}
diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index b6c7a91..debe45d 100644
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -200,7 +200,8 @@ public class ConsensusThread extends AlignCalcWorker
   {
 
     long nseq = getSequences().length;
-    AAFrequency.completeConsensus(consensusAnnotation, hconsensus, 0,
+    AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
+            hconsensus.getStartColumn(),
             hconsensus.getEndColumn() + 1,
             alignViewport.isIgnoreGapsConsensus(),
             alignViewport.isShowSequenceLogo(), nseq);
-- 
1.7.10.2