From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 25 Oct 2016 15:21:48 +0000 (+0100)
Subject: JAL-98 javadoc added
X-Git-Tag: Release_2_10_1^2~22^2~3^2~5
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=40eedee78090598059a57f4e4bcfcb1a8f946a5b;p=jalview.git

JAL-98 javadoc added
---

diff --git a/src/jalview/analysis/Profile.java b/src/jalview/analysis/Profile.java
index b27da9f..d94d031 100644
--- a/src/jalview/analysis/Profile.java
+++ b/src/jalview/analysis/Profile.java
@@ -93,26 +93,53 @@ public class Profile
     return pid;
   }
 
+  /**
+   * Returns the full symbol counts for this profile
+   * 
+   * @return
+   */
   public ResidueCount getCounts()
   {
     return counts;
   }
 
+  /**
+   * Returns the number of sequences in the profile
+   * 
+   * @return
+   */
   public int getHeight()
   {
     return height;
   }
 
+  /**
+   * Returns the number of sequences in the profile which had a gap character
+   * (or were too short to be included in this column's profile)
+   * 
+   * @return
+   */
   public int getGapped()
   {
     return gapped;
   }
 
+  /**
+   * Returns the highest count for any symbol(s) in the profile
+   * 
+   * @return
+   */
   public int getMaxCount()
   {
     return maxCount;
   }
 
+  /**
+   * Returns the symbol (or concatenated symbols) which have the highest count
+   * in the profile, or an empty string if there were no symbols counted
+   * 
+   * @return
+   */
   public String getModalResidue()
   {
     return modalResidue;