JAL-2418 source formatting

[jalview.git] / src / jalview / datamodel / Profile.java

diff --git a/src/jalview/datamodel/Profile.java b/src/jalview/datamodel/Profile.java
index 2951e9e..8638896 100644 (file)
--- a/src/jalview/datamodel/Profile.java
+++ b/src/jalview/datamodel/Profile.java
@@ -1,22 +1,40 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
-
 /**
- * A data bean to hold the result of computing a profile for a column of an
- * alignment
+ * A profile for one column of an alignment
  * 
  * @author gmcarstairs
  *
  */
-public class Profile
+public class Profile implements ProfileI
 {
   /*
-   * counts of keys (chars)
+   * an object holding counts of symbols in the profile
    */
   private ResidueCount counts;
 
   /*
-   * the number of sequences in the profile
+   * the number of sequences (gapped or not) in the profile
    */
   private int height;
 
@@ -57,24 +75,19 @@ public class Profile
     this.modalResidue = modalRes;
   }
 
-  /**
-   * Set the full profile of counts
-   * 
-   * @param residueCounts
+  /* (non-Javadoc)
+   * @see jalview.datamodel.ProfileI#setCounts(jalview.datamodel.ResidueCount)
    */
+  @Override
   public void setCounts(ResidueCount residueCounts)
   {
     this.counts = residueCounts;
   }
 
-  /**
-   * Returns the percentage identity of the profile, i.e. the highest proportion
-   * of conserved (equal) symbols. The percentage is as a fraction of all
-   * sequences, or only ungapped sequences if flag ignoreGaps is set true.
-   * 
-   * @param ignoreGaps
-   * @return
+  /* (non-Javadoc)
+   * @see jalview.datamodel.ProfileI#getPercentageIdentity(boolean)
    */
+  @Override
   public float getPercentageIdentity(boolean ignoreGaps)
   {
     if (height == 0)
@@ -93,63 +106,55 @@ public class Profile
     return pid;
   }
 
-  /**
-   * Returns the full symbol counts for this profile
-   * 
-   * @return
+  /* (non-Javadoc)
+   * @see jalview.datamodel.ProfileI#getCounts()
    */
+  @Override
   public ResidueCount getCounts()
   {
     return counts;
   }
 
-  /**
-   * Returns the number of sequences in the profile
-   * 
-   * @return
+  /* (non-Javadoc)
+   * @see jalview.datamodel.ProfileI#getHeight()
    */
+  @Override
   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
+  /* (non-Javadoc)
+   * @see jalview.datamodel.ProfileI#getGapped()
    */
+  @Override
   public int getGapped()
   {
     return gapped;
   }
 
-  /**
-   * Returns the highest count for any symbol(s) in the profile
-   * 
-   * @return
+  /* (non-Javadoc)
+   * @see jalview.datamodel.ProfileI#getMaxCount()
    */
+  @Override
   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
+  /* (non-Javadoc)
+   * @see jalview.datamodel.ProfileI#getModalResidue()
    */
+  @Override
   public String getModalResidue()
   {
     return modalResidue;
   }
 
-  /**
-   * Answers the number of non-gapped sequences in the profile
-   * 
-   * @return
+  /* (non-Javadoc)
+   * @see jalview.datamodel.ProfileI#getNonGapped()
    */
+  @Override
   public int getNonGapped()
   {
     return height - gapped;