JAL-98 ProfileI interface for Profile

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

diff --git a/src/jalview/datamodel/Profile.java b/src/jalview/datamodel/Profile.java
index 2951e9e..5464596 100644 (file)
--- a/src/jalview/datamodel/Profile.java
+++ b/src/jalview/datamodel/Profile.java
@@ -2,21 +2,20 @@ 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 +56,19 @@ 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 +87,55 @@ 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;