Minor documentation changes

sbliven · sbliven · commit 3d69a6bc4730 · 2011-10-08T01:53:27.000Z
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@9303 7c6358e6-4a41-0410-a743-a5b2a554c398
diff --git a/biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleSubstitutionMatrix.java b/biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleSubstitutionMatrix.java
@@ -59,7 +59,7 @@ public class SimpleSubstitutionMatrix<C extends Compound> implements Substitutio
     private List<C> rows, cols;
 
     /**
-     * Creates a substitution matrix using the defaults.
+     * Creates a substitution matrix using the defaults (BLOSUM 62).
      *
      * @throws ClassCastException if type parameter C is not {@link AminoAcidCompound}
      */
diff --git a/biojava3-alignment/src/main/java/org/biojava3/alignment/aaindex/ScaledSubstitutionMatrix.java b/biojava3-alignment/src/main/java/org/biojava3/alignment/aaindex/ScaledSubstitutionMatrix.java
@@ -9,8 +9,14 @@
 import org.biojava3.core.sequence.template.CompoundSet;
 
 
-/** The biojava-alignment module represents substitution matrices with short values. This is for performance reasons. Some substitution matrices however are provided as float values with up to 2 after-comma precision.
- * In order to be able to use them in the alignment module these are scaled in order to be able to represent as short values.  The method {@link #getScale()} provides access to the scaling factor.
+/**
+ * The biojava-alignment module represents substitution matrices with short
+ * values. This is for performance reasons. Some substitution matrices, however,
+ * are provided as float values with up to 2 decimal places.
+ * <p>
+ * In order to be able to use them in the alignment module these are scaled in
+ * order to be able to represent as short values.
+ * The method {@link #getScale()} provides access to the scaling factor.
  *  
  *  
  * @author Andreas Prlic

Original file line number	Diff line number	Diff line change
`@@ -59,7 +59,7 @@ public class SimpleSubstitutionMatrix<C extends Compound> implements Substitutio`
`59`	`59`	`private List<C> rows, cols;`
`60`	`60`
`61`	`61`	`/**`
`62`		`- * Creates a substitution matrix using the defaults.`
	`62`	`+ * Creates a substitution matrix using the defaults (BLOSUM 62).`
`63`	`63`	`*`
`64`	`64`	`* @throws ClassCastException if type parameter C is not {@link AminoAcidCompound}`
`65`	`65`	`*/`