formatting and javadoc

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 4a8955b..8b20554 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -16,7 +16,6 @@
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.analysis;
-
 import java.util.*;
 
 import java.awt.*;
@@ -267,16 +266,11 @@ public class AlignSeq
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param s1
-   *          DOCUMENT ME!
-   * @param string1
-   *          - string to align for sequence1
-   * @param s2
-   *          sequence 2
-   * @param string2
-   *          - string to align for sequence2
+   * Construct score matrix for sequences with standard DNA or PEPTIDE matrix
+   * @param s1 - sequence 1
+   * @param string1 - string to use for s1
+   * @param s2 - sequence 2
+   * @param string2 - string to use for s2
    * @param type
    *          DNA or PEPTIDE
    */
@@ -289,6 +283,14 @@ public class AlignSeq
     SeqInit(string1, string2);
   }
 
+  /**
+   * Construct score matrix for sequences with custom substitution matrix
+   * @param s1 - sequence 1
+   * @param string1 - string to use for s1
+   * @param s2 - sequence 2
+   * @param string2 - string to use for s2
+   * @param scoreMatrix - substitution matrix to use for alignment
+   */
   public void SeqInit(SequenceI s1, String string1, SequenceI s2,
           String string2, ScoreMatrix scoreMatrix)
   {
@@ -302,7 +304,7 @@ public class AlignSeq
    * construct score matrix for string1 and string2 (after removing any existing
    * gaps
    * 
-   * @param string1
+   * @param string1 
    * @param string2
    */
   private void SeqInit(String string1, String string2)