From 0dd0a6bb09fa26b634b04051e0a539f527feaf2a Mon Sep 17 00:00:00 2001 From: jprocter Date: Sat, 17 Nov 2012 18:33:46 +0000 Subject: [PATCH] formatting and javadoc --- src/jalview/analysis/AlignSeq.java | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java index 4a8955b..8b20554 100755 --- 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 . */ 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) -- 1.7.10.2