X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=ab6fae85bbcdd095a9d02d27c5a7d0e03ab5aac4;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=b9119ed2187946080b4b2eef9dceeb7832915430;hpb=1889827c44c51f6353fe8619e5d44b421158af23;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index b9119ed..ab6fae8 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -19,6 +19,7 @@
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
+
 import java.util.*;
 
 import java.awt.*;
@@ -270,10 +271,15 @@ public class AlignSeq
 
   /**
    * 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 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
    */
@@ -288,11 +294,17 @@ public class AlignSeq
 
   /**
    * 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
+   * 
+   * @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)
@@ -307,7 +319,7 @@ 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)
@@ -972,7 +984,7 @@ public class AlignSeq
       {
         lastmatch = true;
         // extend mapping interval.
-        if (lp1 + 1 != alignpos || lp2+1 !=pdbpos)
+        if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos)
         {
           as1.add(Integer.valueOf(alignpos));
           as2.add(Integer.valueOf(pdbpos));