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[jalview.git] / src / jalview / analysis / AlignSeq.java

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index c9ae044..15727ef 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * 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;
 
@@ -113,17 +112,17 @@ public class AlignSeq
 
   String type;
 
-  private  int[] charToInt;
+  private int[] charToInt;
 
   /**
    * Creates a new AlignSeq object.
    * 
    * @param s1
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param s2
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param type
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public AlignSeq(SequenceI s1, SequenceI s2, String type)
   {
@@ -135,11 +134,11 @@ public class AlignSeq
    * Creates a new AlignSeq object.
    * 
    * @param s1
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param s2
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param type
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public AlignSeq(SequenceI s1, String string1, SequenceI s2,
           String string2, String type)
@@ -271,15 +270,15 @@ public class AlignSeq
    * DOCUMENT ME!
    * 
    * @param s1
-   *                DOCUMENT ME!
-   * @param string1 -
-   *                string to align for sequence1
+   *          DOCUMENT ME!
+   * @param string1
+   *          - string to align for sequence1
    * @param s2
-   *                sequence 2
-   * @param string2 -
-   *                string to align for sequence2
+   *          sequence 2
+   * @param string2
+   *          - string to align for sequence2
    * @param type
-   *                DNA or PEPTIDE
+   *          DNA or PEPTIDE
    */
   public void SeqInit(SequenceI s1, String string1, SequenceI s2,
           String string2, String type)
@@ -604,7 +603,7 @@ public class AlignSeq
    * DOCUMENT ME!
    * 
    * @param mat
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void printScoreMatrix(int[][] mat)
   {
@@ -644,9 +643,9 @@ public class AlignSeq
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param j
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -718,7 +717,7 @@ public class AlignSeq
     {
       E[i][0] = -gapOpen;
       F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend);
-      
+
       score[i][0] = max(lookup[seq1[i]][seq2[0]] * 10, E[i][0], F[i][0]);
       traceback[i][0] = -1;
     }
@@ -742,9 +741,9 @@ public class AlignSeq
    * DOCUMENT ME!
    * 
    * @param gapChar
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param seq
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -765,11 +764,11 @@ public class AlignSeq
    * DOCUMENT ME!
    * 
    * @param i1
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param i2
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param i3
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -794,9 +793,9 @@ public class AlignSeq
    * DOCUMENT ME!
    * 
    * @param i1
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param i2
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -816,9 +815,9 @@ public class AlignSeq
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param type
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -839,11 +838,12 @@ public class AlignSeq
       try
       {
         seq1[i] = charToInt[c]; // set accordingly from setType
-        if (seq1[i]<0 || seq1[i] > defInt) // set from setType: 23 for peptides, or 4 for NA.
+        if (seq1[i] < 0 || seq1[i] > defInt) // set from setType: 23 for
+                                             // peptides, or 4 for NA.
         {
           seq1[i] = defInt;
         }
-      
+
       } catch (Exception e)
       {
         seq1[i] = defInt;
@@ -857,15 +857,15 @@ public class AlignSeq
    * DOCUMENT ME!
    * 
    * @param g
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param mat
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param n
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param m
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param psize
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public static void displayMatrix(Graphics g, int[][] mat, int n, int m,
           int psize)