JAL-2416 remove unused pep, dna alphabets, unused methods, code format

tidy

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index ed4e3bc..86dd3bc 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -20,7 +20,6 @@
  */
 package jalview.analysis;
 
-import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
 import jalview.analysis.scoremodels.ScoreMatrix;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.datamodel.AlignmentAnnotation;
@@ -55,12 +54,6 @@ public class AlignSeq
 
   private static final String NEWLINE = System.lineSeparator();
 
-  static String[] dna = { "A", "C", "G", "T", "-" };
-
-  // "C", "T", "A", "G", "-"};
-  static String[] pep = { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I",
-      "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-" };
-
   float[][] score;
 
   float[][] E;
@@ -120,10 +113,6 @@ public class AlignSeq
 
   float[][] lookup = ScoreModels.getInstance().getBlosum62().getMatrix();
 
-  // ResidueProperties.getBLOSUM62();
-
-  String[] intToStr = pep;
-
   int defInt = 23;
 
   StringBuffer output = new StringBuffer();
@@ -144,7 +133,7 @@ public class AlignSeq
    */
   public AlignSeq(SequenceI s1, SequenceI s2, String type)
   {
-    SeqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(),
+    seqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(),
             type);
   }
 
@@ -161,7 +150,7 @@ public class AlignSeq
   public AlignSeq(SequenceI s1, String string1, SequenceI s2,
           String string2, String type)
   {
-    SeqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type);
+    seqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type);
   }
 
   /**
@@ -265,26 +254,6 @@ public class AlignSeq
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public SequenceI getS1()
-  {
-    return s1;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public SequenceI getS2()
-  {
-    return s2;
-  }
-
-  /**
    * 
    * @return aligned instance of Seq 1
    */
@@ -326,36 +295,13 @@ public class AlignSeq
    * @param type
    *          DNA or PEPTIDE
    */
-  public void SeqInit(SequenceI s1, String string1, SequenceI s2,
+  public void seqInit(SequenceI s1, String string1, SequenceI s2,
           String string2, String type)
   {
     this.s1 = s1;
     this.s2 = s2;
     setDefaultParams(type);
-    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)
-  {
-    this.s1 = s1;
-    this.s2 = s2;
-    setType(scoreMatrix.isDNA() ? AlignSeq.DNA : AlignSeq.PEP);
-    lookup = scoreMatrix.getMatrix();
+    seqInit(string1, string2);
   }
 
   /**
@@ -365,7 +311,7 @@ public class AlignSeq
    * @param string1
    * @param string2
    */
-  private void SeqInit(String string1, String string2)
+  private void seqInit(String string1, String string2)
   {
     s1str = extractGaps(jalview.util.Comparison.GapChars, string1);
     s2str = extractGaps(jalview.util.Comparison.GapChars, string2);
@@ -440,13 +386,11 @@ public class AlignSeq
     this.type = type2;
     if (type.equals(AlignSeq.PEP))
     {
-      intToStr = pep;
       charToInt = ResidueProperties.aaIndex;
       defInt = ResidueProperties.maxProteinIndex;
     }
     else if (type.equals(AlignSeq.DNA))
     {
-      intToStr = dna;
       charToInt = ResidueProperties.nucleotideIndex;
       defInt = ResidueProperties.maxNucleotideIndex;
     }
@@ -603,7 +547,7 @@ public class AlignSeq
             .append(String.valueOf(s2str.length())).append(")")
             .append(NEWLINE).append(NEWLINE);
 
-    PairwiseSeqScoreModel pam250 = ScoreModels.getInstance().getPam250();
+    ScoreMatrix pam250 = ScoreModels.getInstance().getPam250();
 
     for (int j = 0; j < nochunks; j++)
     {
@@ -686,46 +630,6 @@ public class AlignSeq
   /**
    * DOCUMENT ME!
    * 
-   * @param mat
-   *          DOCUMENT ME!
-   */
-  public void printScoreMatrix(int[][] mat)
-  {
-    int n = seq1.length;
-    int m = seq2.length;
-
-    for (int i = 0; i < n; i++)
-    {
-      // Print the top sequence
-      if (i == 0)
-      {
-        Format.print(System.out, "%8s", s2str.substring(0, 1));
-
-        for (int jj = 1; jj < m; jj++)
-        {
-          Format.print(System.out, "%5s", s2str.substring(jj, jj + 1));
-        }
-
-        System.out.println();
-      }
-
-      for (int j = 0; j < m; j++)
-      {
-        if (j == 0)
-        {
-          Format.print(System.out, "%3s", s1str.substring(i, i + 1));
-        }
-
-        Format.print(System.out, "%3d ", mat[i][j] / 10);
-      }
-
-      System.out.println();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @param i
    *          DOCUMENT ME!
    * @param j
@@ -860,7 +764,7 @@ public class AlignSeq
    * 
    * @return DOCUMENT ME!
    */
-  public float max(float f1, float f2, float f3)
+  private static float max(float f1, float f2, float f3)
   {
     float max = f1;
 
@@ -887,7 +791,7 @@ public class AlignSeq
    * 
    * @return DOCUMENT ME!
    */
-  public float max(float f1, float f2)
+  private static float max(float f1, float f2)
   {
     float max = f1;
 
@@ -909,7 +813,7 @@ public class AlignSeq
    * 
    * @return DOCUMENT ME!
    */
-  public int[] stringToInt(String s, String type)
+  int[] stringToInt(String s, String type)
   {
     int[] seq1 = new int[s.length()];