Formatting changes to Comparison class

lafita · lafita · commit d527cf60444d · 2015-11-16T17:35:14.000+01:00
diff --git a/biojava-phylo/src/main/java/org/biojava/nbio/phylo/Comparison.java b/biojava-phylo/src/main/java/org/biojava/nbio/phylo/Comparison.java
@@ -22,94 +22,90 @@
  * To change this template, choose Tools | Templates
  * and open the template in the editor.
  */
-
 package org.biojava.nbio.phylo;
 
 /**
- *
- * @author willishf
+ * This class provides static methods for the calculation of the percentage of
+ * identity between two aligned sequences.
+ * <p>
+ * Since 4.1.1 the methods for distance inference in forester are also used in
+ * BioJava, so this implementation of percentage of identity is not needed
+ * anymore. However, the code is maintained as the own BioJava implementation.
+ * 
+ * @author Scooter Willis
+ * 
  */
 public class Comparison {
 
-
-  /**
-   * this is a gapped PID calculation
-   *
-   * @param s1
-   *                SequenceI
-   * @param s2
-   *                SequenceI
-   * @return float
-   */
-  public final static float PID(String seq1, String seq2)
-  {
-    return PID(seq1, seq2, 0, seq1.length());
-  }
-
-  static final int caseShift = 'a' - 'A';
-
-  // Another pid with region specification
-  public final static float PID(String seq1, String seq2, int start, int end)
-  {
-
-    int s1len = seq1.length();
-    int s2len = seq2.length();
-
-    int len = Math.min(s1len, s2len);
-
-    if (end < len)
-    {
-      len = end;
-    }
-
-    if (len < start)
-    {
-      start = len - 1; // we just use a single residue for the difference
-    }
-
-    int bad = 0;
-    char chr1;
-    char chr2;
-
-    for (int i = start; i < len; i++)
-    {
-      chr1 = seq1.charAt(i);
-
-      chr2 = seq2.charAt(i);
-
-      if ('a' <= chr1 && chr1 <= 'z')
-      {
-        // TO UPPERCASE !!!
-        // Faster than toUpperCase
-        chr1 -= caseShift;
-      }
-      if ('a' <= chr2 && chr2 <= 'z')
-      {
-        // TO UPPERCASE !!!
-        // Faster than toUpperCase
-        chr2 -= caseShift;
-      }
-
-      if (chr1 != chr2 && !isGap(chr1) && !isGap(chr2))
-      {
-        bad++;
-      }
-    }
-
-    return ((float) 100 * (len - bad)) / len;
-  }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param c
-   *                DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public static final boolean isGap(char c)
-  {
-    return (c == '-' || c == '.' || c == ' ') ? true : false;
-  }
+	private static final int caseShift = 'a' - 'A';
+
+	/**
+	 * this is a gapped PID calculation
+	 *
+	 * @param s1
+	 *            SequenceI
+	 * @param s2
+	 *            SequenceI
+	 * @return float
+	 */
+	public final static float PID(String seq1, String seq2) {
+		return PID(seq1, seq2, 0, seq1.length());
+	}
+
+	// Another pid with region specification
+	public final static float PID(String seq1, String seq2, int start, int end) {
+
+		int s1len = seq1.length();
+		int s2len = seq2.length();
+
+		int len = Math.min(s1len, s2len);
+
+		if (end < len) {
+			len = end;
+		}
+
+		if (len < start) {
+			start = len - 1; // we just use a single residue for the difference
+		}
+
+		int bad = 0;
+		char chr1;
+		char chr2;
+
+		for (int i = start; i < len; i++) {
+
+			chr1 = seq1.charAt(i);
+			chr2 = seq2.charAt(i);
+
+			if ('a' <= chr1 && chr1 <= 'z') {
+				// TO UPPERCASE !!!
+				// Faster than toUpperCase
+				chr1 -= caseShift;
+			}
+			if ('a' <= chr2 && chr2 <= 'z') {
+				// TO UPPERCASE !!!
+				// Faster than toUpperCase
+				chr2 -= caseShift;
+			}
+
+			if (chr1 != chr2 && !isGap(chr1) && !isGap(chr2)) {
+				bad++;
+			}
+		}
+
+		return ((float) 100 * (len - bad)) / len;
+	}
+
+	/**
+	 * Method that determines if a character means a gap in the alignment.
+	 *
+	 * @param c
+	 *            gap character is one of the symbols in {' ','-','.'}
+	 *
+	 * @return true if it is a gap, false otherwise
+	 */
+	public static final boolean isGap(char c) {
+		return (c == '-' || c == '.' || c == ' ') ? true : false;
+	}
 
 }
