JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / src / jalview / util / Comparison.java

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 1934583..c491be4 100644 (file)
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,18 +20,28 @@
  */
 package jalview.util;
 
-import jalview.datamodel.*;
+import jalview.datamodel.SequenceI;
+
+import java.util.ArrayList;
+import java.util.List;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * Assorted methods for analysing or comparing sequences.
  */
 public class Comparison
 {
-  /** DOCUMENT ME!! */
-  public static final String GapChars = " .-";
+  private static final int EIGHTY_FIVE = 85;
+
+  private static final int TO_UPPER_CASE = 'a' - 'A';
+
+  private static final char GAP_SPACE = ' ';
+
+  private static final char GAP_DOT = '.';
+
+  private static final char GAP_DASH = '-';
+
+  public static final String GapChars = new String(new char[] { GAP_SPACE,
+      GAP_DOT, GAP_DASH });
 
   /**
    * DOCUMENT ME!
@@ -69,12 +79,12 @@ public class Comparison
     int ilen = si.length() - 1;
     int jlen = sj.length() - 1;
 
-    while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))
+    while (Comparison.isGap(si.charAt(start + ilen)))
     {
       ilen--;
     }
 
-    while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
+    while (Comparison.isGap(sj.charAt(start + jlen)))
     {
       jlen--;
     }
@@ -225,47 +235,66 @@ public class Comparison
   }
 
   /**
-   * DOCUMENT ME!
+   * Answers true if the supplied character is a recognised gap character, else
+   * false. Currently hard-coded to recognise '-', '-' or ' ' (hyphen / dot /
+   * space).
    * 
    * @param c
-   *          DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
   public static final boolean isGap(char c)
   {
-    return (c == '-' || c == '.' || c == ' ') ? true : false;
+    return (c == GAP_DASH || c == GAP_DOT || c == GAP_SPACE) ? true : false;
   }
 
+  /**
+   * Answers true if more than 85% of the sequence residues (ignoring gaps) are
+   * A, G, C, T or U, else false. This is just a heuristic guess and may give a
+   * wrong answer (as AGCT are also amino acid codes).
+   * 
+   * @param seqs
+   * @return
+   */
   public static final boolean isNucleotide(SequenceI[] seqs)
   {
-    int i = 0, iSize = seqs.length, j, jSize;
-    float nt = 0, aa = 0;
-    char c;
-    while (i < iSize)
+    if (seqs == null)
+    {
+      return false;
+    }
+    int ntCount = 0;
+    int aaCount = 0;
+    for (SequenceI seq : seqs)
     {
-      jSize = seqs[i].getLength();
-      for (j = 0; j < jSize; j++)
+      if (seq == null)
+      {
+        continue;
+      }
+      // TODO could possibly make an informed guess just from the first sequence
+      // to save a lengthy calculation
+      for (char c : seq.getSequence())
       {
-        c = seqs[i].getCharAt(j);
         if ('a' <= c && c <= 'z')
         {
-          c -= ('a' - 'A');
+          c -= TO_UPPER_CASE;
         }
 
         if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U')
         {
-          nt++;
+          ntCount++;
         }
-        else if (!jalview.util.Comparison.isGap(seqs[i].getCharAt(j)))
+        else if (!Comparison.isGap(c))
         {
-          aa++;
+          aaCount++;
         }
       }
-      i++;
     }
 
-    if ((nt / (nt + aa)) > 0.85f)
+    /*
+     * Check for nucleotide count > 85% of total count (in a form that evades
+     * int / float conversion or divide by zero).
+     */
+    if (ntCount * 100 > EIGHTY_FIVE * (ntCount + aaCount))
     {
       return true;
     }
@@ -275,4 +304,29 @@ public class Comparison
     }
 
   }
+
+  /**
+   * Convenience overload of isNucleotide
+   * 
+   * @param seqs
+   * @return
+   */
+  public static boolean isNucleotide(SequenceI[][] seqs)
+  {
+    if (seqs == null)
+    {
+      return false;
+    }
+    List<SequenceI> flattened = new ArrayList<SequenceI>();
+    for (SequenceI[] ss : seqs)
+    {
+      for (SequenceI s : ss)
+      {
+        flattened.add(s);
+      }
+    }
+    final SequenceI[] oneDArray = flattened.toArray(new SequenceI[flattened
+            .size()]);
+    return isNucleotide(oneDArray);
+  }
 }