From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 31 Aug 2018 15:56:56 +0000 (+0100)
Subject: JAL-2996 JAL-3053 ~ | : [] {} () treated as gap characters.
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=refs%2Fheads%2Fpatch%2FJAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars

JAL-2996 JAL-3053 ~ | : [] {} () treated as gap characters.
---

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index d4fc233..aa6bcd4 100644
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -40,9 +40,29 @@ public class Comparison
 
   public static final char GAP_DASH = '-';
 
+  public static final char GAP_TILDE = '~';
+
+  public static final char GAP_PIPE = '|';
+
+  public static final char GAP_COLON = ':';
+
+  public static final char GAP_LPAREN = '(';
+
+  public static final char GAP_RPAREN = ')';
+
+  public static final char GAP_LSQBR = '[';
+
+  public static final char GAP_RSQBR = ']';
+
+  public static final char GAP_LBRACE = '{';
+
+  public static final char GAP_RBRACE = '}';
+
   public static final String GapChars = new String(
           new char[]
-          { GAP_SPACE, GAP_DOT, GAP_DASH });
+          { GAP_SPACE, GAP_DOT, GAP_DASH, GAP_TILDE, GAP_PIPE, GAP_COLON,
+              GAP_LPAREN,
+              GAP_RPAREN, GAP_LSQBR, GAP_RSQBR, GAP_LBRACE, GAP_RBRACE });
 
   /**
    * DOCUMENT ME!
@@ -256,7 +276,24 @@ public class Comparison
    */
   public static final boolean isGap(char c)
   {
-    return (c == GAP_DASH || c == GAP_DOT || c == GAP_SPACE) ? true : false;
+    switch (c)
+    {
+    case GAP_SPACE:
+    case GAP_DOT:
+    case GAP_DASH:
+    case GAP_TILDE:
+    case GAP_PIPE:
+    case GAP_COLON:
+    case GAP_LPAREN:
+    case GAP_RPAREN:
+    case GAP_LSQBR:
+    case GAP_RSQBR:
+    case GAP_LBRACE:
+    case GAP_RBRACE:
+      return true;
+    default:
+      return false;
+    }
   }
 
   /**
@@ -391,7 +428,7 @@ public class Comparison
     {
       return false;
     }
-    List<SequenceI> flattened = new ArrayList<SequenceI>();
+    List<SequenceI> flattened = new ArrayList<>();
     for (SequenceI[] ss : seqs)
     {
       for (SequenceI s : ss)
diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java
index 6f6841d..bd3b52e 100644
--- a/test/jalview/util/ComparisonTest.java
+++ b/test/jalview/util/ComparisonTest.java
@@ -28,6 +28,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.gui.JvOptionPane;
 
+import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -51,6 +52,23 @@ public class ComparisonTest
     assertFalse(Comparison.isGap('x'));
     assertFalse(Comparison.isGap('*'));
     assertFalse(Comparison.isGap('G'));
+
+    // consistency - test Comparison.isGap covers all gapChars
+    StringBuilder missing = new StringBuilder();
+    for (int i = 0, iSize = Comparison.GapChars.length(); i < iSize; i++)
+    {
+      char gc = Comparison.GapChars.charAt(i);
+      if (!Comparison.isGap(gc))
+      {
+        missing.append(gc);
+      }
+    }
+    if (missing.length() > 0)
+    {
+      Assert.fail(
+              "Comparison.GapChars contains symbols not covered by Comparison.isGap: '"
+              + missing.toString() + "'");
+    }
   }
 
   /**