From 3a20b7a1383c3b62cb91bc21e8aef8bbcd8c21a8 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 21 Jan 2016 14:40:17 +0000
Subject: [PATCH] JAL-1705 isFromForwardStrand added; toString (for debug)
 tweaked

---
 src/jalview/util/MapList.java      |   29 +++++++++++++++++++++++++++--
 test/jalview/util/MapListTest.java |   26 +++++++++++++++++++++++---
 2 files changed, 50 insertions(+), 5 deletions(-)

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index e0cad6e..c32447c 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -889,8 +889,7 @@ public class MapList
   public String toString()
   {
     StringBuilder sb = new StringBuilder(64);
-    sb.append("From (").append(fromRatio).append(":").append(toRatio)
-            .append(") [");
+    sb.append("[");
     for (int[] shift : fromShifts)
     {
       sb.append(" ").append(Arrays.toString(shift));
@@ -975,4 +974,30 @@ public class MapList
      */
     addTo.add(range);
   }
+
+  /**
+   * Returns true if mapping is from forward strand, false if from reverse
+   * strand. Result is just based on the first 'from' range that is not a single
+   * position. Default is true unless proven to be false. Behaviour is not well
+   * defined if the mapping has a mixture of forward and reverse ranges.
+   * 
+   * @return
+   */
+  public boolean isFromForwardStrand()
+  {
+    boolean forwardStrand = true;
+    for (int[] range : getFromRanges())
+    {
+      if (range[1] > range[0])
+      {
+        break; // forward strand confirmed
+      }
+      else if (range[1] < range[0])
+      {
+        forwardStrand = false;
+        break; // reverse strand confirmed
+      }
+    }
+    return forwardStrand;
+  }
 }
diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index 54e8311..22a3ad9 100644
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -534,7 +534,7 @@ public class MapListTest
     MapList ml = new MapList(new int[] { 1, 5, 10, 15, 25, 20 }, new int[] {
         51, 1 }, 1, 3);
     String s = ml.toString();
-    assertEquals("From (1:3) [ [1, 5] [10, 15] [25, 20] ] To [ [51, 1] ]",
+    assertEquals("[ [1, 5] [10, 15] [25, 20] ] To [ [51, 1] ]",
             s);
   }
 
@@ -558,7 +558,7 @@ public class MapListTest
 
     String s = ml.toString();
     assertEquals(
-            "From (1:3) [ [11, 15] [20, 25] [35, 30] [2, 4] [37, 40] ] To [ [72, 22] [12, 17] [78, 83] [88, 96] ]",
+            "[ [11, 15] [20, 25] [35, 30] [2, 4] [37, 40] ] To [ [72, 22] [12, 17] [78, 83] [88, 96] ]",
             s);
   }
 
@@ -571,7 +571,7 @@ public class MapListTest
     MapList ml2 = new MapList(new int[] { 15, 16 }, new int[] { 58, 53 },
             1, 3);
     ml.addMapList(ml2);
-    assertEquals("From (1:3) [ [11, 16] ] To [ [72, 53] ]", ml.toString());
+    assertEquals("[ [11, 16] ] To [ [72, 53] ]", ml.toString());
   }
 
   @Test(groups = "Functional")
@@ -646,4 +646,24 @@ public class MapListTest
     assertEquals(79, ml.getToLowest());
     assertEquals(100, ml.getToHighest());
   }
+
+  /**
+   * Test that method that inspects for the (first) forward or reverse from
+   * range. Single position ranges are ignored.
+   */
+  @Test(groups = { "Functional" })
+  public void testIsFromForwardStrand()
+  {
+    MapList ml = new MapList(new int[] { 2, 2, 3, 9, 12, 11 },
+            new int[] { 20, 11 }, 1, 1);
+    assertTrue(ml.isFromForwardStrand());
+
+    ml = new MapList(new int[] { 2, 2, 11, 5, 13, 14 },
+            new int[] { 20, 11 }, 1, 1);
+    assertFalse(ml.isFromForwardStrand());
+
+    ml = new MapList(new int[] { 2, 2, 4, 4, 6, 6 }, new int[] { 3, 1 }, 1,
+            1);
+    assertTrue(ml.isFromForwardStrand());
+  }
 }
-- 
1.7.10.2