From 6d0af2bcecfa9eabab29c659ca151008db6379b2 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Sat, 23 Apr 2016 18:36:11 +0100
Subject: [PATCH] JAL-2075 findPosition for SeqCigar (with test)

---
 src/jalview/datamodel/SeqCigar.java      |   37 ++++++++++++++++++++++++++++++
 test/jalview/datamodel/SeqCigarTest.java |   25 ++++++++++++++++++++
 2 files changed, 62 insertions(+)

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 31957d7..98b0de5 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -68,6 +68,43 @@ public class SeqCigar extends CigarSimple
   }
 
   /**
+   * 
+   * @param column
+   * @return position in sequence for column (or -1 if no match state exists)
+   */
+  public int findPosition(int column)
+  {
+    int w = 0, ew, p = refseq.findPosition(start);
+    if (column < 0)
+    {
+      return -1;
+    }
+    if (range != null)
+    {
+      for (int i = 0; i < length; i++)
+      {
+        if (operation[i] == M || operation[i] == D)
+        {
+          p += range[i];
+        }
+        if (operation[i] == M || operation[i] == I)
+        {
+          ew = w + range[i];
+          if (column < ew)
+          {
+            if (operation[i] == I)
+            {
+              return -1;
+            }
+            return p - (ew - column);
+          }
+          w = ew;
+        }
+      }
+    }
+    return -1;
+  }
+
   /**
    * Returns sequence as a string with cigar operations applied to it
    * 
diff --git a/test/jalview/datamodel/SeqCigarTest.java b/test/jalview/datamodel/SeqCigarTest.java
index 705c773..8d3c878 100644
--- a/test/jalview/datamodel/SeqCigarTest.java
+++ b/test/jalview/datamodel/SeqCigarTest.java
@@ -23,6 +23,8 @@ package jalview.datamodel;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 
+import jalview.util.Comparison;
+
 import org.testng.annotations.Test;
 
 /**
@@ -30,6 +32,29 @@ import org.testng.annotations.Test;
  */
 public class SeqCigarTest
 {
+  @Test(groups = { "Functional" })
+  public void testFindPosition()
+  {
+    SequenceI oseq = new Sequence("MySeq", "ASD---ASD---ASD", 37, 45);
+    oseq.createDatasetSequence();
+    SeqCigar cs = new SeqCigar(oseq);
+    assertEquals(oseq.getSequenceAsString(), cs.getSequenceString('-'));
+    for (int c = 0, cLen = oseq.getLength(); c < cLen; c++)
+    {
+      int os_p = oseq.findPosition(c);
+      int cigar_p = cs.findPosition(c);
+      if (Comparison.isGap(oseq.getCharAt(c)))
+      {
+        assertEquals("Expected gap at position " + os_p + " column " + c,
+                -1, cigar_p);
+      }
+      else
+      {
+        assertEquals("Positions don't match for at column " + c, os_p,
+                cigar_p);
+      }
+    }
+  }
   /*
    * refactored 'as is' from main method
    * 
-- 
1.7.10.2