JAL-1499 replace identity symbols when parsing

diff --git a/src/jalview/io/MegaFile.java b/src/jalview/io/MegaFile.java
index 2f48bf5..2f5e35a 100644 (file)
--- a/src/jalview/io/MegaFile.java
+++ b/src/jalview/io/MegaFile.java
@@ -134,6 +134,9 @@ public class MegaFile extends AlignFile
   // gap character may be explicitly declared, if not we infer it
   private Character gapCharacter;
 
+  // identity character if declared
+  private char identityCharacter = 0;
+
   // this can be True, False or null (meaning not asserted in file)
   private Boolean nucleotide;
 
@@ -465,9 +468,7 @@ public class MegaFile extends AlignFile
 
     StringBuilder sb = getSequenceDataBuffer(seqData, currentId);
 
-    /*
-     * Add the current line of data to the sequence.
-     */
+    dataLine = reformatSequenceData(dataLine, sb.length(), seqData);
     sb.append(dataLine);
 
     setPositionsPerLine(Math.max(positionsPerLine, dataLine.length()));
@@ -529,10 +530,7 @@ public class MegaFile extends AlignFile
      */
     if (data != null && data.length() > 0)
     {
-      if (data.indexOf(SPACE) != -1)
-      {
-        data = data.replace(SPACE, "");
-      }
+      data = reformatSequenceData(data, sb.length(), seqData);
       sb.append(data);
       setPositionsPerLine(Math.max(positionsPerLine, data.length()));
       assertInterleaved(true, dataLine);
@@ -540,6 +538,41 @@ public class MegaFile extends AlignFile
   }
 
   /**
+   * Reformat input sequence data by removing any internal formatting spaces,
+   * and converting any 'identity' characters to the corresponding position in
+   * the first sequence.
+   * 
+   * @param data
+   * @param startPos
+   *          the sequence position (base 0) of the start of the data
+   * @param seqData
+   * @return
+   */
+  protected String reformatSequenceData(String data, int startPos, Map<String, StringBuilder> seqData)
+  {
+    String formatted = data.replace(SPACE, "");
+    if (formatted.indexOf(identityCharacter) > -1)
+    {
+      /*
+       * sequence contains '.' or other identity symbol; replace these with the
+       * same position from the first (reference) sequence
+       */
+      StringBuilder referenceSequence = seqData.values().iterator().next();
+      StringBuilder sb = new StringBuilder(formatted.length());
+      for (int i = 0 ; i < formatted.length() ; i++) {
+        char nextChar = formatted.charAt(i);
+        if (nextChar != identityCharacter) {
+          sb.append(nextChar);
+        } else {
+          sb.append(referenceSequence.charAt(startPos + i));
+        }
+      }
+      formatted = sb.toString();
+    }
+    return formatted;
+  }
+
+  /**
    * If the line begins with (e.g.) "#abcde " then returns "abcde" as the
    * identifier. Else returns null.
    * 
@@ -738,6 +771,7 @@ public class MegaFile extends AlignFile
             || keyword.equalsIgnoreCase("MatchChar"))
     {
       setAlignmentProperty(PROP_IDENTITY, value);
+      this.identityCharacter = value.charAt(0);
       if (!".".equals(value))
       {
         System.err.println("Warning: " + token

diff --git a/test/jalview/io/MegaFileTest.java b/test/jalview/io/MegaFileTest.java
index 948efa8..309ffee 100644 (file)
--- a/test/jalview/io/MegaFileTest.java
+++ b/test/jalview/io/MegaFileTest.java
@@ -491,4 +491,80 @@ public class MegaFileTest
     assertEquals("Roundtrip didn't match", expected,
             formatted);
   }
+
+  //@formatter:on
+  
+  /**
+   * Test paste of interleaved mega format data where the identity character is
+   * used in sequences after the first
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" })
+  public void testParse_interleavedWithIdentity() throws IOException
+  {
+    //@formatter:off
+    MegaFile testee = new MegaFile("#MEGA\n"+ 
+    "!TITLE Interleaved sequence data;\n" +
+    "!Format Identical=.;\n\n" +
+    "#U455   ABCDEF\n" + 
+    "#CPZANT  M..P.R\n\n" + 
+    "#U455   KLMNOP\n" + 
+    "#CPZANT ..YZ..", AppletFormatAdapter.PASTE);
+    //@formatter:on
+    assertEquals("Title not as expected", "Interleaved sequence data",
+            testee.getAlignmentProperty(MegaFile.PROP_TITLE));
+    Vector<SequenceI> seqs = testee.getSeqs();
+    // should be 2 sequences
+    assertEquals("Expected two sequences", 2, seqs.size());
+    // check sequence names correct and order preserved
+    assertEquals("First sequence id wrong", "U455", seqs.get(0).getName());
+    assertEquals("Second sequence id wrong", "CPZANT", seqs.get(1)
+            .getName());
+    // check sequence data
+    assertEquals("First sequence data wrong", "ABCDEFKLMNOP", seqs.get(0)
+            .getSequenceAsString());
+    assertEquals("Second sequence data wrong", "MBCPERKLYZOP", seqs.get(1)
+            .getSequenceAsString());
+    assertTrue("File format is not flagged as interleaved",
+            testee.isInterleaved());
+  }
+
+  /**
+   * Test paste of noninterleaved format data including identity symbol
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" })
+  public void testParse_nonInterleavedWithIdentity() throws IOException
+  {
+    //@formatter:off
+    MegaFile testee = new MegaFile("#MEGA\n"
+    + "!TITLE Noninterleaved sequence data;\n"
+    + "!Format MatchChar=.;\n"
+    + "#U455  \n"
+    + "ABCFEDHIJ\n" 
+    + "MNOPQR\n\n" 
+    + "#CPZANT \n" 
+    + "KL..O..XYZ\n" 
+    + "CG..C\n",
+            AppletFormatAdapter.PASTE);
+    //@formatter:on
+    assertEquals("Title not as expected", "Noninterleaved sequence data",
+            testee.getAlignmentProperty(MegaFile.PROP_TITLE));
+    Vector<SequenceI> seqs = testee.getSeqs();
+    // should be 2 sequences
+    assertEquals("Expected two sequences", 2, seqs.size());
+    // check sequence names correct and order preserved
+    assertEquals("First sequence id wrong", "U455", seqs.get(0).getName());
+    assertEquals("Second sequence id wrong", "CPZANT", seqs.get(1)
+            .getName());
+    // check sequence data
+    assertEquals("First sequence data wrong", "ABCFEDHIJMNOPQR", seqs
+            .get(0).getSequenceAsString());
+    assertEquals("Second sequence data wrong", "KLCFODHXYZCGPQC",
+            seqs.get(1).getSequenceAsString());
+    assertFalse("File format is not flagged as noninterleaved",
+            testee.isInterleaved());
+  }
 }