From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 1 Oct 2015 08:33:02 +0000 (+0100)
Subject: JAL-1499 write position numbers at end of each line (interleaved)
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=db6df7f531341ba6a7ade77103cf071cfb25e543

JAL-1499 write position numbers at end of each line (interleaved)
---

diff --git a/src/jalview/io/MegaFile.java b/src/jalview/io/MegaFile.java
index af9889b..2f48bf5 100644
--- a/src/jalview/io/MegaFile.java
+++ b/src/jalview/io/MegaFile.java
@@ -143,6 +143,9 @@ public class MegaFile extends AlignFile
   // this can be True, False or null (meaning we don't know yet)
   private Boolean interleaved;
 
+  // write end of line positions as a comment
+  private boolean writePositionNumbers = true;
+
   public MegaFile()
   {
   }
@@ -891,17 +894,17 @@ public class MegaFile extends AlignFile
     int maxSequenceLength = getMaxSequenceLength(s);
     int numLines = maxSequenceLength / positionsPerLine + 3; // approx
 
-    /*
-     * Size a buffer to hold the whole output
-     */
-    StringBuilder sb = new StringBuilder(numLines
-            * (maxIdLength + 2 + positionsPerLine));
-
     int numDataBlocks = (maxSequenceLength - 1) / positionsPerLine + 1;
     int spaceEvery = this.nucleotide != null && this.nucleotide ? 3 : 10;
     int chunksPerLine = (positionsPerLine + spaceEvery - 1) / spaceEvery;
 
     /*
+     * Roughly size a buffer to hold the whole output
+     */
+    StringBuilder sb = new StringBuilder(numLines
+            * (maxIdLength + positionsPerLine + chunksPerLine + 10));
+
+    /*
      * Output as: #Seqid CGT AGC ACT ... or blocks of 10 for peptide
      */
     int from = 0;
@@ -936,6 +939,12 @@ public class MegaFile extends AlignFile
             advancedBy += subSequence.length;
           }
         }
+        // write last position as a comment
+        if (writePositionNumbers)
+        {
+          sb.append(SPACE).append(COMMENT_START).append(from + advancedBy)
+                  .append(COMMENT_END);
+        }
         sb.append(newline);
         first = false;
       }
diff --git a/test/jalview/io/MegaFileTest.java b/test/jalview/io/MegaFileTest.java
index fef8337..948efa8 100644
--- a/test/jalview/io/MegaFileTest.java
+++ b/test/jalview/io/MegaFileTest.java
@@ -231,8 +231,9 @@ public class MegaFileTest
     // normally output should match input
     // we cheated here with a number of short input lines
     // nb don't get Title in output if not calling print(AlignmentI)
-    String expected = "#MEGA\n\n" + "#U455   ABCDEF\n"
-            + "#CPZANT MNOPQR\n\n" + "#U455   KLMNOP\n" + "#CPZANT WXYZGC"
+    String expected = "#MEGA\n\n" + "#U455   ABCDEF [6]\n"
+            + "#CPZANT MNOPQR [6]\n\n" + "#U455   KLMNOP [12]\n"
+            + "#CPZANT WXYZGC [12]"
             + "\n";
     assertEquals("Print format wrong", expected, printed);
   }
@@ -250,8 +251,14 @@ public class MegaFileTest
     String printed = testee.print();
     System.out.println(printed);
 
-    assertEquals("Print format wrong", "#MEGA\n\n" + INTERLEAVED_NOHEADERS,
+    //@formatter:off
+    assertEquals("Print format wrong", 
+    "#MEGA\n\n" + "#U455   ABCDEF [6]\n" 
+    + "#CPZANT MNOPQR [6]\n\n" 
+    + "#U455   KLMNOP [12]\n"
+    + "#CPZANT WXYZGC [12]\n",
             printed);
+    //@formatter:on
   }
 
   /**
@@ -297,12 +304,12 @@ public class MegaFileTest
     //0123456789klmnopqrstABCDEFGHIJ9876543210abcdefghij
     String expected = 
             "#MEGA\n\n" + 
-            "#U455   0123456789 klmnopqrst\n" + // first 20
-            "#CPZANT 9876543210 abcdefghij\n\n" +
-            "#U455   ABCDEFGHIJ 9876543210\n" + // next 20
-            "#CPZANT 0123456789 klmnopqrst\n\n" +
-            "#U455   abcdefghij\n" + // last 10
-            "#CPZANT ABCDEFGHIJ\n";
+            "#U455   0123456789 klmnopqrst [20]\n" + // first 20
+            "#CPZANT 9876543210 abcdefghij [20]\n\n" +
+            "#U455   ABCDEFGHIJ 9876543210 [40]\n" + // next 20
+            "#CPZANT 0123456789 klmnopqrst [40]\n\n" +
+            "#U455   abcdefghij [50]\n" + // last 10
+            "#CPZANT ABCDEFGHIJ [50]\n";
     //@formatter:on
     assertEquals("Print format wrong", expected, printed);
   }
@@ -426,10 +433,10 @@ public class MegaFileTest
          "    DataType=DNA CodeTable=Standard\n" +
          "    NSeqs=2 NSites=12\n" +
          "    Indel=- Identical=. Missing=?;\n\n" +
-         "#U455   CGC GTA\n" +
-         "#CPZANT ATC GGG\n\n" +
-         "#U455   CGA TTT\n" +
-         "#CPZANT CAA TGC\n";
+         "#U455   CGC GTA [6]\n" +
+         "#CPZANT ATC GGG [6]\n\n" +
+         "#U455   CGA TTT [12]\n" +
+         "#CPZANT CAA TGC [12]\n";
     //@formatter:on
     assertEquals("Roundtrip didn't match", expected,
             formatted);
@@ -476,10 +483,10 @@ public class MegaFileTest
          "    DataType=DNA CodeTable=Standard\n" +
          "    NSeqs=2 NSites=12\n" +
          "    Indel=- Identical=. Missing=?;\n\n" +
-         "#U455   CGC GTA\n" +
-         "#CPZANT ATC GGG\n\n" +
-         "#U455   CGA TTT\n" +
-         "#CPZANT CAA TGC\n";
+         "#U455   CGC GTA [6]\n" +
+         "#CPZANT ATC GGG [6]\n\n" +
+         "#U455   CGA TTT [12]\n" +
+         "#CPZANT CAA TGC [12]\n";
     //@formatter:on
     assertEquals("Roundtrip didn't match", expected,
             formatted);