Bump version and update changelog; also update some comments

Author: FarmGeek4Life

docs/Changelog.html

@@ -13,6 +13,13 @@ <h1 class="pagetitle">MS-GF+ ChangeLog</h1>
         <a href="index.html">MS-GF+ Documentation home</a>
     </p>
 
+    <p>
+        <b>v2019.02.28</b>
+    </p>
+    <ul>
+        <li>Fix a math error that introduced new erroneous output.</li>
+    </ul>
+
     <p>
         <b>v2019.02.27</b>
     </p>

src/main/java/edu/ucsd/msjava/mzid/MZIdentMLGen.java

@@ -634,11 +634,10 @@ public List<PeptideEvidenceRef> getPeptideEvidenceList(DatabaseMatch match, Pept
                 if (sa.getSequence().getByteAt(index) == 0 && sa.getSequence().getCharAt(index + 1) == 'M') {
                     // match.isNTermMetCleaved() is specific to only one of the matched peptides in most cases
                     // Do a double-check that the index/protein match is correct for the sequence by checking
-                    // the first residue (if not 'M') or matching the peptide sequence to sequence at index + 1
+                    // the first residue (if not 'M') or matching the peptide sequence to sequence at index + 2
                     isNTermMetCleaved = match.isNTermMetCleaved() || peptide.getPeptideSequence().charAt(0) != 'M';
                     if (!isNTermMetCleaved) {
                         // peptideSequence begins with M
-                        // TODO: is this considered possible (N-Term Methionine cleavage and peptide begins with M)?
                         // check if the sequence starting at index + 2 matches the provided peptide sequence
                         String matchSequence = sa.getSequence().getSubsequence(index + 2, index + 3 + peptide.getPeptideSequence().length());
                         isNTermMetCleaved = matchSequence.startsWith(peptide.getPeptideSequence());

src/main/java/edu/ucsd/msjava/ui/MSGFPlus.java

@@ -22,8 +22,8 @@
 
 
 public class MSGFPlus {
-    public static final String VERSION = "Release (v2019.02.27)";
-    public static final String RELEASE_DATE = "27 February 2019";
+    public static final String VERSION = "Release (v2019.02.28)";
+    public static final String RELEASE_DATE = "28 February 2019";
 
     public static final String DECOY_DB_EXTENSION = ".revCat.fasta";
     public static final String DEFAULT_DECOY_PROTEIN_PREFIX = "XXX";