From 89f9ad40a3e1d7f1765f3bf5369dcc3636a824ff Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 22 Aug 2019 09:06:23 +0100
Subject: [PATCH] JAL-3187 one more obsolete method removed

---
 src/jalview/analysis/AlignmentUtils.java |   91 ------------------------------
 1 file changed, 91 deletions(-)

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 55efaa5..fdf66d0 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2389,97 +2389,6 @@ public class AlignmentUtils
   }
 
   /**
-   * Helper method that adds a peptide variant feature. ID and
-   * clinical_significance attributes of the dna variant (if present) are copied
-   * to the new feature.
-   * 
-   * @param peptide
-   * @param peptidePos
-   * @param residue
-   * @param var
-   * @param codon
-   *          the variant codon e.g. aCg
-   * @param canonical
-   *          the 'normal' codon e.g. aTg
-   * @return true if a feature was added, else false
-   */
-  static boolean addPeptideVariant(SequenceI peptide, int peptidePos,
-          String residue, DnaVariant var, String codon, String canonical)
-  {
-    /*
-     * get peptide translation of codon e.g. GAT -> D
-     * note that variants which are not single alleles,
-     * e.g. multibase variants or HGMD_MUTATION etc
-     * are currently ignored here
-     */
-    String trans = codon.contains("-") ? null
-            : (codon.length() > CODON_LENGTH ? null
-                    : ResidueProperties.codonTranslate(codon));
-    if (trans == null)
-    {
-      return false;
-    }
-    String desc = canonical + "/" + codon;
-    String featureType = "";
-    if (trans.equals(residue))
-    {
-      featureType = SequenceOntologyI.SYNONYMOUS_VARIANT;
-    }
-    else if (ResidueProperties.STOP.equals(trans))
-    {
-      featureType = SequenceOntologyI.STOP_GAINED;
-    }
-    else
-    {
-      String residue3Char = StringUtils
-              .toSentenceCase(ResidueProperties.aa2Triplet.get(residue));
-      String trans3Char = StringUtils
-              .toSentenceCase(ResidueProperties.aa2Triplet.get(trans));
-      desc = "p." + residue3Char + peptidePos + trans3Char;
-      featureType = SequenceOntologyI.NONSYNONYMOUS_VARIANT;
-    }
-    SequenceFeature sf = new SequenceFeature(featureType, desc, peptidePos,
-            peptidePos, var.getSource());
-
-    StringBuilder attributes = new StringBuilder(32);
-    String id = (String) var.variant.getValue(VARIANT_ID);
-    if (id != null)
-    {
-      if (id.startsWith(SEQUENCE_VARIANT))
-      {
-        id = id.substring(SEQUENCE_VARIANT.length());
-      }
-      sf.setValue(VARIANT_ID, id);
-      attributes.append(VARIANT_ID).append("=").append(id);
-      // TODO handle other species variants JAL-2064
-      StringBuilder link = new StringBuilder(32);
-      try
-      {
-        link.append(desc).append(" ").append(id).append(
-                "|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=")
-                .append(URLEncoder.encode(id, "UTF-8"));
-        sf.addLink(link.toString());
-      } catch (UnsupportedEncodingException e)
-      {
-        // as if
-      }
-    }
-    String clinSig = (String) var.variant.getValue(CLINICAL_SIGNIFICANCE);
-    if (clinSig != null)
-    {
-      sf.setValue(CLINICAL_SIGNIFICANCE, clinSig);
-      attributes.append(";").append(CLINICAL_SIGNIFICANCE).append("=")
-              .append(clinSig);
-    }
-    peptide.addSequenceFeature(sf);
-    if (attributes.length() > 0)
-    {
-      sf.setAttributes(attributes.toString());
-    }
-    return true;
-  }
-
-  /**
    * Makes an alignment with a copy of the given sequences, adding in any
    * non-redundant sequences which are mapped to by the cross-referenced
    * sequences.
-- 
1.7.10.2