From 8cc8f6f1a4bba3d2c97a1a349970597edbb6af68 Mon Sep 17 00:00:00 2001 From: Fengchao Date: Mon, 29 Feb 2016 15:30:59 +0800 Subject: [PATCH] Adjust amino acid and position based on Unimod. --- .../pride/utilities/pridemod/model/Specificity.java | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/src/main/java/uk/ac/ebi/pride/utilities/pridemod/model/Specificity.java b/src/main/java/uk/ac/ebi/pride/utilities/pridemod/model/Specificity.java index 2dca822..ac6e3e7 100755 --- a/src/main/java/uk/ac/ebi/pride/utilities/pridemod/model/Specificity.java +++ b/src/main/java/uk/ac/ebi/pride/utilities/pridemod/model/Specificity.java @@ -82,14 +82,14 @@ public int compareTo(Object o) { } public enum Position { - CTERM, NTERM, PCTERM, PNTERM, NONE + CTERM, NTERM, PCTERM, PNTERM, ANYWHERE, NONE } /** * To use the same notation of PSI-MOD we decide to include the X as aminoacid. PSI-Mod use X for N-Term position. */ public enum AminoAcid { - A, R, N, D, C, E, Q, G, H, K, I, L, M, F, P, S, T, W, Y, V, X, NONE + A, R, N, D, C, E, Q, G, H, K, I, L, M, F, P, S, T, W, Y, V, X, NTERM, CTERM, NONE } @@ -122,6 +122,8 @@ public static AminoAcid parseAminoAcid(String s) { if (s.compareToIgnoreCase("Y") == 0) return AminoAcid.Y; if (s.compareToIgnoreCase("V") == 0) return AminoAcid.V; if (s.compareToIgnoreCase("X") == 0) return AminoAcid.X; + if (s.compareToIgnoreCase("C-term") == 0) return AminoAcid.CTERM; + if (s.compareToIgnoreCase("N-term") == 0) return AminoAcid.NTERM; return AminoAcid.NONE; } @@ -133,10 +135,11 @@ public static AminoAcid parseAminoAcid(String s) { */ public static Position parsePositon(String s) { if (s != null) { - if (s.compareToIgnoreCase("N-Term") == 0) return Position.NTERM; - if (s.compareToIgnoreCase("C-Term") == 0) return Position.CTERM; + if (s.compareToIgnoreCase("Any N-Term") == 0) return Position.NTERM; + if (s.compareToIgnoreCase("Any C-Term") == 0) return Position.CTERM; if (s.compareToIgnoreCase("Protein N-term") == 0) return Position.PNTERM; if (s.compareToIgnoreCase("Protein C-Term") == 0) return Position.PCTERM; + if (s.compareToIgnoreCase("Anywhere") == 0) return Position.ANYWHERE; } return Position.NONE; }