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Adjust amino acid and position based on Unimod. #3

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Adjust amino acid and position based on Unimod. #3

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8cc8f6f
Adjust amino acid and position based on Unimod.
fcyu Feb 29, 2016
ac63fc3
Merge remote-tracking branch 'upstream/master'
fcyu Feb 29, 2016
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11 changes: 7 additions & 4 deletions src/main/java/uk/ac/ebi/pride/utilities/pridemod/model/Specificity.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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

}

Expand Down Expand Up @@ -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;
}

Expand All @@ -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;
}
Expand Down