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JAL-2629 choice of hmm profile now a parameter not a selection, apis simplified
[jalview.git]
/
src
/
jalview
/
schemes
/
ResidueProperties.java
diff --git
a/src/jalview/schemes/ResidueProperties.java
b/src/jalview/schemes/ResidueProperties.java
index
60fd25c
..
9b0489e
100755
(executable)
--- a/
src/jalview/schemes/ResidueProperties.java
+++ b/
src/jalview/schemes/ResidueProperties.java
@@
-32,6
+32,13
@@
import java.util.Vector;
public class ResidueProperties
{
public class ResidueProperties
{
+ // alphabet names used in Hidden Markov Model files
+ public static final String ALPHABET_RNA = "RNA";
+
+ public static final String ALPHABET_DNA = "DNA";
+
+ public static final String ALPHABET_AMINO = "amino";
+
// Stores residue codes/names and colours and other things
public static final int[] aaIndex; // aaHash version 2.1.1 and below
// Stores residue codes/names and colours and other things
public static final int[] aaIndex; // aaHash version 2.1.1 and below
@@
-2543,7
+2550,7
@@
public class ResidueProperties
amino.put('I', 0.0593f);
amino.put('P', 0.0472f);
amino.put('V', 0.0686f);
amino.put('I', 0.0593f);
amino.put('P', 0.0472f);
amino.put('V', 0.0686f);
- backgroundFrequencies.put("amino", amino);
+ backgroundFrequencies.put(ALPHABET_AMINO, amino);
// todo: these don't match https://www.ebi.ac.uk/uniprot/TrEMBLstats - what
// are they?
}
// todo: these don't match https://www.ebi.ac.uk/uniprot/TrEMBLstats - what
// are they?
}
@@
-2557,7
+2564,7
@@
public class ResidueProperties
dna.put('C', 0.25f);
dna.put('T', 0.25f);
dna.put('G', 0.25f);
dna.put('C', 0.25f);
dna.put('T', 0.25f);
dna.put('G', 0.25f);
- backgroundFrequencies.put("DNA", dna);
+ backgroundFrequencies.put(ALPHABET_DNA, dna);
}
}
@@
-2568,7
+2575,7
@@
public class ResidueProperties
rna.put('C', 0.25f);
rna.put('T', 0.25f);
rna.put('G', 0.25f);
rna.put('C', 0.25f);
rna.put('T', 0.25f);
rna.put('G', 0.25f);
- backgroundFrequencies.put("RNA", rna);
+ backgroundFrequencies.put(ALPHABET_RNA, rna);
}
}