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JAL-4001 Added useful props information
[jalview.git]
/
src
/
jalview
/
schemes
/
ResidueProperties.java
diff --git
a/src/jalview/schemes/ResidueProperties.java
b/src/jalview/schemes/ResidueProperties.java
index
73b48a9
..
42d03ec
100755
(executable)
--- a/
src/jalview/schemes/ResidueProperties.java
+++ b/
src/jalview/schemes/ResidueProperties.java
@@
-48,6
+48,8
@@
public class ResidueProperties
public static final Map<String, String> nucleotideName = new HashMap<>();
public static final Map<String, String> nucleotideName = new HashMap<>();
+ public static final Map<String, String> nucleotideAmbiguityName = new HashMap<>();
+
// lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
public static final Map<String, String> modifications = new HashMap<>();
// lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
public static final Map<String, String> modifications = new HashMap<>();
@@
-123,16
+125,14
@@
public class ResidueProperties
static
{
static
{
-
- String[][] namesArray = { { "a", "Adenine" }, { "g", "Guanine" },
- { "c", "Cytosine" },
+ String[][] namesArray = { { "a", "Adenine" }, { "c", "Cytosine" },
+ { "g", "Guanine" },
{ "t", "Thymine" },
{ "u", "Uracil" },
{ "i", "Inosine" },
{ "x", "Xanthine" },
{ "r", "Unknown Purine" },
{ "y", "Unknown Pyrimidine" },
{ "t", "Thymine" },
{ "u", "Uracil" },
{ "i", "Inosine" },
{ "x", "Xanthine" },
{ "r", "Unknown Purine" },
{ "y", "Unknown Pyrimidine" },
- { "n", "Unknown" },
{ "w", "Weak nucleotide (A or T)" },
{ "s", "Strong nucleotide (G or C)" },
{ "m", "Amino (A or C)" },
{ "w", "Weak nucleotide (A or T)" },
{ "s", "Strong nucleotide (G or C)" },
{ "m", "Amino (A or C)" },
@@
-140,10
+140,10
@@
public class ResidueProperties
{ "b", "Not A (G or C or T)" },
{ "h", "Not G (A or C or T)" },
{ "d", "Not C (A or G or T)" },
{ "b", "Not A (G or C or T)" },
{ "h", "Not G (A or C or T)" },
{ "d", "Not C (A or G or T)" },
- { "v", "Not T (A or G or C" } };
-
+ { "v", "Not T (A or G or C)" },
+ { "n", "Unknown" } };
// "gap" index
// "gap" index
- maxNucleotideIndex = namesArray.length + 1;
+ maxNucleotideIndex = namesArray.length;
nucleotideIndex = new int[255];
for (int i = 0; i < 255; i++)
nucleotideIndex = new int[255];
for (int i = 0; i < 255; i++)
@@
-162,6
+162,7
@@
public class ResidueProperties
nucleotideName.put(namesArray[i][0].toUpperCase(Locale.ROOT),
namesArray[i][1]);
}
nucleotideName.put(namesArray[i][0].toUpperCase(Locale.ROOT),
namesArray[i][1]);
}
+
}
static
}
static
@@
-349,17
+350,17
@@
public class ResidueProperties
Color.white, // Gap
};
Color.white, // Gap
};
+ // this colour scheme devised by sduce
public static final Color[] nucleotideAmbiguity = {
Color.decode("#f0fff0"), // a
public static final Color[] nucleotideAmbiguity = {
Color.decode("#f0fff0"), // a
- Color.decode("#f0fff0"), // g
Color.decode("#f0fff0"), // c
Color.decode("#f0fff0"), // c
+ Color.decode("#f0fff0"), // g
Color.decode("#f0fff0"), // t
Color.decode("#f0fff0"), // u
Color.decode("#ffffff"), // i
Color.decode("#f0fff0"), // t
Color.decode("#f0fff0"), // u
Color.decode("#ffffff"), // i
- Color.decode("#ffffff"), // x
+ Color.decode("#4f6f6f"), // x
Color.decode("#CD5C5C"), // r
Color.decode("#008000"), // y
Color.decode("#CD5C5C"), // r
Color.decode("#008000"), // y
- Color.decode("#2f4f4f"), // n
Color.decode("#4682B4"), // w
Color.decode("#FF8C00"), // s
Color.decode("#9ACD32"), // m
Color.decode("#4682B4"), // w
Color.decode("#FF8C00"), // s
Color.decode("#9ACD32"), // m
@@
-368,6
+369,7
@@
public class ResidueProperties
Color.decode("#808080"), // h
Color.decode("#483D8B"), // d
Color.decode("#b8860b"), // v
Color.decode("#808080"), // h
Color.decode("#483D8B"), // d
Color.decode("#b8860b"), // v
+ Color.decode("#2f4f4f"), // n
Color.white, // Gap
};
Color.white, // Gap
};