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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git]
/
src
/
jalview
/
schemes
/
ResidueProperties.java
diff --git
a/src/jalview/schemes/ResidueProperties.java
b/src/jalview/schemes/ResidueProperties.java
index
2ce3e6d
..
e297ff6
100755
(executable)
--- a/
src/jalview/schemes/ResidueProperties.java
+++ b/
src/jalview/schemes/ResidueProperties.java
@@
-140,7
+140,7
@@
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
maxNucleotideIndex = namesArray.length;
{ "n", "Unknown" } };
// "gap" index
maxNucleotideIndex = namesArray.length;
@@
-350,17
+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
@@
-369,6
+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
};
@@
-2413,7
+2414,7
@@
public class ResidueProperties
public static void main(String[] args)
{
Hashtable<String, Vector<String>> aaProps = new Hashtable<>();
public static void main(String[] args)
{
Hashtable<String, Vector<String>> aaProps = new Hashtable<>();
- System.out.println("my %aa = {");
+ jalview.bin.Console.outPrintln("my %aa = {");
// invert property hashes
for (String pname : propHash.keySet())
{
// invert property hashes
for (String pname : propHash.keySet())
{
@@
-2445,12
+2446,13
@@
public class ResidueProperties
System.out.print("'" + props.nextElement() + "'");
if (props.hasMoreElements())
{
System.out.print("'" + props.nextElement() + "'");
if (props.hasMoreElements())
{
- System.out.println(", ");
+ jalview.bin.Console.outPrintln(", ");
}
}
}
}
- System.out.println("]" + (res.hasMoreElements() ? "," : ""));
+ jalview.bin.Console
+ .outPrintln("]" + (res.hasMoreElements() ? "," : ""));
}
}
- System.out.println("};");
+ jalview.bin.Console.outPrintln("};");
}
// to here
}
// to here