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Merge branch 'develop' into features/JAL-4219_extended_fasta_rna_ss
[jalview.git]
/
src
/
jalview
/
schemes
/
ResidueProperties.java
diff --git
a/src/jalview/schemes/ResidueProperties.java
b/src/jalview/schemes/ResidueProperties.java
index
42d03ec
..
2fcb95f
100755
(executable)
--- a/
src/jalview/schemes/ResidueProperties.java
+++ b/
src/jalview/schemes/ResidueProperties.java
@@
-41,6
+41,8
@@
public class ResidueProperties
public static final int[] nucleotideIndex;
public static final int[] purinepyrimidineIndex;
public static final int[] nucleotideIndex;
public static final int[] purinepyrimidineIndex;
+
+ public static final int[] secondaryStructureIndex;
public static final Map<String, Integer> aa3Hash = new HashMap<>();
public static final Map<String, Integer> aa3Hash = new HashMap<>();
@@
-195,6
+197,19
@@
public class ResidueProperties
purinepyrimidineIndex['N'] = 2;
purinepyrimidineIndex['n'] = 2;
}
purinepyrimidineIndex['N'] = 2;
purinepyrimidineIndex['n'] = 2;
}
+
+ static
+ {
+ secondaryStructureIndex = new int[255];
+ for (int i = 0; i < 255; i++)
+ {
+ secondaryStructureIndex[i] = 3;
+ }
+
+ secondaryStructureIndex['H'] = 0;
+ secondaryStructureIndex['E'] = 1;
+ secondaryStructureIndex['C'] = 2;
+ }
private static final Integer ONE = Integer.valueOf(1);
private static final Integer ONE = Integer.valueOf(1);
@@
-383,6
+398,12
@@
public class ResidueProperties
Color.white, // all other nucleotides
Color.white // Gap
};
Color.white, // all other nucleotides
Color.white // Gap
};
+
+ //Secondary structure
+ public static final Color[] secondarystructure = { Color.red, // H
+ Color.green, // E
+ Color.gray // C
+ };
// Zappo
public static final Color[] zappo = { Color.pink, // A
// Zappo
public static final Color[] zappo = { Color.pink, // A
@@
-2414,7
+2435,7
@@
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())
{
@@
-2446,12
+2467,13
@@
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