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JAL-2759 First pass instantiate hiddenColumns collection in constructor
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignedCodon.java
diff --git
a/src/jalview/datamodel/AlignedCodon.java
b/src/jalview/datamodel/AlignedCodon.java
index
6179831
..
39a1853
100644
(file)
--- a/
src/jalview/datamodel/AlignedCodon.java
+++ b/
src/jalview/datamodel/AlignedCodon.java
@@
-27,32
+27,38
@@
package jalview.datamodel;
*
* Example: in "G-AT-C-GA" the aligned codons are (0, 2, 3) and (5, 7, 8).
*
*
* Example: in "G-AT-C-GA" the aligned codons are (0, 2, 3) and (5, 7, 8).
*
- * JBPComment: Is this useful anywhere other than jalview.analysis.Dna ?
- *
* @author gmcarstairs
*
*/
public final class AlignedCodon
{
* @author gmcarstairs
*
*/
public final class AlignedCodon
{
+ // base 1 aligned sequence position (base 0)
public final int pos1;
public final int pos1;
+ // base 2 aligned sequence position (base 0)
public final int pos2;
public final int pos2;
+ // base 3 aligned sequence position (base 0)
public final int pos3;
public final int pos3;
+ // peptide aligned sequence position (base 0)
+ public final int peptideCol;
+
+ // peptide coded for by this codon
public final String product;
public AlignedCodon(int i, int j, int k)
{
public final String product;
public AlignedCodon(int i, int j, int k)
{
- this(i, j, k, null);
+ this(i, j, k, null, 0);
}
}
- public AlignedCodon(int i, int j, int k, String prod)
+ public AlignedCodon(int i, int j, int k, String prod, int prodCol)
{
pos1 = i;
pos2 = j;
pos3 = k;
product = prod;
{
pos1 = i;
pos2 = j;
pos3 = k;
product = prod;
+ peptideCol = prodCol;
}
/**
}
/**