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JAL-3033 updated classlist for loading the example file (jim's kitchensink corefile)
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignmentUtils.java
diff --git
a/src/jalview/analysis/AlignmentUtils.java
b/src/jalview/analysis/AlignmentUtils.java
index
8fd961e
..
2946ba2
100644
(file)
--- a/
src/jalview/analysis/AlignmentUtils.java
+++ b/
src/jalview/analysis/AlignmentUtils.java
@@
-74,12
+74,15
@@
import java.util.TreeMap;
*/
public class AlignmentUtils
{
*/
public class AlignmentUtils
{
-
private static final int CODON_LENGTH = 3;
private static final String SEQUENCE_VARIANT = "sequence_variant:";
private static final int CODON_LENGTH = 3;
private static final String SEQUENCE_VARIANT = "sequence_variant:";
- private static final String ID = "ID";
+ /*
+ * the 'id' attribute is provided for variant features fetched from
+ * Ensembl using its REST service with JSON format
+ */
+ public static final String VARIANT_ID = "id";
/**
* A data model to hold the 'normal' base value at a position, and an optional
/**
* A data model to hold the 'normal' base value at a position, and an optional
@@
-2583,15
+2586,15
@@
public class AlignmentUtils
peptidePos, var.getSource());
StringBuilder attributes = new StringBuilder(32);
peptidePos, var.getSource());
StringBuilder attributes = new StringBuilder(32);
- String id = (String) var.variant.getValue(ID);
+ String id = (String) var.variant.getValue(VARIANT_ID);
if (id != null)
{
if (id.startsWith(SEQUENCE_VARIANT))
{
id = id.substring(SEQUENCE_VARIANT.length());
}
if (id != null)
{
if (id.startsWith(SEQUENCE_VARIANT))
{
id = id.substring(SEQUENCE_VARIANT.length());
}
- sf.setValue(ID, id);
- attributes.append(ID).append("=").append(id);
+ sf.setValue(VARIANT_ID, id);
+ attributes.append(VARIANT_ID).append("=").append(id);
// TODO handle other species variants JAL-2064
StringBuilder link = new StringBuilder(32);
try
// TODO handle other species variants JAL-2064
StringBuilder link = new StringBuilder(32);
try