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JAL-2041 add ID,clinical_significance to feature attributes (for export)
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignmentUtils.java
diff --git
a/src/jalview/analysis/AlignmentUtils.java
b/src/jalview/analysis/AlignmentUtils.java
index
fa135f8
..
42a1201
100644
(file)
--- a/
src/jalview/analysis/AlignmentUtils.java
+++ b/
src/jalview/analysis/AlignmentUtils.java
@@
-20,6
+20,8
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
+import static jalview.io.gff.GffConstants.CLINICAL_SIGNIFICANCE;
+
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
@@
-69,7
+71,6
@@
public class AlignmentUtils
private static final String SEQUENCE_VARIANT = "sequence_variant:";
private static final String ID = "ID";
private static final String SEQUENCE_VARIANT = "sequence_variant:";
private static final String ID = "ID";
- private static final String CLINICAL_SIGNIFICANCE = "clinical_significance";
/**
* 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
@@
-1927,10
+1928,11
@@
public class AlignmentUtils
if (trans != null && !trans.equals(residue))
{
String desc = residue + "->" + trans;
if (trans != null && !trans.equals(residue))
{
String desc = residue + "->" + trans;
- // set score to 0f so 'graduated colour' option is offered!
+ // set score to 0f so 'graduated colour' option is offered! JAL-2060
SequenceFeature sf = new SequenceFeature(
SequenceOntologyI.SEQUENCE_VARIANT, desc, peptidePos,
peptidePos, 0f, null);
SequenceFeature sf = new SequenceFeature(
SequenceOntologyI.SEQUENCE_VARIANT, desc, peptidePos,
peptidePos, 0f, null);
+ StringBuilder attributes = new StringBuilder(32);
String id = (String) var.variant.getValue(ID);
if (id != null)
{
String id = (String) var.variant.getValue(ID);
if (id != null)
{
@@
-1939,6
+1941,7
@@
public class AlignmentUtils
id = id.substring(SEQUENCE_VARIANT.length());
}
sf.setValue(ID, id);
id = id.substring(SEQUENCE_VARIANT.length());
}
sf.setValue(ID, id);
+ attributes.append(ID).append("=").append(id);
// TODO handle other species variants
StringBuilder link = new StringBuilder(32);
try
// TODO handle other species variants
StringBuilder link = new StringBuilder(32);
try
@@
-1957,8
+1960,14
@@
public class AlignmentUtils
if (clinSig != null)
{
sf.setValue(CLINICAL_SIGNIFICANCE, clinSig);
if (clinSig != null)
{
sf.setValue(CLINICAL_SIGNIFICANCE, clinSig);
+ attributes.append(";").append(CLINICAL_SIGNIFICANCE).append("=")
+ .append(clinSig);
}
peptide.addSequenceFeature(sf);
}
peptide.addSequenceFeature(sf);
+ if (attributes.length() > 0)
+ {
+ sf.setAttributes(attributes.toString());
+ }
return true;
}
return false;
return true;
}
return false;