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Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups
[jalview.git]
/
src
/
jalview
/
ws
/
dbsources
/
EBIAlfaFold.java
diff --git
a/src/jalview/ws/dbsources/EBIAlfaFold.java
b/src/jalview/ws/dbsources/EBIAlfaFold.java
index
a734f52
..
fd10c79
100644
(file)
--- a/
src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/
src/jalview/ws/dbsources/EBIAlfaFold.java
@@
-44,6
+44,7
@@
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GroupSet;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
@@
-447,7
+448,7
@@
public class EBIAlfaFold extends EbiFileRetrievedProxy
}
ContactMatrixI matrix = new PAEContactMatrix(sequence,
(Map<String, Object>) paeDict);
}
ContactMatrixI matrix = new PAEContactMatrix(sequence,
(Map<String, Object>) paeDict);
- ((PAEContactMatrix) matrix).makeGroups(5f, true);
+ matrix.setGroupSet(GroupSet.makeGroups(matrix, 5f, true));
AlignmentAnnotation cmannot = sequence.addContactList(matrix);
if (label != null)
AlignmentAnnotation cmannot = sequence.addContactList(matrix);
if (label != null)
@@
-505,8
+506,8
@@
public class EBIAlfaFold extends EbiFileRetrievedProxy
SequenceI seq = sm.getSequence();
ContactMatrixI matrix = new PAEContactMatrix(seq,
(Map<String, Object>) pae_obj);
SequenceI seq = sm.getSequence();
ContactMatrixI matrix = new PAEContactMatrix(seq,
(Map<String, Object>) pae_obj);
- ((PAEContactMatrix) matrix).makeGroups(5f, true);
- AlignmentAnnotation cmannot = seq.addContactList(matrix);
+ matrix.setGroupSet(GroupSet.makeGroups(matrix, 5f, true));
+ AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
/* this already happens in Sequence.addContactList()
seq.addAlignmentAnnotation(cmannot);
*/
/* this already happens in Sequence.addContactList()
seq.addAlignmentAnnotation(cmannot);
*/