package jalview.ext.forester;
-import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
import jalview.math.MatrixI;
import jalview.util.MessageManager;
private final MatrixI jalviewMatrix;
-
private final String[] identifiers;
public ForesterMatrix(final MatrixI jalviewInputMatrix,
- final Sequence[] matrixSequences)
+ final SequenceI[] matrixSequences)
{
this.jalviewMatrix = jalviewInputMatrix;
this.identifiers = new String[matrixSequences.length];
int i = 0;
-
- for (Sequence sequence : matrixSequences)
+ for (SequenceI sequence : matrixSequences)
{
identifiers[i] = sequence.getName();
i++;
@Override
public String getIdentifier(final int i)
{
- return identifiers[i];
+ return identifiers[i]; // add handling if index is out of bounds
}
}
+ public static DistanceMatrix convertJalviewToForester(
+ final MatrixI jalviewInputMatrix,
+ final SequenceI[] matrixSequences)
+ {
+ return DataConversions.createForesterDistanceMatrix(
+ jalviewInputMatrix, matrixSequences);
+
+ }
+
+ public static DistanceMatrix convertJalviewToForester(
+ final MatrixI jalviewInputMatrix,
+ final String[] matrixIdentifiers)
+ {
+ return DataConversions.createForesterDistanceMatrix(
+ jalviewInputMatrix, matrixIdentifiers);
+
+ }
+
}
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