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JAL-1479 improved SiftsClient test coverage and implemented previously unimplemented...
[jalview.git]
/
src
/
jalview
/
datamodel
/
HiddenSequences.java
diff --git
a/src/jalview/datamodel/HiddenSequences.java
b/src/jalview/datamodel/HiddenSequences.java
index
dcc5f26
..
db4c858
100755
(executable)
--- a/
src/jalview/datamodel/HiddenSequences.java
+++ b/
src/jalview/datamodel/HiddenSequences.java
@@
-254,6
+254,12
@@
public class HiddenSequences
return alignmentIndex;
}
return alignmentIndex;
}
+ /**
+ * makes a copy of the alignment with hidden sequences included. Using the
+ * copy for anything other than simple output is not recommended. Note - this
+ * method DOES NOT USE THE AlignmentI COPY CONSTRUCTOR!
+ * @return
+ */
public AlignmentI getFullAlignment()
{
int isize = hiddenSequences.length;
public AlignmentI getFullAlignment()
{
int isize = hiddenSequences.length;
@@
-277,6
+283,7
@@
public class HiddenSequences
fAlignmt.alignmentProperties = alignment.getProperties();
fAlignmt.groups = alignment.getGroups();
fAlignmt.hasRNAStructure = alignment.hasRNAStructure();
fAlignmt.alignmentProperties = alignment.getProperties();
fAlignmt.groups = alignment.getGroups();
fAlignmt.hasRNAStructure = alignment.hasRNAStructure();
+ fAlignmt.setSeqrep(alignment.getSeqrep());
return fAlignmt;
}
return fAlignmt;
}