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Merge branch 'features/JAL-1641_JSON_' into develop
[jalview.git]
/
src
/
jalview
/
io
/
AlignFile.java
diff --git
a/src/jalview/io/AlignFile.java
b/src/jalview/io/AlignFile.java
index
e902ccf
..
b2f8b2b
100755
(executable)
--- a/
src/jalview/io/AlignFile.java
+++ b/
src/jalview/io/AlignFile.java
@@
-22,13
+22,17
@@
package jalview.io;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import java.io.IOException;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import java.io.IOException;
+import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
/**
import java.util.Vector;
/**
@@
-54,6
+58,11
@@
public abstract class AlignFile extends FileParse
protected Vector<AlignmentAnnotation> annotations;
/**
protected Vector<AlignmentAnnotation> annotations;
/**
+ * SequenceGroups to be added to the alignment object
+ */
+ protected List<SequenceGroup> seqGroups;
+
+ /**
* Properties to be added to generated alignment object
*/
protected Hashtable properties;
* Properties to be added to generated alignment object
*/
protected Hashtable properties;
@@
-165,6
+174,11
@@
public abstract class AlignFile extends FileParse
return seqs;
}
return seqs;
}
+ public List<SequenceGroup> getSeqGroups()
+ {
+ return seqGroups;
+ }
+
/**
* Return the Sequences in the seqs Vector as an array of Sequences
*/
/**
* Return the Sequences in the seqs Vector as an array of Sequences
*/
@@
-206,6
+220,12
@@
public abstract class AlignFile extends FileParse
}
}
+ public void addSeqGroups(AlignmentI al)
+ {
+ this.seqGroups = al.getGroups();
+
+ }
+
/**
* Add any additional information extracted from the file to the alignment
* properties.
/**
* Add any additional information extracted from the file to the alignment
* properties.
@@
-269,6
+289,7
@@
public abstract class AlignFile extends FileParse
{
seqs = new Vector();
annotations = new Vector();
{
seqs = new Vector();
annotations = new Vector();
+ seqGroups = new ArrayList<SequenceGroup>();
parseCalled=false;
}
parseCalled=false;
}