git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2428 simplify TreeModel constructors, add getOriginalData
[jalview.git]
/
src
/
jalview
/
analysis
/
TreeModel.java
diff --git
a/src/jalview/analysis/TreeModel.java
b/src/jalview/analysis/TreeModel.java
index
2f8d788
..
62b0594
100644
(file)
--- a/
src/jalview/analysis/TreeModel.java
+++ b/
src/jalview/analysis/TreeModel.java
@@
-46,7
+46,7
@@
public class TreeModel
* SequenceData is a string representation of what the user
* sees. The display may contain hidden columns.
*/
* SequenceData is a string representation of what the user
* sees. The display may contain hidden columns.
*/
- public AlignmentView seqData;
+ private AlignmentView seqData;
int noseqs;
int noseqs;
@@
-68,7
+68,7
@@
public class TreeModel
/**
* Create a new TreeModel object with leaves associated with sequences in
/**
* Create a new TreeModel object with leaves associated with sequences in
- * seqs, and original alignment data represented by Cigar strings
+ * seqs, and (optionally) original alignment data represented by Cigar strings
*
* @param seqs
* SequenceI[]
*
* @param seqs
* SequenceI[]
@@
-79,22
+79,9
@@
public class TreeModel
*/
public TreeModel(SequenceI[] seqs, AlignmentView odata, NewickFile treefile)
{
*/
public TreeModel(SequenceI[] seqs, AlignmentView odata, NewickFile treefile)
{
- this(seqs, treefile);
- seqData = odata;
- }
-
- /**
- * Creates a new TreeModel object from a tree from an external source
- *
- * @param seqs
- * SequenceI which should be associated with leafs of treefile
- * @param treefile
- * A parsed tree
- */
- public TreeModel(SequenceI[] seqs, NewickFile treefile)
- {
this(seqs, treefile.getTree(), treefile.HasDistances(), treefile
.HasBootstrap(), treefile.HasRootDistance());
this(seqs, treefile.getTree(), treefile.HasDistances(), treefile
.HasBootstrap(), treefile.HasRootDistance());
+ seqData = odata;
associateLeavesToSequences(seqs);
}
associateLeavesToSequences(seqs);
}
@@
-468,15
+455,6
@@
public class TreeModel
}
/**
}
/**
- *
- * @return true if original sequence data can be recovered
- */
- public boolean hasOriginalSequenceData()
- {
- return seqData != null;
- }
-
- /**
* Returns original alignment data used for calculation - or null where not
* available.
*
* Returns original alignment data used for calculation - or null where not
* available.
*
@@
-710,4
+688,9
@@
public class TreeModel
;
}
}
;
}
}
+
+ public AlignmentView getOriginalData()
+ {
+ return seqData;
+ }
}
}