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
Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure
[jalview.git]
/
src
/
jalview
/
io
/
packed
/
JalviewDataset.java
diff --git
a/src/jalview/io/packed/JalviewDataset.java
b/src/jalview/io/packed/JalviewDataset.java
index
63263d2
..
9f84c16
100644
(file)
--- a/
src/jalview/io/packed/JalviewDataset.java
+++ b/
src/jalview/io/packed/JalviewDataset.java
@@
-20,6
+20,7
@@
*/
package jalview.io.packed;
*/
package jalview.io.packed;
+import jalview.analysis.TreeModel;
import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
@@
-151,8
+152,7
@@
public class JalviewDataset
{
// the following works because all trees are already had node/SequenceI
// associations created.
{
// the following works because all trees are already had node/SequenceI
// associations created.
- jalview.analysis.NJTree njt = new jalview.analysis.NJTree(
- al.getSequencesArray(), nf);
+ TreeModel njt = new TreeModel(al.getSequencesArray(), null, nf);
// this just updates the displayed leaf name on the tree according to
// the SequenceIs.
njt.renameAssociatedNodes();
// this just updates the displayed leaf name on the tree according to
// the SequenceIs.
njt.renameAssociatedNodes();
@@
-211,8
+211,7
@@
public class JalviewDataset
* @param parentAlignment
*/
public JalviewDataset(AlignmentI aldataset,
* @param parentAlignment
*/
public JalviewDataset(AlignmentI aldataset,
- Map<String, FeatureColourI> fc,
- Hashtable seqDets)
+ Map<String, FeatureColourI> fc, Hashtable seqDets)
{
// TODO not used - remove?
this(aldataset, fc, seqDets, null);
{
// TODO not used - remove?
this(aldataset, fc, seqDets, null);
@@
-234,8
+233,8
@@
public class JalviewDataset
* with.
*/
public JalviewDataset(AlignmentI aldataset,
* with.
*/
public JalviewDataset(AlignmentI aldataset,
- Map<String, FeatureColourI> fc,
- Hashtable seqDets, AlignmentI parentAlignment)
+ Map<String, FeatureColourI> fc, Hashtable seqDets,
+ AlignmentI parentAlignment)
{
this();
parentDataset = aldataset;
{
this();
parentDataset = aldataset;