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JAL-3676 Documentation in Help for Java Console, Logging and Reporting Bugs
[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
817ba9c
..
9f84c16
100644
(file)
--- a/
src/jalview/io/packed/JalviewDataset.java
+++ b/
src/jalview/io/packed/JalviewDataset.java
@@
-20,6
+20,8
@@
*/
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.io.NewickFile;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.NewickFile;
@@
-57,7
+59,7
@@
public class JalviewDataset
/**
* @return the featureColours
*/
/**
* @return the featureColours
*/
- public Map<String, Object> getFeatureColours()
+ public Map<String, FeatureColourI> getFeatureColours()
{
return featureColours;
}
{
return featureColours;
}
@@
-66,7
+68,7
@@
public class JalviewDataset
* @param featureColours
* the featureColours to set
*/
* @param featureColours
* the featureColours to set
*/
- public void setFeatureColours(Map<String, Object> featureColours)
+ public void setFeatureColours(Map<String, FeatureColourI> featureColours)
{
this.featureColours = featureColours;
}
{
this.featureColours = featureColours;
}
@@
-150,8
+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();
@@
-187,7
+188,7
@@
public class JalviewDataset
/**
* current set of feature colours
*/
/**
* current set of feature colours
*/
- Map<String, Object> featureColours;
+ Map<String, FeatureColourI> featureColours;
/**
* original identity of each sequence in results
/**
* original identity of each sequence in results
@@
-201,7
+202,7
@@
public class JalviewDataset
seqDetails = new Hashtable();
al = new ArrayList<AlignmentSet>();
parentDataset = null;
seqDetails = new Hashtable();
al = new ArrayList<AlignmentSet>();
parentDataset = null;
- featureColours = new HashMap<String, Object>();
+ featureColours = new HashMap<String, FeatureColourI>();
}
/**
}
/**
@@
-209,8
+210,8
@@
public class JalviewDataset
*
* @param parentAlignment
*/
*
* @param parentAlignment
*/
- public JalviewDataset(AlignmentI aldataset, Map<String, Object> fc,
- Hashtable seqDets)
+ public JalviewDataset(AlignmentI aldataset,
+ Map<String, FeatureColourI> fc, Hashtable seqDets)
{
// TODO not used - remove?
this(aldataset, fc, seqDets, null);
{
// TODO not used - remove?
this(aldataset, fc, seqDets, null);
@@
-231,8
+232,9
@@
public class JalviewDataset
* (may be null) alignment to associate new annotation and trees
* with.
*/
* (may be null) alignment to associate new annotation and trees
* with.
*/
- public JalviewDataset(AlignmentI aldataset, Map<String, Object> fc,
- Hashtable seqDets, AlignmentI parentAlignment)
+ public JalviewDataset(AlignmentI aldataset,
+ Map<String, FeatureColourI> fc, Hashtable seqDets,
+ AlignmentI parentAlignment)
{
this();
parentDataset = aldataset;
{
this();
parentDataset = aldataset;