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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
ad5bb24
..
9f84c16
100644
(file)
--- a/
src/jalview/io/packed/JalviewDataset.java
+++ b/
src/jalview/io/packed/JalviewDataset.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,13
+20,17
@@
*/
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 java.util.ArrayList;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.NewickFile;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
public class JalviewDataset
{
public class JalviewDataset
{
@@
-55,7
+59,7
@@
public class JalviewDataset
/**
* @return the featureColours
*/
/**
* @return the featureColours
*/
- public Hashtable getFeatureColours()
+ public Map<String, FeatureColourI> getFeatureColours()
{
return featureColours;
}
{
return featureColours;
}
@@
-64,7
+68,7
@@
public class JalviewDataset
* @param featureColours
* the featureColours to set
*/
* @param featureColours
* the featureColours to set
*/
- public void setFeatureColours(Hashtable featureColours)
+ public void setFeatureColours(Map<String, FeatureColourI> featureColours)
{
this.featureColours = featureColours;
}
{
this.featureColours = featureColours;
}
@@
-148,8
+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();
@@
-185,7
+188,7
@@
public class JalviewDataset
/**
* current set of feature colours
*/
/**
* current set of feature colours
*/
- Hashtable featureColours;
+ Map<String, FeatureColourI> featureColours;
/**
* original identity of each sequence in results
/**
* original identity of each sequence in results
@@
-199,7
+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 Hashtable();
+ featureColours = new HashMap<String, FeatureColourI>();
}
/**
}
/**
@@
-207,9
+210,10
@@
public class JalviewDataset
*
* @param parentAlignment
*/
*
* @param parentAlignment
*/
- public JalviewDataset(AlignmentI aldataset, Hashtable fc,
- Hashtable seqDets)
+ public JalviewDataset(AlignmentI aldataset,
+ Map<String, FeatureColourI> fc, Hashtable seqDets)
{
{
+ // TODO not used - remove?
this(aldataset, fc, seqDets, null);
}
this(aldataset, fc, seqDets, null);
}
@@
-228,8
+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, Hashtable fc,
- Hashtable seqDets, AlignmentI parentAlignment)
+ public JalviewDataset(AlignmentI aldataset,
+ Map<String, FeatureColourI> fc, Hashtable seqDets,
+ AlignmentI parentAlignment)
{
this();
parentDataset = aldataset;
{
this();
parentDataset = aldataset;