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Merge branch 'releases/Release_2_10_0_Branch'
[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
1906fff
..
c79c63a
100644
(file)
--- a/
src/jalview/io/packed/JalviewDataset.java
+++ b/
src/jalview/io/packed/JalviewDataset.java
@@
-1,5
+1,5
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
* Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
@@
-20,13
+20,16
@@
*/
package jalview.io.packed;
*/
package jalview.io.packed;
+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
+58,7
@@
public class JalviewDataset
/**
* @return the featureColours
*/
/**
* @return the featureColours
*/
- public Hashtable getFeatureColours()
+ public Map<String, FeatureColourI> getFeatureColours()
{
return featureColours;
}
{
return featureColours;
}
@@
-64,7
+67,7
@@
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;
}
@@
-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;