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-1761 backbone type parameter for configuring which atoms are used for superpositi...
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceGroup.java
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
1e579ec
..
861595c
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-25,7
+25,6
@@
import jalview.analysis.Conservation;
import jalview.renderer.ResidueShader;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
import jalview.renderer.ResidueShader;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
-import jalview.ws.params.InvalidArgumentException;
import java.awt.Color;
import java.beans.PropertyChangeListener;
import java.awt.Color;
import java.beans.PropertyChangeListener;
@@
-89,7
+88,7
@@
public class SequenceGroup implements AnnotatedCollectionI
/**
* group members
*/
/**
* group members
*/
- private List<SequenceI> sequences = new ArrayList<>();
+ private List<SequenceI> sequences;
/**
* representative sequence for this group (if any)
/**
* representative sequence for this group (if any)
@@
-163,6
+162,7
@@
public class SequenceGroup implements AnnotatedCollectionI
{
groupName = "JGroup:" + this.hashCode();
cs = new ResidueShader();
{
groupName = "JGroup:" + this.hashCode();
cs = new ResidueShader();
+ sequences = new ArrayList<>();
}
/**
}
/**
@@
-244,6
+244,17
@@
public class SequenceGroup implements AnnotatedCollectionI
}
}
}
}
+ /**
+ * Constructor that copies the given list of sequences
+ *
+ * @param seqs
+ */
+ public SequenceGroup(List<SequenceI> seqs)
+ {
+ this();
+ this.sequences.addAll(seqs);
+ }
+
public boolean isShowSequenceLogo()
{
return showSequenceLogo;
public boolean isShowSequenceLogo()
{
return showSequenceLogo;
@@
-262,7
+273,7
@@
public class SequenceGroup implements AnnotatedCollectionI
if (seqipos != null)
{
seqipos.setDescription(seq.getDescription());
if (seqipos != null)
{
seqipos.setDescription(seq.getDescription());
- seqipos.getDBRefsFrom(seq);
+ seqipos.setDBRefs(seq.getDBRefs());
seqipos.setSequenceFeatures(seq.getSequenceFeatures());
if (seq.getDatasetSequence() != null)
{
seqipos.setSequenceFeatures(seq.getSequenceFeatures());
if (seq.getDatasetSequence() != null)
{