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Merge branch 'documentation/JAL-3111_release_211' into bug/JAL-2830_editManglesDatase...
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceGroup.java
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
944f263
..
3bf7bc4
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-88,7
+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)
@@
-102,11
+102,15
@@
public class SequenceGroup implements AnnotatedCollectionI
*/
public ResidueShaderI cs;
*/
public ResidueShaderI cs;
- // start column (base 0)
- int startRes = 0;
+ /**
+ * start column (base 0)
+ */
+ private int startRes = 0;
- // end column (base 0)
- int endRes = 0;
+ /**
+ * end column (base 0)
+ */
+ private int endRes = 0;
public Color outlineColour = Color.black;
public Color outlineColour = Color.black;
@@
-158,6
+162,7
@@
public class SequenceGroup implements AnnotatedCollectionI
{
groupName = "JGroup:" + this.hashCode();
cs = new ResidueShader();
{
groupName = "JGroup:" + this.hashCode();
cs = new ResidueShader();
+ sequences = new ArrayList<>();
}
/**
}
/**
@@
-209,6
+214,7
@@
public class SequenceGroup implements AnnotatedCollectionI
displayBoxes = seqsel.displayBoxes;
displayText = seqsel.displayText;
colourText = seqsel.colourText;
displayBoxes = seqsel.displayBoxes;
displayText = seqsel.displayText;
colourText = seqsel.colourText;
+
startRes = seqsel.startRes;
endRes = seqsel.endRes;
cs = new ResidueShader((ResidueShader) seqsel.cs);
startRes = seqsel.startRes;
endRes = seqsel.endRes;
cs = new ResidueShader((ResidueShader) seqsel.cs);
@@
-238,6
+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;
@@
-752,13
+769,16
@@
public class SequenceGroup implements AnnotatedCollectionI
/**
* Set the first column selected by this group. Runs from 0<=i<N_cols
*
/**
* Set the first column selected by this group. Runs from 0<=i<N_cols
*
- * @param i
+ * @param newStart
*/
*/
- public void setStartRes(int i)
+ public void setStartRes(int newStart)
{
int before = startRes;
{
int before = startRes;
- startRes = i;
- changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+ startRes= Math.max(0,newStart); // sanity check for negative start column positions
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+
+
+
}
/**
}
/**