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JAL-1942 JAL-1479 refactored SequenceI.getDBRef/SequenceI.setDBRef to SequenceI.getDB...
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceGroup.java
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
feb714a
..
0e8fa17
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-76,8
+76,10
@@
public class SequenceGroup implements AnnotatedCollectionI
*/
public ColourSchemeI cs;
*/
public ColourSchemeI cs;
+ // start column (base 0)
int startRes = 0;
int startRes = 0;
+ // end column (base 0)
int endRes = 0;
public Color outlineColour = Color.black;
int endRes = 0;
public Color outlineColour = Color.black;
@@
-207,7
+209,7
@@
public class SequenceGroup implements AnnotatedCollectionI
if (seqs[ipos] != null)
{
seqs[ipos].setDescription(seq.getDescription());
if (seqs[ipos] != null)
{
seqs[ipos].setDescription(seq.getDescription());
- seqs[ipos].setDBRef(seq.getDBRef());
+ seqs[ipos].setDBRefs(seq.getDBRefs());
seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
if (seq.getDatasetSequence() != null)
{
seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
if (seq.getDatasetSequence() != null)
{
@@
-611,13
+613,13
@@
public class SequenceGroup implements AnnotatedCollectionI
{
synchronized (sequences)
{
{
synchronized (sequences)
{
- if (sequences.contains(s))
- {
- deleteSequence(s, recalc);
- }
- else
- {
- addSequence(s, recalc);
+ if (sequences.contains(s))
+ {
+ deleteSequence(s, recalc);
+ }
+ else
+ {
+ addSequence(s, recalc);
}
}
}
}
}
}
@@
-773,8
+775,9
@@
public class SequenceGroup implements AnnotatedCollectionI
synchronized (sequences)
{
// MC This needs to get reset when characters are inserted and deleted
synchronized (sequences)
{
// MC This needs to get reset when characters are inserted and deleted
- boolean first=true;
- for (SequenceI seq:sequences) {
+ boolean first = true;
+ for (SequenceI seq : sequences)
+ {
if (first || seq.getLength() > width)
{
width = seq.getLength();
if (first || seq.getLength() > width)
{
width = seq.getLength();