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Implemented CIGAR representation of an Alignment view for passing to
[jalview.git]
/
src
/
jalview
/
datamodel
/
Sequence.java
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
615f670
..
562440f
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-40,7
+40,7
@@
public class Sequence implements SequenceI
Color color = Color.white;
\r
Vector pdbIds;
\r
String vamsasId;
\r
Color color = Color.white;
\r
Vector pdbIds;
\r
String vamsasId;
\r
- Vector dbrefs;
\r
+ DBRefEntry [] dbrefs;
\r
\r
/** This annotation is displayed below the alignment but the
\r
* positions are tied to the residues of this sequence */
\r
\r
/** This annotation is displayed below the alignment but the
\r
* positions are tied to the residues of this sequence */
\r
@@
-560,11
+560,12
@@
public class Sequence implements SequenceI
vamsasId = id;
\r
}
\r
\r
vamsasId = id;
\r
}
\r
\r
- public void setDBRef(Vector dbref)
\r
+ public void setDBRef(DBRefEntry [] dbref)
\r
{
\r
dbrefs = dbref;
\r
}
\r
{
\r
dbrefs = dbref;
\r
}
\r
- public Vector getDBRef()
\r
+
\r
+ public DBRefEntry [] getDBRef()
\r
{
\r
return dbrefs;
\r
}
\r
{
\r
return dbrefs;
\r
}
\r
@@
-572,9
+573,14
@@
public class Sequence implements SequenceI
public void addDBRef(DBRefEntry entry)
\r
{
\r
if(dbrefs == null)
\r
public void addDBRef(DBRefEntry entry)
\r
{
\r
if(dbrefs == null)
\r
- dbrefs = new Vector();
\r
+ dbrefs = new DBRefEntry[0];
\r
+
\r
+ DBRefEntry [] temp = new DBRefEntry[dbrefs.length+1];
\r
+ System.arraycopy(dbrefs, 0, temp, 0, dbrefs.length);
\r
+
\r
+ temp[temp.length-1] = entry;
\r
\r
\r
- dbrefs.addElement(entry);
\r
+ dbrefs = temp;
\r
}
\r
\r
public void setDatasetSequence(SequenceI seq)
\r
}
\r
\r
public void setDatasetSequence(SequenceI seq)
\r