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Merge branch 'JAL-1445' into develop
[jalview.git]
/
src
/
jalview
/
datamodel
/
Sequence.java
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
23c3de7
..
c31dd3e
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-23,6
+23,8
@@
import jalview.analysis.AlignSeq;
import java.util.Enumeration;
import java.util.Vector;
import java.util.Enumeration;
import java.util.Vector;
+import fr.orsay.lri.varna.models.rna.RNA;
+
/**
*
* Implements the SequenceI interface for a char[] based sequence object.
/**
*
* Implements the SequenceI interface for a char[] based sequence object.
@@
-49,6
+51,8
@@
public class Sequence implements SequenceI
String vamsasId;
DBRefEntry[] dbrefs;
String vamsasId;
DBRefEntry[] dbrefs;
+
+ RNA rna;
/**
* This annotation is displayed below the alignment but the positions are tied
/**
* This annotation is displayed below the alignment but the positions are tied
@@
-61,7
+65,7
@@
public class Sequence implements SequenceI
*/
int index = -1;
*/
int index = -1;
- /** array of seuqence features - may not be null for a valid sequence object */
+ /** array of sequence features - may not be null for a valid sequence object */
public SequenceFeature[] sequenceFeatures;
/**
public SequenceFeature[] sequenceFeatures;
/**
@@
-708,6
+712,7
@@
public class Sequence implements SequenceI
{
tmp = new char[i];
System.arraycopy(sequence, 0, tmp, 0, i);
{
tmp = new char[i];
System.arraycopy(sequence, 0, tmp, 0, i);
+ j=sequence.length;
}
else
{
}
else
{
@@
-716,6
+721,9
@@
public class Sequence implements SequenceI
System.arraycopy(sequence, j, tmp, i, sequence.length - j);
}
boolean createNewDs = false;
System.arraycopy(sequence, j, tmp, i, sequence.length - j);
}
boolean createNewDs = false;
+ // TODO: take a look at the new dataset creation validation method below -
+ // this could become time comsuming for large sequences - consider making it
+ // more efficient
for (int s = i; s < j; s++)
{
if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
for (int s = i; s < j; s++)
{
if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
@@
-1201,4
+1209,9
@@
public class Sequence implements SequenceI
{
index = value;
}
{
index = value;
}
+
+ public void setRNA(RNA r){rna=r;}
+
+ public RNA getRNA() { return rna; }
+
}
}