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JAl-1705 ENSEMBL cDNA type cannot be queried with peptide IDs
[jalview.git]
/
src
/
jalview
/
io
/
AlignFile.java
diff --git
a/src/jalview/io/AlignFile.java
b/src/jalview/io/AlignFile.java
index
b66fb11
..
d221d37
100755
(executable)
--- a/
src/jalview/io/AlignFile.java
+++ b/
src/jalview/io/AlignFile.java
@@
-20,7
+20,6
@@
*/
package jalview.io;
*/
package jalview.io;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
@@
-48,7
+47,8
@@
public abstract class AlignFile extends FileParse
int maxLength = 0;
/**
int maxLength = 0;
/**
- * Sequences to be added to form a new alignment.
+ * Sequences to be added to form a new alignment. TODO: remove vector in this
+ * class
*/
protected Vector<SequenceI> seqs;
*/
protected Vector<SequenceI> seqs;
@@
-200,7
+200,7
@@
public abstract class AlignFile extends FileParse
*
* @param al
*/
*
* @param al
*/
- public void addAnnotations(Alignment al)
+ public void addAnnotations(AlignmentI al)
{
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
{
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
@@
-220,6
+220,11
@@
public abstract class AlignFile extends FileParse
}
}
+ /**
+ * register sequence groups on the alignment for **output**
+ *
+ * @param al
+ */
public void addSeqGroups(AlignmentI al)
{
this.seqGroups = al.getGroups();
public void addSeqGroups(AlignmentI al)
{
this.seqGroups = al.getGroups();
@@
-233,7
+238,7
@@
public abstract class AlignFile extends FileParse
* @note implicitly called by addAnnotations()
* @param al
*/
* @note implicitly called by addAnnotations()
* @param al
*/
- public void addProperties(Alignment al)
+ public void addProperties(AlignmentI al)
{
if (properties != null && properties.size() > 0)
{
{
if (properties != null && properties.size() > 0)
{
@@
-378,4
+383,13
@@
public abstract class AlignFile extends FileParse
return newickStrings == null ? 0 : newickStrings.size();
}
return newickStrings == null ? 0 : newickStrings.size();
}
+ public void addGroups(AlignmentI al)
+ {
+
+ for (SequenceGroup sg : getSeqGroups())
+ {
+ al.addGroup(sg);
+ }
+ }
+
}
}