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Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
[jalview.git]
/
src
/
jalview
/
io
/
AMSAFile.java
diff --git
a/src/jalview/io/AMSAFile.java
b/src/jalview/io/AMSAFile.java
index
f82407e
..
34eace4
100644
(file)
--- a/
src/jalview/io/AMSAFile.java
+++ b/
src/jalview/io/AMSAFile.java
@@
-22,6
+22,9
@@
package jalview.io;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
public class AMSAFile extends jalview.io.FastaFile
{
public class AMSAFile extends jalview.io.FastaFile
{
@@
-36,14
+39,26
@@
public class AMSAFile extends jalview.io.FastaFile
this.al = al;
}
this.al = al;
}
+ public AMSAFile(String inFile, DataSourceType sourceType)
+ throws IOException
+ {
+ super(inFile, sourceType);
+ }
+
+ public AMSAFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public String print()
+ @Override
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
{
- super.print(getSeqsAsArray());
+ super.print(sqs, jvsuffix);
AlignmentAnnotation aa;
if (al.getAlignmentAnnotation() != null)
AlignmentAnnotation aa;
if (al.getAlignmentAnnotation() != null)