* @author $author$
* @version $Revision$
*/
-public abstract class AlignFile extends FileParse implements AlignmentFileI
+public abstract class AlignFile extends FileParse
+ implements AlignmentFileReaderI, AlignmentFileWriterI
{
int noSeqs = 0;
/**
* Properties to be added to generated alignment object
*/
- protected Hashtable properties;
+ private Hashtable properties;
long start;
long end;
- boolean jvSuffix = true;
-
private boolean parseCalled;
/**
initData();
}
+ public AlignFile(SequenceI[] seqs)
+ {
+ this();
+ setSeqs(seqs);
+ }
+
/**
* Constructor which parses the data from a file of some specified type.
*
* @throws IOException
*/
public AlignFile(boolean parseImmediately, String dataObject,
- DataSourceType sourceType)
- throws IOException
+ DataSourceType sourceType) throws IOException
{
super(dataObject, sourceType);
initData();
{
if (key == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_cannot_have_null_alignment"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_cannot_have_null_alignment"));
}
if (value == null)
{
public abstract void parse() throws IOException;
/**
- * Print out in alignment file format the Sequences in the seqs Vector.
- */
- @Override
- public abstract String print();
-
- @Override
- public void addJVSuffix(boolean b)
- {
- jvSuffix = b;
- }
-
- /**
* A general parser for ids.
*
* @String id Id to be parsed
}
/**
- * Creates the output id. Adds prefix Uniprot format source|id And suffix
- * Jalview /start-end
+ * Creates the output id. Adds prefix Uniprot format source|id and optionally
+ * suffix Jalview /start-end
+ *
+ * @param jvsuffix
*
* @String id Id to be parsed
*/
+ String printId(SequenceI seq, boolean jvsuffix)
+ {
+ return seq.getDisplayId(jvsuffix);
+ }
+
String printId(SequenceI seq)
{
- return seq.getDisplayId(jvSuffix);
+ return printId(seq, true);
}
/**
}
}
+ protected void addSequence(SequenceI seq)
+ {
+ seqs.add(seq);
+ }
}