* @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;
* @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)
{
}
/**
- * 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
*
return seq.getDisplayId(jvsuffix);
}
+ String printId(SequenceI seq)
+ {
+ return printId(seq, true);
+ }
+
/**
* vector of String[] treeName, newickString pairs
*/
}
}
+ protected void addSequence(SequenceI seq)
+ {
+ seqs.add(seq);
+ }
}