* @author $author$
* @version $Revision$
*/
-public abstract class AlignFile extends FileParse
+public abstract class AlignFile extends FileParse implements AlignmentFileI
{
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.
*
* @param dataObject
* Filename, URL or Pasted String to read from.
- * @param type
+ * @param sourceType
* What type of file to read from (File, URL, Pasted String)
*/
- public AlignFile(String dataObject, String type) throws IOException
+ public AlignFile(String dataObject, DataSourceType sourceType)
+ throws IOException
{
- this(true, dataObject, type);
+ this(true, dataObject, sourceType);
}
/**
* if false, need to call 'doParse()' to begin parsing data
* @param dataObject
* Filename, URL or Pasted String to read from.
- * @param type
+ * @param sourceType
* What type of file to read from (File, URL)
* @throws IOException
*/
- public AlignFile(boolean parseImmediately, String dataObject, String type)
+ public AlignFile(boolean parseImmediately, String dataObject,
+ DataSourceType sourceType)
throws IOException
{
- super(dataObject, type);
+ super(dataObject, sourceType);
initData();
if (parseImmediately)
{
/**
* Return the Sequences in the seqs Vector as an array of Sequences
*/
+ @Override
public SequenceI[] getSeqsAsArray()
{
SequenceI[] s = new SequenceI[seqs.size()];
*
* @param al
*/
+ @Override
public void addAnnotations(AlignmentI al)
{
addProperties(al);
* @param s
* DOCUMENT ME!
*/
- protected void setSeqs(SequenceI[] s)
+ @Override
+ public void setSeqs(SequenceI[] s)
{
seqs = new Vector<SequenceI>();
public abstract void parse() throws IOException;
/**
- * Print out in alignment file format the Sequences in the seqs Vector.
- */
- public abstract String print();
-
- 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);
}
/**
return newickStrings == null ? 0 : newickStrings.size();
}
+ @Override
public void addGroups(AlignmentI al)
{