import java.util.Hashtable;
import java.util.Vector;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
+
/**
* DOCUMENT ME!
*
*/
public AlignFile()
{
+ // Shouldn't we init data structures
+ initData();
}
/**
* Filename to read from.
* @param type
* What type of file to read from (File, URL)
+ * @throws SAXException
+ * @throws ParserConfigurationException
+ * @throws ExceptionFileFormatOrSyntax
+ * @throws ExceptionLoadingFailed
+ * @throws ExceptionPermissionDenied
*/
- public AlignFile(String inFile, String type) throws IOException
+ public AlignFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
{
super(inFile, type);
initData();
*
* @param source
* @throws IOException
+ * @throws SAXException
+ * @throws ParserConfigurationException
+ * @throws ExceptionFileFormatOrSyntax
+ * @throws ExceptionLoadingFailed
+ * @throws ExceptionPermissionDenied
*/
- public AlignFile(FileParse source) throws IOException
+ public AlignFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
{
super(source);
initData();
/**
* This method must be implemented to parse the contents of the file.
+ * @throws ExceptionFileFormatOrSyntax
+ * @throws SAXException
+ * @throws ParserConfigurationException
+ * @throws ExceptionLoadingFailed
+ * @throws ExceptionPermissionDenied
*/
- public abstract void parse() throws IOException;
+ public abstract void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed;
/**
* Print out in alignment file format the Sequences in the seqs Vector.