*/
package jalview.io;
-import java.io.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.io.IOException;
/**
* DOCUMENT ME!
* @throws IOException
* DOCUMENT ME!
*/
+ @Override
public void parse() throws IOException
{
StringBuffer sb = new StringBuffer();
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
{
- AlignmentAnnotation aa = (AlignmentAnnotation) annotations
- .elementAt(i);
+ AlignmentAnnotation aa = annotations.elementAt(i);
aa.setPadGaps(true, al.getGapCharacter());
al.addAnnotation(aa);
}
out.append(newline);
- int nochunks = (s[i].getLength() / len) + 1;
+ int nochunks = (s[i].getLength() / len)
+ + (s[i].getLength() % len > 0 ? 1 : 0);
for (int j = 0; j < nochunks; j++)
{
*
* @return DOCUMENT ME!
*/
+ @Override
public String print()
{
return print(getSeqsAsArray());