}
/**
- * DOCUMENT ME!
+ * Returns the given sequence with all of the given gap characters removed.
*
- * @param gapChar
- * DOCUMENT ME!
+ * @param gapChars
+ * a string of characters to be treated as gaps
* @param seq
- * DOCUMENT ME!
+ * the input sequence
*
- * @return DOCUMENT ME!
+ * @return
*/
- public static String extractGaps(String gapChar, String seq)
+ public static String extractGaps(String gapChars, String seq)
{
- StringTokenizer str = new StringTokenizer(seq, gapChar);
- StringBuffer newString = new StringBuffer();
+ if (gapChars == null || seq == null)
+ {
+ return null;
+ }
+ StringTokenizer str = new StringTokenizer(seq, gapChars);
+ StringBuilder newString = new StringBuilder(seq.length());
while (str.hasMoreTokens())
{
if (allowmismatch || c1 == c2)
{
- lastmatch = true;
- // extend mapping interval.
+ // extend mapping interval
if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos)
{
as1.add(Integer.valueOf(alignpos));
as2.add(Integer.valueOf(pdbpos));
}
+ lastmatch = true;
lp1 = alignpos;
lp2 = pdbpos;
}
else
{
+ // extend mapping interval
+ if (lastmatch)
+ {
+ as1.add(Integer.valueOf(lp1));
+ as2.add(Integer.valueOf(lp2));
+ }
lastmatch = false;
}
}
// construct range pairs
+
int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)], mapseq2 = new int[as2
.size() + (lastmatch ? 1 : 0)];
int i = 0;
ap++;
}
}
- if (sq.getAnnotation() != null)
+ if (sq.getAnnotation() != null && sq.getAnnotation().length > 0)
{
- annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+ annotations.addAll(inspos == -1 ? annotations.size() : inspos,
+ Arrays.asList(sq.getAnnotation()));
}
}
}