+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
import jalview.util.Comparison;
/**
* A class to count occurrences of residues in a profile, optimised for speed
* and memory footprint.
+ *
* @author gmcarstairs
*
*/
*/
private static final String AAS = "ACDEFGHIKLMNPQRSTUVWXY";
- private static final int GAP_COUNT = 0;
+ static final int GAP_COUNT = 0;
/*
* fast lookup tables holding the index into our count
{
if (intCounts[i] == count)
{
- modal.append(isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1));
+ modal.append(
+ isNucleotide ? NUCS.charAt(i - 1) : AAS.charAt(i - 1));
}
}
}
{
if (counts[i] == count)
{
- modal.append(isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1));
+ modal.append(
+ isNucleotide ? NUCS.charAt(i - 1) : AAS.charAt(i - 1));
}
}
}
*
* @return
*/
- public int size() {
+ public int size()
+ {
int size = 0;
if (useIntCounts)
{
{
if (intCounts[i] > 0)
{
- char symbol = isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1);
+ char symbol = isNucleotide ? NUCS.charAt(i - 1)
+ : AAS.charAt(i - 1);
symbols[j] = symbol;
values[j] = intCounts[i];
j++;
{
if (counts[i] > 0)
{
- char symbol = isNucleotide ? NUCS.charAt(i - 1) : AAS
- .charAt(i - 1);
+ char symbol = isNucleotide ? NUCS.charAt(i - 1)
+ : AAS.charAt(i - 1);
symbols[j] = symbol;
values[j] = counts[i];
j++;