- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
- * 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
+ * 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
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * 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.
* returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
* This class is used extensively in calculating alignment colourschemes that
* depend on the amount of conservation in each alignment column.
* returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
* This class is used extensively in calculating alignment colourschemes that
* depend on the amount of conservation in each alignment column.
{
return calculate(list, start, end, false);
}
{
return calculate(list, start, end, false);
}
- public static final Hashtable[] calculate(List<SequenceI> sequences, int start,
- int end, boolean profile)
+ public static final Hashtable[] calculate(List<SequenceI> sequences,
+ int start, int end, boolean profile)
- calculate(seqs, start, end, reply, profile);
- return reply;
- }
+ calculate(seqs, start, end, reply, profile);
+ return reply;
+ }
Hashtable residueHash;
int maxCount, nongap, i, j, v, jSize = sequences.length;
String maxResidue;
Hashtable residueHash;
int maxCount, nongap, i, j, v, jSize = sequences.length;
String maxResidue;
- if (values[v] > maxCount)
- {
- maxResidue = String.valueOf((char) v);
- }
- else if (values[v] == maxCount)
- {
- maxResidue += String.valueOf((char) v);
+ if (values[v] > maxCount)
+ {
+ maxResidue = String.valueOf((char) v);
+ }
+ else if (values[v] == maxCount)
+ {
+ maxResidue += String.valueOf((char) v);
+ }
+ maxCount = values[v];
percentage = ((float) maxCount * 100) / jSize;
residueHash.put(PID_GAPS, new Float(percentage));
percentage = ((float) maxCount * 100) / jSize;
residueHash.put(PID_GAPS, new Float(percentage));
*/
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
*/
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
{
completeConsensus(consensus, hconsensus, iStart, width,
{
completeConsensus(consensus, hconsensus, iStart, width,
- ignoreGapsInConsensusCalculation, includeAllConsSymbols, null); // new
- // char[]
+ ignoreGapsInConsensusCalculation, includeAllConsSymbols, null,
+ nseq); // new
+ // char[]
// { 'A', 'C', 'G', 'T', 'U' });
}
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
// { 'A', 'C', 'G', 'T', 'U' });
}
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
boolean ignoreGapsInConsensusCalculation,
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);
}
consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
value);
for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
{
if (((char[]) ca[c])[0] != '-')
for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
{
if (((char[]) ca[c])[0] != '-')
rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
rtnval[rtnval[0]] = (int) (profile[0][((char[]) ca[c])[0]] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);
rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
rtnval[rtnval[0]] = (int) (profile[0][((char[]) ca[c])[0]] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
: 0]);