/*
- * 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
*
* 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.
- *
+ * 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/>.
+ * 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.analysis;
int s, sSize = sequences.size();
SequenceI[] sarray = new SequenceI[sSize];
this.sequences = sarray;
- try {
- for (s = 0; s < sSize; s++)
+ try
{
- sarray[s] = (SequenceI) sequences.get(s);
- if (sarray[s].getLength() > maxLength)
+ for (s = 0; s < sSize; s++)
{
- maxLength = sarray[s].getLength();
+ sarray[s] = (SequenceI) sequences.get(s);
+ if (sarray[s].getLength() > maxLength)
+ {
+ maxLength = sarray[s].getLength();
+ }
}
- }
} catch (ArrayIndexOutOfBoundsException ex)
{
- // bail - another thread has modified the sequence array, so the current calculation is probably invalid.
- this.sequences=new SequenceI[0];
- maxLength=0;
+ // bail - another thread has modified the sequence array, so the current
+ // calculation is probably invalid.
+ this.sequences = new SequenceI[0];
+ maxLength = 0;
}
}
}
}
- if (total.length>0) {
+ if (total.length > 0)
+ {
total[i - start] = resultHash;
}
}
}
}
}
+
+ /**
+ * construct and call the calculation methods on a new Conservation object
+ *
+ * @param name
+ * - name of conservation
+ * @param consHash
+ * - hash table of properties for each amino acid (normally
+ * ResidueProperties.propHash)
+ * @param threshold
+ * - minimum number of conserved residues needed to indicate
+ * conservation (typically 3)
+ * @param seqs
+ * @param start
+ * first column in calculation window
+ * @param end
+ * last column in calculation window
+ * @param posOrNeg
+ * positive (true) or negative (false) conservation
+ * @param consPercGaps
+ * percentage of gaps tolerated in column
+ * @param calcQuality
+ * flag indicating if alignment quality should be calculated
+ * @return Conservation object ready for use in visualization
+ */
+ public static Conservation calculateConservation(String name,
+ Hashtable consHash, int threshold, List<SequenceI> seqs,
+ int start, int end, boolean posOrNeg, int consPercGaps,
+ boolean calcQuality)
+ {
+ Conservation cons = new Conservation(name, consHash, threshold, seqs,
+ start, end);
+ return calculateConservation(cons, posOrNeg, consPercGaps, calcQuality);
+ }
+
+ /**
+ * @param b
+ * positive (true) or negative (false) conservation
+ * @param consPercGaps
+ * percentage of gaps tolerated in column
+ * @param calcQuality
+ * flag indicating if alignment quality should be calculated
+ * @return Conservation object ready for use in visualization
+ */
+ public static Conservation calculateConservation(Conservation cons,
+ boolean b, int consPercGaps, boolean calcQuality)
+ {
+ cons.calculate();
+ cons.verdict(b, consPercGaps);
+
+ if (calcQuality)
+ {
+ cons.findQuality();
+ }
+
+ return cons;
+ }
}