/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.awt.Color;
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
/**
* Calculates conservation values for a given set of sequences
int[][] cons2;
+ private String[] consSymbs;
+
/**
* Creates a new Conservation object.
*
* @param name
- * Name of conservation
+ * Name of conservation
* @param propHash
- * hash of properties for each symbol
+ * hash of properties for each symbol
* @param threshold
- * to count the residues in residueHash(). commonly used value
- * is 3
+ * to count the residues in residueHash(). commonly used value is 3
* @param sequences
- * sequences to be used in calculation
+ * sequences to be used in calculation
* @param start
- * start residue position
+ * start residue position
* @param end
- * end residue position
+ * end residue position
*/
public Conservation(String name, Hashtable propHash, int threshold,
- Vector sequences, int start, int end)
+ List<SequenceI> sequences, int start, int end)
{
-
this.name = name;
this.propHash = propHash;
this.threshold = threshold;
int s, sSize = sequences.size();
SequenceI[] sarray = new SequenceI[sSize];
this.sequences = sarray;
-
- for (s = 0; s < sSize; s++)
+ try
{
- sarray[s] = (SequenceI) sequences.elementAt(s);
- if (sarray[s].getLength() > maxLength)
+ for (s = 0; s < sSize; s++)
{
- maxLength = sarray[s].getLength();
+ sarray[s] = 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;
}
}
resultHash.put(type, ht.get("-"));
}
}
- else if (((Integer) resultHash.get(type)).equals((Integer) ht
- .get(res)) == false)
+ else if (((Integer) resultHash.get(type)).equals(ht.get(res)) == false)
{
resultHash.put(type, new Integer(-1));
}
}
}
- total[i - start] = resultHash;
+ if (total.length > 0)
+ {
+ total[i - start] = resultHash;
+ }
}
}
* Calculates the conservation sequence
*
* @param consflag
- * if true, poitiveve conservation; false calculates negative
- * conservation
+ * if true, poitiveve conservation; false calculates negative
+ * conservation
* @param percentageGaps
- * commonly used value is 25
+ * commonly used value is 25
*/
public void verdict(boolean consflag, float percentageGaps)
{
{
consString.append('-');
}
-
+ consSymbs = new String[end - start + 1];
for (int i = start; i <= end; i++)
{
gapcons = countConsNGaps(i);
totGaps = gapcons[1];
- pgaps = ((float) totGaps * 100) / (float) sequences.length;
+ pgaps = ((float) totGaps * 100) / sequences.length;
+ consSymbs[i - start] = new String();
if (percentageGaps > pgaps)
{
resultHash = total[i - start];
-
// Now find the verdict
count = 0;
enumeration = resultHash.keys();
{
type = (String) enumeration.nextElement();
result = (Integer) resultHash.get(type);
-
// Do we want to count +ve conservation or +ve and -ve cons.?
if (consflag)
{
if (result.intValue() == 1)
{
+ consSymbs[i - start] = type + " " + consSymbs[i - start];
count++;
}
}
{
if (result.intValue() != -1)
{
+ {
+ if (result.intValue() == 0)
+ {
+ consSymbs[i - start] = consSymbs[i - start] + " !" + type;
+ }
+ else
+ {
+ consSymbs[i - start] = type + " " + consSymbs[i - start];
+ }
+ }
+
count++;
}
}
* Calculates the quality of the set of sequences
*
* @param start
- * Start residue
+ * Start residue
* @param end
- * End residue
+ * End residue
*/
public void findQuality(int start, int end)
{
}
/**
- * complete the given consensus and quuality annotation rows
- * @param conservation conservation annotation row
- * @param quality2 (optional - may be null)
- * @param alWidth extent of consensus
+ * complete the given consensus and quuality annotation rows. Note: currently
+ * this method will enlarge the given annotation row if it is too small,
+ * otherwise will leave its length unchanged.
+ *
+ * @param conservation
+ * conservation annotation row
+ * @param quality2
+ * (optional - may be null)
+ * @param istart
+ * first column for conservation
+ * @param alWidth
+ * extent of conservation
*/
public void completeAnnotations(AlignmentAnnotation conservation,
- AlignmentAnnotation quality2, int alWidth)
+ AlignmentAnnotation quality2, int istart, int alWidth)
{
char[] sequence = getConsSequence().getSequence();
float minR;
maxR = 1.0f - minR;
maxG = 0.9f - minG;
maxB = 0f - minB; // scalable range for colouring both Conservation and
- // Quality
+ // Quality
float min = 0f;
float max = 11f;
char c;
- conservation.annotations = new Annotation[alWidth];
+ if (conservation.annotations != null
+ && conservation.annotations.length < alWidth)
+ {
+ conservation.annotations = new Annotation[alWidth];
+ }
if (quality2 != null)
{
quality2.graphMax = qualityRange[1].floatValue();
- quality2.annotations = new Annotation[alWidth];
+ if (quality2.annotations != null
+ && quality2.annotations.length < alWidth)
+ {
+ quality2.annotations = new Annotation[alWidth];
+ }
qmin = qualityRange[0].floatValue();
qmax = qualityRange[1].floatValue();
}
if (Character.isDigit(c))
{
- value = (int) (c - '0');
+ value = c - '0';
}
else if (c == '*')
{
float vprop = value - min;
vprop /= max;
+ int consp = i - start;
+ String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
+ : "";
conservation.annotations[i] = new Annotation(String.valueOf(c),
- String.valueOf(value), ' ', value, new Color(minR
- + (maxR * vprop), minG + (maxG * vprop), minB
- + (maxB * vprop)));
+ conssym, ' ', value, new Color(minR + (maxR * vprop), minG
+ + (maxG * vprop), minB + (maxB * vprop)));
// Quality calc
if (quality2 != null)
{
- value = ((Double) quality.get(i)).floatValue();
+ value = ((Double) quality.elementAt(i)).floatValue();
vprop = value - qmin;
vprop /= qmax;
- quality2.annotations[i] = new Annotation(" ", String
- .valueOf(value), ' ', value, new Color(minR
- + (maxR * vprop), minG + (maxG * vprop), minB
- + (maxB * vprop)));
+ quality2.annotations[i] = new Annotation(" ",
+ String.valueOf(value), ' ', value, new Color(minR
+ + (maxR * vprop), minG + (maxG * vprop), minB
+ + (maxB * vprop)));
}
}
}
+
+ /**
+ * 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff