X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=6957b5cb0e3f6ba119dc7c08e18a1a866fe0008d;hb=3e51d4b043f8ac3e262f9b3660ec1f8561d1db93;hp=31a4b6659e81b4f9a67d6dac9e6207c37fd4dd1d;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 31a4b66..6957b5c 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,23 +1,23 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
*
- * 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.
*
- * 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
+ * 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 .
*/
package jalview.analysis;
+import java.awt.Color;
import java.util.*;
import jalview.datamodel.*;
@@ -72,23 +72,21 @@ public class Conservation
* 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 sequences, int start, int end)
{
-
this.name = name;
this.propHash = propHash;
this.threshold = threshold;
@@ -101,15 +99,21 @@ public class Conservation
int s, sSize = sequences.size();
SequenceI[] sarray = new SequenceI[sSize];
this.sequences = sarray;
-
+ try {
for (s = 0; s < sSize; s++)
{
- sarray[s] = (SequenceI) sequences.elementAt(s);
+ 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;
+ }
}
/**
@@ -272,7 +276,9 @@ public class Conservation
}
}
- total[i - start] = resultHash;
+ if (total.length>0) {
+ total[i - start] = resultHash;
+ }
}
}
@@ -331,10 +337,10 @@ public class Conservation
* 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)
{
@@ -488,9 +494,9 @@ public class Conservation
* 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)
{
@@ -591,4 +597,139 @@ public class Conservation
qualityRange[0] = new Double(0);
qualityRange[1] = new Double(newmax);
}
+
+ /**
+ * 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 istart, int alWidth)
+ {
+ char[] sequence = getConsSequence().getSequence();
+ float minR;
+ float minG;
+ float minB;
+ float maxR;
+ float maxG;
+ float maxB;
+ minR = 0.3f;
+ minG = 0.0f;
+ minB = 0f;
+ maxR = 1.0f - minR;
+ maxG = 0.9f - minG;
+ maxB = 0f - minB; // scalable range for colouring both Conservation and
+ // Quality
+
+ float min = 0f;
+ float max = 11f;
+ float qmin = 0f;
+ float qmax = 0f;
+
+ char c;
+
+ if (conservation.annotations != null
+ && conservation.annotations.length < alWidth)
+ {
+ conservation.annotations = new Annotation[alWidth];
+ }
+
+ if (quality2 != null)
+ {
+ quality2.graphMax = qualityRange[1].floatValue();
+ if (quality2.annotations != null
+ && quality2.annotations.length < alWidth)
+ {
+ quality2.annotations = new Annotation[alWidth];
+ }
+ qmin = qualityRange[0].floatValue();
+ qmax = qualityRange[1].floatValue();
+ }
+
+ for (int i = 0; i < alWidth; i++)
+ {
+ float value = 0;
+
+ c = sequence[i];
+
+ if (Character.isDigit(c))
+ {
+ value = (int) (c - '0');
+ }
+ else if (c == '*')
+ {
+ value = 11;
+ }
+ else if (c == '+')
+ {
+ value = 10;
+ }
+
+ float vprop = value - min;
+ vprop /= max;
+ conservation.annotations[i] = new Annotation(String.valueOf(c),
+ String.valueOf(value), ' ', value, new Color(minR
+ + (maxR * vprop), minG + (maxG * vprop), minB
+ + (maxB * vprop)));
+
+ // Quality calc
+ if (quality2 != null)
+ {
+ 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)));
+ }
+ }
+ }
+
+ /**
+ * 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 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;
+ }
}