X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=66a6d78987d69047947255cf4a669935442612c5;hb=18ab877a5f32de9dbf0a999f8b4623706f4ad2db;hp=9e9471f2e3018820f93be08805113c402be5956e;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 9e9471f..66a6d78 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
@@ -68,6 +71,8 @@ public class Conservation
int[][] cons2;
+ private String[] consSymbs;
+
/**
* Creates a new Conservation object.
*
@@ -85,9 +90,8 @@ public class Conservation
* 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;
@@ -100,14 +104,22 @@ public class Conservation
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] = (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;
}
}
@@ -271,7 +283,10 @@ public class Conservation
}
}
- total[i - start] = resultHash;
+ if (total.length > 0)
+ {
+ total[i - start] = resultHash;
+ }
}
}
@@ -353,17 +368,17 @@ public class Conservation
{
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;
-
+ consSymbs[i-start]=new String();
+
if (percentageGaps > pgaps)
{
resultHash = total[i - start];
-
// Now find the verdict
count = 0;
enumeration = resultHash.keys();
@@ -372,12 +387,12 @@ public class Conservation
{
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++;
}
}
@@ -385,6 +400,14 @@ public class Conservation
{
if (result.intValue() != -1)
{
+ {
+ if (result.intValue()==0) {
+ consSymbs[i-start] = consSymbs[i-start]+ " !"+type;
+ } else {
+ consSymbs[i-start] = type+" "+consSymbs[i-start];
+ }
+ }
+
count++;
}
}
@@ -670,7 +693,7 @@ public class Conservation
float vprop = value - min;
vprop /= max;
conservation.annotations[i] = new Annotation(String.valueOf(c),
- String.valueOf(value), ' ', value, new Color(minR
+ consSymbs[i-start], ' ', value, new Color(minR
+ (maxR * vprop), minG + (maxG * vprop), minB
+ (maxB * vprop)));
@@ -687,4 +710,61 @@ public class Conservation
}
}
}
+
+ /**
+ * 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;
+ }
}