/*
- * 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 2.7)
+ * 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 <http://www.gnu.org/licenses/>.
*/
package jalview.analysis;
* 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)
{
-
this.name = name;
this.propHash = propHash;
this.threshold = threshold;
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);
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;
+ }
}
/**
}
}
- 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)
{
* 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();
}
// 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)));
}
}
}
git://source.jalview.org / jalview.git / blobdiff