X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=69d32cb3efd05661837c3472816d5c38fc4b2e69;hb=0b6b6af8bfba4edda36fef12a26c7526f4ee9555;hp=36534a36a9eaed2a7da3acb49c312974dc1e948a;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 36534a3..69d32cb 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,25 +1,28 @@
/*
- * 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 2.8.2)
+ * Copyright (C) 2014 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
import java.util.*;
+import jalview.util.Format;
import jalview.datamodel.*;
/**
@@ -43,39 +46,55 @@ public class AAFrequency
public static final String PID_NOGAPS = "N";
- public static final Hashtable[] calculate(Vector sequences, int start,
- int end)
+ public static final String PROFILE = "P";
+
+ public static final Hashtable[] calculate(List list,
+ int start, int end)
+ {
+ return calculate(list, start, end, false);
+ }
+
+ public static final Hashtable[] calculate(List sequences,
+ int start, int end, boolean profile)
{
SequenceI[] seqs = new SequenceI[sequences.size()];
int width = 0;
- for (int i = 0; i < sequences.size(); i++)
+ synchronized (sequences)
{
- seqs[i] = (SequenceI) sequences.elementAt(i);
- if (seqs[i].getLength() > width)
+ for (int i = 0; i < sequences.size(); i++)
{
- width = seqs[i].getLength();
+ seqs[i] = sequences.get(i);
+ if (seqs[i].getLength() > width)
+ {
+ width = seqs[i].getLength();
+ }
}
- }
-
- Hashtable[] reply = new Hashtable[width];
- if (end >= width)
- {
- end = width;
- }
+ Hashtable[] reply = new Hashtable[width];
- calculate(seqs, start, end, reply);
+ if (end >= width)
+ {
+ end = width;
+ }
- return reply;
+ calculate(seqs, start, end, reply, profile);
+ return reply;
+ }
}
public static final void calculate(SequenceI[] sequences, int start,
int end, Hashtable[] result)
{
+ calculate(sequences, start, end, result, false);
+ }
+
+ public static final void calculate(SequenceI[] sequences, int start,
+ int end, Hashtable[] result, boolean profile)
+ {
Hashtable residueHash;
int maxCount, nongap, i, j, v, jSize = sequences.length;
String maxResidue;
- char c;
+ char c = '-';
float percentage;
int[] values = new int[255];
@@ -92,6 +111,12 @@ public class AAFrequency
for (j = 0; j < jSize; j++)
{
+ if (sequences[j] == null)
+ {
+ System.err
+ .println("WARNING: Consensus skipping null sequence - possible race condition.");
+ continue;
+ }
seq = sequences[j].getSequence();
if (seq.length > i)
{
@@ -121,39 +146,239 @@ public class AAFrequency
values['-']++;
}
}
-
- for (v = 'A'; v < 'Z'; v++)
+ if (jSize == 1)
+ {
+ maxResidue = String.valueOf(c);
+ maxCount = 1;
+ }
+ else
{
- if (values[v] < 2 || values[v] < maxCount)
+ for (v = 'A'; v < 'Z'; v++)
{
- continue;
- }
+ if (values[v] < 2 || values[v] < maxCount)
+ {
+ continue;
+ }
- if (values[v] > maxCount)
- {
- maxResidue = String.valueOf((char) v);
- }
- else if (values[v] == maxCount)
- {
- maxResidue += String.valueOf((char) v);
+ if (values[v] > maxCount)
+ {
+ maxResidue = String.valueOf((char) v);
+ }
+ else if (values[v] == maxCount)
+ {
+ maxResidue += String.valueOf((char) v);
+ }
+ maxCount = values[v];
}
- maxCount = values[v];
}
-
if (maxResidue.length() == 0)
{
maxResidue = "-";
}
-
+ if (profile)
+ {
+ residueHash.put(PROFILE, new int[][]
+ { values, new int[]
+ { jSize, nongap } });
+ }
residueHash.put(MAXCOUNT, new Integer(maxCount));
residueHash.put(MAXRESIDUE, maxResidue);
- percentage = ((float) maxCount * 100) / (float) jSize;
+ percentage = ((float) maxCount * 100) / jSize;
residueHash.put(PID_GAPS, new Float(percentage));
- percentage = ((float) maxCount * 100) / (float) nongap;
+ if (nongap > 0)
+ {
+ // calculate for non-gapped too
+ percentage = ((float) maxCount * 100) / nongap;
+ }
residueHash.put(PID_NOGAPS, new Float(percentage));
+
result[i] = residueHash;
}
}
+
+ /**
+ * Compute all or part of the annotation row from the given consensus
+ * hashtable
+ *
+ * @param consensus
+ * - pre-allocated annotation row
+ * @param hconsensus
+ * @param iStart
+ * @param width
+ * @param ignoreGapsInConsensusCalculation
+ * @param includeAllConsSymbols
+ * @param nseq
+ */
+ public static void completeConsensus(AlignmentAnnotation consensus,
+ Hashtable[] hconsensus, int iStart, int width,
+ boolean ignoreGapsInConsensusCalculation,
+ boolean includeAllConsSymbols, long nseq)
+ {
+ completeConsensus(consensus, hconsensus, iStart, width,
+ ignoreGapsInConsensusCalculation, includeAllConsSymbols, null,
+ nseq); // new
+ // char[]
+ // { 'A', 'C', 'G', 'T', 'U' });
+ }
+
+ public static void completeConsensus(AlignmentAnnotation consensus,
+ Hashtable[] hconsensus, int iStart, int width,
+ boolean ignoreGapsInConsensusCalculation,
+ boolean includeAllConsSymbols, char[] alphabet, long nseq)
+ {
+ float tval, value;
+ if (consensus == null || consensus.annotations == null
+ || consensus.annotations.length < width)
+ {
+ // called with a bad alignment annotation row - wait for it to be
+ // initialised properly
+ return;
+ }
+ String fmtstr = "%3.1f";
+ int precision = 0;
+ while (nseq >= 10)
+ {
+ precision++;
+ nseq /= 10;
+ }
+ final Format fmt;
+ if (precision > 1)
+ {
+ // if (precision>2)
+ {
+ fmtstr = "%" + (2 + precision) + "." + (precision) + "f";
+ }
+ fmt = new Format(fmtstr);
+ }
+ else
+ {
+ fmt = null;
+ }
+ for (int i = iStart; i < width; i++)
+ {
+ Hashtable hci;
+ if (i >= hconsensus.length || ((hci = hconsensus[i]) == null))
+ {
+ // happens if sequences calculated over were shorter than alignment
+ // width
+ consensus.annotations[i] = null;
+ continue;
+ }
+ value = 0;
+ Float fv;
+ if (ignoreGapsInConsensusCalculation)
+ {
+ fv = (Float) hci.get(AAFrequency.PID_NOGAPS);
+ }
+ else
+ {
+ fv = (Float) hci.get(AAFrequency.PID_GAPS);
+ }
+ if (fv == null)
+ {
+ consensus.annotations[i] = null;
+ // data has changed below us .. give up and
+ continue;
+ }
+ value = fv.floatValue();
+ String maxRes = hci.get(AAFrequency.MAXRESIDUE).toString();
+ String mouseOver = hci.get(AAFrequency.MAXRESIDUE) + " ";
+ if (maxRes.length() > 1)
+ {
+ mouseOver = "[" + maxRes + "] ";
+ maxRes = "+";
+ }
+ int[][] profile = (int[][]) hci.get(AAFrequency.PROFILE);
+ if (profile != null && includeAllConsSymbols)
+ {
+ mouseOver = "";
+ if (alphabet != null)
+ {
+ for (int c = 0; c < alphabet.length; c++)
+ {
+ tval = profile[0][alphabet[c]] * 100f
+ / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
+ mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
+ + ((fmt != null) ? fmt.form(tval) : ((int) tval)) + "%";
+ }
+ }
+ else
+ {
+ Object[] ca = new Object[profile[0].length];
+ float[] vl = new float[profile[0].length];
+ for (int c = 0; c < ca.length; c++)
+ {
+ ca[c] = new char[]
+ { (char) c };
+ vl[c] = profile[0][c];
+ }
+ ;
+ jalview.util.QuickSort.sort(vl, ca);
+ for (int p = 0, c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
+ {
+ if (((char[]) ca[c])[0] != '-')
+ {
+ tval = profile[0][((char[]) ca[c])[0]]
+ * 100f
+ / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
+ mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
+ + " "
+ + ((fmt != null) ? fmt.form(tval) : ((int) tval))
+ + "%";
+ p++;
+
+ }
+ }
+
+ }
+ }
+ else
+ {
+ mouseOver += ((fmt != null) ? fmt.form(value) : ((int) value))
+ + "%";
+ }
+ consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
+ value);
+ }
+ }
+
+ /**
+ * get the sorted profile for the given position of the consensus
+ *
+ * @param hconsensus
+ * @return
+ */
+ public static int[] extractProfile(Hashtable hconsensus,
+ boolean ignoreGapsInConsensusCalculation)
+ {
+ int[] rtnval = new int[64];
+ int[][] profile = (int[][]) hconsensus.get(AAFrequency.PROFILE);
+ if (profile == null)
+ return null;
+ Object[] ca = new Object[profile[0].length];
+ float[] vl = new float[profile[0].length];
+ for (int c = 0; c < ca.length; c++)
+ {
+ ca[c] = new char[]
+ { (char) c };
+ vl[c] = profile[0][c];
+ }
+ ;
+ jalview.util.QuickSort.sort(vl, ca);
+ rtnval[0] = 2;
+ rtnval[1] = 0;
+ for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
+ {
+ if (((char[]) ca[c])[0] != '-')
+ {
+ rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
+ rtnval[rtnval[0]] = (int) (profile[0][((char[]) ca[c])[0]] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0]);
+ rtnval[1] += rtnval[rtnval[0]++];
+ }
+ }
+ return rtnval;
+ }
}