X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=11e7a3d8514be3d0e14e3c249278a64dce353c1e;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=6c21c749f416220a6a7f987b884a9cd64434b1c4;hpb=c9fc6a5f7f6fc4ffb29830500dc5a61111e6a44f;p=jalview.git
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 6c21c74..11e7a3d 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,20 +1,19 @@
/*
- * 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 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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;
@@ -43,9 +42,17 @@ public class AAFrequency
public static final String PID_NOGAPS = "N";
+ public static final String PROFILE = "P";
+
public static final Hashtable[] calculate(Vector sequences, int start,
int end)
{
+ return calculate(sequences, start, end, false);
+ }
+
+ public static final Hashtable[] calculate(Vector sequences, int start,
+ int end, boolean profile)
+ {
SequenceI[] seqs = new SequenceI[sequences.size()];
int width = 0;
for (int i = 0; i < sequences.size(); i++)
@@ -64,7 +71,7 @@ public class AAFrequency
end = width;
}
- calculate(seqs, start, end, reply);
+ calculate(seqs, start, end, reply, profile);
return reply;
}
@@ -72,6 +79,12 @@ public class AAFrequency
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;
@@ -144,7 +157,12 @@ public class AAFrequency
{
maxResidue = "-";
}
-
+ if (profile)
+ {
+ residueHash.put(PROFILE, new int[][]
+ { values, new int[]
+ { jSize, nongap } });
+ }
residueHash.put(MAXCOUNT, new Integer(maxCount));
residueHash.put(MAXRESIDUE, maxResidue);
@@ -158,20 +176,47 @@ public class AAFrequency
}
/**
- * Compute all or part of the annotation row from the given consensus hashtable
- * @param consensus - pre-allocated annotation row
+ * 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
*/
public static void completeConsensus(AlignmentAnnotation consensus,
Hashtable[] hconsensus, int iStart, int width,
- boolean ignoreGapsInConsensusCalculation)
+ boolean ignoreGapsInConsensusCalculation,
+ boolean includeAllConsSymbols)
{
+ completeConsensus(consensus, hconsensus, iStart, width,
+ ignoreGapsInConsensusCalculation, includeAllConsSymbols, null); // 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)
+ {
+ float tval, value;
+ if (consensus==null || consensus.annotations==null || consensus.annotations.length=hconsensus.length) {
+ // happens if sequences calculated over were shorter than alignment width
+ consensus.annotations[i]=null;
+ continue;
+ }
+ value = 0;
if (ignoreGapsInConsensusCalculation)
{
value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS))
@@ -183,20 +228,100 @@ public class AAFrequency
.floatValue();
}
- String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE)
- .toString();
- String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE)
- + " ";
-
+ String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
+ String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
if (maxRes.length() > 1)
{
mouseOver = "[" + maxRes + "] ";
maxRes = "+";
}
+ int[][] profile = (int[][]) hconsensus[i].get(AAFrequency.PROFILE);
+ if (profile != null && includeAllConsSymbols)
+ {
+ mouseOver = "";
+ if (alphabet != null)
+ {
+ for (int c = 0; c < alphabet.length; c++)
+ {
+ tval = ((float) profile[0][alphabet[c]])
+ * 100f
+ / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0];
+ mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
+ + ((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] = (float) 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 = ((float) profile[0][((char[]) ca[c])[0]])
+ * 100f
+ / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0];
+ mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
+ + " " + ((int) tval) + "%";
+ p++;
- mouseOver += ((int) value + "%");
+ }
+ }
+
+ }
+ }
+ else
+ {
+ mouseOver += ((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] = (float) profile[0][c];
+ }
+ ;
+ jalview.util.QuickSort.sort(vl, ca);
+ rtnval[0] = 1;
+ 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) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+ : 0]);
+ }
+ }
+ return rtnval;
+ }
}