-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.analysis;\r
-\r
-import jalview.analysis.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-/**\r
- * Takes in a vector of sequences and column start and column end\r
- * and returns a vector of size (end-start+1). Each element of the\r
- * vector contains a hashtable with the keys being residues and\r
- * the values being the count of each residue in that column.\r
- * This class is used extensively in calculating alignment colourschemes\r
- * that depend on the amount of conservation in each alignment column.\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class AAFrequency\r
-{\r
- /** Takes in a vector of sequences and column start and column end\r
- * and returns a vector of size (end-start+1). Each element of the\r
- * vector contains a hashtable with the keys being residues and\r
- * the values being the count of each residue in that column.\r
- * This class is used extensively in calculating alignment colourschemes\r
- * that depend on the amount of conservation in each alignment column. */\r
- public static Vector calculate(Vector sequences, int start, int end)\r
- {\r
- Vector result = new Vector();\r
- Hashtable residueHash;\r
- int count, maxCount, nongap, i, j, jSize = sequences.size();\r
- String maxResidue, sequence, res;\r
- float percentage;\r
-\r
- for (i = start; i <= end; i++)\r
- {\r
- residueHash = new Hashtable();\r
- maxCount = 0;\r
- maxResidue = "-";\r
- nongap = 0;\r
-\r
- for (j = 0; j < jSize; j++)\r
- {\r
- if (sequences.elementAt(j) instanceof Sequence)\r
- {\r
- sequence = ((Sequence) sequences.elementAt(j)).getSequence();\r
-\r
- if (sequence.length() > i)\r
- {\r
- res = sequence.substring(i,i+1);\r
-\r
- if (jalview.util.Comparison.isGap(res.charAt(0)))\r
- {\r
- res = "-"; // we always use this for gaps in the property vectors\r
- }\r
- else\r
- { nongap++; }\r
-\r
- if (residueHash.containsKey(res))\r
- {\r
- count = ((Integer) residueHash.get(res)).intValue();\r
- count++;\r
-\r
- if (!jalview.util.Comparison.isGap(res.charAt(0)) &&\r
- (count >= maxCount))\r
- {\r
- if (count > maxCount)\r
- {\r
- maxResidue = res;\r
- }\r
- else if (maxResidue.indexOf(res) == -1)\r
- {\r
- maxResidue += res;\r
- }\r
-\r
- maxCount = count;\r
- }\r
-\r
- residueHash.put(res, new Integer(count));\r
- }\r
- else\r
- {\r
- residueHash.put(res, new Integer(1));\r
- }\r
- }\r
- else\r
- {\r
- if (residueHash.containsKey("-"))\r
- {\r
- count = ((Integer) residueHash.get("-")).intValue();\r
- count++;\r
- residueHash.put("-", new Integer(count));\r
- }\r
- else\r
- {\r
- residueHash.put("-", new Integer(1));\r
- }\r
- }\r
- }\r
- }\r
-\r
- residueHash.put("maxCount", new Integer(maxCount));\r
- residueHash.put("maxResidue", maxResidue);\r
-\r
-\r
- //Size is redundant at present if we calculate percentage here\r
- //residueHash.put("size", new Integer(jSize));\r
- //residueHash.put("nogaps", new Integer(nongap));\r
-\r
- percentage = ((float)maxCount*100) / (float)jSize;\r
- residueHash.put("pid_gaps", new Float(percentage) );\r
-\r
- percentage = ((float)maxCount*100) / (float)nongap;\r
- residueHash.put("pid_nogaps", new Float(percentage) );\r
- result.addElement(residueHash);\r
- }\r
-\r
-\r
-\r
- return result;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, 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 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.
+ *
+ * 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
+ */
+package jalview.analysis;
+
+import java.util.*;
+
+import jalview.datamodel.*;
+
+/**
+ * Takes in a vector or array of sequences and column start and column end and
+ * returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
+ * This class is used extensively in calculating alignment colourschemes that
+ * depend on the amount of conservation in each alignment column.
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AAFrequency
+{
+ // No need to store 1000s of strings which are not
+ // visible to the user.
+ public static final String MAXCOUNT = "C";
+
+ public static final String MAXRESIDUE = "R";
+
+ public static final String PID_GAPS = "G";
+
+ public static final String PID_NOGAPS = "N";
+
+ public static final Hashtable[] calculate(Vector sequences, int start,
+ int end)
+ {
+ SequenceI[] seqs = new SequenceI[sequences.size()];
+ int width = 0;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ seqs[i] = (SequenceI) sequences.elementAt(i);
+ if (seqs[i].getLength() > width)
+ {
+ width = seqs[i].getLength();
+ }
+ }
+
+ Hashtable[] reply = new Hashtable[width];
+
+ if (end >= width)
+ {
+ end = width;
+ }
+
+ calculate(seqs, start, end, reply);
+
+ return reply;
+ }
+
+ public static final void calculate(SequenceI[] sequences, int start,
+ int end, Hashtable[] result)
+ {
+ Hashtable residueHash;
+ int maxCount, nongap, i, j, v, jSize = sequences.length;
+ String maxResidue;
+ char c;
+ float percentage;
+
+ int[] values = new int[255];
+
+ char[] seq;
+
+ for (i = start; i < end; i++)
+ {
+ residueHash = new Hashtable();
+ maxCount = 0;
+ maxResidue = "";
+ nongap = 0;
+ values = new int[255];
+
+ for (j = 0; j < jSize; j++)
+ {
+ seq = sequences[j].getSequence();
+ if (seq.length > i)
+ {
+ c = seq[i];
+
+ if (c == '.' || c == ' ')
+ {
+ c = '-';
+ }
+
+ if (c == '-')
+ {
+ values['-']++;
+ continue;
+ }
+ else if ('a' <= c && c <= 'z')
+ {
+ c -= 32; // ('a' - 'A');
+ }
+
+ nongap++;
+ values[c]++;
+
+ }
+ else
+ {
+ values['-']++;
+ }
+ }
+
+ for (v = 'A'; v < 'Z'; v++)
+ {
+ 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);
+ }
+ maxCount = values[v];
+ }
+
+ if (maxResidue.length() == 0)
+ {
+ maxResidue = "-";
+ }
+
+ residueHash.put(MAXCOUNT, new Integer(maxCount));
+ residueHash.put(MAXRESIDUE, maxResidue);
+
+ percentage = ((float) maxCount * 100) / (float) jSize;
+ residueHash.put(PID_GAPS, new Float(percentage));
+
+ percentage = ((float) maxCount * 100) / (float) nongap;
+ residueHash.put(PID_NOGAPS, new Float(percentage));
+ result[i] = residueHash;
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff