-/*\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 = String.valueOf(Character.toUpperCase(sequence.charAt(i)));\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
+* Copyright (C) 2006 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 jalview.datamodel.*;
+
+import java.util.*;
+
+
+/**
+ * Takes in a vector of sequences and column start and column end
+ * and returns a vector of size (end-start+1). Each element of the
+ * vector contains a hashtable with the keys being residues and
+ * the values being the count of each residue in that column.
+ * 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
+{
+ /** Takes in a vector of sequences and column start and column end
+ * and returns a vector of size (end-start+1). Each element of the
+ * vector contains a hashtable with the keys being residues and
+ * the values being the count of each residue in that column.
+ * This class is used extensively in calculating alignment colourschemes
+ * that depend on the amount of conservation in each alignment column. */
+ public static final Vector calculate(Vector sequences, int start, int end)
+ {
+ Vector result = new Vector();
+ Hashtable residueHash;
+ int count, maxCount, nongap, i, j, jSize = sequences.size();
+ String maxResidue, sequence, res;
+ float percentage;
+
+ for (i = start; i <= end; i++)
+ {
+ residueHash = new Hashtable();
+ maxCount = 0;
+ maxResidue = "-";
+ nongap = 0;
+
+ for (j = 0; j < jSize; j++)
+ {
+ if (sequences.elementAt(j) instanceof Sequence)
+ {
+ sequence = ((Sequence) sequences.elementAt(j)).getSequence();
+
+ if (sequence.length() > i)
+ {
+ res = String.valueOf(Character.toUpperCase(sequence.charAt(i)));
+
+ if (jalview.util.Comparison.isGap(res.charAt(0)))
+ {
+ res = "-"; // we always use this for gaps in the property vectors
+ }
+ else
+ { nongap++; }
+
+ if (residueHash.containsKey(res))
+ {
+ count = ((Integer) residueHash.get(res)).intValue();
+ count++;
+
+ if (!jalview.util.Comparison.isGap(res.charAt(0)) &&
+ (count >= maxCount))
+ {
+ if (count > maxCount)
+ {
+ maxResidue = res;
+ }
+ else if (maxResidue.indexOf(res) == -1)
+ {
+ maxResidue += res;
+ }
+
+ maxCount = count;
+ }
+
+ residueHash.put(res, new Integer(count));
+ }
+ else
+ {
+ residueHash.put(res, new Integer(1));
+ }
+ }
+ else
+ {
+ if (residueHash.containsKey("-"))
+ {
+ count = ((Integer) residueHash.get("-")).intValue();
+ count++;
+ residueHash.put("-", new Integer(count));
+ }
+ else
+ {
+ residueHash.put("-", new Integer(1));
+ }
+ }
+ }
+ }
+
+ residueHash.put("maxCount", new Integer(maxCount));
+ residueHash.put("maxResidue", maxResidue);
+
+
+ //Size is redundant at present if we calculate percentage here
+ //residueHash.put("size", new Integer(jSize));
+ //residueHash.put("nogaps", new Integer(nongap));
+
+ 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.addElement(residueHash);
+ }
+
+
+
+ return result;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff