/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 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
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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.datamodel.*;\r
-\r
import java.util.*;\r
\r
+import jalview.datamodel.*;\r
\r
/**\r
* Takes in a vector or array of sequences and column start and column end\r
//No need to store 1000s of strings which are not\r
//visible to the user.\r
public static final String MAXCOUNT = "C";\r
- public static final String MAXRESIDUE="R";\r
+ public static final String MAXRESIDUE = "R";\r
public static final String PID_GAPS = "G";\r
- public static final String PID_NOGAPS="N";\r
-\r
- public static final Hashtable [] calculate(Vector sequences, int start, int end)\r
- {\r
- SequenceI [] seqs = new SequenceI[sequences.size()];\r
- int width = 0;\r
- for(int i=0; i<sequences.size(); i++)\r
- {\r
- seqs[i] = (SequenceI) sequences.elementAt(i);\r
- if(seqs[i].getLength()>width)\r
- width = seqs[i].getLength();\r
- }\r
-\r
- Hashtable [] reply = new Hashtable[width];\r
-\r
- if(end>=width)\r
- {\r
- end = width;\r
- }\r
-\r
- calculate(seqs, start, end, reply);\r
-\r
- return reply;\r
- }\r
-\r
-public static final void calculate(SequenceI[] sequences,\r
- int start, int end,\r
- Hashtable [] result)\r
-{\r
- Hashtable residueHash;\r
- int maxCount, nongap, i, j, v, jSize = sequences.length;\r
- String maxResidue;\r
- char c;\r
- float percentage;\r
+ public static final String PID_NOGAPS = "N";\r
\r
- int[] values = new int[255];\r
+ public static final Hashtable[] calculate(Vector sequences, int start,\r
+ int end)\r
+ {\r
+ SequenceI[] seqs = new SequenceI[sequences.size()];\r
+ int width = 0;\r
+ for (int i = 0; i < sequences.size(); i++)\r
+ {\r
+ seqs[i] = (SequenceI) sequences.elementAt(i);\r
+ if (seqs[i].getLength() > width)\r
+ {\r
+ width = seqs[i].getLength();\r
+ }\r
+ }\r
\r
- char [] seq;\r
+ Hashtable[] reply = new Hashtable[width];\r
\r
- for (i = start; i < end; i++)\r
+ if (end >= width)\r
+ {\r
+ end = width;\r
+ }\r
+\r
+ calculate(seqs, start, end, reply);\r
+\r
+ return reply;\r
+ }\r
+\r
+ public static final void calculate(SequenceI[] sequences,\r
+ int start, int end,\r
+ Hashtable[] result)\r
{\r
- residueHash = new Hashtable();\r
- maxCount = 0;\r
- maxResidue = "";\r
- nongap = 0;\r
- values = new int[255];\r
+ Hashtable residueHash;\r
+ int maxCount, nongap, i, j, v, jSize = sequences.length;\r
+ String maxResidue;\r
+ char c;\r
+ float percentage;\r
+\r
+ int[] values = new int[255];\r
+\r
+ char[] seq;\r
\r
- for (j = 0; j < jSize; j++)\r
+ for (i = start; i < end; i++)\r
{\r
- seq = sequences[j].getSequence();\r
- if (seq.length > i)\r
- {\r
- c = seq[i];\r
+ residueHash = new Hashtable();\r
+ maxCount = 0;\r
+ maxResidue = "";\r
+ nongap = 0;\r
+ values = new int[255];\r
\r
- if(c == '.' || c==' ')\r
- c = '-';\r
+ for (j = 0; j < jSize; j++)\r
+ {\r
+ seq = sequences[j].getSequence();\r
+ if (seq.length > i)\r
+ {\r
+ c = seq[i];\r
+\r
+ if (c == '.' || c == ' ')\r
+ {\r
+ c = '-';\r
+ }\r
+\r
+ if (c == '-')\r
+ {\r
+ values['-']++;\r
+ continue;\r
+ }\r
+ else if ('a' <= c && c <= 'z')\r
+ {\r
+ c -= 32; //('a' - 'A');\r
+ }\r
+\r
+ nongap++;\r
+ values[c]++;\r
\r
- if(c=='-')\r
+ }\r
+ else\r
{\r
values['-']++;\r
- continue;\r
}\r
- else if ('a' <= c && c <= 'z')\r
+ }\r
+\r
+ for (v = 'A'; v < 'Z'; v++)\r
+ {\r
+ if (values[v] < 2 || values[v] < maxCount)\r
{\r
- c -= 32 ;//('a' - 'A');\r
+ continue;\r
}\r
\r
- nongap++;\r
- values[c]++;\r
-\r
- }\r
- else\r
- {\r
- values['-']++;\r
+ if (values[v] > maxCount)\r
+ {\r
+ maxResidue = String.valueOf( (char) v);\r
+ }\r
+ else if (values[v] == maxCount)\r
+ {\r
+ maxResidue += String.valueOf( (char) v);\r
+ }\r
+ maxCount = values[v];\r
}\r
- }\r
-\r
- for (v = 'A'; v < 'Z'; v++)\r
- {\r
- if (values[v] < 2 || values[v] < maxCount)\r
- continue;\r
\r
- if (values[v] > maxCount)\r
+ if (maxResidue.length() == 0)\r
{\r
- maxResidue = String.valueOf( (char) v);\r
+ maxResidue = "-";\r
}\r
- else if (values[v] == maxCount)\r
- {\r
- maxResidue += String.valueOf( (char) v);\r
- }\r
- maxCount = values[v];\r
- }\r
\r
- if(maxResidue.length()==0)\r
- maxResidue = "-";\r
+ residueHash.put(MAXCOUNT, new Integer(maxCount));\r
+ residueHash.put(MAXRESIDUE, maxResidue);\r
\r
- residueHash.put(MAXCOUNT, new Integer(maxCount));\r
- residueHash.put(MAXRESIDUE, maxResidue);\r
+ percentage = ( (float) maxCount * 100) / (float) jSize;\r
+ residueHash.put(PID_GAPS, new Float(percentage));\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[i] = residueHash;\r
+ percentage = ( (float) maxCount * 100) / (float) nongap;\r
+ residueHash.put(PID_NOGAPS, new Float(percentage));\r
+ result[i] = residueHash;\r
+ }\r
}\r
}\r
-}\r
-\r
-\r
git://source.jalview.org / jalview.git / blobdiff