-/*\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.util;\r
-\r
-import jalview.datamodel.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class Comparison\r
-{\r
- /** DOCUMENT ME!! */\r
- public static String GapChars = " .-";\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param ii DOCUMENT ME!\r
- * @param jj DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static float compare(SequenceI ii, SequenceI jj)\r
- {\r
- return Comparison.compare(ii, jj, 0, ii.getLength() - 1);\r
- }\r
-\r
- /**\r
- * this was supposed to be an ungapped pid calculation\r
- * @param ii SequenceI\r
- * @param jj SequenceI\r
- * @param start int\r
- * @param end int\r
- * @return float\r
- */\r
- public static float compare(SequenceI ii, SequenceI jj, int start, int end)\r
- {\r
- String si = ii.getSequence();\r
- String sj = jj.getSequence();\r
-\r
- int ilen = si.length() - 1;\r
- int jlen = sj.length() - 1;\r
-\r
- while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))\r
- {\r
- ilen--;\r
- }\r
-\r
- while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))\r
- {\r
- jlen--;\r
- }\r
-\r
- int count = 0;\r
- int match = 0;\r
- float pid = -1;\r
-\r
- if (ilen > jlen)\r
- {\r
- for (int j = 0; j < jlen; j++)\r
- {\r
- if (si.substring(start + j, start + j + 1).equals(sj.substring(start +\r
- j, start + j + 1)))\r
- {\r
- match++;\r
- }\r
-\r
- count++;\r
- }\r
-\r
- pid = (float) match / (float) ilen * 100;\r
- }\r
- else\r
- {\r
- for (int j = 0; j < jlen; j++)\r
- {\r
- if (si.substring(start + j, start + j + 1).equals(sj.substring(start +\r
- j, start + j + 1)))\r
- {\r
- match++;\r
- }\r
-\r
- count++;\r
- }\r
-\r
- pid = (float) match / (float) jlen * 100;\r
- }\r
-\r
- return pid;\r
- }\r
-\r
- /**\r
- * this is a gapped PID calculation\r
- *\r
- * @param s1 SequenceI\r
- * @param s2 SequenceI\r
- * @return float\r
- */\r
- public static float PID(SequenceI s1, SequenceI s2)\r
- {\r
- int len;\r
-\r
- if (s1.getSequence().length() > s2.getSequence().length())\r
- {\r
- len = s1.getSequence().length();\r
- }\r
- else\r
- {\r
- len = s2.getSequence().length();\r
- }\r
-\r
- int bad = 0;\r
-\r
- for (int i = 0; i < len; i++)\r
- {\r
- char chr1;\r
- char chr2;\r
-\r
- if (i < s1.getSequence().length())\r
- {\r
- chr1 = Character.toUpperCase(s1.getSequence().charAt(i));\r
- }\r
- else\r
- {\r
- chr1 = '.';\r
- }\r
-\r
- if (i < s2.getSequence().length())\r
- {\r
- chr2 = Character.toUpperCase(s2.getSequence().charAt(i));\r
- }\r
- else\r
- {\r
- chr2 = '.';\r
- }\r
-\r
- if (! (jalview.util.Comparison.isGap(chr1)) &&\r
- ! (jalview.util.Comparison.isGap(chr2)))\r
- {\r
- if (chr1 != chr2)\r
- {\r
- bad++;\r
- }\r
- }\r
- }\r
-\r
- return ( (float) 100 * (len - bad)) / len;\r
- }\r
-\r
- // Another pid with region specification\r
- public static float PID(SequenceI s1, SequenceI s2, int start, int end)\r
- {\r
- int len;\r
-\r
- if (s1.getSequence().length() > s2.getSequence().length())\r
- {\r
- len = s1.getSequence().length();\r
- }\r
- else\r
- {\r
- len = s2.getSequence().length();\r
- }\r
-\r
- if (end < len)\r
- {\r
- len = end;\r
- }\r
-\r
- if (len < start)\r
- {\r
- start = len - 1; // we just use a single residue for the difference\r
- }\r
-\r
- int bad = 0;\r
-\r
- for (int i = start; i < len; i++)\r
- {\r
- char chr1;\r
- char chr2;\r
-\r
- if (i < s1.getSequence().length())\r
- {\r
- chr1 = Character.toUpperCase(s1.getSequence().charAt(i));\r
- }\r
- else\r
- {\r
- chr1 = '.';\r
- }\r
-\r
- if (i < s2.getSequence().length())\r
- {\r
- chr2 = Character.toUpperCase(s2.getSequence().charAt(i));\r
- }\r
- else\r
- {\r
- chr2 = '.';\r
- }\r
-\r
- if (! (jalview.util.Comparison.isGap(chr1)) &&\r
- ! (jalview.util.Comparison.isGap(chr2)))\r
- {\r
- if (chr1 != chr2)\r
- {\r
- bad++;\r
- }\r
- }\r
- }\r
-\r
- return ( (float) 100 * (len - bad)) / len;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param c DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static boolean isGap(char c)\r
- {\r
- return (c == '-' || c == '.' || c == ' ') ? true : false;\r
- }\r
-\r
- public static boolean isNucleotide(SequenceI [] seqs)\r
- {\r
- int i = 0, iSize = seqs.length, j, jSize;\r
- float nt = 0, aa = 0;\r
- char c;\r
- while (i < iSize)\r
- {\r
- jSize = seqs[i].getLength();\r
- for (j = 0; j < jSize; j++)\r
- {\r
- c = seqs[i].getCharAt(j);\r
- if ('a' <= c && c <= 'z')\r
- c -= ('a' - 'A');\r
-\r
- if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U')\r
- nt++;\r
- else if (!jalview.util.Comparison.isGap( seqs[i].getCharAt(j)))\r
- {\r
- aa++;\r
- }\r
- }\r
- i++;\r
- }\r
-\r
- if ( (nt / (nt + aa)) > 0.85f)\r
- return true;\r
- else\r
- return false;\r
-\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.util;
+
+import jalview.datamodel.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Comparison
+{
+ /** DOCUMENT ME!! */
+ public static String GapChars = " .-";
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ii DOCUMENT ME!
+ * @param jj DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static float compare(SequenceI ii, SequenceI jj)
+ {
+ return Comparison.compare(ii, jj, 0, ii.getLength() - 1);
+ }
+
+ /**
+ * this was supposed to be an ungapped pid calculation
+ * @param ii SequenceI
+ * @param jj SequenceI
+ * @param start int
+ * @param end int
+ * @return float
+ */
+ public static float compare(SequenceI ii, SequenceI jj, int start, int end)
+ {
+ String si = ii.getSequence();
+ String sj = jj.getSequence();
+
+ int ilen = si.length() - 1;
+ int jlen = sj.length() - 1;
+
+ while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))
+ {
+ ilen--;
+ }
+
+ while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
+ {
+ jlen--;
+ }
+
+ int count = 0;
+ int match = 0;
+ float pid = -1;
+
+ if (ilen > jlen)
+ {
+ for (int j = 0; j < jlen; j++)
+ {
+ if (si.substring(start + j, start + j + 1).equals(sj.substring(start +
+ j, start + j + 1)))
+ {
+ match++;
+ }
+
+ count++;
+ }
+
+ pid = (float) match / (float) ilen * 100;
+ }
+ else
+ {
+ for (int j = 0; j < jlen; j++)
+ {
+ if (si.substring(start + j, start + j + 1).equals(sj.substring(start +
+ j, start + j + 1)))
+ {
+ match++;
+ }
+
+ count++;
+ }
+
+ pid = (float) match / (float) jlen * 100;
+ }
+
+ return pid;
+ }
+
+ /**
+ * this is a gapped PID calculation
+ *
+ * @param s1 SequenceI
+ * @param s2 SequenceI
+ * @return float
+ */
+ public final static float PID(String seq1, String seq2)
+ {
+ return PID(seq1, seq2, 0, seq1.length());
+ }
+
+ static final int caseShift = 'a' - 'A';
+
+ // Another pid with region specification
+ public final static float PID(String seq1, String seq2, int start, int end)
+ {
+
+ int s1len = seq1.length();
+ int s2len = seq2.length();
+
+ int len = Math.min(s1len, s2len);
+
+ if (end < len)
+ {
+ len = end;
+ }
+
+ if (len < start)
+ {
+ start = len - 1; // we just use a single residue for the difference
+ }
+
+
+ int bad = 0;
+ char chr1;
+ char chr2;
+
+
+ for (int i = start; i < len; i++)
+ {
+ chr1 = seq1.charAt(i) ;
+
+ chr2 = seq2.charAt(i) ;
+
+ if ('a' <= chr1 && chr1 <= 'z')
+ {
+ // TO UPPERCASE !!!
+ //Faster than toUpperCase
+ chr1 -= caseShift;
+ }
+ if ('a' <= chr2 && chr2 <= 'z')
+ {
+ // TO UPPERCASE !!!
+ //Faster than toUpperCase
+ chr2 -= caseShift;
+ }
+
+
+ if (chr1!=chr2 && !isGap(chr1) && !isGap(chr2) )
+ {
+ bad++;
+ }
+ }
+
+ return ( (float) 100 * (len - bad)) / len;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static boolean isGap(char c)
+ {
+ return (c == '-' || c == '.' || c == ' ') ? true : false;
+ }
+
+ public static boolean isNucleotide(SequenceI [] seqs)
+ {
+ int i = 0, iSize = seqs.length, j, jSize;
+ float nt = 0, aa = 0;
+ char c;
+ while (i < iSize)
+ {
+ jSize = seqs[i].getLength();
+ for (j = 0; j < jSize; j++)
+ {
+ c = seqs[i].getCharAt(j);
+ if ('a' <= c && c <= 'z')
+ c -= ('a' - 'A');
+
+ if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U')
+ nt++;
+ else if (!jalview.util.Comparison.isGap( seqs[i].getCharAt(j)))
+ {
+ aa++;
+ }
+ }
+ i++;
+ }
+
+ if ( (nt / (nt + aa)) > 0.85f)
+ return true;
+ else
+ return false;
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff