* 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
-\r
package jalview.util;\r
\r
import jalview.datamodel.*;\r
\r
+\r
public class Comparison {\r
+ public static String GapChars = " .-";\r
\r
- public static float compare(SequenceI ii, SequenceI jj)\r
- {\r
- return Comparison.compare(ii,jj,0,ii.getLength()-1);\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
- if (si.substring(start + j,start + j+1).equals(sj.substring(start + j,start + j+1))) {\r
- match++;\r
- }\r
- count++;\r
- }\r
- pid = (float)match/(float)ilen * 100;\r
- } else {\r
- for (int j = 0; j < jlen; j++) {\r
- if (si.substring(start + j,start + j+1).equals(sj.substring(start + j,start + j+1))) {\r
- match++;\r
- }\r
- count++;\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
- len = s1.getSequence().length();\r
- else\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
- chr1 = s1.getSequence().charAt(i);\r
- else\r
- chr1 = '.';\r
-\r
-\r
- if (i < s2.getSequence().length())\r
- chr2 = s2.getSequence().charAt(i);\r
- else\r
- chr2 = '.';\r
-\r
-\r
- if (!(jalview.util.Comparison.isGap( chr1 )) && !(jalview.util.Comparison.isGap( chr2 )))\r
- {\r
- if (chr1!=chr2)\r
- bad++;\r
- }\r
+ public static float compare(SequenceI ii, SequenceI jj) {\r
+ return Comparison.compare(ii, jj, 0, ii.getLength() - 1);\r
}\r
\r
- return (float)100*(len-bad)/len;\r
- }\r
-\r
- // Another pid with region specification\r
-\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
- len = s1.getSequence().length();\r
- else\r
- len = s2.getSequence().length();\r
-\r
- if (end<len)\r
- len=end;\r
-\r
- if (len<start) {\r
- start = len - 1; // we just use a single residue for the difference\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
+ 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
+ ilen--;\r
+ }\r
+\r
+ while (jalview.util.Comparison.isGap(sj.charAt(start + jlen))) {\r
+ jlen--;\r
+ }\r
+\r
+ int count = 0;\r
+ int match = 0;\r
+ float pid = -1;\r
+\r
+ if (ilen > jlen) {\r
+ for (int j = 0; j < jlen; j++) {\r
+ if (si.substring(start + j, start + j + 1).equals(sj.substring(start +\r
+ j, start + j + 1))) {\r
+ match++;\r
+ }\r
+\r
+ count++;\r
+ }\r
+\r
+ pid = (float) match / (float) ilen * 100;\r
+ } else {\r
+ for (int j = 0; j < jlen; j++) {\r
+ if (si.substring(start + j, start + j + 1).equals(sj.substring(start +\r
+ j, start + j + 1))) {\r
+ match++;\r
+ }\r
+\r
+ count++;\r
+ }\r
+\r
+ pid = (float) match / (float) jlen * 100;\r
+ }\r
+\r
+ return pid;\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
- chr1 = s1.getSequence().charAt(i);\r
- else\r
- chr1 = '.';\r
-\r
-\r
- if (i < s2.getSequence().length())\r
- chr2 = s2.getSequence().charAt(i);\r
- else\r
- chr2 = '.';\r
-\r
-\r
- if (!(jalview.util.Comparison.isGap( chr1 )) && !(jalview.util.Comparison.isGap( chr2 )))\r
- {\r
- if (chr1!=chr2)\r
- bad++;\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
+ int len;\r
+\r
+ if (s1.getSequence().length() > s2.getSequence().length()) {\r
+ len = s1.getSequence().length();\r
+ } else {\r
+ len = s2.getSequence().length();\r
+ }\r
+\r
+ int bad = 0;\r
+\r
+ for (int i = 0; i < len; i++) {\r
+ char chr1;\r
+ char chr2;\r
+\r
+ if (i < s1.getSequence().length()) {\r
+ chr1 = s1.getSequence().charAt(i);\r
+ } else {\r
+ chr1 = '.';\r
+ }\r
+\r
+ if (i < s2.getSequence().length()) {\r
+ chr2 = s2.getSequence().charAt(i);\r
+ } else {\r
+ chr2 = '.';\r
+ }\r
+\r
+ if (!(jalview.util.Comparison.isGap(chr1)) &&\r
+ !(jalview.util.Comparison.isGap(chr2))) {\r
+ if (chr1 != chr2) {\r
+ bad++;\r
+ }\r
+ }\r
+ }\r
+\r
+ return ((float) 100 * (len - bad)) / len;\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
+ int len;\r
+\r
+ if (s1.getSequence().length() > s2.getSequence().length()) {\r
+ len = s1.getSequence().length();\r
+ } else {\r
+ len = s2.getSequence().length();\r
+ }\r
+\r
+ if (end < len) {\r
+ len = end;\r
+ }\r
+\r
+ if (len < start) {\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
+ char chr1;\r
+ char chr2;\r
+\r
+ if (i < s1.getSequence().length()) {\r
+ chr1 = s1.getSequence().charAt(i);\r
+ } else {\r
+ chr1 = '.';\r
+ }\r
+\r
+ if (i < s2.getSequence().length()) {\r
+ chr2 = s2.getSequence().charAt(i);\r
+ } else {\r
+ chr2 = '.';\r
+ }\r
+\r
+ if (!(jalview.util.Comparison.isGap(chr1)) &&\r
+ !(jalview.util.Comparison.isGap(chr2))) {\r
+ if (chr1 != chr2) {\r
+ bad++;\r
+ }\r
+ }\r
+ }\r
+\r
+ return ((float) 100 * (len - bad)) / len;\r
+ }\r
\r
- public static String GapChars = " .-";\r
- public static boolean isGap(char c)\r
- {\r
- return (c != '.' && c != '-' && c != ' ') ? false : true;\r
- }\r
+ public static boolean isGap(char c) {\r
+ return ((c != '.') && (c != '-') && (c != ' ')) ? false : true;\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff