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author
jprocter
<Jim Procter>
Mon, 30 May 2005 16:33:29 +0000
(16:33 +0000)
committer
jprocter
<Jim Procter>
Mon, 30 May 2005 16:33:29 +0000
(16:33 +0000)
src/jalview/util/Comparison.java
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diff --git
a/src/jalview/util/Comparison.java
b/src/jalview/util/Comparison.java
index
0366430
..
03abd0c
100755
(executable)
--- a/
src/jalview/util/Comparison.java
+++ b/
src/jalview/util/Comparison.java
@@
-8,6
+8,14
@@
public class Comparison {
{
\r
return Comparison.compare(ii,jj,0,ii.getLength()-1);
\r
}
\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
public static float compare(SequenceI ii, SequenceI jj, int start, int end) {
\r
\r
String si = ii.getSequence();
\r
@@
-52,7
+60,13
@@
public class Comparison {
return pid;
\r
}
\r
\r
return pid;
\r
}
\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
public static float PID(SequenceI s1 , SequenceI s2)
\r
{
\r
int len;
\r