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[jalview.git]
/
src
/
jalview
/
util
/
Comparison.java
diff --git
a/src/jalview/util/Comparison.java
b/src/jalview/util/Comparison.java
index
50f2a0b
..
50472a5
100755
(executable)
--- a/
src/jalview/util/Comparison.java
+++ b/
src/jalview/util/Comparison.java
@@
-30,7
+30,7
@@
import jalview.datamodel.*;
public class Comparison
\r
{
\r
/** DOCUMENT ME!! */
\r
public class Comparison
\r
{
\r
/** DOCUMENT ME!! */
\r
- public static String GapChars = " .-";
\r
+ public static final String GapChars = " .-";
\r
\r
/**
\r
* DOCUMENT ME!
\r
\r
/**
\r
* DOCUMENT ME!
\r
@@
-40,7
+40,7
@@
public class Comparison
*
\r
* @return DOCUMENT ME!
\r
*/
\r
*
\r
* @return DOCUMENT ME!
\r
*/
\r
- public static float compare(SequenceI ii, SequenceI jj)
\r
+ public static final float compare(SequenceI ii, SequenceI jj)
\r
{
\r
return Comparison.compare(ii, jj, 0, ii.getLength() - 1);
\r
}
\r
{
\r
return Comparison.compare(ii, jj, 0, ii.getLength() - 1);
\r
}
\r
@@
-55,8
+55,8
@@
public class Comparison
*/
\r
public static float compare(SequenceI ii, SequenceI jj, int start, int end)
\r
{
\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
+ String si = ii.getSequenceAsString();
\r
+ String sj = jj.getSequenceAsString();
\r
\r
int ilen = si.length() - 1;
\r
int jlen = sj.length() - 1;
\r
\r
int ilen = si.length() - 1;
\r
int jlen = sj.length() - 1;
\r
@@
-184,12
+184,12
@@
public class Comparison
*
\r
* @return DOCUMENT ME!
\r
*/
\r
*
\r
* @return DOCUMENT ME!
\r
*/
\r
- public static boolean isGap(char c)
\r
+ public static final boolean isGap(char c)
\r
{
\r
return (c == '-' || c == '.' || c == ' ') ? true : false;
\r
}
\r
\r
{
\r
return (c == '-' || c == '.' || c == ' ') ? true : false;
\r
}
\r
\r
- public static boolean isNucleotide(SequenceI [] seqs)
\r
+ public static final boolean isNucleotide(SequenceI [] seqs)
\r
{
\r
int i = 0, iSize = seqs.length, j, jSize;
\r
float nt = 0, aa = 0;
\r
{
\r
int i = 0, iSize = seqs.length, j, jSize;
\r
float nt = 0, aa = 0;
\r