git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2418 source formatting
[jalview.git]
/
src
/
jalview
/
util
/
Comparison.java
diff --git
a/src/jalview/util/Comparison.java
b/src/jalview/util/Comparison.java
index
22e1ab7
..
17d3a70
100644
(file)
--- a/
src/jalview/util/Comparison.java
+++ b/
src/jalview/util/Comparison.java
@@
-40,8
+40,9
@@
public class Comparison
public static final char GAP_DASH = '-';
public static final char GAP_DASH = '-';
- public static final String GapChars = new String(new char[] { GAP_SPACE,
- GAP_DOT, GAP_DASH });
+ public static final String GapChars = new String(
+ new char[]
+ { GAP_SPACE, GAP_DOT, GAP_DASH });
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-71,7
+72,8
@@
public class Comparison
* int
* @return float
*/
* int
* @return float
*/
- public static float compare(SequenceI ii, SequenceI jj, int start, int end)
+ public static float compare(SequenceI ii, SequenceI jj, int start,
+ int end)
{
String si = ii.getSequenceAsString();
String sj = jj.getSequenceAsString();
{
String si = ii.getSequenceAsString();
String sj = jj.getSequenceAsString();
@@
-97,8
+99,8
@@
public class Comparison
{
for (int j = 0; j < jlen; j++)
{
{
for (int j = 0; j < jlen; j++)
{
- if (si.substring(start + j, start + j + 1).equals(
- sj.substring(start + j, start + j + 1)))
+ if (si.substring(start + j, start + j + 1)
+ .equals(sj.substring(start + j, start + j + 1)))
{
match++;
}
{
match++;
}
@@
-112,8
+114,8
@@
public class Comparison
{
for (int j = 0; j < jlen; j++)
{
{
for (int j = 0; j < jlen; j++)
{
- if (si.substring(start + j, start + j + 1).equals(
- sj.substring(start + j, start + j + 1)))
+ if (si.substring(start + j, start + j + 1)
+ .equals(sj.substring(start + j, start + j + 1)))
{
match++;
}
{
match++;
}
@@
-150,7
+152,8
@@
public class Comparison
* @deprecated use PIDModel.computePID()
*/
@Deprecated
* @deprecated use PIDModel.computePID()
*/
@Deprecated
- public final static float PID(String seq1, String seq2, int start, int end)
+ public final static float PID(String seq1, String seq2, int start,
+ int end)
{
return PID(seq1, seq2, start, end, true, false);
}
{
return PID(seq1, seq2, start, end, true, false);
}
@@
-419,8
+422,8
@@
public class Comparison
flattened.add(s);
}
}
flattened.add(s);
}
}
- final SequenceI[] oneDArray = flattened.toArray(new SequenceI[flattened
- .size()]);
+ final SequenceI[] oneDArray = flattened
+ .toArray(new SequenceI[flattened.size()]);
return isNucleotide(oneDArray);
}
return isNucleotide(oneDArray);
}