git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
9f6812a
)
JAL-98 wording "negatively conserved" now "absence conserved"
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 2 Nov 2016 10:04:18 +0000
(10:04 +0000)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 2 Nov 2016 10:04:18 +0000
(10:04 +0000)
src/jalview/analysis/Conservation.java
patch
|
blob
|
history
diff --git
a/src/jalview/analysis/Conservation.java
b/src/jalview/analysis/Conservation.java
index
73a9dee
..
027a096
100755
(executable)
--- a/
src/jalview/analysis/Conservation.java
+++ b/
src/jalview/analysis/Conservation.java
@@
-60,7
+60,7
@@
public class Conservation
/*
* a map per column with {property, conservation} where conservation value is
/*
* a map per column with {property, conservation} where conservation value is
- * 1 (property is conserved), 0 (property is negatively conserved) or -1
+ * 1 (property is conserved), 0 (absence of property is conserved) or -1
* (property is not conserved i.e. column has residues with and without it)
*/
Map<String, Integer>[] total;
* (property is not conserved i.e. column has residues with and without it)
*/
Map<String, Integer>[] total;
@@
-214,7
+214,7
@@
public class Conservation
/*
* check observed residues in column and record whether each
/*
* check observed residues in column and record whether each
- * physico-chemical property is conserved (+1), negatively conserved (0),
+ * physico-chemical property is conserved (+1), absence conserved (0),
* or not conserved (-1)
* Using TreeMap means properties are displayed in alphabetical order
*/
* or not conserved (-1)
* Using TreeMap means properties are displayed in alphabetical order
*/
@@
-442,7
+442,7
@@
public class Conservation
if (result == -1)
{
/*
if (result == -1)
{
/*
- * not conserved either positively or negatively
+ * not conserved (present or absent)
*/
continue;
}
*/
continue;
}
@@
-458,7
+458,7
@@
public class Conservation
if (result == 0 && !positiveOnly)
{
/*
if (result == 0 && !positiveOnly)
{
/*
- * negatively conserved property (all residues lack it)
+ * absense of property is conserved (all residues lack it)
*/
negatives.append(negatives.length() == 0 ? "" : " ");
negatives.append("!").append(type);
*/
negatives.append(negatives.length() == 0 ? "" : " ");
negatives.append("!").append(type);
@@
-816,7
+816,8
@@
public class Conservation
/**
* Returns the computed tooltip (annotation description) for a given column.
* The tip is empty if the conservation score is zero, otherwise holds the
/**
* Returns the computed tooltip (annotation description) for a given column.
* The tip is empty if the conservation score is zero, otherwise holds the
- * positively (and, optionally, negatively) conserved properties.
+ * conserved properties (and, optionally, properties whose absence is
+ * conserved).
*
* @param column
* @return
*
* @param column
* @return