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JAL-98 javadoc / comments updated
[jalview.git]
/
src
/
jalview
/
analysis
/
AAFrequency.java
diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
5ecd644
..
569b036
100755
(executable)
--- a/
src/jalview/analysis/AAFrequency.java
+++ b/
src/jalview/analysis/AAFrequency.java
@@
-111,7
+111,9
@@
public class AAFrequency
*
* @param sequences
* @param start
*
* @param sequences
* @param start
+ * start column (inclusive, base zero)
* @param end
* @param end
+ * end column (exclusive)
* @param result
* array in which to store profile per column
* @param saveFullProfile
* @param result
* array in which to store profile per column
* @param saveFullProfile
@@
-169,8
+171,7
@@
public class AAFrequency
else
{
/*
else
{
/*
- * here we count a gap if the sequence doesn't
- * reach this column (is that correct?)
+ * count a gap if the sequence doesn't reach this column
*/
residueCounts.addGap();
}
*/
residueCounts.addGap();
}
@@
-220,8
+221,8
@@
public class AAFrequency
/**
* Derive the consensus annotations to be added to the alignment for display.
* This does not recompute the raw data, but may be called on a change in
/**
* Derive the consensus annotations to be added to the alignment for display.
* This does not recompute the raw data, but may be called on a change in
- * display options, such as 'show logo', which may in turn result in a change
- * in the derived values.
+ * display options, such as 'ignore gaps', which may in turn result in a
+ * change in the derived values.
*
* @param consensus
* the annotation row to add annotations to
*
* @param consensus
* the annotation row to add annotations to