From b197f605c73927b107d69044cfd593293c2e8c00 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 25 Oct 2016 10:00:25 +0100 Subject: [PATCH] JAL-98 javadoc / comments updated --- src/jalview/analysis/AAFrequency.java | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index 5ecd644..569b036 100755 --- a/src/jalview/analysis/AAFrequency.java +++ b/src/jalview/analysis/AAFrequency.java @@ -111,7 +111,9 @@ public class AAFrequency * * @param sequences * @param start + * start column (inclusive, base zero) * @param end + * end column (exclusive) * @param result * array in which to store profile per column * @param saveFullProfile @@ -169,8 +171,7 @@ public class AAFrequency 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(); } @@ -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 - * 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 -- 1.7.10.2