From aaa5a9341963ac324baa558bf3f5b744cfdee9c7 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 16 Mar 2017 17:42:25 +0000 Subject: [PATCH] JAL-1933 refactor parameter for code clarity --- src/jalview/analysis/AAFrequency.java | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index ffa413b..ee16f94 100755 --- a/src/jalview/analysis/AAFrequency.java +++ b/src/jalview/analysis/AAFrequency.java @@ -291,7 +291,7 @@ public class AAFrequency /** * Derive the gap count annotation row. * - * @param consensus + * @param gaprow * the annotation row to add annotations to * @param profiles * the source consensus data @@ -300,11 +300,11 @@ public class AAFrequency * @param endCol * end column (exclusive) */ - public static void completeGapAnnot(AlignmentAnnotation consensus, + public static void completeGapAnnot(AlignmentAnnotation gaprow, ProfilesI profiles, int startCol, int endCol, long nseq) { - if (consensus == null || consensus.annotations == null - || consensus.annotations.length < endCol) + if (gaprow == null || gaprow.annotations == null + || gaprow.annotations.length < endCol) { /* * called with a bad alignment annotation row @@ -313,8 +313,8 @@ public class AAFrequency return; } // always set ranges again - consensus.graphMax = nseq; - consensus.graphMin = 0; + gaprow.graphMax = nseq; + gaprow.graphMin = 0; for (int i = startCol; i < endCol; i++) { ProfileI profile = profiles.get(i); @@ -324,7 +324,7 @@ public class AAFrequency * happens if sequences calculated over were * shorter than alignment width */ - consensus.annotations[i] = null; + gaprow.annotations[i] = null; return; } @@ -332,7 +332,7 @@ public class AAFrequency String description = String.valueOf(gapped); - consensus.annotations[i] = new Annotation(description, description, + gaprow.annotations[i] = new Annotation(description, description, '\0', gapped); } -- 1.7.10.2