From 6099817bf611097b9db77237cabddcdb63d0ad14 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 27 Feb 2018 16:18:31 +0000 Subject: [PATCH] JAL-2668 method name change for clarity --- src/jalview/datamodel/ResidueCount.java | 2 +- src/jalview/schemes/HMMERAlignmentColourScheme.java | 2 +- test/jalview/datamodel/ResidueCountTest.java | 5 ++++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/src/jalview/datamodel/ResidueCount.java b/src/jalview/datamodel/ResidueCount.java index aaf6988..047b7e7 100644 --- a/src/jalview/datamodel/ResidueCount.java +++ b/src/jalview/datamodel/ResidueCount.java @@ -666,7 +666,7 @@ public class ResidueCount * * @return */ - public int getTotalCount() + public int getTotalResidueCount() { int total = 0; for (char symbol : this.getSymbolCounts().symbols) diff --git a/src/jalview/schemes/HMMERAlignmentColourScheme.java b/src/jalview/schemes/HMMERAlignmentColourScheme.java index 52ee6e5..d5bbe0c 100644 --- a/src/jalview/schemes/HMMERAlignmentColourScheme.java +++ b/src/jalview/schemes/HMMERAlignmentColourScheme.java @@ -164,7 +164,7 @@ public class HMMERAlignmentColourScheme extends ResidueColourScheme public void countFrequencies(AnnotatedCollectionI sg) { ResidueCount counts = new ResidueCount(sg.getSequences()); - int total = counts.getTotalCount(); // excludes gaps + int total = counts.getTotalResidueCount(); // excludes gaps for (char symbol : counts.getSymbolCounts().symbols) { diff --git a/test/jalview/datamodel/ResidueCountTest.java b/test/jalview/datamodel/ResidueCountTest.java index 462104f..9a8f93d 100644 --- a/test/jalview/datamodel/ResidueCountTest.java +++ b/test/jalview/datamodel/ResidueCountTest.java @@ -71,6 +71,7 @@ public class ResidueCountTest assertEquals(rc.getCount('N'), 1); assertEquals(rc.getCount('?'), 0); assertEquals(rc.getCount('-'), 0); + assertEquals(rc.getTotalResidueCount(), 11); assertFalse(rc.isCountingInts()); assertFalse(rc.isUsingOtherData()); @@ -92,6 +93,7 @@ public class ResidueCountTest assertEquals(rc.getCount(' '), 4); assertEquals(rc.getCount('-'), 4); assertEquals(rc.getCount('.'), 4); + assertEquals(rc.getTotalResidueCount(), 0); assertFalse(rc.isUsingOtherData()); assertFalse(rc.isCountingInts()); } @@ -160,6 +162,7 @@ public class ResidueCountTest assertEquals(rc.getCount('m'), 13); assertEquals(rc.getCount('G'), 0); assertEquals(rc.getCount('-'), 0); + assertEquals(rc.getTotalResidueCount(), 27); assertFalse(rc.isCountingInts()); assertFalse(rc.isUsingOtherData()); @@ -450,7 +453,7 @@ public class ResidueCountTest ResidueCount rc = new ResidueCount(Arrays.asList(seq1, seq2)); assertEquals(rc.getGapCount(), 7); - assertEquals(rc.getTotalCount(), 15); // excludes gaps + assertEquals(rc.getTotalResidueCount(), 15); // excludes gaps assertEquals(rc.getCount('a'), 2); assertEquals(rc.getCount('A'), 2); assertEquals(rc.getCount('B'), 3); -- 1.7.10.2