JAL-2668 method name change for clarity

diff --git a/src/jalview/datamodel/ResidueCount.java b/src/jalview/datamodel/ResidueCount.java
index aaf6988..047b7e7 100644 (file)
--- 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 (file)
--- 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 (file)
--- 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);