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JAL-1933 refactor parameter for code clarity
[jalview.git]
/
src
/
jalview
/
analysis
/
AAFrequency.java
diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
ffa413b
..
ee16f94
100755
(executable)
--- 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.
*
/**
* Derive the gap count annotation row.
*
- * @param consensus
+ * @param gaprow
* the annotation row to add annotations to
* @param profiles
* the source consensus data
* 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)
*/
* @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)
{
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
{
/*
* called with a bad alignment annotation row
@@
-313,8
+313,8
@@
public class AAFrequency
return;
}
// always set ranges again
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);
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
*/
* happens if sequences calculated over were
* shorter than alignment width
*/
- consensus.annotations[i] = null;
+ gaprow.annotations[i] = null;
return;
}
return;
}
@@
-332,7
+332,7
@@
public class AAFrequency
String description = String.valueOf(gapped);
String description = String.valueOf(gapped);
- consensus.annotations[i] = new Annotation(description, description,
+ gaprow.annotations[i] = new Annotation(description, description,
'\0',
gapped);
}
'\0',
gapped);
}