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JAL-3761 more consistent parameter naming
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Sat, 26 Dec 2020 08:51:37 +0000
(08:51 +0000)
committer
Ben Soares
<b.soares@dundee.ac.uk>
Thu, 16 Sep 2021 09:23:46 +0000
(10:23 +0100)
src/jalview/util/MapList.java
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diff --git
a/src/jalview/util/MapList.java
b/src/jalview/util/MapList.java
index
745f367
..
3555e52
100644
(file)
--- a/
src/jalview/util/MapList.java
+++ b/
src/jalview/util/MapList.java
@@
-427,8
+427,8
@@
public class MapList
* @return int[] { from, to pos in range }, int[range.to-range.from+1]
* returning mapped position
*/
* @return int[] { from, to pos in range }, int[range.to-range.from+1]
* returning mapped position
*/
- private int[][] posMap(List<int[]> shiftTo, int ratio,
- List<int[]> shiftFrom, int toRatio)
+ private int[][] posMap(List<int[]> shiftTo, int sourceRatio,
+ List<int[]> shiftFrom, int targetRatio)
{
// TODO only used for test - remove??
int iv = 0, ivSize = shiftTo.size();
{
// TODO only used for test - remove??
int iv = 0, ivSize = shiftTo.size();
@@
-467,7
+467,7
@@
public class MapList
int mp[][] = new int[to - from + 2][];
for (int i = 0; i < mp.length; i++)
{
int mp[][] = new int[to - from + 2][];
for (int i = 0; i < mp.length; i++)
{
- int[] m = shift(i + from, shiftTo, ratio, shiftFrom, toRatio);
+ int[] m = shift(i + from, shiftTo, sourceRatio, shiftFrom, targetRatio);
if (m != null)
{
if (i == 0)
if (m != null)
{
if (i == 0)
@@
-1244,20
+1244,20
@@
public class MapList
*
* @param start
* @param end
*
* @param start
* @param end
- * @param ranges
- * @param wordLengthFrom
- * @param wordLengthTo
+ * @param sourceRange
+ * @param sourceWordLength
+ * @param targetWordLength
* @return
*/
protected final static BitSet getMappedOffsetsForPositions(int start,
* @return
*/
protected final static BitSet getMappedOffsetsForPositions(int start,
- int end, List<int[]> ranges, int wordLengthFrom, int wordLengthTo)
+ int end, List<int[]> sourceRange, int sourceWordLength, int targetWordLength)
{
BitSet overlaps = new BitSet();
int offset = 0;
{
BitSet overlaps = new BitSet();
int offset = 0;
- final int s1 = ranges.size();
+ final int s1 = sourceRange.size();
for (int i = 0; i < s1; i++)
{
for (int i = 0; i < s1; i++)
{
- int[] range = ranges.get(i);
+ int[] range = sourceRange.get(i);
final int offset1 = offset;
int overlapStartOffset = -1;
int overlapEndOffset = -1;
final int offset1 = offset;
int overlapStartOffset = -1;
int overlapEndOffset = -1;
@@
-1300,24
+1300,24
@@
public class MapList
/*
* found an overlap
*/
/*
* found an overlap
*/
- if (wordLengthFrom != wordLengthTo)
+ if (sourceWordLength != targetWordLength)
{
/*
* convert any overlap found to whole words in the target range
* (e.g. treat any partial codon overlap as if the whole codon)
*/
{
/*
* convert any overlap found to whole words in the target range
* (e.g. treat any partial codon overlap as if the whole codon)
*/
- overlapStartOffset -= overlapStartOffset % wordLengthFrom;
- overlapStartOffset = overlapStartOffset / wordLengthFrom
- * wordLengthTo;
+ overlapStartOffset -= overlapStartOffset % sourceWordLength;
+ overlapStartOffset = overlapStartOffset / sourceWordLength
+ * targetWordLength;
/*
* similar calculation for range end, adding
* (wordLength2 - 1) for end of mapped word
*/
/*
* similar calculation for range end, adding
* (wordLength2 - 1) for end of mapped word
*/
- overlapEndOffset -= overlapEndOffset % wordLengthFrom;
- overlapEndOffset = overlapEndOffset / wordLengthFrom
- * wordLengthTo;
- overlapEndOffset += wordLengthTo - 1;
+ overlapEndOffset -= overlapEndOffset % sourceWordLength;
+ overlapEndOffset = overlapEndOffset / sourceWordLength
+ * targetWordLength;
+ overlapEndOffset += targetWordLength - 1;
}
overlaps.set(overlapStartOffset, overlapEndOffset + 1);
}
}
overlaps.set(overlapStartOffset, overlapEndOffset + 1);
}
@@
-1328,15
+1328,15
@@
public class MapList
/**
* Returns a (possibly empty) list of the [start-end] values (positions) at
/**
* Returns a (possibly empty) list of the [start-end] values (positions) at
- * offsets in the {@code ranges} list that are marked by 'on' bits in the
+ * offsets in the {@code targetRange} list that are marked by 'on' bits in the
* {@code offsets} bitset.
*
* {@code offsets} bitset.
*
- * @param ranges
+ * @param targetRange
* @param offsets
* @return
*/
protected final static List<int[]> getPositionsForOffsets(
* @param offsets
* @return
*/
protected final static List<int[]> getPositionsForOffsets(
- List<int[]> ranges, BitSet offsets)
+ List<int[]> targetRange, BitSet offsets)
{
List<int[]> mapped = new ArrayList<>();
if (offsets.isEmpty())
{
List<int[]> mapped = new ArrayList<>();
if (offsets.isEmpty())
@@
-1356,10
+1356,10
@@
public class MapList
*/
final int toAdd = offsets.cardinality();
int added = 0;
*/
final int toAdd = offsets.cardinality();
int added = 0;
- final int s2 = ranges.size();
+ final int s2 = targetRange.size();
for (int i = 0; added < toAdd && i < s2; i++)
{
for (int i = 0; added < toAdd && i < s2; i++)
{
- int[] range = ranges.get(i);
+ int[] range = targetRange.get(i);
added += addOffsetPositions(mapped, traversed, range, offsets);
traversed += Math.abs(range[1] - range[0]) + 1;
}
added += addOffsetPositions(mapped, traversed, range, offsets);
traversed += Math.abs(range[1] - range[0]) + 1;
}