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JAL-2759 Rename hideInsertionsFor to hideList, after review
author
kiramt
<k.mourao@dundee.ac.uk>
Mon, 15 Jan 2018 13:38:56 +0000
(13:38 +0000)
committer
kiramt
<k.mourao@dundee.ac.uk>
Mon, 15 Jan 2018 13:38:56 +0000
(13:38 +0000)
src/jalview/datamodel/Alignment.java
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src/jalview/datamodel/HiddenColumns.java
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src/jalview/io/AnnotationFile.java
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test/jalview/datamodel/HiddenColumnsTest.java
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diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
f052c05
..
7cc2125
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-1920,7
+1920,7
@@
public class Alignment implements AlignmentI
SequenceI repseq = getSequenceAt(0);
setSeqrep(repseq);
HiddenColumns cs = new HiddenColumns();
SequenceI repseq = getSequenceAt(0);
setSeqrep(repseq);
HiddenColumns cs = new HiddenColumns();
- cs.hideInsertionsFor(repseq.getInsertions());
+ cs.hideList(repseq.getInsertions());
setHiddenColumns(cs);
}
}
setHiddenColumns(cs);
}
}
diff --git
a/src/jalview/datamodel/HiddenColumns.java
b/src/jalview/datamodel/HiddenColumns.java
index
2b5185f
..
4a1a9a3
100644
(file)
--- a/
src/jalview/datamodel/HiddenColumns.java
+++ b/
src/jalview/datamodel/HiddenColumns.java
@@
-300,17
+300,16
@@
public class HiddenColumns
}
/**
}
/**
- * mark the columns corresponding to gap characters as hidden in the column
- * selection
+ * hide a list of ranges
*
*
- * @param insertions
+ * @param ranges
*/
*/
- public void hideInsertionsFor(List<int[]> inserts)
+ public void hideList(List<int[]> ranges)
{
try
{
LOCK.writeLock().lock();
{
try
{
LOCK.writeLock().lock();
- for (int[] r : inserts)
+ for (int[] r : ranges)
{
hideColumns(r[0], r[1]);
}
{
hideColumns(r[0], r[1]);
}
diff --git
a/src/jalview/io/AnnotationFile.java
b/src/jalview/io/AnnotationFile.java
index
885a298
..
e578a45
100755
(executable)
--- a/
src/jalview/io/AnnotationFile.java
+++ b/
src/jalview/io/AnnotationFile.java
@@
-968,7
+968,7
@@
public class AnnotationFile
else
{
// consider deferring this till after the file has been parsed ?
else
{
// consider deferring this till after the file has been parsed ?
- hidden.hideInsertionsFor(sr.getInsertions());
+ hidden.hideList(sr.getInsertions());
}
}
modified = true;
}
}
modified = true;
diff --git
a/test/jalview/datamodel/HiddenColumnsTest.java
b/test/jalview/datamodel/HiddenColumnsTest.java
index
a31d527
..
e6c9b32
100644
(file)
--- a/
test/jalview/datamodel/HiddenColumnsTest.java
+++ b/
test/jalview/datamodel/HiddenColumnsTest.java
@@
-420,7
+420,7
@@
public class HiddenColumnsTest
new SequenceI[]
{ new Sequence("refseqGaptest", "KTDVTI----------NFI-----G----L") });
HiddenColumns cs = new HiddenColumns();
new SequenceI[]
{ new Sequence("refseqGaptest", "KTDVTI----------NFI-----G----L") });
HiddenColumns cs = new HiddenColumns();
- cs.hideInsertionsFor(al.getSequenceAt(0).getInsertions());
+ cs.hideList(al.getSequenceAt(0).getInsertions());
assertEquals("G", ""
+ al.getSequenceAt(0).getCharAt(cs.visibleToAbsoluteColumn(9)));
assertEquals("G", ""
+ al.getSequenceAt(0).getCharAt(cs.visibleToAbsoluteColumn(9)));
@@
-1139,10
+1139,10
@@
public class HiddenColumnsTest
SequenceI seq1 = new Sequence("TEST1", "GAL---MFW-KQESPVICY--HRNDT");
SequenceI seq2 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
SequenceI seq1 = new Sequence("TEST1", "GAL---MFW-KQESPVICY--HRNDT");
SequenceI seq2 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
- h.hideInsertionsFor(seq2.getInsertions());
+ h.hideList(seq2.getInsertions());
assertTrue(h.equals(h2));
assertTrue(h.equals(h2));
- h.hideInsertionsFor(seq1.getInsertions());
+ h.hideList(seq1.getInsertions());
h2.hideColumns(3, 5);
h2.hideColumns(9, 9);
h2.hideColumns(19, 20);
h2.hideColumns(3, 5);
h2.hideColumns(9, 9);
h2.hideColumns(19, 20);