git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Jalview 2.6 source licence
[jalview.git]
/
src
/
jalview
/
datamodel
/
ColumnSelection.java
diff --git
a/src/jalview/datamodel/ColumnSelection.java
b/src/jalview/datamodel/ColumnSelection.java
index
4371994
..
546ba1a
100644
(file)
--- a/
src/jalview/datamodel/ColumnSelection.java
+++ b/
src/jalview/datamodel/ColumnSelection.java
@@
-1,5
+1,5
@@
/*
\r
/*
\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
\r
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
\r
*
\r
* This file is part of Jalview.
\r
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
\r
*
\r
* This file is part of Jalview.
\r
@@
-508,8
+508,8
@@
public class ColumnSelection
}
\r
\r
/**
\r
}
\r
\r
/**
\r
- * Use this method to find out where a visible column is in the alignment when
\r
- * hidden columns exist
\r
+ * Use this method to find out where a column will appear in the visible alignment when
\r
+ * hidden columns exist. If the column is not visible, then the left-most visible column will always be returned.
\r
*
\r
* @param hiddenColumn
\r
* int
\r
*
\r
* @param hiddenColumn
\r
* int
\r
@@
-521,21
+521,21
@@
public class ColumnSelection
if (hiddenColumns != null)
\r
{
\r
int index = 0;
\r
if (hiddenColumns != null)
\r
{
\r
int index = 0;
\r
- int gaps = 0;
\r
+ int[] region;
\r
do
\r
{
\r
do
\r
{
\r
- int[] region = (int[]) hiddenColumns.elementAt(index);
\r
+ region = (int[]) hiddenColumns.elementAt(index++);
\r
if (hiddenColumn > region[1])
\r
{
\r
result -= region[1] + 1 - region[0];
\r
}
\r
if (hiddenColumn > region[1])
\r
{
\r
result -= region[1] + 1 - region[0];
\r
}
\r
- index++;
\r
- } while (index < hiddenColumns.size());
\r
-
\r
- result -= gaps;
\r
+ } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
\r
+ if (hiddenColumn>region[0] && hiddenColumn<region[1])
\r
+ {
\r
+ return region[0]+hiddenColumn-result;
\r
+ }
\r
}
\r
}
\r
-
\r
- return result;
\r
+ return result; // return the shifted position after removing hidden columns.
\r
}
\r
\r
/**
\r
}
\r
\r
/**
\r