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JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob
[jalview.git]
/
src
/
jalview
/
datamodel
/
ColumnSelection.java
diff --git
a/src/jalview/datamodel/ColumnSelection.java
b/src/jalview/datamodel/ColumnSelection.java
index
3916b7d
..
15bbffa
100644
(file)
--- a/
src/jalview/datamodel/ColumnSelection.java
+++ b/
src/jalview/datamodel/ColumnSelection.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-486,6
+486,7
@@
public class ColumnSelection
/**
* This Method is used to return all the HiddenColumn regions
/**
* This Method is used to return all the HiddenColumn regions
+ *
* @return empty list or List of hidden column intervals
*/
public List<int[]> getHiddenColumns()
* @return empty list or List of hidden column intervals
*/
public List<int[]> getHiddenColumns()
@@
-666,8
+667,7
@@
public class ColumnSelection
}
else if (end < region[0] && start < region[0])
{
}
else if (end < region[0] && start < region[0])
{
- hiddenColumns.insertElementAt(new int[]
- { start, end }, i);
+ hiddenColumns.insertElementAt(new int[] { start, end }, i);
added = true;
break;
}
added = true;
break;
}
@@
-679,8
+679,7
@@
public class ColumnSelection
}
else if (!added)
{
}
else if (!added)
{
- hiddenColumns.addElement(new int[]
- { start, end });
+ hiddenColumns.addElement(new int[] { start, end });
}
}
}
}
@@
-909,16
+908,14
@@
public class ColumnSelection
}
if (hideStart > vstart)
{
}
if (hideStart > vstart)
{
- visiblecontigs.add(new int[]
- { vstart, hideStart - 1 });
+ visiblecontigs.add(new int[] { vstart, hideStart - 1 });
}
vstart = hideEnd + 1;
}
if (vstart < end)
{
}
vstart = hideEnd + 1;
}
if (vstart < end)
{
- visiblecontigs.add(new int[]
- { vstart, end - 1 });
+ visiblecontigs.add(new int[] { vstart, end - 1 });
}
int[] vcontigs = new int[visiblecontigs.size() * 2];
for (int i = 0, j = visiblecontigs.size(); i < j; i++)
}
int[] vcontigs = new int[visiblecontigs.size() * 2];
for (int i = 0, j = visiblecontigs.size(); i < j; i++)
@@
-933,8
+930,7
@@
public class ColumnSelection
}
else
{
}
else
{
- return new int[]
- { start, end - 1 };
+ return new int[] { start, end - 1 };
}
}
}
}
@@
-975,7
+971,7
@@
public class ColumnSelection
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
// then mangle the alignmentAnnotation annotation array
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
// then mangle the alignmentAnnotation annotation array
- Vector<Annotation []> annels = new Vector<Annotation []>();
+ Vector<Annotation[]> annels = new Vector<Annotation[]>();
Annotation[] els = null;
List<int[]> regions = getHiddenColumns();
int blockStart = start, blockEnd = end;
Annotation[] els = null;
List<int[]> regions = getHiddenColumns();
int blockStart = start, blockEnd = end;
@@
-1035,7
+1031,7
@@
public class ColumnSelection
alignmentAnnotation.annotations = new Annotation[w];
w = 0;
alignmentAnnotation.annotations = new Annotation[w];
w = 0;
- for (Annotation [] chnk : annels)
+ for (Annotation[] chnk : annels)
{
System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
chnk.length);
{
System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
chnk.length);
@@
-1284,7
+1280,7
@@
public class ColumnSelection
{
return hiddenColumns != null && hiddenColumns.size() > 0;
}
{
return hiddenColumns != null && hiddenColumns.size() > 0;
}
-
+
/**
*
* @return true if there are more than one set of columns hidden
/**
*
* @return true if there are more than one set of columns hidden
@@
-1308,7
+1304,7
@@
public class ColumnSelection
hideColumns(r[0], r[1]);
}
}
hideColumns(r[0], r[1]);
}
}
-
+
public boolean filterAnnotations(Annotation[] annotations,
AnnotationFilterParameter filterParams)
{
public boolean filterAnnotations(Annotation[] annotations,
AnnotationFilterParameter filterParams)
{