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JAL-2609 process only up to end of alignment when shifting sequences
[jalview.git]
/
src
/
jalview
/
javascript
/
JsSelectionSender.java
diff --git
a/src/jalview/javascript/JsSelectionSender.java
b/src/jalview/javascript/JsSelectionSender.java
index
57da5b4
..
fdf8b58
100644
(file)
--- a/
src/jalview/javascript/JsSelectionSender.java
+++ b/
src/jalview/javascript/JsSelectionSender.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-23,6
+23,7
@@
package jalview.javascript;
import jalview.appletgui.AlignFrame;
import jalview.bin.JalviewLite;
import jalview.datamodel.ColumnSelection;
import jalview.appletgui.AlignFrame;
import jalview.bin.JalviewLite;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceGroup;
import jalview.structure.SelectionSource;
import jalview.datamodel.SequenceGroup;
import jalview.structure.SelectionSource;
@@
-44,13
+45,12
@@
public class JsSelectionSender extends JSFunctionExec implements
@Override
public void selection(SequenceGroup seqsel, ColumnSelection colsel,
@Override
public void selection(SequenceGroup seqsel, ColumnSelection colsel,
- SelectionSource source)
+ HiddenColumns hidden, SelectionSource source)
{
// System.err.println("Testing selection event relay to jsfunction:"+_listener);
try
{
String setid = "";
{
// System.err.println("Testing selection event relay to jsfunction:"+_listener);
try
{
String setid = "";
- String viewid = "";
AlignFrame src = _af;
if (source != null)
{
AlignFrame src = _af;
if (source != null)
{
@@
-82,19
+82,16
@@
public class JsSelectionSender extends JSFunctionExec implements
end = seqsel.getEndRes();
}
}
end = seqsel.getEndRes();
}
}
- if (colsel != null && colsel.size() > 0)
+ if (colsel != null && !colsel.isEmpty())
{
if (end == -1)
{
end = colsel.getMax() + 1;
}
cols = new String[colsel.getSelected().size()];
{
if (end == -1)
{
end = colsel.getMax() + 1;
}
cols = new String[colsel.getSelected().size()];
- int d = 0, r = -1;
for (int i = 0; i < cols.length; i++)
{
for (int i = 0; i < cols.length; i++)
{
- cols[i] = ""
- + (1 + ((Integer) colsel.getSelected().elementAt(i))
- .intValue());
+ cols[i] = "" + (1 + colsel.getSelected().get(i).intValue());
}
}
else
}
}
else