private boolean isNa = false;
/**
- * reference to the complementary CDS/Protein alignment for this alignment, if available
- */
- private AlignmentView complementView=null;
-
- /**
- * setter for
- * @param complementView
- */
- public void setComplement(AlignmentView complementView)
- {
- this.complementView = complementView;
-
- }
- /**
- *
- * @return true if a complement is available
- */
- public boolean hasComplementView()
- {
- return complementView!=null;
- }
- /**
- *
- * @return the complement view or null
- */
- public AlignmentView getComplementView()
- {
- return complementView;
- }
-
- /**
* false if the view concerns peptides
*
* @return
public static void testSelectionViews(AlignmentI alignment,
HiddenColumns hidden, SequenceGroup selection)
{
- System.out.println("Testing standard view creation:\n");
+ jalview.bin.Console.outPrintln("Testing standard view creation:\n");
AlignmentView view = null;
try
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"View with no hidden columns, no limit to selection, no groups to be collected:");
view = new AlignmentView(alignment, hidden, selection, false, false,
false);
} catch (Exception e)
{
e.printStackTrace();
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to generate alignment with selection but no groups marked.");
}
try
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"View with no hidden columns, no limit to selection, and all groups to be collected:");
view = new AlignmentView(alignment, hidden, selection, false, false,
true);
} catch (Exception e)
{
e.printStackTrace();
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to generate alignment with selection marked but no groups marked.");
}
try
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"View with no hidden columns, limited to selection and no groups to be collected:");
view = new AlignmentView(alignment, hidden, selection, false, true,
false);
} catch (Exception e)
{
e.printStackTrace();
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to generate alignment with selection restricted but no groups marked.");
}
try
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"View with no hidden columns, limited to selection, and all groups to be collected:");
view = new AlignmentView(alignment, hidden, selection, false, true,
true);
} catch (Exception e)
{
e.printStackTrace();
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to generate alignment with selection restricted and groups marked.");
}
try
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"View *with* hidden columns, no limit to selection, no groups to be collected:");
view = new AlignmentView(alignment, hidden, selection, true, false,
false);
} catch (Exception e)
{
e.printStackTrace();
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to generate alignment with selection but no groups marked.");
}
try
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"View *with* hidden columns, no limit to selection, and all groups to be collected:");
view = new AlignmentView(alignment, hidden, selection, true, false,
true);
} catch (Exception e)
{
e.printStackTrace();
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to generate alignment with selection marked but no groups marked.");
}
try
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"View *with* hidden columns, limited to selection and no groups to be collected:");
view = new AlignmentView(alignment, hidden, selection, true, true,
false);
} catch (Exception e)
{
e.printStackTrace();
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to generate alignment with selection restricted but no groups marked.");
}
try
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"View *with* hidden columns, limited to selection, and all groups to be collected:");
view = new AlignmentView(alignment, hidden, selection, true, true,
true);
} catch (Exception e)
{
e.printStackTrace();
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Failed to generate alignment with selection restricted and groups marked.");
}