private void buildSkipList()
{
skipList = new Hashtable();
- AlignFrame[] al = Desktop.getAlignFrames();
+ AlignFrame[] al = Desktop.getDesktopAlignFrames();
for (int f = 0; al != null && f < al.length; f++)
{
skipList.put(al[f].getViewport().getSequenceSetId(), al[f]);
{
// removeValignmentSequences(alignment, docseqs);
docseqs.removeAllElements();
- System.out.println(
+ jalview.bin.Console.outPrintln(
"Sequence deletion from alignment is not implemented.");
}
}
if (alismod)
{
- System.out.println("update alignment in document.");
+ jalview.bin.Console.outPrintln("update alignment in document.");
}
else
{
- System.out.println("alignment in document left unchanged.");
+ jalview.bin.Console.outPrintln("alignment in document left unchanged.");
}
}
else
// unbind alignment from view.
// create new binding and new alignment.
// mark trail on new alignment as being derived from old ?
- System.out.println(
+ jalview.bin.Console.outPrintln(
"update edited alignment to new alignment in document.");
}
}
// METHODS)
{
// verify existing alignment sequence annotation is up to date
- System.out.println("update dataset sequence annotation.");
+ jalview.bin.Console.outPrintln("update dataset sequence annotation.");
}
else
{
// verify existing alignment sequence annotation is up to date
- System.out.println(
+ jalview.bin.Console.outPrintln(
"make new alignment dataset sequence annotation if modification has happened.");
}
}
// METHODS)
{
// verify existing alignment sequence annotation is up to date
- System.out.println("update alignment sequence annotation.");
+ jalview.bin.Console.outPrintln("update alignment sequence annotation.");
}
else
{
// verify existing alignment sequence annotation is up to date
- System.out.println(
+ jalview.bin.Console.outPrintln(
"make new alignment sequence annotation if modification has happened.");
}
}