.getStructureSelectionManager(Desktop.instance);
SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
ssm.computeMapping(false, new SequenceI[] { seq }, null,
- openFile, DataSourceType.FILE, null);
+ openFile, DataSourceType.FILE, null, null, null);
}
}
else
{
Console.info("***** Attaching paeFile '" + paePath + "' to "
+ "structfile=" + subVals.get("structfile"));
- EBIAlfaFold.addAlphaFoldPAEToStructure(
- af.getCurrentView().getAlignment(), paeFile,
- subVals.getIndex(), subVals.get("structfile"), false);
+ EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+ paeFile, subVals.getIndex(), subVals.get("structfile"),
+ true, false);
}
else if (subVals.has("structid"))
{
Console.info("***** Attaching paeFile '" + paePath + "' to "
+ "structid=" + subVals.get("structid"));
- EBIAlfaFold.addAlphaFoldPAEToStructure(
- af.getCurrentView().getAlignment(), paeFile,
- subVals.getIndex(), subVals.get("structid"), true);
+ EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+ paeFile, subVals.getIndex(), subVals.get("structid"),
+ true, true);
}
else
{
Console.debug("***** Attaching paeFile '" + paePath
+ "' to sequence index " + subVals.getIndex());
- EBIAlfaFold.addAlphaFoldPAEToSequence(
- af.getCurrentView().getAlignment(), paeFile,
- subVals.getIndex(), null);
+ EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+ paeFile, subVals.getIndex(), null, false, false);
// required to readjust the height and position of the pAE
// annotation
}