import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.io.PDBFeatureSettings;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;
Console.debug("Downloading pae from " + paeURL + " to " + pae.toString()
+ "");
UrlDownloadClient.download(paeURL, pae);
- addAlphaFoldPAE(pdbAlignment, pae, 0, null);
+ addAlphaFoldPAEToSequence(pdbAlignment, pae, 0, null);
}
- public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae,
- int index, String seqId)
+ public static void addAlphaFoldPAEToSequence(AlignmentI pdbAlignment,
+ File pae, int index, String seqId)
{
FileInputStream pae_input = null;
try
}
+ public static void addAlphaFoldPAEToStructure(AlignmentI pdbAlignment,
+ File pae, int index, String structId)
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ if (ssm != null)
+ {
+ /*
+ ssm.setAddTempFacAnnot(showTemperatureFactor);
+ ssm.setProcessSecondaryStructure(showSecondaryStructure);
+ */
+ }
+
+ }
+
/**
* parses the given pAE matrix and adds it to sequence 0 in the given
* alignment
Console.debug("***** Got sequence at index " + seqToGet + ": "
+ (sequence == null ? null : sequence.getName()));
}
- else
+ if (sequence == null)
{
Console.debug("***** Looking for sequence with id '" + seqId + "'");