import jalview.datamodel.AlignmentI;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
AlignmentI pdbAlignment, String retrievalUrl) throws IOException
{
File pae = fetchAlphaFoldPAE(id, retrievalUrl);
AlignmentI pdbAlignment, String retrievalUrl) throws IOException
{
File pae = fetchAlphaFoldPAE(id, retrievalUrl);
- addAlphaFoldPAE(pdbAlignment, pae, 0, null, false, false);
+ addAlphaFoldPAE(pdbAlignment, pae, 0, null, false, false, null);
- int index, String id, boolean isStruct, boolean isStructId)
+ int index, String id, boolean isStruct, boolean isStructId,
+ String label)
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
if (ssm != null)
{
String structFilename = isStructId ? ssm.findFileForPDBId(id) : id;
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
if (ssm != null)
{
String structFilename = isStructId ? ssm.findFileForPDBId(id) : id;
*/
public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input, int index,
*/
public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input, int index,
}
public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input,
}
public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input,
- SequenceI sequence) throws IOException, ParseException
+ SequenceI sequence, String label)
+ throws IOException, ParseException
}
ContactMatrixI matrix = new PAEContactMatrix(sequence,
(Map<String, Object>) paeDict);
}
ContactMatrixI matrix = new PAEContactMatrix(sequence,
(Map<String, Object>) paeDict);
throws IOException, ParseException
{
boolean someDone = false;
for (StructureMapping sm : smArray)
{
boolean thisDone = importPaeJSONAsContactMatrixToStructure(sm,
throws IOException, ParseException
{
boolean someDone = false;
for (StructureMapping sm : smArray)
{
boolean thisDone = importPaeJSONAsContactMatrixToStructure(sm,
throws IOException, ParseException
{
JSONObject pae_obj = parseJSONtoPAEContactMatrix(paeInput);
throws IOException, ParseException
{
JSONObject pae_obj = parseJSONtoPAEContactMatrix(paeInput);