import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JmolParser;
import jalview.gui.IProgressIndicator;
+import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.util.MappingUtils;
{
for (StructureMapping sm : mappings)
{
- if (sm.getPdbId().equalsIgnoreCase(pdbid))
+ if (sm.getPdbId().equals(pdbid))
{
return sm.pdbfile;
}
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
+ sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
pdb = new JmolParser(pdbFile, sourceType);
if (pdb.getId() != null && pdb.getId().trim().length() > 0
* Attempt pairwise alignment of the sequence with each chain in the PDB,
* and remember the highest scoring chain
*/
- int max = -10;
+ float max = -10;
AlignSeq maxAlignseq = null;
String maxChainId = " ";
PDBChain maxChain = null;
return pdb;
}
- private boolean isCIFFile(String filename)
+ public void addStructureMapping(StructureMapping sm)
{
- String fileExt = filename.substring(filename.lastIndexOf(".") + 1,
- filename.length());
- return "cif".equalsIgnoreCase(fileExt);
+ mappings.add(sm);
}
/**
if (listeners.elementAt(i) instanceof StructureListener)
{
sl = (StructureListener) listeners.elementAt(i);
- for (String pdbfile : sl.getPdbFile())
+ for (String pdbfile : sl.getStructureFiles())
{
pdbs.remove(pdbfile);
}
* @param atoms
* @return
*/
- public SearchResults findAlignmentPositionsForStructurePositions(
+ public SearchResultsI findAlignmentPositionsForStructurePositions(
List<AtomSpec> atoms)
{
- SearchResults results = new SearchResults();
+ SearchResultsI results = new SearchResults();
for (AtomSpec atom : atoms)
{
SequenceI lastseq = null;
public synchronized void sendSelection(
jalview.datamodel.SequenceGroup selection,
- jalview.datamodel.ColumnSelection colsel, SelectionSource source)
+ jalview.datamodel.ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source)
{
for (SelectionListener slis : sel_listeners)
{
if (slis != source)
{
- slis.selection(selection, colsel, source);
+ slis.selection(selection, colsel, hidden, source);
}
}
}