import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.io.DataSourceType;
import jalview.jbgui.GStructureChooser;
-import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
-import jalview.ws.DBRefFetcher;
-import jalview.ws.sifts.SiftsSettings;
import java.awt.event.ItemEvent;
import java.util.ArrayList;
{
private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
- private static int MAX_QLENGTH = 7820;
+ private static final int MAX_QLENGTH = 7820;
- private SequenceI selectedSequence;
+ protected SequenceI selectedSequence;
- private SequenceI[] selectedSequences;
+ public SequenceI[] selectedSequences;
private IProgressIndicator progressIndicator;
- private Collection<FTSData> discoveredStructuresSet;
+ protected Collection<FTSData> discoveredStructuresSet;
- private FTSRestRequest lastPdbRequest;
+ protected FTSRestRequest lastPdbRequest;
- private FTSRestClientI pdbRestClient;
+ protected FTSRestClientI pdbRestClient;
- private String selectedPdbFileName;
+ protected String selectedPdbFileName;
- private boolean isValidPBDEntry;
+ protected boolean isValidPBDEntry;
- private boolean cachedPDBExists;
-
- private static StructureViewer lastTargetedView = null;
+ protected boolean cachedPDBExists;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
* structures may be added. If this list is empty then it, and the 'Add'
* button, are hidden.
*/
- private void discoverStructureViews()
+ protected void discoverStructureViews()
{
- if (Desktop.instance != null)
+ Desktop desktop = Desktop.getInstance();
+ if (desktop != null)
{
targetView.removeAllItems();
- if (lastTargetedView != null && !lastTargetedView.isVisible())
+ if (desktop.lastTargetedView != null
+ && !desktop.lastTargetedView.isVisible())
{
- lastTargetedView = null;
+ desktop.lastTargetedView = null;
}
int linkedViewsAt = 0;
- for (StructureViewerBase view : Desktop.instance
+ for (StructureViewerBase view : desktop
.getStructureViewers(null, null))
{
- StructureViewer viewHandler = (lastTargetedView != null
- && lastTargetedView.sview == view) ? lastTargetedView
+ StructureViewer viewHandler = (desktop.lastTargetedView != null
+ && desktop.lastTargetedView.sview == view)
+ ? desktop.lastTargetedView
: StructureViewer.reconfigure(view);
if (view.isLinkedWith(ap))
if (targetView.getItemCount() > 0)
{
targetView.setVisible(true);
- if (lastTargetedView != null)
+ if (desktop.lastTargetedView != null)
{
- targetView.setSelectedItem(lastTargetedView);
+ targetView.setSelectedItem(desktop.lastTargetedView);
}
else
{
/**
* structure viewer opened by this dialog, or null
*/
- private StructureViewer sViewer = null;
+ protected StructureViewer sViewer = null;
public void showStructures(boolean waitUntilFinished)
{
- final StructureSelectionManager ssm = ap.getStructureSelectionManager();
-
final int preferredHeight = pnl_filter.getHeight();
Runnable viewStruc = new Runnable()
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+ sViewer = launchStructureViewer(ap, pdbEntriesToView,
selectedSeqs);
}
else if (currentView == VIEWS_LOCAL_PDB)
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+ sViewer = launchStructureViewer(ap, pdbEntriesToView,
selectedSeqs);
}
else if (currentView == VIEWS_ENTER_ID)
}
PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
- sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+ sViewer = launchStructureViewer(ap, pdbEntriesToView,
new SequenceI[]
{ selectedSequence });
}
{
selectedSequence = userSelectedSeq;
}
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+ PDBEntry fileEntry = AssociatePdbFileWithSeq
.associatePdbWithSeq(selectedPdbFileName,
- DataSourceType.FILE, selectedSequence, true,
- Desktop.instance);
+ DataSourceType.FILE, selectedSequence, true);
sViewer = launchStructureViewer(
- ssm, new PDBEntry[]
- { fileEntry }, ap,
+ ap, new PDBEntry[]
+ { fileEntry },
new SequenceI[]
{ selectedSequence });
}
}
}
- private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
+ protected PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
{
Objects.requireNonNull(id);
Objects.requireNonNull(pdbEntries);
* Answers a structure viewer (new or existing) configured to superimpose
* added structures or not according to the user's choice
*
- * @param ssm
* @return
*/
- StructureViewer getTargetedStructureViewer(
- StructureSelectionManager ssm)
+ StructureViewer getTargetedStructureViewer()
{
- Object sv = targetView.getSelectedItem();
+ final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+ Object sv = (targetView == null ? null : targetView.getSelectedItem());
return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
}
/**
* Adds PDB structures to a new or existing structure viewer
*
- * @param ssm
+ * @param ap
* @param pdbEntriesToView
- * @param alignPanel
* @param sequences
- * @return
+ * @param superimpose
+ * @return viewer
*/
- private StructureViewer launchStructureViewer(
- StructureSelectionManager ssm,
- final PDBEntry[] pdbEntriesToView,
- final AlignmentPanel alignPanel, SequenceI[] sequences)
+ protected StructureViewer launchStructureViewer(
+ AlignmentPanel ap, PDBEntry[] pdbEntriesToView,
+ SequenceI[] selectedSeqs)
{
- long progressId = sequences.hashCode();
- setProgressBar(MessageManager
- .getString("status.launching_3d_structure_viewer"), progressId);
- final StructureViewer theViewer = getTargetedStructureViewer(ssm);
boolean superimpose = chk_superpose.isSelected();
- theViewer.setSuperpose(superimpose);
-
/*
* remember user's choice of superimpose or not
*/
Cache.setProperty(AUTOSUPERIMPOSE,
Boolean.valueOf(superimpose).toString());
-
- setProgressBar(null, progressId);
- if (SiftsSettings.isMapWithSifts())
- {
- List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
- int p = 0;
- // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
- // real PDB ID. For moment, we can also safely do this if there is already
- // a known mapping between the PDBEntry and the sequence.
- for (SequenceI seq : sequences)
- {
- PDBEntry pdbe = pdbEntriesToView[p++];
- if (pdbe != null && pdbe.getFile() != null)
- {
- StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
- if (smm != null && smm.length > 0)
- {
- for (StructureMapping sm : smm)
- {
- if (sm.getSequence() == seq)
- {
- continue;
- }
- }
- }
- }
- if (seq.getPrimaryDBRefs().isEmpty())
- {
- seqsWithoutSourceDBRef.add(seq);
- continue;
- }
- }
- if (!seqsWithoutSourceDBRef.isEmpty())
- {
- int y = seqsWithoutSourceDBRef.size();
- setProgressBar(MessageManager.formatMessage(
- "status.fetching_dbrefs_for_sequences_without_valid_refs",
- y), progressId);
- SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
- .toArray(new SequenceI[y]);
- DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
- dbRefFetcher.fetchDBRefs(true);
-
- setProgressBar("Fetch complete.", progressId); // todo i18n
- }
- }
- if (pdbEntriesToView.length > 1)
- {
- setProgressBar(MessageManager.getString(
- "status.fetching_3d_structures_for_selected_entries"),
- progressId);
- theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
- }
- else
- {
- setProgressBar(MessageManager.formatMessage(
- "status.fetching_3d_structures_for",
- pdbEntriesToView[0].getId()),progressId);
- theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
- }
- setProgressBar(null, progressId);
- // remember the last viewer we used...
- lastTargetedView = theViewer;
- return theViewer;
+ return StructureViewer.launchStructureViewer(ap, pdbEntriesToView, selectedSeqs,
+ superimpose, getTargetedStructureViewer(), progressBar);
}
/**
protected void txt_search_ActionPerformed()
{
String text = txt_search.getText().trim();
- if (text.length() >= PDB_ID_MIN)
+ if (text.length() >= PDB_ID_MIN)
+ {
new Thread()
{
}
}.start();
}
+ }
@Override
protected void tabRefresh()
@Override
public void setProgressBar(String message, long id)
{
- progressBar.setProgressBar(message, id);
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(message, id);
+ }
}
@Override
git://source.jalview.org / jalview.git / blobdiff