package jalview.gui;
import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
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;
public class StructureChooser extends GStructureChooser
implements IProgressIndicator
{
- private static int MAX_QLENGTH = 7820;
+ private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
- private SequenceI selectedSequence;
+ private static final int MAX_QLENGTH = 7820;
- private SequenceI[] selectedSequences;
+ protected SequenceI selectedSequence;
+
+ public SequenceI[] selectedSequences;
private IProgressIndicator progressIndicator;
- private Collection<FTSData> discoveredStructuresSet;
+ protected Collection<FTSData> discoveredStructuresSet;
- private FTSRestRequest lastPdbRequest;
+ protected FTSRestRequest lastPdbRequest;
- private FTSRestClientI pdbRestCleint;
+ protected FTSRestClientI pdbRestClient;
- private String selectedPdbFileName;
+ protected String selectedPdbFileName;
- private boolean isValidPBDEntry;
+ protected boolean isValidPBDEntry;
- private boolean cachedPDBExists;
+ protected boolean cachedPDBExists;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
/**
* Initializes parameters used by the Structure Chooser Panel
*/
- public void init()
+ protected void init()
{
if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
}
+ chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
+
// ensure a filter option is in force for search
populateFilterComboBox(true, cachedPDBExists);
Thread discoverPDBStructuresThread = new Thread(new Runnable()
discoverPDBStructuresThread.start();
}
- private void discoverStructureViews()
+ /**
+ * Builds a drop-down choice list of existing structure viewers to which new
+ * structures may be added. If this list is empty then it, and the 'Add'
+ * button, are hidden.
+ */
+ protected void discoverStructureViews()
{
- if (Desktop.instance != null)
+ Desktop desktop = Desktop.getInstance();
+ if (desktop != null)
{
targetView.removeAllItems();
- targetView.addItem(
- new StructureViewer(ap.getStructureSelectionManager()));
- if (lastTargetedView != null && !lastTargetedView.isVisible())
+ if (desktop.lastTargetedView != null
+ && !desktop.lastTargetedView.isVisible())
{
- lastTargetedView = null;
+ desktop.lastTargetedView = null;
}
- int linkedViewsAt = 1;
- for (StructureViewerBase view : Desktop.instance
+ int linkedViewsAt = 0;
+ 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))
targetView.addItem(viewHandler);
}
}
- targetView.setVisible(targetView.getItemCount() > 1);
- // finally, restore last targeted view by default.
- if (lastTargetedView != null)
+ /*
+ * show option to Add to viewer if at least 1 viewer found
+ */
+ targetView.setVisible(false);
+ if (targetView.getItemCount() > 0)
{
- targetView.setSelectedItem(lastTargetedView);
+ targetView.setVisible(true);
+ if (desktop.lastTargetedView != null)
+ {
+ targetView.setSelectedItem(desktop.lastTargetedView);
+ }
+ else
+ {
+ targetView.setSelectedIndex(0);
+ }
}
+ btn_add.setVisible(targetView.isVisible());
}
}
- private static StructureViewer lastTargetedView = null;
-
/**
* Updates the progress indicator with the specified message
*
* @param id
* unique handle for this indicator
*/
- public void updateProgressIndicator(String message, long id)
+ protected void updateProgressIndicator(String message, long id)
{
if (progressIndicator != null)
{
* Retrieve meta-data for all the structure(s) for a given sequence(s) in a
* selection group
*/
- public void fetchStructuresMetaData()
+ void fetchStructuresMetaData()
{
long startTime = System.currentTimeMillis();
- pdbRestCleint = PDBFTSRestClient.getInstance();
+ pdbRestClient = PDBFTSRestClient.getInstance();
Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
.getStructureSummaryFields();
FTSRestResponse resultList;
try
{
- resultList = pdbRestCleint.executeRequest(pdbRequest);
+ resultList = pdbRestClient.executeRequest(pdbRequest);
} catch (Exception e)
{
e.printStackTrace();
}
}
- public void loadLocalCachedPDBEntries()
+ protected void loadLocalCachedPDBEntries()
{
ArrayList<CachedPDB> entries = new ArrayList<>();
for (SequenceI seq : selectedSequences)
* @return the built query string
*/
- public static String buildQuery(SequenceI seq)
+ static String buildQuery(SequenceI seq)
{
boolean isPDBRefsFound = false;
boolean isUniProtRefsFound = false;
}
}
- if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
+ List<DBRefEntry> refs = seq.getDBRefs();
+ if (refs != null && refs.size() != 0)
{
- for (DBRefEntry dbRef : seq.getDBRefs())
+ for (int ib = 0, nb = refs.size(); ib < nb; ib++)
{
+ DBRefEntry dbRef = refs.get(ib);
if (isValidSeqName(getDBRefId(dbRef))
&& queryBuilder.length() < MAX_QLENGTH)
{
* @param seqName
* @return
*/
- public static boolean isValidSeqName(String seqName)
+ static boolean isValidSeqName(String seqName)
{
// System.out.println("seqName : " + seqName);
String ignoreList = "pdb,uniprot,swiss-prot";
return true;
}
- public static String getDBRefId(DBRefEntry dbRef)
+ static String getDBRefId(DBRefEntry dbRef)
{
String ref = dbRef.getAccessionId().replaceAll("GO:", "");
return ref;
* @param fieldToFilterBy
* the field to filter by
*/
- public void filterResultSet(final String fieldToFilterBy)
+ void filterResultSet(final String fieldToFilterBy)
{
Thread filterThread = new Thread(new Runnable()
{
public void run()
{
long startTime = System.currentTimeMillis();
- pdbRestCleint = PDBFTSRestClient.getInstance();
+ pdbRestClient = PDBFTSRestClient.getInstance();
lbl_loading.setVisible(true);
Collection<FTSDataColumnI> wantedFields = pdbDocFieldPrefs
.getStructureSummaryFields();
FTSRestResponse resultList;
try
{
- resultList = pdbRestCleint.executeRequest(pdbRequest);
+ resultList = pdbRestClient.executeRequest(pdbRequest);
} catch (Exception e)
{
e.printStackTrace();
* Handles action event for btn_pdbFromFile
*/
@Override
- public void pdbFromFile_actionPerformed()
+ protected void pdbFromFile_actionPerformed()
{
+ // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and StructureChooser
+ // works
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
}
/**
- * Validates user selection and activates the view button if all parameters
- * are correct
+ * Validates user selection and enables the 'Add' and 'New View' buttons if
+ * all parameters are correct (the Add button will only be visible if there is
+ * at least one existing structure viewer open). This basically means at least
+ * one structure selected and no error messages.
+ * <p>
+ * The 'Superpose Structures' option is enabled if either more than one
+ * structure is selected, or the 'Add' to existing view option is enabled, and
+ * disabled if the only option is to open a new view of a single structure.
*/
@Override
- public void validateSelections()
+ protected void validateSelections()
{
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
- btn_view.setEnabled(false);
+ btn_add.setEnabled(false);
String currentView = selectedFilterOpt.getView();
+ int selectedCount = 0;
if (currentView == VIEWS_FILTER)
{
- if (getResultTable().getSelectedRows().length > 0)
+ selectedCount = getResultTable().getSelectedRows().length;
+ if (selectedCount > 0)
{
- btn_view.setEnabled(true);
+ btn_add.setEnabled(true);
}
}
else if (currentView == VIEWS_LOCAL_PDB)
{
- if (tbl_local_pdb.getSelectedRows().length > 0)
+ selectedCount = tbl_local_pdb.getSelectedRows().length;
+ if (selectedCount > 0)
{
- btn_view.setEnabled(true);
+ btn_add.setEnabled(true);
}
}
else if (currentView == VIEWS_ENTER_ID)
{
validateAssociationFromFile();
}
+
+ btn_newView.setEnabled(btn_add.isEnabled());
+
+ /*
+ * enable 'Superpose' option if more than one structure is selected,
+ * or there are view(s) available to add structure(s) to
+ */
+ chk_superpose
+ .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0);
}
/**
* Validates inputs from the Manual PDB entry panel
*/
- public void validateAssociationEnterPdb()
+ protected void validateAssociationEnterPdb()
{
AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
.getCmb_assSeq().getSelectedItem();
txt_search.setEnabled(true);
if (isValidPBDEntry)
{
- btn_view.setEnabled(true);
+ btn_add.setEnabled(true);
lbl_pdbManualFetchStatus.setToolTipText("");
lbl_pdbManualFetchStatus.setIcon(goodImage);
}
/**
* Validates inputs for the manual PDB file selection options
*/
- public void validateAssociationFromFile()
+ protected void validateAssociationFromFile()
{
AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
.getCmb_assSeq().getSelectedItem();
btn_pdbFromFile.setEnabled(true);
if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
{
- btn_view.setEnabled(true);
+ btn_add.setEnabled(true);
lbl_fromFileStatus.setIcon(goodImage);
}
}
}
@Override
- public void cmbAssSeqStateChanged()
+ protected void cmbAssSeqStateChanged()
{
validateSelections();
}
}
return found;
}
+
+ /**
+ * Handles the 'New View' action
+ */
+ @Override
+ protected void newView_ActionPerformed()
+ {
+ targetView.setSelectedItem(null);
+ showStructures(false);
+ }
+
/**
- * Handles action event for btn_ok
+ * Handles the 'Add to existing viewer' action
*/
@Override
- public void ok_ActionPerformed()
+ protected void add_ActionPerformed()
{
showStructures(false);
}
/**
* 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);
return foundEntry;
}
- public StructureViewer getTargetedStructureViewer(
- StructureSelectionManager ssm)
+ /**
+ * Answers a structure viewer (new or existing) configured to superimpose
+ * added structures or not according to the user's choice
+ *
+ * @return
+ */
+ StructureViewer getTargetedStructureViewer()
{
- Object _sv = targetView.getSelectedItem();
+ final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+ Object sv = (targetView == null ? null : targetView.getSelectedItem());
- if (_sv == null)
- {
- return new StructureViewer(ssm);
- } else {
- return (StructureViewer) _sv;
- }
+ return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
}
- private StructureViewer launchStructureViewer(
- StructureSelectionManager ssm,
- final PDBEntry[] pdbEntriesToView,
- final AlignmentPanel alignPanel, SequenceI[] sequences)
- {
- long progressId = sequences.hashCode();
- setProgressBar(MessageManager
- .getString("status.launching_3d_structure_viewer"), progressId);
- final StructureViewer sViewer = getTargetedStructureViewer(ssm);
-
- 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().size() == 0)
- {
- 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 = new SequenceI[y];
- int x = 0;
- for (SequenceI fSeq : seqsWithoutSourceDBRef)
- {
- seqWithoutSrcDBRef[x++] = fSeq;
- }
-
- 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);
- sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
- }
- else
- {
- setProgressBar(MessageManager.formatMessage(
- "status.fetching_3d_structures_for",
- pdbEntriesToView[0].getId()),progressId);
- sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
- }
- setProgressBar(null, progressId);
- // remember the last viewer we used...
- lastTargetedView = sViewer;
- return sViewer;
+ /**
+ * Adds PDB structures to a new or existing structure viewer
+ *
+ * @param ap
+ * @param pdbEntriesToView
+ * @param sequences
+ * @param superimpose
+ * @return viewer
+ */
+ protected StructureViewer launchStructureViewer(
+ AlignmentPanel ap, PDBEntry[] pdbEntriesToView,
+ SequenceI[] selectedSeqs)
+ {
+ boolean superimpose = chk_superpose.isSelected();
+ /*
+ * remember user's choice of superimpose or not
+ */
+ Cache.setProperty(AUTOSUPERIMPOSE,
+ Boolean.valueOf(superimpose).toString());
+ return StructureViewer.launchStructureViewer(ap, pdbEntriesToView, selectedSeqs,
+ superimpose, getTargetedStructureViewer(), progressBar);
}
/**
* a unique sequence when more than one sequence selection is made.
*/
@Override
- public void populateCmbAssociateSeqOptions(
+ protected void populateCmbAssociateSeqOptions(
JComboBox<AssociateSeqOptions> cmb_assSeq,
JLabel lbl_associateSeq)
{
}
}
- public boolean isStructuresDiscovered()
+ protected boolean isStructuresDiscovered()
{
return discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty();
}
- public Collection<FTSData> getDiscoveredStructuresSet()
- {
- return discoveredStructuresSet;
- }
+ protected int PDB_ID_MIN = 3;// or: (Jalview.isJS() ? 3 : 1); // Bob proposes this.
+ // Doing a search for "1" or "1c" is valuable?
+ // Those work but are enormously slow.
@Override
protected void txt_search_ActionPerformed()
{
+ String text = txt_search.getText().trim();
+ if (text.length() >= PDB_ID_MIN)
+ {
new Thread()
{
- @Override
+
+ @Override
public void run()
{
errorWarning.setLength(0);
isValidPBDEntry = false;
- if (txt_search.getText().length() > 0)
+ if (text.length() > 0)
{
- String searchTerm = txt_search.getText().toLowerCase();
+ String searchTerm = text.toLowerCase();
searchTerm = searchTerm.split(":")[0];
// System.out.println(">>>>> search term : " + searchTerm);
List<FTSDataColumnI> wantedFields = new ArrayList<>();
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(searchTerm + ")");
pdbRequest.setAssociatedSequence(selectedSequence);
- pdbRestCleint = PDBFTSRestClient.getInstance();
- wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
+ pdbRestClient = PDBFTSRestClient.getInstance();
+ wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
FTSRestResponse resultList;
try
{
- resultList = pdbRestCleint.executeRequest(pdbRequest);
+ resultList = pdbRestClient.executeRequest(pdbRequest);
} catch (Exception e)
{
errorWarning.append(e.getMessage());
}
}.start();
}
+ }
@Override
- public void tabRefresh()
+ protected void tabRefresh()
{
if (selectedSequences != null)
{
@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