--- /dev/null
+package jalview.gui.structurechooser;
+
+import java.util.Locale;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Objects;
+import java.util.Vector;
+
+import javax.swing.JTable;
+import javax.swing.table.TableModel;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSDataColumnPreferences;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.jbgui.FilterOption;
+
+/**
+ * logic for querying sources of structural data for structures of sequences
+ *
+ * @author jprocter
+ *
+ * @param <T>
+ */
+public abstract class StructureChooserQuerySource
+{
+
+ protected FTSDataColumnPreferences docFieldPrefs;
+
+ /**
+ * max length of a GET URL (probably :( )
+ */
+ protected static int MAX_QLENGTH = 7820;
+
+ public StructureChooserQuerySource()
+ {
+ }
+
+ public static StructureChooserQuerySource getPDBfts()
+ {
+ return new PDBStructureChooserQuerySource();
+ }
+
+ public static StructureChooserQuerySource getTDBfts()
+ {
+ return new ThreeDBStructureChooserQuerySource();
+ }
+
+ public FTSDataColumnPreferences getDocFieldPrefs()
+ {
+ return docFieldPrefs;
+ }
+
+ public void setDocFieldPrefs(FTSDataColumnPreferences docFieldPrefs)
+ {
+ this.docFieldPrefs = docFieldPrefs;
+ }
+
+ public FTSDataColumnPreferences getInitialFieldPreferences()
+ {
+ return docFieldPrefs;
+ }
+
+ /**
+ * Builds a query string for a given sequences using its DBRef entries
+ *
+ * @param seq
+ * the sequences to build a query for
+ * @return the built query string
+ */
+
+ public abstract String buildQuery(SequenceI seq);
+
+ /**
+ * Remove the following special characters from input string +, -, &, !, (, ),
+ * {, }, [, ], ^, ", ~, *, ?, :, \
+ *
+ * @param seqName
+ * @return
+ */
+ public static String sanitizeSeqName(String seqName)
+ {
+ Objects.requireNonNull(seqName);
+ return seqName.replaceAll("\\[\\d*\\]", "")
+ .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
+ }
+
+ /**
+ * Ensures sequence ref names are not less than 3 characters and does not
+ * contain a database name
+ *
+ * @param seqName
+ * @return
+ */
+ static boolean isValidSeqName(String seqName)
+ {
+ // System.out.println("seqName : " + seqName);
+ String ignoreList = "pdb,uniprot,swiss-prot";
+ if (seqName.length() < 3)
+ {
+ return false;
+ }
+ if (seqName.contains(":"))
+ {
+ return false;
+ }
+ seqName = seqName.toLowerCase(Locale.ROOT);
+ for (String ignoredEntry : ignoreList.split(","))
+ {
+ if (seqName.contains(ignoredEntry))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ static String getDBRefId(DBRefEntry dbRef)
+ {
+ String ref = dbRef.getAccessionId().replaceAll("GO:", "");
+ return ref;
+ }
+
+ static PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
+ {
+ Objects.requireNonNull(id);
+ Objects.requireNonNull(pdbEntries);
+ PDBEntry foundEntry = null;
+ for (PDBEntry entry : pdbEntries)
+ {
+ if (entry.getId().equalsIgnoreCase(id))
+ {
+ return entry;
+ }
+ }
+ return foundEntry;
+ }
+
+ /**
+ * FTSRestClient specific query builder to recover associated structure data
+ * records for a sequence
+ *
+ * @param seq
+ * - seq to generate a query for
+ * @param wantedFields
+ * - fields to retrieve
+ * @param selectedFilterOpt
+ * - criterion for ranking results (e.g. resolution)
+ * @param b
+ * - sort ascending or descending
+ * @return
+ * @throws Exception
+ */
+ public abstract FTSRestResponse fetchStructuresMetaData(SequenceI seq,
+ Collection<FTSDataColumnI> wantedFields,
+ FilterOption selectedFilterOpt, boolean b) throws Exception;
+
+ /**
+ * FTSRestClient specific query builder to pick top ranked entry from a
+ * fetchStructuresMetaData query
+ *
+ * @param seq
+ * - seq to generate a query for
+ * @param discoveredStructuresSet
+ * - existing set of entries - allows client side selection
+ * @param wantedFields
+ * - fields to retrieve
+ * @param selectedFilterOpt
+ * - criterion for ranking results (e.g. resolution)
+ * @param b
+ * - sort ascending or descending
+ * @return
+ * @throws Exception
+ */
+ public abstract FTSRestResponse selectFirstRankedQuery(SequenceI seq,
+ Collection<FTSData> discoveredStructuresSet,
+ Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
+ boolean b) throws Exception;
+
+ /**
+ *
+ * @param discoveredStructuresSet
+ * @return the table model for the given result set for this engine
+ */
+ public TableModel getTableModel(
+ Collection<FTSData> discoveredStructuresSet)
+ {
+ return FTSRestResponse.getTableModel(getLastFTSRequest(),
+ discoveredStructuresSet);
+ }
+
+ protected abstract FTSRestRequest getLastFTSRequest();
+
+ public abstract PDBEntry[] collectSelectedRows(JTable restable,
+ int[] selectedRows, List<SequenceI> selectedSeqsToView);
+
+ /**
+ * @param VIEWS_FILTER
+ * - a String key that can be used by the caller to tag the returned
+ * filter options to distinguish them in a collection
+ * @return list of FilterOption - convention is that the last one in the list
+ * will be constructed with 'addSeparator==true'
+ */
+ public abstract List<FilterOption> getAvailableFilterOptions(
+ String VIEWS_FILTER);
+
+ /**
+ * construct a structure chooser query source for the given set of sequences
+ *
+ * @param selectedSeqs
+ * @return PDBe or 3DB query source
+ */
+ public static StructureChooserQuerySource getQuerySourceFor(
+ SequenceI[] selectedSeqs)
+ {
+ ThreeDBStructureChooserQuerySource tdbSource = new ThreeDBStructureChooserQuerySource();
+ boolean hasUniprot = false, hasCanonical = false;
+ boolean hasNA = false, hasProtein = false;
+ int protWithoutUni = 0;
+ int protWithoutCanon = 0;
+ for (SequenceI seq : selectedSeqs)
+ {
+ hasNA |= !seq.isProtein();
+ hasProtein |= seq.isProtein();
+ if (seq.isProtein())
+ {
+ int refsAvailable = ThreeDBStructureChooserQuerySource
+ .checkUniprotRefs(seq.getDBRefs());
+ if (refsAvailable > -2)
+ {
+ if (refsAvailable > -1)
+ {
+ hasCanonical = true;
+ } else {
+ protWithoutCanon++;
+ }
+ hasUniprot = true;
+ } else {
+ protWithoutUni++;
+
+ }
+ }
+ }
+ //
+ // logic: all canonicals - no fetchdb
+ // some uniprot no canonicals: defer to PDB, user can optionally fetch
+ //
+ if (hasProtein && hasCanonical && !hasNA && protWithoutCanon == 0 && protWithoutUni == 0)
+
+ {
+ return tdbSource;
+ }
+ return new PDBStructureChooserQuerySource();
+ }
+
+ /**
+ * some filter options may mean the original query needs to be executed again.
+ *
+ * @param selectedFilterOpt
+ * @return true if the fetchStructuresMetadata method needs to be called again
+ */
+ public abstract boolean needsRefetch(FilterOption selectedFilterOpt);
+
+ public void updateAvailableFilterOptions(String VIEWS_FILTER,
+ List<FilterOption> xtantOptions, Collection<FTSData> lastFTSData)
+ {
+ // TODO Auto-generated method stub
+
+ }
+}
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git://source.jalview.org / jalview.git / blobdiff