+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.gui.structurechooser;
+import java.util.Locale;
+
import java.util.Collection;
import java.util.List;
import java.util.Objects;
public static StructureChooserQuerySource getPDBfts()
{
- return new PDBStructureChooserQuerySource();
+ return new PDBStructureChooserQuerySource();
}
public static StructureChooserQuerySource getTDBfts()
return docFieldPrefs;
}
-
/**
* Builds a query string for a given sequences using its DBRef entries
*
*/
public abstract String buildQuery(SequenceI seq);
-
/**
* Remove the following special characters from input string +, -, &, !, (, ),
{
return false;
}
- seqName = seqName.toLowerCase();
+ seqName = seqName.toLowerCase(Locale.ROOT);
for (String ignoredEntry : ignoreList.split(","))
{
if (seqName.contains(ignoredEntry))
*
* @param seq
* - seq to generate a query for
- * @param discoveredStructuresSet - existing set of entries - allows client side selection
+ * @param discoveredStructuresSet
+ * - existing set of entries - allows client side selection
* @param wantedFields
* - fields to retrieve
* @param selectedFilterOpt
* @throws Exception
*/
public abstract FTSRestResponse selectFirstRankedQuery(SequenceI seq,
- Collection<FTSData> discoveredStructuresSet, Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
+ Collection<FTSData> discoveredStructuresSet,
+ Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
boolean b) throws Exception;
/**
/**
* @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
+ * - 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);
+ 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
*/
SequenceI[] selectedSeqs)
{
ThreeDBStructureChooserQuerySource tdbSource = new ThreeDBStructureChooserQuerySource();
- boolean hasUniprot=false,hasCanonical=false;
- boolean hasNA=false,hasProtein=false;
- int protWithoutUni=0;
+ 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());
+ int refsAvailable = ThreeDBStructureChooserQuerySource
+ .checkUniprotRefs(seq.getDBRefs());
if (refsAvailable > -2)
{
if (refsAvailable > -1)
+ {
hasCanonical = true;
+ }
+ else
+ {
+ protWithoutCanon++;
+ }
+ hasUniprot = true;
+ }
+ else
+ {
+ protWithoutUni++;
+
}
- hasUniprot = true;
- }
- else
- {
- protWithoutUni++;
}
}
//
// logic: all canonicals - no fetchdb
- // some uniprot no canonicals: prompt do fetchDb for remaining
- // no uniprot but protein: offer 3d-beacons search
+ // some uniprot no canonicals: defer to PDB, user can optionally fetch
//
- if (hasProtein && hasUniprot && !hasNA)
+ if (hasProtein && hasCanonical && !hasNA && protWithoutCanon == 0
+ && protWithoutUni == 0)
+
{
return tdbSource;
}
}
/**
- * some filter options may mean the original query needs to be executed again.
+ * 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
-
- }}
\ No newline at end of file
+
+ }
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff