/*
* 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 .
* 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;
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
*/
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)
{
// jalview.bin.Console.outPrintln("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 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 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 discoveredStructuresSet,
Collection 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 discoveredStructuresSet)
{
return FTSRestResponse.getTableModel(getLastFTSRequest(),
discoveredStructuresSet);
}
protected abstract FTSRestRequest getLastFTSRequest();
public abstract PDBEntry[] collectSelectedRows(JTable restable,
int[] selectedRows, List 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 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 xtantOptions, Collection lastFTSData)
{
// TODO Auto-generated method stub
}
}