import java.util.Set;
import javax.swing.JTable;
-import javax.swing.table.TableModel;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.jbgui.FilterOption;
+import jalview.struture.PDBEntryUtils;
import jalview.util.MessageManager;
/**
PDBFTSRestClient.getInstance());
}
-
+
/**
* Builds a query string for a given sequences using its DBRef entries
*
boolean isUniProtRefsFound = false;
StringBuilder queryBuilder = new StringBuilder();
Set<String> seqRefs = new LinkedHashSet<>();
-
+ SequenceI ds = seq.getDatasetSequence();
+ while (ds.getDatasetSequence()!=null) {
+ ds = ds.getDatasetSequence();
+ }
+
/*
* note PDBs as DBRefEntry so they are not duplicated in query
*/
Set<String> pdbids = new HashSet<>();
-
- if (seq.getAllPDBEntries() != null
- && queryBuilder.length() < MAX_QLENGTH)
+ if (queryBuilder.length() < MAX_QLENGTH)
{
- for (PDBEntry entry : seq.getAllPDBEntries())
+ Set<PDBEntry> gatheredEntries = PDBEntryUtils.gatherPDBEntries(seq, true);
+ for (PDBEntry entry : gatheredEntries)
{
if (isValidSeqName(entry.getId()))
{
pdbids.add(id);
}
}
- }
-
+ }
+
List<DBRefEntry> refs = seq.getDBRefs();
if (refs != null && refs.size() != 0)
{
}
}
}
-
+
if (!isPDBRefsFound && !isUniProtRefsFound)
{
String seqName = seq.getName();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
int idColumnIndex = -1;
- boolean fromTDB = true;
idColumnIndex = restable.getColumn("PDB Id").getModelIndex();
for (int row : selectedRows)
import java.util.Collections;
import java.util.Enumeration;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
+import java.util.Set;
import java.util.Vector;
import jalview.analysis.AlignSeq;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.structure.StructureImportSettings.TFType;
+import jalview.struture.PDBEntryUtils;
import jalview.util.MapList;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
{
ds = ds.getDatasetSequence();
}
-
+ List <PDBEntry> putativePDBe = PDBEntryUtils.selectPutativePDBe(seq,ds, pdb);
+
if (targetChainIds != null && targetChainIds[s] != null)
{
infChain = false;
targetChainId = targetChainIds[s];
}
- else if (seq.getName().indexOf("|") > -1)
- {
- targetChainId = seq.getName()
- .substring(seq.getName().lastIndexOf("|") + 1);
- if (targetChainId.length() > 1)
- {
- if (targetChainId.trim().length() == 0)
- {
- targetChainId = " ";
- }
- else
- {
- // not a valid chain identifier
- targetChainId = "";
- }
- }
- }
- else
- {
- targetChainId = "";
+ else {
+ targetChainId = PDBEntryUtils.inferChainId(seq);
}
/*
{
continue; // don't try to map chains don't match.
}
+ PDBEntry putativeChain = null;
+ if (!putativePDBe.isEmpty() && (putativeChain = PDBEntryUtils
+ .selectPutativePDBEntry(putativePDBe, chain)) == null)
+ {
+ continue;
+ }
// TODO: correctly determine sequence type for mixed na/peptide
// structures
final String type = chain.isNa ? AlignSeq.DNA : AlignSeq.PEP;
}
else
{
+ if (maxAlignseq.getS1Coverage()<0.15 && maxAlignseq.getS2Coverage()<0.15)
+ {
+ // skip this - the NW alignment is spurious
+ continue;
+ }
// Construct a needleman wunsch mapping instead.
if (progress != null)
{
--- /dev/null
+/*
+ * 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.struture;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import com.google.common.collect.Lists;
+
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.StructureFile;
+import mc_view.PDBChain;
+
+public class PDBEntryUtils
+{
+
+ public static String inferChainId(SequenceI seq)
+ {
+ String targetChainId;
+ if (seq.getName().indexOf("|") > -1)
+ {
+ targetChainId = seq.getName()
+ .substring(seq.getName().lastIndexOf("|") + 1);
+ if (targetChainId.length() > 1)
+ {
+ if (targetChainId.trim().length() == 0)
+ {
+ targetChainId = " ";
+ }
+ else
+ {
+ // not a valid chain identifier
+ targetChainId = "";
+ }
+ }
+ }
+ else
+ {
+ targetChainId = "";
+ }
+ return targetChainId;
+ }
+ protected static Pattern id_and_chain=Pattern.compile("(\\d[0-9A-Za-z]{3})[_:]?(.+)*");
+
+ public static List<PDBEntry> inferPDBEntry(SequenceI seq)
+ {
+ Matcher matcher = id_and_chain.matcher(seq.getName());
+ if (matcher.matches())
+ {
+ String id = matcher.group(1);
+ PDBEntry pdbe = new PDBEntry();
+ pdbe.setId(id);
+ if (matcher.groupCount() > 1)
+ {
+ pdbe.setChainCode(matcher.group(2));
+ }
+
+ return List.of(pdbe);
+ }
+ return List.of();
+ }
+
+
+ /**
+ * generate likely PDB IDs & chain codes from seq and ds that fit pdb
+ * @param seq
+ * @param ds
+ * @param pdb
+ * @return empty list or one or more PDBEntry which match pdb.getId()
+ */
+ public static List<PDBEntry> selectPutativePDBe(SequenceI seq,
+ SequenceI ds, StructureFile pdb)
+ {
+ List<PDBEntry> putativePDBe = new ArrayList<PDBEntry>();
+ Set<PDBEntry> possiblePDBe=PDBEntryUtils.gatherPDBEntries(seq,true);
+ for (PDBEntry infPDBe: possiblePDBe)
+ {
+ if (infPDBe.getId().equalsIgnoreCase(pdb.getId()))
+ {
+ putativePDBe.add(infPDBe);
+ }
+ }
+ return putativePDBe;
+ }
+
+
+ public static Set<PDBEntry> gatherPDBEntries(SequenceI seq,boolean inferFromName)
+ {
+ Set<PDBEntry> possiblePDBe=new HashSet<PDBEntry>();
+ while (seq!=null)
+ {
+ if (seq.getAllPDBEntries()!=null) {
+ possiblePDBe.addAll(seq.getAllPDBEntries());
+ }
+ if (inferFromName)
+ {
+ possiblePDBe.addAll(PDBEntryUtils.inferPDBEntry(seq));
+ }
+ seq = seq.getDatasetSequence();
+ }
+ return possiblePDBe;
+ }
+
+
+ public static PDBEntry selectPutativePDBEntry(List<PDBEntry> putativePDBe,
+ PDBChain chain)
+ {
+ if (putativePDBe.isEmpty())
+ {
+ return null;
+ }
+
+ // check if there's a chaincode
+ PDBEntry putativeEntry = null;
+ boolean hasChainCodes;
+ // check for a chaincode mapping
+ for (PDBEntry pdbe : putativePDBe)
+ {
+ if (pdbe.getChainCode() != null)
+ {
+ hasChainCodes = true;
+ if (pdbe.getChainCode().equals(chain.id))
+ {
+ putativeEntry = pdbe;
+ return putativeEntry;
+ }
+ }
+ }
+ return null;
+ }
+}
git://source.jalview.org / jalview.git / commitdiff