*/
package jalview.structure;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.IdentityHashMap;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Vector;
+
import jalview.analysis.AlignSeq;
import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.OrderCommand;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JmolParser;
import jalview.gui.IProgressIndicator;
+import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.ws.sifts.SiftsClient;
import jalview.ws.sifts.SiftsException;
import jalview.ws.sifts.SiftsSettings;
-
-import java.io.PrintStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.IdentityHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Vector;
-
-import MCview.Atom;
-import MCview.PDBChain;
-import MCview.PDBfile;
+import mc_view.Atom;
+import mc_view.PDBChain;
+import mc_view.PDBfile;
public class StructureSelectionManager
{
static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
- private List<StructureMapping> mappings = new ArrayList<StructureMapping>();
+ private List<StructureMapping> mappings = new ArrayList<>();
private boolean processSecondaryStructure = false;
private boolean addTempFacAnnot = false;
- private IProgressIndicator progressIndicator;
-
- private SiftsClient siftsClient = null;
-
- private long progressSessionId;
-
/*
* Set of any registered mappings between (dataset) sequences.
*/
- private List<AlignedCodonFrame> seqmappings = new ArrayList<AlignedCodonFrame>();
+ private List<AlignedCodonFrame> seqmappings = new ArrayList<>();
- private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
+ private List<CommandListener> commandListeners = new ArrayList<>();
- private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
+ private List<SelectionListener> sel_listeners = new ArrayList<>();
/**
* @return true if will try to use external services for processing secondary
}
else
{
- System.err.println("reportMapping: There are " + mappings.size()
- + " mappings.");
+ System.err.println(
+ "reportMapping: There are " + mappings.size() + " mappings.");
int i = 0;
for (StructureMapping sm : mappings)
{
* map between the PDB IDs (or structure identifiers) used by Jalview and the
* absolute filenames for PDB data that corresponds to it
*/
- Map<String, String> pdbIdFileName = new HashMap<String, String>();
+ Map<String, String> pdbIdFileName = new HashMap<>();
- Map<String, String> pdbFileNameId = new HashMap<String, String>();
+ Map<String, String> pdbFileNameId = new HashMap<>();
public void registerPDBFile(String idForFile, String absoluteFile)
{
{
if (instances != null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_structure_selection_manager_null"),
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_structure_selection_manager_null"),
new NullPointerException(MessageManager
.getString("exception.ssm_context_is_null")));
}
}
if (instances == null)
{
- instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager>();
+ instances = new java.util.IdentityHashMap<>();
}
StructureSelectionManager instance = instances.get(context);
if (instance == null)
}
/**
- * Returns the file name for a mapped PDB id (or null if not mapped).
+ * Returns the filename the PDB id is already mapped to if known, or null if
+ * it is not mapped
*
* @param pdbid
* @return
{
for (StructureMapping sm : mappings)
{
- if (sm.getPdbId().equals(pdbid))
+ if (sm.getPdbId().equalsIgnoreCase(pdbid))
{
return sm.pdbfile;
}
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile setMapping(SequenceI[] sequence,
- String[] targetChains, String pdbFile, DataSourceType protocol)
+ String[] targetChains, String pdbFile, DataSourceType protocol,
+ IProgressIndicator progress)
{
- return setMapping(true, sequence, targetChains, pdbFile, protocol);
+ return computeMapping(true, sequence, targetChains, pdbFile, protocol,
+ progress);
+ }
+
+ /**
+ * Import a single structure file and register sequence structure mappings for
+ * broadcasting colouring, mouseovers and selection events (convenience
+ * wrapper).
+ *
+ * @param forStructureView
+ * when true, record the mapping for use in mouseOvers
+ * @param sequence
+ * - one or more sequences to be mapped to pdbFile
+ * @param targetChains
+ * - optional chain specification for mapping each sequence to pdb
+ * (may be nill, individual elements may be nill)
+ * @param pdbFile
+ * - structure data resource
+ * @param protocol
+ * - how to resolve data from resource
+ * @return null or the structure data parsed as a pdb file
+ */
+ synchronized public StructureFile setMapping(boolean forStructureView,
+ SequenceI[] sequenceArray, String[] targetChainIds,
+ String pdbFile, DataSourceType sourceType)
+ {
+ return computeMapping(forStructureView, sequenceArray, targetChainIds,
+ pdbFile, sourceType, null);
}
/**
* create sequence structure mappings between each sequence and the given
- * pdbFile (retrieved via the given protocol).
+ * pdbFile (retrieved via the given protocol). Either constructs a mapping
+ * using NW alignment or derives one from any available SIFTS mapping data.
*
* @param forStructureView
* when true, record the mapping for use in mouseOvers
* - one or more sequences to be mapped to pdbFile
* @param targetChainIds
* - optional chain specification for mapping each sequence to pdb
- * (may be nill, individual elements may be nill)
+ * (may be nill, individual elements may be nill) - JBPNote: JAL-2693
+ * - this should be List<List<String>>, empty lists indicate no
+ * predefined mappings
* @param pdbFile
* - structure data resource
* @param sourceType
* - how to resolve data from resource
+ * @param IProgressIndicator
+ * reference to UI component that maintains a progress bar for the
+ * mapping operation
* @return null or the structure data parsed as a pdb file
*/
- synchronized public StructureFile setMapping(boolean forStructureView,
- SequenceI[] sequenceArray, String[] targetChainIds,
- String pdbFile, DataSourceType sourceType)
+ synchronized public StructureFile computeMapping(
+ boolean forStructureView, SequenceI[] sequenceArray,
+ String[] targetChainIds, String pdbFile, DataSourceType sourceType,
+ IProgressIndicator progress)
{
- /*
- * There will be better ways of doing this in the future, for now we'll use
- * the tried and tested MCview pdb mapping
+ long progressSessionId = System.currentTimeMillis() * 3;
+
+ /**
+ * do we extract and transfer annotation from 3D data ?
*/
- boolean parseSecStr = processSecondaryStructure;
- if (isPDBFileRegistered(pdbFile))
- {
- for (SequenceI sq : sequenceArray)
- {
- SequenceI ds = sq;
- while (ds.getDatasetSequence() != null)
- {
- ds = ds.getDatasetSequence();
- }
- ;
- if (ds.getAnnotation() != null)
- {
- for (AlignmentAnnotation ala : ds.getAnnotation())
- {
- // false if any annotation present from this structure
- // JBPNote this fails for jmol/chimera view because the *file* is
- // passed, not the structure data ID -
- if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
- {
- parseSecStr = false;
- }
- }
- }
- }
- }
+ // FIXME: possibly should just delete
+
+ boolean parseSecStr = processSecondaryStructure
+ ? isStructureFileProcessed(pdbFile, sequenceArray)
+ : false;
+
StructureFile pdb = null;
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
- pdb = new JmolParser(pdbFile, sourceType);
-
+ // FIXME if sourceType is not null, we've lost data here
+ sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
+ pdb = new JmolParser(false, pdbFile, sourceType);
+ pdb.addSettings(parseSecStr && processSecondaryStructure,
+ parseSecStr && addTempFacAnnot,
+ parseSecStr && secStructServices);
+ pdb.doParse();
if (pdb.getId() != null && pdb.getId().trim().length() > 0
&& DataSourceType.FILE == sourceType)
{
registerPDBFile(pdb.getId().trim(), pdbFile);
}
// if PDBId is unavailable then skip SIFTS mapping execution path
- isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable();
+ // TODO: JAL-3868 need to know if structure is actually from
+ // PDB (has valid PDB ID and has provenance suggesting it
+ // actually came from PDB)
+ boolean isProtein = false;
+ for (SequenceI s:sequenceArray) {
+ if (s.isProtein()) {
+ isProtein = true;
+ break;
+ }
+ }
+ isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable() && !pdb.getId().startsWith("AF-") && isProtein;
} catch (Exception ex)
{
ex.printStackTrace();
return null;
}
-
+ /*
+ * sifts client - non null if SIFTS mappings are to be used
+ */
+ SiftsClient siftsClient = null;
try
{
if (isMapUsingSIFTs)
} catch (SiftsException e)
{
isMapUsingSIFTs = false;
- e.printStackTrace();
+ Cache.error("SIFTS mapping failed", e);
+ Cache.error("Falling back on Needleman & Wunsch alignment");
+ siftsClient = null;
}
String targetChainId;
}
else if (seq.getName().indexOf("|") > -1)
{
- targetChainId = seq.getName().substring(
- seq.getName().lastIndexOf("|") + 1);
+ targetChainId = seq.getName()
+ .substring(seq.getName().lastIndexOf("|") + 1);
if (targetChainId.length() > 1)
{
if (targetChainId.trim().length() == 0)
* Attempt pairwise alignment of the sequence with each chain in the PDB,
* and remember the highest scoring chain
*/
- int max = -10;
+ float max = -10;
AlignSeq maxAlignseq = null;
String maxChainId = " ";
PDBChain maxChain = null;
pdbFile = "INLINE" + pdb.getId();
}
- List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+ List<StructureMapping> seqToStrucMapping = new ArrayList<>();
if (isMapUsingSIFTs && seq.isProtein())
{
- setProgressBar(null);
- setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_sifts"));
+ if (progress!=null) {
+ progress.setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_sifts"),
+ progressSessionId);
+ }
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
if (targetChainId != null && !targetChainId.trim().isEmpty())
try
{
siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
- pdb, maxChain, sqmpping, maxAlignseq);
+ pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
seqToStrucMapping.add(siftsMapping);
- maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
- // "IEA:SIFTS" ?
- maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
+ maxChain.makeExactMapping(siftsMapping, seq);
+ maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId().toLowerCase(Locale.ROOT));
+ maxChain.transferResidueAnnotation(siftsMapping, null);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
} catch (SiftsException e)
{
// fall back to NW alignment
- System.err.println(e.getMessage());
+ Cache.error(e.getMessage());
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
targetChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+ maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is
+ // this
// "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
}
else
{
- List<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+ List<StructureMapping> foundSiftsMappings = new ArrayList<>();
for (PDBChain chain : pdb.getChains())
{
+ StructureMapping siftsMapping = null;
try
{
- StructureMapping siftsMapping = getStructureMapping(seq,
- pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
+ siftsMapping = getStructureMapping(seq,
+ pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq,
+ siftsClient);
foundSiftsMappings.add(siftsMapping);
+ chain.makeExactMapping(siftsMapping, seq);
+ chain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId().toLowerCase(Locale.ROOT));// FIXME: is this
+ // "IEA:SIFTS" ?
+ chain.transferResidueAnnotation(siftsMapping, null);
} catch (SiftsException e)
{
System.err.println(e.getMessage());
}
+ catch (Exception e)
+ {
+ System.err
+ .println(
+ "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
+ System.err.println(e.getMessage());
+ }
}
if (!foundSiftsMappings.isEmpty())
{
seqToStrucMapping.addAll(foundSiftsMappings);
- maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
- // "IEA:SIFTS" ?
- maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
- sqmpping);
ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0));
}
else
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
maxChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
- maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+ maxChain.transferRESNUMFeatures(seq, null,pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is this
// "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
}
else
{
- setProgressBar(null);
- setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_nw_alignment"));
- StructureMapping nwMapping = getNWMappings(seq, pdbFile,
- maxChainId, maxChain, pdb, maxAlignseq);
+ if (progress != null)
+ {
+ progress.setProgressBar(MessageManager
+ .getString("status.obtaining_mapping_with_nw_alignment"),
+ progressSessionId);
+ }
+ StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId,
+ maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
-
}
-
if (forStructureView)
{
- mappings.addAll(seqToStrucMapping);
+ for (StructureMapping sm : seqToStrucMapping)
+ {
+ addStructureMapping(sm); // not addAll!
+ }
+ }
+ if (progress != null)
+ {
+ progress.setProgressBar(null, progressSessionId);
}
}
return pdb;
}
+ /**
+ * check if we need to extract secondary structure from given pdbFile and
+ * transfer to sequences
+ *
+ * @param pdbFile
+ * @param sequenceArray
+ * @return
+ */
+ private boolean isStructureFileProcessed(String pdbFile,
+ SequenceI[] sequenceArray)
+ {
+ boolean parseSecStr = true;
+ if (isPDBFileRegistered(pdbFile))
+ {
+ for (SequenceI sq : sequenceArray)
+ {
+ SequenceI ds = sq;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+ ;
+ if (ds.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation ala : ds.getAnnotation())
+ {
+ // false if any annotation present from this structure
+ // JBPNote this fails for jmol/chimera view because the *file* is
+ // passed, not the structure data ID -
+ if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
+ {
+ parseSecStr = false;
+ }
+ }
+ }
+ }
+ }
+ return parseSecStr;
+ }
+
public void addStructureMapping(StructureMapping sm)
{
- mappings.add(sm);
+ if (!mappings.contains(sm))
+ {
+ mappings.add(sm);
+ }
}
/**
* @param maxChain
* @param sqmpping
* @param maxAlignseq
+ * @param siftsClient
+ * client for retrieval of SIFTS mappings for this structure
* @return
* @throws SiftsException
*/
private StructureMapping getStructureMapping(SequenceI seq,
String pdbFile, String targetChainId, StructureFile pdb,
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
- AlignSeq maxAlignseq) throws SiftsException
+ AlignSeq maxAlignseq, SiftsClient siftsClient) throws SiftsException
{
StructureMapping curChainMapping = siftsClient
.getSiftsStructureMapping(seq, pdbFile, targetChainId);
PDBChain chain = pdb.findChain(targetChainId);
if (chain != null)
{
- chain.transferResidueAnnotation(curChainMapping, sqmpping);
+ chain.transferResidueAnnotation(curChainMapping, null);
}
} catch (Exception e)
{
AlignSeq maxAlignseq)
{
final StringBuilder mappingDetails = new StringBuilder(128);
- mappingDetails.append(NEWLINE).append(
- "Sequence \u27f7 Structure mapping details");
+ mappingDetails.append(NEWLINE)
+ .append("Sequence \u27f7 Structure mapping details");
mappingDetails.append(NEWLINE);
mappingDetails
.append("Method: inferred with Needleman & Wunsch alignment");
.append(" ");
mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
mappingDetails.append(NEWLINE).append("SEQ start/end ");
- mappingDetails.append(
- String.valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
+ mappingDetails
+ .append(String
+ .valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
.append(" ");
- mappingDetails.append(String.valueOf(maxAlignseq.seq1end
- + (seq.getStart() - 1)));
+ mappingDetails.append(
+ String.valueOf(maxAlignseq.seq1end + (seq.getStart() - 1)));
mappingDetails.append(NEWLINE);
maxChain.makeExactMapping(maxAlignseq, seq);
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
- maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferRESNUMFeatures(seq, null, pdb.getId().toLowerCase(Locale.ROOT));
- HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
+ HashMap<Integer, int[]> mapping = new HashMap<>();
int resNum = -10000;
int index = 0;
char insCode = ' ';
insCode = tmp.insCode;
if (tmp.alignmentMapping >= -1)
{
- mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber,
- tmp.atomIndex });
+ mapping.put(tmp.alignmentMapping + 1,
+ new int[]
+ { tmp.resNumber, tmp.atomIndex });
}
}
* Remove mappings to the closed listener's PDB files, but first check if
* another listener is still interested
*/
- List<String> pdbs = new ArrayList<String>(Arrays.asList(pdbfiles));
+ List<String> pdbs = new ArrayList<>(Arrays.asList(pdbfiles));
StructureListener sl;
for (int i = 0; i < listeners.size(); i++)
if (listeners.elementAt(i) instanceof StructureListener)
{
sl = (StructureListener) listeners.elementAt(i);
- for (String pdbfile : sl.getPdbFile())
+ for (String pdbfile : sl.getStructureFiles())
{
pdbs.remove(pdbfile);
}
*/
if (pdbs.size() > 0)
{
- List<StructureMapping> tmp = new ArrayList<StructureMapping>();
+ List<StructureMapping> tmp = new ArrayList<>();
for (StructureMapping sm : mappings)
{
if (!pdbs.contains(sm.pdbfile))
* @param pdbResNum
* @param chain
* @param pdbfile
+ * @return
*/
- public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
+ public String mouseOverStructure(int pdbResNum, String chain,
+ String pdbfile)
{
AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
List<AtomSpec> atoms = Collections.singletonList(atomSpec);
- mouseOverStructure(atoms);
+ return mouseOverStructure(atoms);
}
/**
*
* @param atoms
*/
- public void mouseOverStructure(List<AtomSpec> atoms)
+ public String mouseOverStructure(List<AtomSpec> atoms)
{
if (listeners == null)
{
// old or prematurely sent event
- return;
+ return null;
}
boolean hasSequenceListener = false;
for (int i = 0; i < listeners.size(); i++)
}
if (!hasSequenceListener)
{
- return;
+ return null;
}
- SearchResultsI results = findAlignmentPositionsForStructurePositions(atoms);
+ SearchResultsI results = findAlignmentPositionsForStructurePositions(
+ atoms);
+ String result = null;
for (Object li : listeners)
{
if (li instanceof SequenceListener)
{
- ((SequenceListener) li).highlightSequence(results);
+ String s = ((SequenceListener) li).highlightSequence(results);
+ if (s != null)
+ {
+ result = s;
+ }
}
}
+ return result;
}
/**
&& sm.pdbchain.equals(atom.getChain()))
{
int indexpos = sm.getSeqPos(atom.getPdbResNum());
- if (lastipos != indexpos && lastseq != sm.sequence)
+ if (lastipos != indexpos || lastseq != sm.sequence)
{
results.addResult(sm.sequence, indexpos, indexpos);
lastipos = indexpos;
return;
}
int atomNo;
- List<AtomSpec> atoms = new ArrayList<AtomSpec>();
+ List<AtomSpec> atoms = new ArrayList<>();
for (StructureMapping sm : mappings)
{
- if (sm.sequence == seq
- || sm.sequence == seq.getDatasetSequence()
+ if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()
|| (sm.sequence.getDatasetSequence() != null && sm.sequence
.getDatasetSequence() == seq.getDatasetSequence()))
{
if (atomNo > 0)
{
- atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
- .getPDBResNum(index), atomNo));
+ atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain,
+ sm.getPDBResNum(index), atomNo));
}
}
}
public StructureMapping[] getMapping(String pdbfile)
{
- List<StructureMapping> tmp = new ArrayList<StructureMapping>();
+ List<StructureMapping> tmp = new ArrayList<>();
for (StructureMapping sm : mappings)
{
if (sm.pdbfile.equals(pdbfile))
StringBuilder sb = new StringBuilder(64);
for (StructureMapping sm : mappings)
{
- if (sm.pdbfile.equals(pdbfile) && seqs.contains(sm.sequence))
+ if (Platform.pathEquals(sm.pdbfile, pdbfile)
+ && seqs.contains(sm.sequence))
{
sb.append(sm.mappingDetails);
sb.append(NEWLINE);
public synchronized void sendSelection(
jalview.datamodel.SequenceGroup selection,
- jalview.datamodel.ColumnSelection colsel, SelectionSource source)
+ jalview.datamodel.ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source)
{
for (SelectionListener slis : sel_listeners)
{
if (slis != source)
{
- slis.selection(selection, colsel, source);
+ slis.selection(selection, colsel, hidden, source);
}
}
}
- Vector<AlignmentViewPanelListener> view_listeners = new Vector<AlignmentViewPanelListener>();
+ Vector<AlignmentViewPanelListener> view_listeners = new Vector<>();
public synchronized void sendViewPosition(
jalview.api.AlignmentViewPanel source, int startRes, int endRes,
instances.remove(jalviewLite);
try
{
- mnger.finalize();
+ /* bsoares 2019-03-20 finalize deprecated, no apparent external
+ * resources to close
+ */
+ // mnger.finalize();
} catch (Throwable x)
{
}
{
if (command instanceof EditCommand)
{
- return MappingUtils.mapEditCommand((EditCommand) command, undo,
- mapTo, gapChar, seqmappings);
+ return MappingUtils.mapEditCommand((EditCommand) command, undo, mapTo,
+ gapChar, seqmappings);
}
else if (command instanceof OrderCommand)
{
return null;
}
- public IProgressIndicator getProgressIndicator()
- {
- return progressIndicator;
- }
-
- public void setProgressIndicator(IProgressIndicator progressIndicator)
- {
- this.progressIndicator = progressIndicator;
- }
-
- public long getProgressSessionId()
- {
- return progressSessionId;
- }
-
- public void setProgressSessionId(long progressSessionId)
- {
- this.progressSessionId = progressSessionId;
- }
-
- public void setProgressBar(String message)
- {
- if (progressIndicator == null)
- {
- return;
- }
- progressIndicator.setProgressBar(message, progressSessionId);
- }
-
public List<AlignedCodonFrame> getSequenceMappings()
{
return seqmappings;
git://source.jalview.org / jalview.git / blobdiff