-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.structure;\r
-\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-import MCview.*;\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-\r
-public class StructureSelectionManager\r
-{\r
- static StructureSelectionManager instance;\r
- StructureMapping[] mappings;\r
- Hashtable mappingData = new Hashtable();\r
-\r
- public static StructureSelectionManager getStructureSelectionManager()\r
- {\r
- if (instance == null)\r
- {\r
- instance = new StructureSelectionManager();\r
- }\r
-\r
- return instance;\r
- }\r
-\r
- Vector listeners = new Vector();\r
- public void addStructureViewerListener(Object svl)\r
- {\r
- if (!listeners.contains(svl))\r
- {\r
- listeners.addElement(svl);\r
- }\r
- }\r
-\r
- public String alreadyMappedToFile(String pdbid)\r
- {\r
- if (mappings != null)\r
- {\r
- for (int i = 0; i < mappings.length; i++)\r
- {\r
- if (mappings[i].getPdbId().equals(pdbid))\r
- {\r
- return mappings[i].pdbfile;\r
- }\r
- }\r
- }\r
- return null;\r
- }\r
-\r
- /*\r
- There will be better ways of doing this in the future, for now we'll use\r
- the tried and tested MCview pdb mapping\r
- */\r
- public MCview.PDBfile setMapping(SequenceI[] sequence,\r
- String pdbFile,\r
- String protocol)\r
- {\r
- MCview.PDBfile pdb = null;\r
- try\r
- {\r
- pdb = new MCview.PDBfile(pdbFile, protocol);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- return null;\r
- }\r
-\r
- for (int s = 0; s < sequence.length; s++)\r
- {\r
- String targetChain = "";\r
-\r
- if (sequence[s].getName().indexOf("|") > -1)\r
- {\r
- targetChain = sequence[s].getName().substring(\r
- sequence[s].getName().lastIndexOf("|") + 1);\r
- }\r
-\r
- int max = -10;\r
- AlignSeq maxAlignseq = null;\r
- String maxChainId = " ";\r
- PDBChain maxChain = null;\r
-\r
- for (int i = 0; i < pdb.chains.size(); i++)\r
- {\r
- AlignSeq as = new AlignSeq(sequence[s],\r
- ( (PDBChain) pdb.chains.elementAt(i)).\r
- sequence,\r
- AlignSeq.PEP);\r
- as.calcScoreMatrix();\r
- as.traceAlignment();\r
- PDBChain chain = ( (PDBChain) pdb.chains.elementAt(i));\r
-\r
- if (as.maxscore > max\r
- || (as.maxscore == max && chain.id.equals(targetChain)))\r
- {\r
- maxChain = chain;\r
- max = as.maxscore;\r
- maxAlignseq = as;\r
- maxChainId = chain.id;\r
- }\r
- }\r
-\r
- final StringBuffer mappingDetails = new StringBuffer();\r
- mappingDetails.append("\n\nPDB Sequence is :\nSequence = " +\r
- maxChain.sequence.getSequenceAsString());\r
- mappingDetails.append("\nNo of residues = " +\r
- maxChain.residues.\r
- size() +\r
- "\n\n");\r
- PrintStream ps = new PrintStream(System.out)\r
- {\r
- public void print(String x)\r
- {\r
- mappingDetails.append(x);\r
- }\r
-\r
- public void println()\r
- {\r
- mappingDetails.append("\n");\r
- }\r
- };\r
-\r
- maxAlignseq.printAlignment(ps);\r
-\r
- mappingDetails.append("\nPDB start/end " + maxAlignseq.seq2start + " " +\r
- maxAlignseq.seq2end);\r
- mappingDetails.append("\nSEQ start/end "\r
- + (maxAlignseq.seq1start + sequence[s].getStart() - 1) +\r
- " "\r
- + (maxAlignseq.seq1end + sequence[s].getEnd() - 1));\r
-\r
- maxChain.makeExactMapping(maxAlignseq, sequence[s]);\r
-\r
- // maxChain.transferRESNUMFeatures(sequence[s], null);\r
-\r
- int[][] mapping = new int[sequence[s].getEnd() + 2][2];\r
- int resNum = -10000;\r
- int index = 0;\r
-\r
-\r
- do\r
- {\r
- Atom tmp = (Atom) maxChain.atoms.elementAt(index);\r
- if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)\r
- {\r
- resNum = tmp.resNumber;\r
- mapping[tmp.alignmentMapping+1][0] = tmp.resNumber;\r
- mapping[tmp.alignmentMapping+1][1] = tmp.atomIndex;\r
- }\r
-\r
- index++;\r
- }\r
- while(index < maxChain.atoms.size());\r
-\r
- if (mappings == null)\r
- {\r
- mappings = new StructureMapping[1];\r
- }\r
- else\r
- {\r
- StructureMapping[] tmp = new StructureMapping[mappings.length + 1];\r
- System.arraycopy(mappings, 0, tmp, 0, mappings.length);\r
- mappings = tmp;\r
- }\r
-\r
- if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))\r
- pdbFile = "INLINE"+pdb.id;\r
-\r
- mappings[mappings.length - 1]\r
- = new StructureMapping(sequence[s], pdbFile, pdb.id, maxChainId,\r
- mapping, mappingDetails.toString());\r
- }\r
- /////////\r
-\r
- return pdb;\r
- }\r
-\r
- public void removeStructureViewerListener(Object svl, String pdbfile)\r
- {\r
- listeners.removeElement(svl);\r
-\r
- boolean removeMapping = true;\r
-\r
- StructureListener sl;\r
- for (int i = 0; i < listeners.size(); i++)\r
- {\r
- if (listeners.elementAt(i) instanceof StructureListener)\r
- {\r
- sl = (StructureListener) listeners.elementAt(i);\r
- if (sl.getPdbFile().equals(pdbfile))\r
- {\r
- removeMapping = false;\r
- break;\r
- }\r
- }\r
- }\r
-\r
- if (removeMapping && mappings!=null)\r
- {\r
- Vector tmp = new Vector();\r
- for (int i = 0; i < mappings.length; i++)\r
- {\r
- if (!mappings[i].pdbfile.equals(pdbfile))\r
- {\r
- tmp.addElement(mappings[i]);\r
- }\r
- }\r
-\r
- mappings = new StructureMapping[tmp.size()];\r
- tmp.copyInto(mappings);\r
- }\r
- }\r
-\r
- public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)\r
- {\r
- SequenceListener sl;\r
- for (int i = 0; i < listeners.size(); i++)\r
- {\r
- if (listeners.elementAt(i) instanceof SequenceListener)\r
- {\r
- sl = (SequenceListener) listeners.elementAt(i);\r
-\r
- for (int j = 0; j < mappings.length; j++)\r
- {\r
- if (mappings[j].pdbfile.equals(pdbfile) &&\r
- mappings[j].pdbchain.equals(chain))\r
- {\r
- sl.highlightSequence(mappings[j].sequence,\r
- mappings[j].getSeqPos(pdbResNum));\r
- }\r
- }\r
-\r
- sl.highlightSequence(null, pdbResNum);\r
- }\r
- }\r
- }\r
-\r
- public void mouseOverSequence(SequenceI seq, int index)\r
- {\r
- StructureListener sl;\r
- int atomNo = 0;\r
- for (int i = 0; i < listeners.size(); i++)\r
- {\r
- if (listeners.elementAt(i) instanceof StructureListener)\r
- {\r
- sl = (StructureListener) listeners.elementAt(i);\r
-\r
- for (int j = 0; j < mappings.length; j++)\r
- {\r
- if (mappings[j].sequence == seq)\r
- {\r
- atomNo = mappings[j].getAtomNum(index);\r
-\r
- if (atomNo > 0)\r
- {\r
- sl.highlightAtom(atomNo,\r
- mappings[j].getPDBResNum(index),\r
- mappings[j].pdbchain,\r
- mappings[j].pdbfile);\r
- }\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- public void structureSelectionChanged()\r
- {\r
- StructureListener svl;\r
- for (int i = 0; i < listeners.size(); i++)\r
- {\r
- svl = (StructureListener) listeners.elementAt(i);\r
- }\r
- }\r
-\r
- public void sequenceSelectionChanged()\r
- {\r
- StructureListener svl;\r
- for (int i = 0; i < listeners.size(); i++)\r
- {\r
- svl = (StructureListener) listeners.elementAt(i);\r
- }\r
- }\r
-\r
- public void sequenceColoursChanged(Object source)\r
- {\r
- StructureListener sl;\r
- for (int i = 0; i < listeners.size(); i++)\r
- {\r
- if (listeners.elementAt(i) instanceof StructureListener)\r
- {\r
- sl = (StructureListener) listeners.elementAt(i);\r
- sl.updateColours(source);\r
- }\r
- }\r
- }\r
-\r
- public StructureMapping[] getMapping(String pdbfile)\r
- {\r
- Vector tmp = new Vector();\r
- for (int i = 0; i < mappings.length; i++)\r
- {\r
- if (mappings[i].pdbfile.equals(pdbfile))\r
- {\r
- tmp.addElement(mappings[i]);\r
- }\r
- }\r
-\r
- StructureMapping[] ret = new StructureMapping[tmp.size()];\r
- for (int i = 0; i < tmp.size(); i++)\r
- {\r
- ret[i] = (StructureMapping) tmp.elementAt(i);\r
- }\r
-\r
- return ret;\r
- }\r
-\r
- public String printMapping(String pdbfile)\r
- {\r
- StringBuffer sb = new StringBuffer();\r
- for (int i = 0; i < mappings.length; i++)\r
- {\r
- if (mappings[i].pdbfile.equals(pdbfile))\r
- {\r
- sb.append(mappings[i].mappingDetails);\r
- }\r
- }\r
-\r
- return sb.toString();\r
- }\r
-}\r
+/*
+ * 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.structure;
+
+import jalview.analysis.AlignSeq;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.OrderCommand;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
+import jalview.gui.IProgressIndicator;
+import jalview.io.AppletFormatAdapter;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+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.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
+
+import MCview.Atom;
+import MCview.PDBChain;
+import MCview.PDBfile;
+
+public class StructureSelectionManager
+{
+ public final static String NEWLINE = System.lineSeparator();
+
+ static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
+
+ private List<StructureMapping> mappings = new ArrayList<StructureMapping>();
+
+ private boolean processSecondaryStructure = false;
+
+ private boolean secStructServices = false;
+
+ private boolean addTempFacAnnot = false;
+
+ private IProgressIndicator progressIndicator;
+
+ private long progressSessionId;
+
+ /*
+ * Set of any registered mappings between (dataset) sequences.
+ */
+ public Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
+
+ private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
+
+ private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
+
+ /**
+ * @return true if will try to use external services for processing secondary
+ * structure
+ */
+ public boolean isSecStructServices()
+ {
+ return secStructServices;
+ }
+
+ /**
+ * control use of external services for processing secondary structure
+ *
+ * @param secStructServices
+ */
+ public void setSecStructServices(boolean secStructServices)
+ {
+ this.secStructServices = secStructServices;
+ }
+
+ /**
+ * flag controlling addition of any kind of structural annotation
+ *
+ * @return true if temperature factor annotation will be added
+ */
+ public boolean isAddTempFacAnnot()
+ {
+ return addTempFacAnnot;
+ }
+
+ /**
+ * set flag controlling addition of structural annotation
+ *
+ * @param addTempFacAnnot
+ */
+ public void setAddTempFacAnnot(boolean addTempFacAnnot)
+ {
+ this.addTempFacAnnot = addTempFacAnnot;
+ }
+
+ /**
+ *
+ * @return if true, the structure manager will attempt to add secondary
+ * structure lines for unannotated sequences
+ */
+
+ public boolean isProcessSecondaryStructure()
+ {
+ return processSecondaryStructure;
+ }
+
+ /**
+ * Control whether structure manager will try to annotate mapped sequences
+ * with secondary structure from PDB data.
+ *
+ * @param enable
+ */
+ public void setProcessSecondaryStructure(boolean enable)
+ {
+ processSecondaryStructure = enable;
+ }
+
+ /**
+ * debug function - write all mappings to stdout
+ */
+ public void reportMapping()
+ {
+ if (mappings.isEmpty())
+ {
+ System.err.println("reportMapping: No PDB/Sequence mappings.");
+ }
+ else
+ {
+ System.err.println("reportMapping: There are " + mappings.size()
+ + " mappings.");
+ int i = 0;
+ for (StructureMapping sm : mappings)
+ {
+ System.err.println("mapping " + i++ + " : " + sm.pdbfile);
+ }
+ }
+ }
+
+ /**
+ * 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> pdbFileNameId = new HashMap<String, String>();
+
+ public void registerPDBFile(String idForFile, String absoluteFile)
+ {
+ pdbIdFileName.put(idForFile, absoluteFile);
+ pdbFileNameId.put(absoluteFile, idForFile);
+ }
+
+ public String findIdForPDBFile(String idOrFile)
+ {
+ String id = pdbFileNameId.get(idOrFile);
+ return id;
+ }
+
+ public String findFileForPDBId(String idOrFile)
+ {
+ String id = pdbIdFileName.get(idOrFile);
+ return id;
+ }
+
+ public boolean isPDBFileRegistered(String idOrFile)
+ {
+ return pdbFileNameId.containsKey(idOrFile)
+ || pdbIdFileName.containsKey(idOrFile);
+ }
+
+ private static StructureSelectionManager nullProvider = null;
+
+ public static StructureSelectionManager getStructureSelectionManager(
+ StructureSelectionManagerProvider context)
+ {
+ if (context == null)
+ {
+ if (nullProvider == null)
+ {
+ if (instances != null)
+ {
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_structure_selection_manager_null"),
+ new NullPointerException(MessageManager
+ .getString("exception.ssm_context_is_null")));
+ }
+ else
+ {
+ nullProvider = new StructureSelectionManager();
+ }
+ return nullProvider;
+ }
+ }
+ if (instances == null)
+ {
+ instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager>();
+ }
+ StructureSelectionManager instance = instances.get(context);
+ if (instance == null)
+ {
+ if (nullProvider != null)
+ {
+ instance = nullProvider;
+ }
+ else
+ {
+ instance = new StructureSelectionManager();
+ }
+ instances.put(context, instance);
+ }
+ return instance;
+ }
+
+ /**
+ * flag controlling whether SeqMappings are relayed from received sequence
+ * mouse over events to other sequences
+ */
+ boolean relaySeqMappings = true;
+
+ /**
+ * Enable or disable relay of seqMapping events to other sequences. You might
+ * want to do this if there are many sequence mappings and the host computer
+ * is slow
+ *
+ * @param relay
+ */
+ public void setRelaySeqMappings(boolean relay)
+ {
+ relaySeqMappings = relay;
+ }
+
+ /**
+ * get the state of the relay seqMappings flag.
+ *
+ * @return true if sequence mouse overs are being relayed to other mapped
+ * sequences
+ */
+ public boolean isRelaySeqMappingsEnabled()
+ {
+ return relaySeqMappings;
+ }
+
+ Vector listeners = new Vector();
+
+ /**
+ * register a listener for alignment sequence mouseover events
+ *
+ * @param svl
+ */
+ public void addStructureViewerListener(Object svl)
+ {
+ if (!listeners.contains(svl))
+ {
+ listeners.addElement(svl);
+ }
+ }
+
+ /**
+ * Returns the file name for a mapped PDB id (or null if not mapped).
+ *
+ * @param pdbid
+ * @return
+ */
+ public String alreadyMappedToFile(String pdbid)
+ {
+ for (StructureMapping sm : mappings)
+ {
+ if (sm.getPdbId().equals(pdbid))
+ {
+ return sm.pdbfile;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Import structure data and register a structure mapping for broadcasting
+ * colouring, mouseovers and selection events (convenience wrapper).
+ *
+ * @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 PDBfile setMapping(SequenceI[] sequence,
+ String[] targetChains, String pdbFile, String protocol)
+ {
+ return setMapping(true, sequence, targetChains, pdbFile, protocol);
+ }
+
+ /**
+ * create sequence structure mappings between each sequence and the given
+ * pdbFile (retrieved via the given protocol).
+ *
+ * @param forStructureView
+ * when true, record the mapping for use in mouseOvers
+ *
+ * @param sequenceArray
+ * - 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)
+ * @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 PDBfile setMapping(boolean forStructureView,
+ SequenceI[] sequenceArray, String[] targetChainIds,
+ String pdbFile,
+ String protocol)
+ {
+ /*
+ * There will be better ways of doing this in the future, for now we'll use
+ * the tried and tested MCview pdb mapping
+ */
+ 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;
+ }
+ }
+ }
+ }
+ }
+ PDBfile pdb = null;
+ boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
+ SiftsClient siftsClient = null;
+ try
+ {
+ pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
+ pdbFile, protocol);
+
+ if (pdb.id != null && pdb.id.trim().length() > 0
+ && AppletFormatAdapter.FILE.equals(protocol))
+ {
+ registerPDBFile(pdb.id.trim(), pdbFile);
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return null;
+ }
+
+ try
+ {
+ if (isMapUsingSIFTs)
+ {
+ siftsClient = new SiftsClient(pdb);
+ }
+ } catch (SiftsException e)
+ {
+ isMapUsingSIFTs = false;
+ e.printStackTrace();
+ }
+
+ String targetChainId;
+ for (int s = 0; s < sequenceArray.length; s++)
+ {
+ boolean infChain = true;
+ final SequenceI seq = sequenceArray[s];
+ 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 = "";
+ }
+
+ /*
+ * Attempt pairwise alignment of the sequence with each chain in the PDB,
+ * and remember the highest scoring chain
+ */
+ int max = -10;
+ AlignSeq maxAlignseq = null;
+ String maxChainId = " ";
+ PDBChain maxChain = null;
+ boolean first = true;
+ for (PDBChain chain : pdb.chains)
+ {
+ if (targetChainId.length() > 0 && !targetChainId.equals(chain.id)
+ && !infChain)
+ {
+ continue; // don't try to map chains don't match.
+ }
+ // TODO: correctly determine sequence type for mixed na/peptide
+ // structures
+ final String type = chain.isNa ? AlignSeq.DNA : AlignSeq.PEP;
+ AlignSeq as = AlignSeq.doGlobalNWAlignment(seq, chain.sequence,
+ type);
+ // equivalent to:
+ // AlignSeq as = new AlignSeq(sequence[s], chain.sequence, type);
+ // as.calcScoreMatrix();
+ // as.traceAlignment();
+
+ if (first || as.maxscore > max
+ || (as.maxscore == max && chain.id.equals(targetChainId)))
+ {
+ first = false;
+ maxChain = chain;
+ max = as.maxscore;
+ maxAlignseq = as;
+ maxChainId = chain.id;
+ }
+ }
+ if (maxChain == null)
+ {
+ continue;
+ }
+
+ if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ {
+ pdbFile = "INLINE" + pdb.id;
+ }
+
+ ArrayList<StructureMapping> seqToStrucMapping = null;
+ if (isMapUsingSIFTs)
+ {
+ setProgressBar(null);
+ setProgressBar("Obtaining mapping with SIFTS");
+ try
+ {
+ jalview.datamodel.Mapping sqmpping = maxAlignseq
+ .getMappingFromS1(false);
+ seqToStrucMapping = new ArrayList<StructureMapping>();
+ if (targetChainId != null && !targetChainId.trim().isEmpty())
+ {
+ StructureMapping curChainMapping = siftsClient
+ .getSiftsStructureMapping(seq, pdbFile, targetChainId);
+ seqToStrucMapping.add(curChainMapping);
+ maxChainId = targetChainId;
+ PDBChain chain = pdb.findChain(targetChainId);
+ if (chain != null)
+ {
+ chain.transferResidueAnnotation(curChainMapping, sqmpping);
+ }
+ }
+ else
+ {
+ for (PDBChain chain : pdb.chains)
+ {
+ StructureMapping curChainMapping = siftsClient
+ .getSiftsStructureMapping(seq, pdbFile, chain.id);
+ seqToStrucMapping.add(curChainMapping);
+ maxChainId = chain.id;
+ chain.transferResidueAnnotation(curChainMapping, sqmpping);
+ }
+ }
+ } catch (SiftsException e)
+ {
+ e.printStackTrace();
+ System.err
+ .println(">>>>>>> SIFTs mapping could not be obtained... Now mapping with NW alignment");
+ setProgressBar(null);
+ setProgressBar("SIFTs mapping could not be obtained... Now mapping with NW alignment");
+ seqToStrucMapping = getNWMappings(seq, pdbFile, maxChainId,
+ maxChain, pdb, maxAlignseq);
+ }
+ }
+ else
+ {
+ setProgressBar(null);
+ setProgressBar("Obtaining mapping with NW alignment");
+ seqToStrucMapping = getNWMappings(seq, pdbFile,
+ maxChainId, maxChain, pdb,
+ maxAlignseq);
+ }
+
+ if (forStructureView)
+ {
+ // mappings.add(seqToStrucMapping);
+ mappings.addAll(seqToStrucMapping);
+ }
+ }
+ return pdb;
+ }
+
+ private ArrayList<StructureMapping> getNWMappings(SequenceI seq,
+ String pdbFile,
+ String maxChainId, PDBChain maxChain, PDBfile pdb,
+ AlignSeq maxAlignseq)
+ {
+ final StringBuilder mappingDetails = new StringBuilder(128);
+ mappingDetails.append(NEWLINE).append(
+ "Sequence \u27f7 Structure mapping details");
+ mappingDetails.append(NEWLINE);
+ mappingDetails
+ .append("Method: inferred with Needleman & Wunsch alignment");
+ mappingDetails.append(NEWLINE).append("PDB Sequence is :")
+ .append(NEWLINE).append("Sequence = ")
+ .append(maxChain.sequence.getSequenceAsString());
+ mappingDetails.append(NEWLINE).append("No of residues = ")
+ .append(maxChain.residues.size()).append(NEWLINE)
+ .append(NEWLINE);
+ PrintStream ps = new PrintStream(System.out)
+ {
+ @Override
+ public void print(String x)
+ {
+ mappingDetails.append(x);
+ }
+
+ @Override
+ public void println()
+ {
+ mappingDetails.append(NEWLINE);
+ }
+ };
+
+ maxAlignseq.printAlignment(ps);
+
+ mappingDetails.append(NEWLINE).append("PDB start/end ");
+ mappingDetails.append(String.valueOf(maxAlignseq.seq2start))
+ .append(" ");
+ mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
+ mappingDetails.append(NEWLINE).append("SEQ start/end ");
+ mappingDetails.append(
+ String.valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
+ .append(" ");
+ 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);
+
+ HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
+ int resNum = -10000;
+ int index = 0;
+
+ do
+ {
+ Atom tmp = maxChain.atoms.elementAt(index);
+ if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
+ {
+ resNum = tmp.resNumber;
+ if (tmp.alignmentMapping >= -1)
+ {
+ // TODO (JAL-1836) address root cause: negative residue no in PDB
+ // file
+ mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber,
+ tmp.atomIndex });
+ }
+ }
+
+ index++;
+ } while (index < maxChain.atoms.size());
+
+ StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
+ pdb.id, maxChainId, mapping, mappingDetails.toString());
+ maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+ ArrayList<StructureMapping> mappings = new ArrayList<StructureMapping>();
+ mappings.add(nwMapping);
+ return mappings;
+ }
+
+ public void removeStructureViewerListener(Object svl, String[] pdbfiles)
+ {
+ listeners.removeElement(svl);
+ if (svl instanceof SequenceListener)
+ {
+ for (int i = 0; i < listeners.size(); i++)
+ {
+ if (listeners.elementAt(i) instanceof StructureListener)
+ {
+ ((StructureListener) listeners.elementAt(i))
+ .releaseReferences(svl);
+ }
+ }
+ }
+
+ if (pdbfiles == null)
+ {
+ return;
+ }
+
+ /*
+ * 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));
+
+ 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())
+ {
+ pdbs.remove(pdbfile);
+ }
+ }
+ }
+
+ /*
+ * Rebuild the mappings set, retaining only those which are for 'other' PDB
+ * files
+ */
+ if (pdbs.size() > 0)
+ {
+ List<StructureMapping> tmp = new ArrayList<StructureMapping>();
+ for (StructureMapping sm : mappings)
+ {
+ if (!pdbs.contains(sm.pdbfile))
+ {
+ tmp.add(sm);
+ }
+ }
+
+ mappings = tmp;
+ }
+ }
+
+ /**
+ * Propagate mouseover of a single position in a structure
+ *
+ * @param pdbResNum
+ * @param chain
+ * @param pdbfile
+ */
+ public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
+ {
+ AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
+ List<AtomSpec> atoms = Collections.singletonList(atomSpec);
+ mouseOverStructure(atoms);
+ }
+
+ /**
+ * Propagate mouseover or selection of multiple positions in a structure
+ *
+ * @param atoms
+ */
+ public void mouseOverStructure(List<AtomSpec> atoms)
+ {
+ if (listeners == null)
+ {
+ // old or prematurely sent event
+ return;
+ }
+ boolean hasSequenceListener = false;
+ for (int i = 0; i < listeners.size(); i++)
+ {
+ if (listeners.elementAt(i) instanceof SequenceListener)
+ {
+ hasSequenceListener = true;
+ }
+ }
+ if (!hasSequenceListener)
+ {
+ return;
+ }
+
+ SearchResults results = new SearchResults();
+ for (AtomSpec atom : atoms)
+ {
+ SequenceI lastseq = null;
+ int lastipos = -1;
+ for (StructureMapping sm : mappings)
+ {
+ if (sm.pdbfile.equals(atom.getPdbFile())
+ && sm.pdbchain.equals(atom.getChain()))
+ {
+ int indexpos = sm.getSeqPos(atom.getPdbResNum());
+ if (lastipos != indexpos && lastseq != sm.sequence)
+ {
+ results.addResult(sm.sequence, indexpos, indexpos);
+ lastipos = indexpos;
+ lastseq = sm.sequence;
+ // construct highlighted sequence list
+ for (AlignedCodonFrame acf : seqmappings)
+ {
+ acf.markMappedRegion(sm.sequence, indexpos, results);
+ }
+ }
+ }
+ }
+ }
+ for (Object li : listeners)
+ {
+ if (li instanceof SequenceListener)
+ {
+ ((SequenceListener) li).highlightSequence(results);
+ }
+ }
+ }
+
+ /**
+ * highlight regions associated with a position (indexpos) in seq
+ *
+ * @param seq
+ * the sequence that the mouse over occurred on
+ * @param indexpos
+ * the absolute position being mouseovered in seq (0 to seq.length())
+ * @param index
+ * the sequence position (if -1, seq.findPosition is called to
+ * resolve the residue number)
+ */
+ public void mouseOverSequence(SequenceI seq, int indexpos, int index,
+ VamsasSource source)
+ {
+ boolean hasSequenceListeners = handlingVamsasMo
+ || !seqmappings.isEmpty();
+ SearchResults results = null;
+ if (index == -1)
+ {
+ index = seq.findPosition(indexpos);
+ }
+ for (int i = 0; i < listeners.size(); i++)
+ {
+ Object listener = listeners.elementAt(i);
+ if (listener == source)
+ {
+ // TODO listener (e.g. SeqPanel) is never == source (AlignViewport)
+ // Temporary fudge with SequenceListener.getVamsasSource()
+ continue;
+ }
+ if (listener instanceof StructureListener)
+ {
+ highlightStructure((StructureListener) listener, seq, index);
+ }
+ else
+ {
+ if (listener instanceof SequenceListener)
+ {
+ final SequenceListener seqListener = (SequenceListener) listener;
+ if (hasSequenceListeners
+ && seqListener.getVamsasSource() != source)
+ {
+ if (relaySeqMappings)
+ {
+ if (results == null)
+ {
+ results = MappingUtils.buildSearchResults(seq, index,
+ seqmappings);
+ }
+ if (handlingVamsasMo)
+ {
+ results.addResult(seq, index, index);
+
+ }
+ if (!results.isEmpty())
+ {
+ seqListener.highlightSequence(results);
+ }
+ }
+ }
+ }
+ else if (listener instanceof VamsasListener && !handlingVamsasMo)
+ {
+ ((VamsasListener) listener).mouseOverSequence(seq, indexpos,
+ source);
+ }
+ else if (listener instanceof SecondaryStructureListener)
+ {
+ ((SecondaryStructureListener) listener).mouseOverSequence(seq,
+ indexpos, index);
+ }
+ }
+ }
+ }
+
+ /**
+ * Send suitable messages to a StructureListener to highlight atoms
+ * corresponding to the given sequence position.
+ *
+ * @param sl
+ * @param seq
+ * @param index
+ */
+ protected void highlightStructure(StructureListener sl, SequenceI seq,
+ int index)
+ {
+ if (!sl.isListeningFor(seq))
+ {
+ return;
+ }
+ int atomNo;
+ List<AtomSpec> atoms = new ArrayList<AtomSpec>();
+ for (StructureMapping sm : mappings)
+ {
+ if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence())
+ {
+ atomNo = sm.getAtomNum(index);
+
+ if (atomNo > 0)
+ {
+ atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
+ .getPDBResNum(index), atomNo));
+ }
+ }
+ }
+ sl.highlightAtoms(atoms);
+ }
+
+ /**
+ * true if a mouse over event from an external (ie Vamsas) source is being
+ * handled
+ */
+ boolean handlingVamsasMo = false;
+
+ long lastmsg = 0;
+
+ /**
+ * as mouseOverSequence but only route event to SequenceListeners
+ *
+ * @param sequenceI
+ * @param position
+ * in an alignment sequence
+ */
+ public void mouseOverVamsasSequence(SequenceI sequenceI, int position,
+ VamsasSource source)
+ {
+ handlingVamsasMo = true;
+ long msg = sequenceI.hashCode() * (1 + position);
+ if (lastmsg != msg)
+ {
+ lastmsg = msg;
+ mouseOverSequence(sequenceI, position, -1, source);
+ }
+ handlingVamsasMo = false;
+ }
+
+ public Annotation[] colourSequenceFromStructure(SequenceI seq,
+ String pdbid)
+ {
+ return null;
+ // THIS WILL NOT BE AVAILABLE IN JALVIEW 2.3,
+ // UNTIL THE COLOUR BY ANNOTATION IS REWORKED
+ /*
+ * Annotation [] annotations = new Annotation[seq.getLength()];
+ *
+ * StructureListener sl; int atomNo = 0; for (int i = 0; i <
+ * listeners.size(); i++) { if (listeners.elementAt(i) instanceof
+ * StructureListener) { sl = (StructureListener) listeners.elementAt(i);
+ *
+ * for (int j = 0; j < mappings.length; j++) {
+ *
+ * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid)
+ * && mappings[j].pdbfile.equals(sl.getPdbFile())) {
+ * System.out.println(pdbid+" "+mappings[j].getPdbId() +"
+ * "+mappings[j].pdbfile);
+ *
+ * java.awt.Color col; for(int index=0; index<seq.getLength(); index++) {
+ * if(jalview.util.Comparison.isGap(seq.getCharAt(index))) continue;
+ *
+ * atomNo = mappings[j].getAtomNum(seq.findPosition(index)); col =
+ * java.awt.Color.white; if (atomNo > 0) { col = sl.getColour(atomNo,
+ * mappings[j].getPDBResNum(index), mappings[j].pdbchain,
+ * mappings[j].pdbfile); }
+ *
+ * annotations[index] = new Annotation("X",null,' ',0,col); } return
+ * annotations; } } } }
+ *
+ * return annotations;
+ */
+ }
+
+ public void structureSelectionChanged()
+ {
+ }
+
+ public void sequenceSelectionChanged()
+ {
+ }
+
+ public void sequenceColoursChanged(Object source)
+ {
+ StructureListener sl;
+ for (int i = 0; i < listeners.size(); i++)
+ {
+ if (listeners.elementAt(i) instanceof StructureListener)
+ {
+ sl = (StructureListener) listeners.elementAt(i);
+ sl.updateColours(source);
+ }
+ }
+ }
+
+ public StructureMapping[] getMapping(String pdbfile)
+ {
+ List<StructureMapping> tmp = new ArrayList<StructureMapping>();
+ for (StructureMapping sm : mappings)
+ {
+ if (sm.pdbfile.equals(pdbfile))
+ {
+ tmp.add(sm);
+ }
+ }
+ return tmp.toArray(new StructureMapping[tmp.size()]);
+ }
+
+ /**
+ * Returns a readable description of all mappings for the given pdbfile to any
+ * of the given sequences
+ *
+ * @param pdbfile
+ * @param seqs
+ * @return
+ */
+ public String printMappings(String pdbfile, List<SequenceI> seqs)
+ {
+ if (pdbfile == null || seqs == null || seqs.isEmpty())
+ {
+ return "";
+ }
+
+ StringBuilder sb = new StringBuilder(64);
+ for (StructureMapping sm : mappings)
+ {
+ if (sm.pdbfile.equals(pdbfile) && seqs.contains(sm.sequence))
+ {
+ sb.append(sm.mappingDetails);
+ sb.append(NEWLINE);
+ // separator makes it easier to read multiple mappings
+ sb.append("=====================");
+ sb.append(NEWLINE);
+ }
+ }
+ sb.append(NEWLINE);
+
+ return sb.toString();
+ }
+
+ /**
+ * Remove the given mapping
+ *
+ * @param acf
+ */
+ public void deregisterMapping(AlignedCodonFrame acf)
+ {
+ if (acf != null)
+ {
+ boolean removed = seqmappings.remove(acf);
+ if (removed && seqmappings.isEmpty())
+ { // debug
+ System.out.println("All mappings removed");
+ }
+ }
+ }
+
+ /**
+ * Add each of the given codonFrames to the stored set, if not aready present.
+ *
+ * @param set
+ */
+ public void registerMappings(Set<AlignedCodonFrame> set)
+ {
+ if (set != null)
+ {
+ for (AlignedCodonFrame acf : set)
+ {
+ registerMapping(acf);
+ }
+ }
+ }
+
+ /**
+ * Add the given mapping to the stored set, unless already stored.
+ */
+ public void registerMapping(AlignedCodonFrame acf)
+ {
+ if (acf != null)
+ {
+ if (!seqmappings.contains(acf))
+ {
+ seqmappings.add(acf);
+ }
+ }
+ }
+
+ /**
+ * Resets this object to its initial state by removing all registered
+ * listeners, codon mappings, PDB file mappings
+ */
+ public void resetAll()
+ {
+ if (mappings != null)
+ {
+ mappings.clear();
+ }
+ if (seqmappings != null)
+ {
+ seqmappings.clear();
+ }
+ if (sel_listeners != null)
+ {
+ sel_listeners.clear();
+ }
+ if (listeners != null)
+ {
+ listeners.clear();
+ }
+ if (commandListeners != null)
+ {
+ commandListeners.clear();
+ }
+ if (view_listeners != null)
+ {
+ view_listeners.clear();
+ }
+ if (pdbFileNameId != null)
+ {
+ pdbFileNameId.clear();
+ }
+ if (pdbIdFileName != null)
+ {
+ pdbIdFileName.clear();
+ }
+ }
+
+ public void addSelectionListener(SelectionListener selecter)
+ {
+ if (!sel_listeners.contains(selecter))
+ {
+ sel_listeners.add(selecter);
+ }
+ }
+
+ public void removeSelectionListener(SelectionListener toremove)
+ {
+ if (sel_listeners.contains(toremove))
+ {
+ sel_listeners.remove(toremove);
+ }
+ }
+
+ public synchronized void sendSelection(
+ jalview.datamodel.SequenceGroup selection,
+ jalview.datamodel.ColumnSelection colsel, SelectionSource source)
+ {
+ for (SelectionListener slis : sel_listeners)
+ {
+ if (slis != source)
+ {
+ slis.selection(selection, colsel, source);
+ }
+ }
+ }
+
+ Vector<AlignmentViewPanelListener> view_listeners = new Vector<AlignmentViewPanelListener>();
+
+ public synchronized void sendViewPosition(
+ jalview.api.AlignmentViewPanel source, int startRes, int endRes,
+ int startSeq, int endSeq)
+ {
+
+ if (view_listeners != null && view_listeners.size() > 0)
+ {
+ Enumeration<AlignmentViewPanelListener> listeners = view_listeners
+ .elements();
+ while (listeners.hasMoreElements())
+ {
+ AlignmentViewPanelListener slis = listeners.nextElement();
+ if (slis != source)
+ {
+ slis.viewPosition(startRes, endRes, startSeq, endSeq, source);
+ }
+ ;
+ }
+ }
+ }
+
+ /**
+ * release all references associated with this manager provider
+ *
+ * @param jalviewLite
+ */
+ public static void release(StructureSelectionManagerProvider jalviewLite)
+ {
+ // synchronized (instances)
+ {
+ if (instances == null)
+ {
+ return;
+ }
+ StructureSelectionManager mnger = (instances.get(jalviewLite));
+ if (mnger != null)
+ {
+ instances.remove(jalviewLite);
+ try
+ {
+ mnger.finalize();
+ } catch (Throwable x)
+ {
+ }
+ }
+ }
+ }
+
+ public void registerPDBEntry(PDBEntry pdbentry)
+ {
+ if (pdbentry.getFile() != null
+ && pdbentry.getFile().trim().length() > 0)
+ {
+ registerPDBFile(pdbentry.getId(), pdbentry.getFile());
+ }
+ }
+
+ public void addCommandListener(CommandListener cl)
+ {
+ if (!commandListeners.contains(cl))
+ {
+ commandListeners.add(cl);
+ }
+ }
+
+ public boolean hasCommandListener(CommandListener cl)
+ {
+ return this.commandListeners.contains(cl);
+ }
+
+ public boolean removeCommandListener(CommandListener l)
+ {
+ return commandListeners.remove(l);
+ }
+
+ /**
+ * Forward a command to any command listeners (except for the command's
+ * source).
+ *
+ * @param command
+ * the command to be broadcast (in its form after being performed)
+ * @param undo
+ * if true, the command was being 'undone'
+ * @param source
+ */
+ public void commandPerformed(CommandI command, boolean undo,
+ VamsasSource source)
+ {
+ for (CommandListener listener : commandListeners)
+ {
+ listener.mirrorCommand(command, undo, this, source);
+ }
+ }
+
+ /**
+ * Returns a new CommandI representing the given command as mapped to the
+ * given sequences. If no mapping could be made, or the command is not of a
+ * mappable kind, returns null.
+ *
+ * @param command
+ * @param undo
+ * @param mapTo
+ * @param gapChar
+ * @return
+ */
+ public CommandI mapCommand(CommandI command, boolean undo,
+ final AlignmentI mapTo, char gapChar)
+ {
+ if (command instanceof EditCommand)
+ {
+ return MappingUtils.mapEditCommand((EditCommand) command, undo,
+ mapTo, gapChar, seqmappings);
+ }
+ else if (command instanceof OrderCommand)
+ {
+ return MappingUtils.mapOrderCommand((OrderCommand) command, undo,
+ mapTo, seqmappings);
+ }
+ 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)
+ {
+ progressIndicator.setProgressBar(message, progressSessionId);
+ }
+
+}