X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEBIAlfaFold.java;h=5ab05e09598353709bdb7a0888044931719a7ae3;hb=a06dd69fae641b3f5a8f202b439796df8469abb6;hp=0e148ff06e9f2e863a01d961acc2124abaabf802;hpb=356ec810340821d8b1b1701aae913b3a58778335;p=jalview.git diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java index 0e148ff..5ab05e0 100644 --- a/src/jalview/ws/dbsources/EBIAlfaFold.java +++ b/src/jalview/ws/dbsources/EBIAlfaFold.java @@ -23,11 +23,19 @@ package jalview.ws.dbsources; import java.io.File; import java.io.FileInputStream; +import java.io.FileNotFoundException; +import java.io.IOException; import java.io.InputStream; import java.util.ArrayList; +import java.util.Date; +import java.util.HashMap; import java.util.List; import java.util.Map; +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.ParseException; + import com.stevesoft.pat.Regex; import jalview.api.FeatureSettingsModelI; @@ -36,14 +44,19 @@ import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.ContactMatrixI; import jalview.datamodel.DBRefEntry; +import jalview.datamodel.GroupSet; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.gui.Desktop; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatI; import jalview.io.FormatAdapter; import jalview.io.PDBFeatureSettings; +import jalview.structure.StructureImportSettings.TFType; +import jalview.structure.StructureMapping; +import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.ws.datamodel.alphafold.PAEContactMatrix; @@ -61,7 +74,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy private static final int PDB_ID_LENGTH = 4; - private static String AF_VERSION = "2"; + private static String AF_VERSION = "3"; public EBIAlfaFold() { @@ -187,6 +200,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy { return null; } + // TODO Get the PAE file somewhere around here and remove from JmolParser pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile, id, chain, getDbSource(), getDbVersion()); @@ -197,7 +211,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy "exception.no_pdb_records_for_chain", new String[] { id, ((chain == null) ? "' '" : chain) })); } - retrieve_AlphaFold_pAE(id, pdbAlignment, retrievalUrl); + // done during structure retrieval + // retrieve_AlphaFold_pAE(id, pdbAlignment, retrievalUrl); } catch (Exception ex) // Problem parsing PDB file { @@ -208,22 +223,22 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy } /** - * get an alphafold pAE for the given id, and add it to sequence 0 in - * pdbAlignment (assuming it came from structurefile parser). + * get an alphafold pAE for the given id and return the File object of the + * downloaded (temp) file * * @param id * @param pdbAlignment * @param retrievalUrl * - URL of .mmcif from EBI-AlphaFold - will be used to generate the * pAE URL automatically + * @throws IOException * @throws Exception */ - public static void retrieve_AlphaFold_pAE(String id, - AlignmentI pdbAlignment, String retrievalUrl) throws Exception + public static File fetchAlphaFoldPAE(String id, String retrievalUrl) + throws IOException { // import PAE as contact matrix - assume this will work if there was a // model - File pae = File.createTempFile(id, "pae_json"); String paeURL = getAlphaFoldPaeDownloadUrl(id, AF_VERSION); if (retrievalUrl != null) @@ -232,26 +247,151 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy paeURL = retrievalUrl.replace("model", "predicted_aligned_error") .replace(".cif", ".json"); } + + // check the cache + File pae = paeDownloadCache.get(paeURL); + if (pae != null && pae.exists() && (new Date().getTime() + - pae.lastModified()) < PAE_CACHE_STALE_TIME) + { + Console.debug( + "Using existing file in PAE cache for '" + paeURL + "'"); + return pae; + } + + try + { + pae = File.createTempFile(id == null ? "af_pae" : id, "pae_json"); + } catch (IOException e) + { + e.printStackTrace(); + } Console.debug("Downloading pae from " + paeURL + " to " + pae.toString() + ""); - try { UrlDownloadClient.download(paeURL, pae); - FileInputStream pae_input = new FileInputStream(pae); + } catch (IOException e) + { + throw e; + } + // cache and it if successful + paeDownloadCache.put(paeURL, pae); + return pae; + } - if (!importPaeJSONAsContactMatrix(pdbAlignment, pae_input)) + /** + * get an alphafold pAE for the given id, and add it to sequence 0 in + * pdbAlignment (assuming it came from structurefile parser). + * + * @param id + * @param pdbAlignment + * @param retrievalUrl + * - URL of .mmcif from EBI-AlphaFold - will be used to generate the + * pAE URL automatically + * @throws IOException + * @throws Exception + */ + public static void retrieve_AlphaFold_pAE(String id, + AlignmentI pdbAlignment, String retrievalUrl) throws IOException + { + File pae = fetchAlphaFoldPAE(id, retrievalUrl); + addAlphaFoldPAE(pdbAlignment, pae, 0, null, false, false, null); + } + + public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae, + int index, String id, boolean isStruct, boolean isStructId, + String label) + { + FileInputStream paeInput = null; + try + { + paeInput = new FileInputStream(pae); + } catch (FileNotFoundException e) + { + Console.error( + "Could not find pAE file '" + pae.getAbsolutePath() + "'", e); + return; + } + + if (isStruct) + { + // ###### WRITE A TEST for this bit of the logic addAlphaFoldPAE with + // different params. + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + if (ssm != null) { - Console.warn("Couln't import contact matrix from " + paeURL - + " (stored in " + pae.toString() + ")"); + String structFilename = isStructId ? ssm.findFileForPDBId(id) : id; + addPAEToStructure(ssm, structFilename, pae, label); } - } catch (Exception pae_ex) + + } + else { - Console.debug("Couldn't download PAE", pae_ex); + // attach to sequence?! + try + { + if (!importPaeJSONAsContactMatrixToSequence(pdbAlignment, paeInput, + index, id, label)) + { + Console.warn("Could not import contact matrix from '" + + pae.getAbsolutePath() + "' to sequence."); + } + } catch (IOException e1) + { + Console.error("Error when importing pAE file '" + + pae.getAbsolutePath() + "'", e1); + } catch (ParseException e2) + { + Console.error("Error when parsing pAE file '" + + pae.getAbsolutePath() + "'", e2); + } } } + public static void addPAEToStructure(StructureSelectionManager ssm, + String structFilename, File pae, String label) + { + FileInputStream paeInput = null; + try + { + paeInput = new FileInputStream(pae); + } catch (FileNotFoundException e) + { + Console.error( + "Could not find pAE file '" + pae.getAbsolutePath() + "'", e); + return; + } + if (ssm == null) + { + ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + } + if (ssm != null) + { + StructureMapping[] smArray = ssm.getMapping(structFilename); + + try + { + if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput, + label)) + { + Console.warn("Could not import contact matrix from '" + + pae.getAbsolutePath() + "' to structure."); + } + } catch (IOException e1) + { + Console.error("Error when importing pAE file '" + + pae.getAbsolutePath() + "'", e1); + } catch (ParseException e2) + { + Console.error("Error when parsing pAE file '" + + pae.getAbsolutePath() + "'", e2); + } + } + } + /** * parses the given pAE matrix and adds it to sequence 0 in the given * alignment @@ -259,26 +399,116 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy * @param pdbAlignment * @param pae_input * @return true if there was a pAE matrix added + * @throws ParseException + * @throws IOException * @throws Exception */ - public static boolean importPaeJSONAsContactMatrix( - AlignmentI pdbAlignment, InputStream pae_input) throws Exception + public static boolean importPaeJSONAsContactMatrixToSequence( + AlignmentI pdbAlignment, InputStream pae_input, int index, + String seqId, String label) throws IOException, ParseException + { + SequenceI sequence = null; + if (seqId == null) + { + int seqToGet = index > 0 ? index : 0; + sequence = pdbAlignment.getSequenceAt(seqToGet); + } + if (sequence == null) + { + SequenceI[] sequences = pdbAlignment.findSequenceMatch(seqId); + if (sequences == null || sequences.length < 1) + { + Console.warn("Could not find sequence with id '" + seqId + + "' to attach pAE matrix to. Ignoring matrix."); + return false; + } + else + { + sequence = sequences[0]; // just use the first sequence with this seqId + } + } + if (sequence == null) + { + return false; + } + return importPaeJSONAsContactMatrixToSequence(pdbAlignment, pae_input, + sequence, label); + } + + public static boolean importPaeJSONAsContactMatrixToSequence( + AlignmentI pdbAlignment, InputStream pae_input, + SequenceI sequence, String label) + throws IOException, ParseException { + JSONObject paeDict = parseJSONtoPAEContactMatrix(pae_input); + if (paeDict == null) + { + Console.debug("JSON file did not parse properly."); + return false; + } + ContactMatrixI matrix = new PAEContactMatrix(sequence, + (Map) paeDict); + + AlignmentAnnotation cmannot = sequence.addContactList(matrix); + if (label != null) + cmannot.label = label; + pdbAlignment.addAnnotation(cmannot); + + return true; + } + + public static JSONObject parseJSONtoPAEContactMatrix( + InputStream pae_input) throws IOException, ParseException + { + Object paeJson = Platform.parseJSON(pae_input); + JSONObject paeDict = null; + if (paeJson instanceof JSONObject) + { + paeDict = (JSONObject) paeJson; + } + else if (paeJson instanceof JSONArray) + { + JSONArray jsonArray = (JSONArray) paeJson; + if (jsonArray.size() > 0) + paeDict = (JSONObject) jsonArray.get(0); + } - List pae_obj = (List) Platform.parseJSON(pae_input); + return paeDict; + } + + // ###### TEST THIS + public static boolean importPaeJSONAsContactMatrixToStructure( + StructureMapping[] smArray, InputStream paeInput, String label) + throws IOException, ParseException + { + boolean someDone = false; + for (StructureMapping sm : smArray) + { + boolean thisDone = importPaeJSONAsContactMatrixToStructure(sm, + paeInput, label); + someDone |= thisDone; + } + return someDone; + } + + public static boolean importPaeJSONAsContactMatrixToStructure( + StructureMapping sm, InputStream paeInput, String label) + throws IOException, ParseException + { + JSONObject pae_obj = parseJSONtoPAEContactMatrix(paeInput); if (pae_obj == null) { + Console.debug("JSON file did not parse properly."); return false; } - ContactMatrixI matrix = new PAEContactMatrix( - pdbAlignment.getSequenceAt(0), - (Map) pae_obj.get(0)); - - // THIS IS NOT GOING TO WORK !!! - // ?? StructureFile assumes sequenceI holds all data, so AlignmentAnnotation - // needs to hold the contact matrix data. - pdbAlignment.getSequenceAt(0) - .addAlignmentAnnotation(pdbAlignment.addContactList(matrix)); + + SequenceI seq = sm.getSequence(); + ContactMatrixI matrix = new PAEContactMatrix(seq, + (Map) pae_obj); + AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix); + /* this already happens in Sequence.addContactList() + seq.addAlignmentAnnotation(cmannot); + */ return true; } @@ -302,8 +532,10 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy String file = tmpFile.getAbsolutePath(); // todo get rid of Type and use FileFormatI instead? FileFormatI fileFormat = FileFormat.MMCif; - AlignmentI pdbAlignment = new FormatAdapter().readFile(tmpFile, - DataSourceType.FILE, fileFormat); + TFType tempfacType = TFType.PLDDT; + AlignmentI pdbAlignment = new FormatAdapter().readFile(tmpFile, file, + DataSourceType.FILE, fileFormat, tempfacType); + if (pdbAlignment != null) { List toremove = new ArrayList(); @@ -316,7 +548,6 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy if (pid.getFile() == file) { chid = pid.getChainCode(); - } } if (chain == null || (chid != null && (chid.equals(chain) @@ -439,4 +670,9 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy return new PDBFeatureSettings(); } + // days * 86400000 + private static final long PAE_CACHE_STALE_TIME = 1 * 86400000; + + private static Map paeDownloadCache = new HashMap<>(); + }