*/
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.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;
-import jalview.bin.Cache;
import jalview.bin.Console;
+import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ContactMatrix;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
-import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.SequenceFeaturesI;
+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.javascript.json.JSON;
-import jalview.structure.StructureImportSettings;
-import jalview.util.HttpUtils;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;
-import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.utils.UrlDownloadClient;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-import org.jmol.adapter.readers.simple.JSONReader;
-
-import com.stevesoft.pat.Regex;
-
/**
* @author JimP
*
private static final int PDB_ID_LENGTH = 4;
+ private static String AF_VERSION = "3";
+
public EBIAlfaFold()
{
super();
return "1";
}
- public static String getAlphaFoldCifDownloadUrl(String id)
+ public static String getAlphaFoldCifDownloadUrl(String id, String vnum)
{
- return "https://alphafold.ebi.ac.uk/files/" + id + "-model_v1.cif";
+ if (vnum == null || vnum.length() == 0)
+ {
+ vnum = AF_VERSION;
+ }
+ return "https://alphafold.ebi.ac.uk/files/" + id + "-model_v" + vnum
+ + ".cif";
}
- public static String getAlphaFoldPaeDownloadUrl(String id)
+ public static String getAlphaFoldPaeDownloadUrl(String id, String vnum)
{
+ if (vnum == null || vnum.length() == 0)
+ {
+ vnum = AF_VERSION;
+ }
return "https://alphafold.ebi.ac.uk/files/" + id
- + "-predicted_aligned_error_v1.json";
+ + "-predicted_aligned_error_v" + vnum + ".json";
}
/*
stopQuery();
return null;
}
- String alphaFoldCif = getAlphaFoldCifDownloadUrl(id);
+ String alphaFoldCif = getAlphaFoldCifDownloadUrl(id, AF_VERSION);
if (retrievalUrl != null)
{
alphaFoldCif = retrievalUrl;
try
{
File tmpFile = File.createTempFile(id, ".cif");
- Console.debug("Retrieving structure file for "+id+" from "+alphaFoldCif);
+ Console.debug("Retrieving structure file for " + id + " from "
+ + alphaFoldCif);
UrlDownloadClient.download(alphaFoldCif, tmpFile);
// may not need this check ?
"exception.no_pdb_records_for_chain", new String[]
{ id, ((chain == null) ? "' '" : chain) }));
}
+ // done during structure retrieval
+ // retrieve_AlphaFold_pAE(id, pdbAlignment, retrievalUrl);
+
+ } catch (Exception ex) // Problem parsing PDB file
+ {
+ stopQuery();
+ throw (ex);
+ }
+ return pdbAlignment;
+ }
+
+ /**
+ * 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
+ {
+ // import PAE as contact matrix - assume this will work if there was a
+ // model
+ String paeURL = getAlphaFoldPaeDownloadUrl(id, AF_VERSION);
+
+ if (retrievalUrl != null)
+ {
+ // manufacture the PAE url from a url like ...-model-vN.cif
+ paeURL = retrievalUrl.replace("model", "predicted_aligned_error")
+ .replace(".cif", ".json");
+ }
+
+ File pae = null;
+ 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()
+ + "");
+ UrlDownloadClient.download(paeURL, pae);
+ addAlphaFoldPAEToSequence(pdbAlignment, pae, 0, null);
+ }
+
+ public static void addAlphaFoldPAEToSequence(AlignmentI pdbAlignment,
+ File pae, int index, String seqId)
+ {
+ addAlphaFoldPAE(pdbAlignment, pae, index, seqId, false, false);
+ }
+
+ public static void addAlphaFoldPAEToStructure(AlignmentI pdbAlignment,
+ File pae, int index, String structIdOrFile, boolean isStructId)
+ {
+ addAlphaFoldPAE(pdbAlignment, pae, index, structIdOrFile, true,
+ isStructId);
+ }
+
+ public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae,
+ int index, String id, boolean isStruct, boolean isStructId)
+ {
+ FileInputStream paeInput = null;
+ try
+ {
+ paeInput = new FileInputStream(pae);
+ } catch (FileNotFoundException e)
+ {
+ Console.error(
+ "Could not find pAE file '" + pae.getAbsolutePath() + "'", e);
+ return;
+ }
+
+ if (isStruct)
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ if (ssm != null)
+ {
+ String structFile = isStructId ? ssm.findFileForPDBId(id) : id;
+ Console.debug("##### AHA! structFile = " + structFile);
+ Console.debug("##### structFile "
+ + (ssm.isPDBFileRegistered(structFile) ? "IS " : "is NOT ")
+ + "registered.");
+
+ StructureMapping[] smArray = ssm.getMapping(structFile);
+ Console.debug("##### AHA! smArray obtained with " + smArray.length
+ + " elements");
+
+ try
+ {
+ if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput))
+ {
+ 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);
+ }
+ }
- // 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);
-
- if (retrievalUrl!=null) {
- // manufacture the PAE url from a url like ...-model-vN.cif
- paeURL = retrievalUrl.replace("model","predicted_aligned_error").replace(".cif",".json");
+ }
+ else
+ {
+ // attach to sequence?!
+ try
+ {
+ if (!importPaeJSONAsContactMatrixToSequence(pdbAlignment, paeInput,
+ index, id))
+ {
+ 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);
}
- Console.debug("Downloading pae from " + paeURL
- + " to " + pae.toString() + "");
+ }
- try {
- UrlDownloadClient.download(paeURL, pae);
- if (!importPaeJSONAsContactMatrix(pdbAlignment, pae))
+ }
+
+ /**
+ * parses the given pAE matrix and adds it to sequence 0 in the given
+ * alignment
+ *
+ * @param pdbAlignment
+ * @param pae_input
+ * @return true if there was a pAE matrix added
+ * @throws ParseException
+ * @throws IOException
+ * @throws Exception
+ */
+ public static boolean importPaeJSONAsContactMatrixToSequence(
+ AlignmentI pdbAlignment, InputStream pae_input)
+ throws IOException, ParseException
+ {
+ return importPaeJSONAsContactMatrixToSequence(pdbAlignment, pae_input,
+ 0, null);
+ }
+
+ public static boolean importPaeJSONAsContactMatrixToSequence(
+ AlignmentI pdbAlignment, InputStream pae_input, int index,
+ String seqId) throws IOException, ParseException
+ {
+ SequenceI sequence = null;
+ /* debugging */
+ SequenceI[] seqs = pdbAlignment.getSequencesArray();
+ if (seqs == null)
+ Console.debug("******* sequences is null");
+ else
+ {
+ for (int i = 0; i < seqs.length; i++)
+ {
+ SequenceI s = seqs[i];
+ }
+ }
+ /* end debug */
+ if (seqId == null)
+ {
+ int seqToGet = index > 0 ? index : 0;
+ sequence = pdbAlignment.getSequenceAt(seqToGet);
+ Console.debug("***** Got sequence at index " + seqToGet + ": "
+ + (sequence == null ? null : sequence.getName()));
+ }
+ if (sequence == null)
+ {
+ SequenceI[] sequences = pdbAlignment.findSequenceMatch(seqId);
+ if (sequences == null || sequences.length < 1)
{
- Console.warn("Couln't import contact matrix from " + paeURL
- + " (stored in " + pae.toString() + ")");
+ Console.warn("Could not find sequence with id '" + seqId
+ + "' to attach pAE matrix to. Ignoring matrix.");
+ return false;
}
- } catch (Exception pae_ex) {
- Console.debug("Couldn't download PAE",pae_ex);
+ else
+ {
+ sequence = sequences[0]; // just use the first sequence with this seqId
}
+ }
- } catch (Exception ex) // Problem parsing PDB file
+ Object paeJson = Platform.parseJSON(pae_input);
+ JSONObject paeDict = null;
+ if (paeJson instanceof JSONObject)
{
- stopQuery();
- throw (ex);
+ Console.debug("***** paeJson is a JSONObject");
+ paeDict = (JSONObject) paeJson;
}
- return pdbAlignment;
+ else if (paeJson instanceof JSONArray)
+ {
+ JSONArray jsonArray = (JSONArray) paeJson;
+ if (jsonArray.size() > 0)
+ paeDict = (JSONObject) jsonArray.get(0);
+ }
+
+ if (paeDict == null)
+ {
+ Console.debug("JSON file did not parse properly.");
+ return false;
+ }
+ ContactMatrixI matrix = new PAEContactMatrix(sequence,
+ (Map<String, Object>) paeDict);
+
+ AlignmentAnnotation cmannot = sequence.addContactList(matrix);
+ pdbAlignment.addAnnotation(cmannot);
+
+ return true;
}
- private boolean importPaeJSONAsContactMatrix(AlignmentI pdbAlignment,
- File pae) throws Exception
+ public static boolean importPaeJSONAsContactMatrixToStructure(
+ StructureMapping[] smArray, InputStream paeInput)
+ throws IOException, ParseException
+ {
+ boolean someDone = false;
+ Console.debug("##### smArray.length=" + smArray.length);
+ for (StructureMapping sm : smArray)
+ {
+ Console.debug("##### sm[n]=" + sm.getPdbId());
+ boolean thisDone = importPaeJSONAsContactMatrixToStructure(sm,
+ paeInput);
+ Console.debug("##### thisDone = " + thisDone);
+ someDone |= thisDone;
+ }
+ return someDone;
+ }
+
+ public static boolean importPaeJSONAsContactMatrixToStructure(
+ StructureMapping sm, InputStream paeInput)
+ throws IOException, ParseException
{
- FileInputStream pae_input = new FileInputStream(pae);
- List<Object> pae_obj = (List<Object>) Platform
- .parseJSON(pae_input);
+ List<Object> pae_obj = (List<Object>) Platform.parseJSON(paeInput);
if (pae_obj == null)
{
+ Console.debug("JSON file did not parse properly.");
return false;
}
- ContactMatrixI matrix = new PAEContactMatrix(
- pdbAlignment.getSequenceAt(0), (Map<String, Object>)pae_obj.get(0));
- pdbAlignment.getSequenceAt(0).addAlignmentAnnotation(pdbAlignment.addContactList(matrix));
+ ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
+ (Map<String, Object>) pae_obj.get(0));
+
+ AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
+ // sm.getSequence().addAlignmentAnnotation(cmannot);
+ sm.transfer(cmannot);
+ // return true;
+
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ List<AlignedCodonFrame> acfList = ssm.getSequenceMappings();
+
return true;
}
git://source.jalview.org / jalview.git / blobdiff