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;
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;
{
return null;
}
+ // TODO Get the PAE file somewhere around here and remove from JmolParser
pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile,
id, chain, getDbSource(), getDbVersion());
}
/**
- * 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)
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)
+ {
+ 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
+ {
+ // 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("Couldn't download PAE", pae_ex);
+ 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);
+ }
+ }
}
/**
* @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);
+ }
- List<Object> pae_obj = (List<Object>) Platform.parseJSON(pae_input);
- if (pae_obj == null)
+ 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(
- pdbAlignment.getSequenceAt(0),
- (Map<String, Object>) pae_obj.get(0));
+ ContactMatrixI matrix = new PAEContactMatrix(sequence,
+ (Map<String, Object>) paeDict);
- AlignmentAnnotation cmannot = pdbAlignment.getSequenceAt(0)
- .addContactList(matrix);
+ 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);
+ }
+
+ return paeDict;
+ }
+
+ 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(sm.getSequence(),
+ (Map<String, Object>) pae_obj);
+
+ AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
+ if (label != null)
+ {
+ Console.debug("Setting annotation label to '" + label + "'");
+ cmannot.label = label;
+ }
+ sm.getSequence().addAlignmentAnnotation(cmannot);
+
return true;
}
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<SequenceI> toremove = new ArrayList<SequenceI>();
if (pid.getFile() == file)
{
chid = pid.getChainCode();
-
}
}
if (chain == null || (chid != null && (chid.equals(chain)
return new PDBFeatureSettings();
}
+ // days * 86400000
+ private static final long PAE_CACHE_STALE_TIME = 1 * 86400000;
+
+ private static Map<String, File> paeDownloadCache = new HashMap<>();
+
}
git://source.jalview.org / jalview.git / blobdiff