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.bin.Console;
-import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ContactMatrixI;
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;
{
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
* @throws IOException
* @throws Exception
*/
- public static void retrieve_AlphaFold_pAE(String id,
- AlignmentI pdbAlignment, String retrievalUrl) throws IOException
+ public static File fetchAlphaFoldPAE(String id, String retrievalUrl)
+ throws IOException
{
// import PAE as contact matrix - assume this will work if there was a
// model
.replace(".cif", ".json");
}
- File pae = null;
+ // 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");
}
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);
+ try
+ {
+ UrlDownloadClient.download(paeURL, pae);
+ } catch (IOException e)
+ {
+ throw e;
+ }
+ // cache and it if successful
+ paeDownloadCache.put(paeURL, pae);
+ return pae;
}
- public static void addAlphaFoldPAEToStructure(AlignmentI pdbAlignment,
- File pae, int index, String structIdOrFile, boolean isStructId)
+ /**
+ * 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
{
- addAlphaFoldPAE(pdbAlignment, pae, index, structIdOrFile, true,
- isStructId);
+ 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)
+ int index, String id, boolean isStruct, boolean isStructId,
+ String label)
{
FileInputStream paeInput = null;
try
.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);
- }
+ String structFilename = isStructId ? ssm.findFileForPDBId(id) : id;
+ addPAEToStructure(ssm, structFilename, pae, label);
}
}
try
{
if (!importPaeJSONAsContactMatrixToSequence(pdbAlignment, paeInput,
- index, id))
+ index, id, label))
{
Console.warn("Could not import contact matrix from '"
+ pae.getAbsolutePath() + "' to sequence.");
}
+ 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
* @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
+ String seqId, String label) 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];
- Console.debug("******* sequences[" + i + "]='" + s.getName() + "'");
- }
- }
- /* 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)
{
- Console.debug("***** Looking for sequence with id '" + seqId + "'");
-
SequenceI[] sequences = pdbAlignment.findSequenceMatch(seqId);
if (sequences == null || sequences.length < 1)
{
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(sequence,
- (Map<String, Object>) pae_obj.get(0));
+ (Map<String, Object>) 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);
+ }
+
+ return paeDict;
+ }
+
public static boolean importPaeJSONAsContactMatrixToStructure(
- StructureMapping[] smArray, InputStream paeInput)
+ StructureMapping[] smArray, InputStream paeInput, String label)
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);
+ paeInput, label);
someDone |= thisDone;
}
return someDone;
}
public static boolean importPaeJSONAsContactMatrixToStructure(
- StructureMapping sm, InputStream paeInput)
+ StructureMapping sm, InputStream paeInput, String label)
throws IOException, ParseException
{
-
- List<Object> pae_obj = (List<Object>) Platform.parseJSON(paeInput);
+ JSONObject pae_obj = parseJSONtoPAEContactMatrix(paeInput);
if (pae_obj == null)
{
Console.debug("JSON file did not parse properly.");
}
ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
- (Map<String, Object>) pae_obj.get(0));
+ (Map<String, Object>) pae_obj);
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();
+ 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