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.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.StructureMapping;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;
Console.debug("Downloading pae from " + paeURL + " to " + pae.toString()
+ "");
UrlDownloadClient.download(paeURL, pae);
- addAlphaFoldPAE(pdbAlignment, pae);
+ addAlphaFoldPAEToSequence(pdbAlignment, pae, 0, null);
}
- public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae)
+ public static void addAlphaFoldPAEToSequence(AlignmentI pdbAlignment,
+ File pae, int index, String seqId)
{
- FileInputStream pae_input = null;
+ 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
{
- pae_input = new FileInputStream(pae);
+ paeInput = new FileInputStream(pae);
} catch (FileNotFoundException e)
{
Console.error(
"Could not find pAE file '" + pae.getAbsolutePath() + "'", e);
+ return;
}
- try
+ if (isStruct)
{
- if (!importPaeJSONAsContactMatrix(pdbAlignment, pae_input))
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ if (ssm != null)
{
- Console.warn("Could not import contact matrix from '"
- + pae.getAbsolutePath() + "'");
+ 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);
+ }
}
- } catch (IOException e1)
- {
- Console.error("Error when importing pAE file '"
- + pae.getAbsolutePath() + "'", e1);
- } catch (ParseException e2)
+
+ }
+ else
{
- Console.error(
- "Error when parsing pAE file '" + pae.getAbsolutePath() + "'",
- e2);
+ // 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);
+ }
}
}
* @throws IOException
* @throws Exception
*/
- public static boolean importPaeJSONAsContactMatrix(
+ public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input)
throws IOException, ParseException
{
+ return importPaeJSONAsContactMatrixToSequence(pdbAlignment, pae_input,
+ 0, null);
+ }
- List<Object> pae_obj = (List<Object>) Platform.parseJSON(pae_input);
+ 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("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
+ }
+ }
+
+ Object paeJson = Platform.parseJSON(pae_input);
+ JSONObject paeDict = null;
+ if (paeJson instanceof JSONObject)
+ {
+ Console.debug("***** paeJson is a JSONObject");
+ paeDict = (JSONObject) paeJson;
+ }
+ 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;
+ }
+
+ 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
+ {
+
+ 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),
+
+ ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
(Map<String, Object>) pae_obj.get(0));
- AlignmentAnnotation cmannot = pdbAlignment.getSequenceAt(0)
- .addContactList(matrix);
- pdbAlignment.addAnnotation(cmannot);
+ 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