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.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.Platform;
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, index,
- seqId))
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ if (ssm != null)
{
- Console.warn("Could not import contact matrix from '"
- + pae.getAbsolutePath() + "'");
- }
- } 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 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");
- public static void addAlphaFoldPAEToStructure(AlignmentI pdbAlignment,
- File pae, int index, String structId)
- {
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- if (ssm != null)
+ 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);
+ }
+ }
+
+ }
+ else
{
- /*
- ssm.setAddTempFacAnnot(showTemperatureFactor);
- ssm.setProcessSecondaryStructure(showSecondaryStructure);
- */
+ // 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 importPaeJSONAsContactMatrix(pdbAlignment, pae_input, 0, null);
+ return importPaeJSONAsContactMatrixToSequence(pdbAlignment, pae_input,
+ 0, null);
}
- public static boolean importPaeJSONAsContactMatrix(
+ public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input, int index,
String seqId) throws IOException, ParseException
{
-
- List<Object> pae_obj = (List<Object>) Platform.parseJSON(pae_input);
- if (pae_obj == null)
- {
- Console.debug("JSON file did not parse properly.");
- return false;
- }
SequenceI sequence = null;
/* debugging */
SequenceI[] seqs = pdbAlignment.getSequencesArray();
sequence = sequences[0]; // just use the first sequence with this seqId
}
}
+
+ List<Object> pae_obj = (List<Object>) Platform.parseJSON(pae_input);
+ if (pae_obj == null)
+ {
+ Console.debug("JSON file did not parse properly.");
+ return false;
+ }
ContactMatrixI matrix = new PAEContactMatrix(sequence,
(Map<String, Object>) pae_obj.get(0));
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(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;
+ }
+
/**
* general purpose structure importer - designed to yield alignment useful for
* transfer of annotation to associated sequences