git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'develop' into bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail...
[jalview.git]
/
src
/
jalview
/
ws
/
dbsources
/
EBIAlfaFold.java
diff --git
a/src/jalview/ws/dbsources/EBIAlfaFold.java
b/src/jalview/ws/dbsources/EBIAlfaFold.java
index
8609046
..
6b27488
100644
(file)
--- a/
src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/
src/jalview/ws/dbsources/EBIAlfaFold.java
@@
-44,6
+44,7
@@
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GroupSet;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
@@
-154,20
+155,12
@@
public class EBIAlfaFold extends EbiFileRetrievedProxy
@Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
@Override
public AlignmentI getSequenceRecords(String queries) throws Exception
{
- // used by the SequenceFetcher. Put forSequencesOnly to true (don't open
- // structure viewer later)
- return getSequenceRecords(queries, null, true);
+ return getSequenceRecords(queries, null);
}
public AlignmentI getSequenceRecords(String queries, String retrievalUrl)
throws Exception
{
}
public AlignmentI getSequenceRecords(String queries, String retrievalUrl)
throws Exception
{
- return getSequenceRecords(queries, retrievalUrl, false);
- }
-
- public AlignmentI getSequenceRecords(String queries, String retrievalUrl,
- boolean forSequencesOnly) throws Exception
- {
AlignmentI pdbAlignment = null;
String chain = null;
String id = null;
AlignmentI pdbAlignment = null;
String chain = null;
String id = null;
@@
-183,7
+176,7
@@
public class EBIAlfaFold extends EbiFileRetrievedProxy
if (!isValidReference(id))
{
if (!isValidReference(id))
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"(AFClient) Ignoring invalid alphafold query: '" + id + "'");
stopQuery();
return null;
"(AFClient) Ignoring invalid alphafold query: '" + id + "'");
stopQuery();
return null;
@@
-226,8
+219,6
@@
public class EBIAlfaFold extends EbiFileRetrievedProxy
stopQuery();
throw (ex);
}
stopQuery();
throw (ex);
}
- // distinguish between AlphaFold cif/pdb opened as structure file or fetched
- // as sequence/alignment
return pdbAlignment;
}
return pdbAlignment;
}
@@
-304,11
+295,12
@@
public class EBIAlfaFold extends EbiFileRetrievedProxy
AlignmentI pdbAlignment, String retrievalUrl) throws IOException
{
File pae = fetchAlphaFoldPAE(id, retrievalUrl);
AlignmentI pdbAlignment, String retrievalUrl) throws IOException
{
File pae = fetchAlphaFoldPAE(id, retrievalUrl);
- addAlphaFoldPAE(pdbAlignment, pae, 0, null, false, false);
+ addAlphaFoldPAE(pdbAlignment, pae, 0, null, false, false, null);
}
public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae,
}
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
{
FileInputStream paeInput = null;
try
@@
-323,12
+315,14
@@
public class EBIAlfaFold extends EbiFileRetrievedProxy
if (isStruct)
{
if (isStruct)
{
+ // ###### WRITE A TEST for this bit of the logic addAlphaFoldPAE with
+ // different params.
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
if (ssm != null)
{
String structFilename = isStructId ? ssm.findFileForPDBId(id) : id;
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
if (ssm != null)
{
String structFilename = isStructId ? ssm.findFileForPDBId(id) : id;
- addPAEToStructure(ssm, structFilename, pae);
+ addPAEToStructure(ssm, structFilename, pae, label);
}
}
}
}
@@
-338,7
+332,7
@@
public class EBIAlfaFold extends EbiFileRetrievedProxy
try
{
if (!importPaeJSONAsContactMatrixToSequence(pdbAlignment, paeInput,
try
{
if (!importPaeJSONAsContactMatrixToSequence(pdbAlignment, paeInput,
- index, id))
+ index, id, label))
{
Console.warn("Could not import contact matrix from '"
+ pae.getAbsolutePath() + "' to sequence.");
{
Console.warn("Could not import contact matrix from '"
+ pae.getAbsolutePath() + "' to sequence.");
@@
-357,7
+351,7
@@
public class EBIAlfaFold extends EbiFileRetrievedProxy
}
public static void addPAEToStructure(StructureSelectionManager ssm,
}
public static void addPAEToStructure(StructureSelectionManager ssm,
- String structFilename, File pae)
+ String structFilename, File pae, String label)
{
FileInputStream paeInput = null;
try
{
FileInputStream paeInput = null;
try
@@
-380,7
+374,8
@@
public class EBIAlfaFold extends EbiFileRetrievedProxy
try
{
try
{
- if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput))
+ if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput,
+ label))
{
Console.warn("Could not import contact matrix from '"
+ pae.getAbsolutePath() + "' to structure.");
{
Console.warn("Could not import contact matrix from '"
+ pae.getAbsolutePath() + "' to structure.");
@@
-410,7
+405,7
@@
public class EBIAlfaFold extends EbiFileRetrievedProxy
*/
public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input, int index,
*/
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;
if (seqId == null)
{
SequenceI sequence = null;
if (seqId == null)
@@
-437,12
+432,13
@@
public class EBIAlfaFold extends EbiFileRetrievedProxy
return false;
}
return importPaeJSONAsContactMatrixToSequence(pdbAlignment, pae_input,
return false;
}
return importPaeJSONAsContactMatrixToSequence(pdbAlignment, pae_input,
- sequence);
+ sequence, label);
}
public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input,
}
public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input,
- SequenceI sequence) throws IOException, ParseException
+ SequenceI sequence, String label)
+ throws IOException, ParseException
{
JSONObject paeDict = parseJSONtoPAEContactMatrix(pae_input);
if (paeDict == null)
{
JSONObject paeDict = parseJSONtoPAEContactMatrix(pae_input);
if (paeDict == null)
@@
-454,6
+450,8
@@
public class EBIAlfaFold extends EbiFileRetrievedProxy
(Map<String, Object>) paeDict);
AlignmentAnnotation cmannot = sequence.addContactList(matrix);
(Map<String, Object>) paeDict);
AlignmentAnnotation cmannot = sequence.addContactList(matrix);
+ if (label != null)
+ cmannot.label = label;
pdbAlignment.addAnnotation(cmannot);
return true;
pdbAlignment.addAnnotation(cmannot);
return true;
@@
-478,22
+476,23
@@
public class EBIAlfaFold extends EbiFileRetrievedProxy
return paeDict;
}
return paeDict;
}
+ // ###### TEST THIS
public static boolean importPaeJSONAsContactMatrixToStructure(
public static boolean importPaeJSONAsContactMatrixToStructure(
- StructureMapping[] smArray, InputStream paeInput)
+ StructureMapping[] smArray, InputStream paeInput, String label)
throws IOException, ParseException
{
boolean someDone = false;
for (StructureMapping sm : smArray)
{
boolean thisDone = importPaeJSONAsContactMatrixToStructure(sm,
throws IOException, ParseException
{
boolean someDone = false;
for (StructureMapping sm : smArray)
{
boolean thisDone = importPaeJSONAsContactMatrixToStructure(sm,
- paeInput);
+ paeInput, label);
someDone |= thisDone;
}
return someDone;
}
public static boolean importPaeJSONAsContactMatrixToStructure(
someDone |= thisDone;
}
return someDone;
}
public static boolean importPaeJSONAsContactMatrixToStructure(
- StructureMapping sm, InputStream paeInput)
+ StructureMapping sm, InputStream paeInput, String label)
throws IOException, ParseException
{
JSONObject pae_obj = parseJSONtoPAEContactMatrix(paeInput);
throws IOException, ParseException
{
JSONObject pae_obj = parseJSONtoPAEContactMatrix(paeInput);
@@
-503,12
+502,13
@@
public class EBIAlfaFold extends EbiFileRetrievedProxy
return false;
}
return false;
}
- ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
+ SequenceI seq = sm.getSequence();
+ ContactMatrixI matrix = new PAEContactMatrix(seq,
(Map<String, Object>) pae_obj);
(Map<String, Object>) pae_obj);
-
AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
- sm.getSequence().addAlignmentAnnotation(cmannot);
-
+ /* this already happens in Sequence.addContactList()
+ seq.addAlignmentAnnotation(cmannot);
+ */
return true;
}
return true;
}