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Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
[jalview.git]
/
src
/
jalview
/
ws
/
sifts
/
SiftsClient.java
diff --git
a/src/jalview/ws/sifts/SiftsClient.java
b/src/jalview/ws/sifts/SiftsClient.java
index
0c707e5
..
24526cf
100644
(file)
--- a/
src/jalview/ws/sifts/SiftsClient.java
+++ b/
src/jalview/ws/sifts/SiftsClient.java
@@
-57,6
+57,7
@@
import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.DBRefEntryI;
import jalview.api.SiftsClientI;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.DBRefEntryI;
import jalview.api.SiftsClientI;
+import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
@@
-116,7
+117,7
@@
public class SiftsClient implements SiftsClientI
private static final String NOT_OBSERVED = "Not_Observed";
private static final String NOT_OBSERVED = "Not_Observed";
- private static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
+ private static final String SIFTS_SPLIT_FTP_BASE_URL = "https://ftp.ebi.ac.uk/pub/databases/msd/sifts/split_xml/";
private final static String NEWLINE = System.lineSeparator();
private final static String NEWLINE = System.lineSeparator();
@@
-305,7
+306,7
@@
public class SiftsClient implements SiftsClientI
pdbId = pdbId.replace(".cif", "");
}
String siftFile = pdbId + ".xml.gz";
pdbId = pdbId.replace(".cif", "");
}
String siftFile = pdbId + ".xml.gz";
- String siftsFileFTPURL = SIFTS_FTP_BASE_URL + siftFile;
+ String siftsFileFTPURL = getDownloadUrlFor(siftFile);
/*
* Download the file from URL to either
/*
* Download the file from URL to either
@@
-348,6
+349,14
@@
public class SiftsClient implements SiftsClientI
return downloadTo;
}
return downloadTo;
}
+ public static String getDownloadUrlFor(String siftFile)
+ {
+ String durl = SIFTS_SPLIT_FTP_BASE_URL+siftFile.substring(1, 3)+"/"+siftFile;
+ Console.trace("SIFTS URL for "+siftFile+" is "+durl);
+ return durl;
+
+ }
+
/**
* Delete the SIFTs file for the given PDB Id in the local SIFTs download
* directory
/**
* Delete the SIFTs file for the given PDB Id in the local SIFTs download
* directory
@@
-535,7
+544,7
@@
public class SiftsClient implements SiftsClientI
if (mapping.isEmpty())
{
if (mapping.isEmpty())
{
- throw new SiftsException("SIFTS mapping failed");
+ throw new SiftsException("SIFTS mapping failed for "+entityId+" and "+seq.getName());
}
// also construct a mapping object between the seq-coord sys and the PDB
// seq's coord sys
}
// also construct a mapping object between the seq-coord sys and the PDB
// seq's coord sys