From: James Procter <j.procter@dundee.ac.uk>
Date: Mon, 17 Jul 2023 10:15:07 +0000 (+0100)
Subject: JAL-4119 TRACE level console message reporting download URL for sifts. Also more... 
X-Git-Tag: Release_2_11_4_0~233
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=11bbccaab947ba4465c27c5d0619ef202fc4e75e;p=jalview.git

JAL-4119 TRACE level console message reporting download URL for sifts. Also more informative message when ‘Sifts Mapping Failed’ is reported as an exception - since this message can be reported when some chains in the PDB file do not match sequences being associated (but others do!!).
---

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 037854b..24526cf 100644
--- 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.bin.Console;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
@@ -350,7 +351,10 @@ public class SiftsClient implements SiftsClientI
 
   public static String getDownloadUrlFor(String siftFile)
   {
-    return SIFTS_SPLIT_FTP_BASE_URL +siftFile.substring(1, 3)+"/"+siftFile;
+    String durl = SIFTS_SPLIT_FTP_BASE_URL+siftFile.substring(1, 3)+"/"+siftFile;
+    Console.trace("SIFTS URL for "+siftFile+" is "+durl);
+    return durl;
+    
   }
 
   /**
@@ -540,7 +544,7 @@ public class SiftsClient implements SiftsClientI
 
     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