From 6bb97547f79105416cba04239855de078ae5dfda Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 11 Jan 2024 17:15:20 +0000
Subject: [PATCH] JAL-4371 make the PDB fetcher use simple naming 1xyzA when
 retrieving 1xyz:A from PDBe - configure via PDB_CHAIN_NAME
 = (SIMPLE|LEGACY)

---
 src/jalview/bin/Cache.java        |    2 ++
 src/jalview/ws/dbsources/Pdb.java |   32 +++++++++++++++++++++++++++++++-
 2 files changed, 33 insertions(+), 1 deletion(-)

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index a64e869..da01018 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1654,6 +1654,8 @@ public class Cache
   private static final Collection<String> bootstrapProperties = new ArrayList<>(
           Arrays.asList(JALVIEWLOGLEVEL, BOOTSTRAP_TEST));
 
+  public static final String PDB_CHAIN_NAME = "PDB_CHAIN_NAME";
+
   public static Properties bootstrapProperties(String filename)
   {
     Properties bootstrapProps = new Properties();
diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 797726f..62d4d68 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -22,6 +22,7 @@
 package jalview.ws.dbsources;
 
 import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -41,6 +42,7 @@ import jalview.ws.ebi.EBIFetchClient;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Locale;
 
 import com.stevesoft.pat.Regex;
 
@@ -113,6 +115,7 @@ public class Pdb extends EbiFileRetrievedProxy
   @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
+    updateConfiguration();
     AlignmentI pdbAlignment = null;
     String chain = null;
     String id = null;
@@ -189,8 +192,19 @@ public class Pdb extends EbiFileRetrievedProxy
           {
             // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
             // TODO: suggest simplify naming to 1qip|A as default name defined
-            pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR + id
+            if (legacyJalviewPDBeName)
+            {
+              pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR + id
                     + SEPARATOR + pdbcs.getName());
+            } else {
+              if (simpleChainName)
+              {
+                int sep_pos = pdbcs.getName().indexOf(SEPARATOR);
+                String cid = pdbcs.getName().substring(0,sep_pos);
+                cid = cid.toLowerCase(Locale.ROOT);
+                pdbcs.setName(cid+"_"+pdbcs.getName().substring(sep_pos+1));
+              };
+            }
             // Might need to add more metadata to the PDBEntry object
             // like below
             /*
@@ -247,6 +261,22 @@ public class Pdb extends EbiFileRetrievedProxy
     }
     return pdbAlignment;
   }
+  
+  boolean simpleChainName=false;
+  boolean legacyJalviewPDBeName=true;
+
+  private static String SIMPLE="SIMPLE";
+  private static String LEGACY="LEGACY";
+  
+  /**
+   * update the chain naming conventions based on the configuration
+   */
+  private void updateConfiguration()
+  {
+    final String nameConf = Cache.getDefault(Cache.PDB_CHAIN_NAME, "SIMPLE");
+    simpleChainName = SIMPLE.equals(nameConf);
+    legacyJalviewPDBeName = LEGACY.equals(nameConf);
+  }
 
   /*
    * (non-Javadoc)
-- 
1.7.10.2