JAL-4366 JAL-4371 refactor and fix up code inferring potential PDB IDs & Chaincode...

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 9906582..a804d84 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -26,10 +26,12 @@ import java.util.Arrays;
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.IdentityHashMap;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
+import java.util.Set;
 import java.util.Vector;
 
 import jalview.analysis.AlignSeq;
@@ -54,6 +56,7 @@ import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.structure.StructureImportSettings.TFType;
+import jalview.struture.PDBEntryUtils;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
@@ -522,32 +525,15 @@ public class StructureSelectionManager
       {
         ds = ds.getDatasetSequence();
       }
-
+      List <PDBEntry> putativePDBe = PDBEntryUtils.selectPutativePDBe(seq,ds, pdb); 
+      
       if (targetChainIds != null && targetChainIds[s] != null)
       {
         infChain = false;
         targetChainId = targetChainIds[s];
       }
-      else if (seq.getName().indexOf("|") > -1)
-      {
-        targetChainId = seq.getName()
-                .substring(seq.getName().lastIndexOf("|") + 1);
-        if (targetChainId.length() > 1)
-        {
-          if (targetChainId.trim().length() == 0)
-          {
-            targetChainId = " ";
-          }
-          else
-          {
-            // not a valid chain identifier
-            targetChainId = "";
-          }
-        }
-      }
-      else
-      {
-        targetChainId = "";
+      else {
+        targetChainId = PDBEntryUtils.inferChainId(seq);
       }
 
       /*
@@ -567,6 +553,12 @@ public class StructureSelectionManager
         {
           continue; // don't try to map chains don't match.
         }
+        PDBEntry putativeChain = null;
+        if (!putativePDBe.isEmpty() && (putativeChain = PDBEntryUtils
+                .selectPutativePDBEntry(putativePDBe, chain)) == null)
+        {
+          continue;
+        }
         // TODO: correctly determine sequence type for mixed na/peptide
         // structures
         final String type = chain.isNa ? AlignSeq.DNA : AlignSeq.PEP;
@@ -685,6 +677,11 @@ public class StructureSelectionManager
         }
         else
         {
+          if (maxAlignseq.getS1Coverage()<0.15 && maxAlignseq.getS2Coverage()<0.15)
+          {
+            // skip this - the NW alignment is spurious
+            continue;
+          }
           // Construct a needleman wunsch mapping instead.
           if (progress != null)
           {