X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=0f82650c2226e3a7acf0e9313fc5a59fbdcf7c8c;hb=9bfda76754fb426a471e1c12c9f0ca0c4c1784bc;hp=6761cc3337c5121e8d64977bd14c77046458488a;hpb=2dc7f485be2afd841461e5eafc71dee47b44f14a;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 6761cc3..0f82650 100644
--- 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;
@@ -522,32 +524,15 @@ 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 +552,12 @@ 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;
@@ -673,7 +664,7 @@ public class StructureSelectionManager
         // Not doing SIFTS, or SIFTS failed for some reason.
         
         // first check if we should use an identity mapping
-        if (idLengthChain != null && maxAlignseq.getS2Coverage() < 0.5)
+        if (idLengthChain != null && maxAlignseq.getS2Coverage() < 0.75)
         {
           Console.info(
                   "Assuming 3Dsi identity mapping between structure and sequence");
@@ -685,6 +676,11 @@ 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)
           {