JAL-2148 fix to heuristically determine chain termination positions. This aids in...

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 9acc2e7..2746807 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -25,7 +25,6 @@ import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
-import jalview.structure.StructureImportSettings;
 import jalview.util.MessageManager;
 
 import java.io.IOException;
@@ -132,8 +131,7 @@ public class PDBfile extends StructureFile
           break;
         }
         if (line.indexOf("ATOM") == 0
-                || (StructureImportSettings.isProcessHETATMs()
-                        && line.indexOf("HETATM") == 0 && !terFlag))
+                || (line.indexOf("HETATM") == 0 && !terFlag))
         {
           terFlag = false;
 

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 23277a4..5f0ed2c 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -433,8 +433,6 @@ public class Cache
     StructureImportSettings
             .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
                     "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
-    StructureImportSettings.setProcessHETATMs(jalview.bin.Cache.getDefault(
-            "PROCESS_HETATM", false));
     // jnlpVersion will be null if we're using InstallAnywhere
     // Dont do this check if running in headless mode
     if (jnlpVersion == null

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index ea347ae..ca412d0 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -31,6 +31,7 @@ import jalview.util.MessageManager;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Vector;
@@ -194,17 +195,17 @@ public class JmolParser extends StructureFile implements JmolStatusListener
   private List<Atom> convertSignificantAtoms(ModelSet ms)
   {
     List<Atom> significantAtoms = new ArrayList<Atom>();
+    HashMap<String, org.jmol.modelset.Atom> chainTerMap = new HashMap<String, org.jmol.modelset.Atom>();
+    org.jmol.modelset.Atom prevAtom = null;
     for (org.jmol.modelset.Atom atom : ms.at)
     {
-      // System.out.println("Seq Id : " + atom.getSeqID());
-      // System.out.println("To String : " + atom.toString());
-      if (!StructureImportSettings.isProcessHETATMs() && atom.isHetero())
-      {
-        continue;
-      }
       if (atom.getAtomName().equalsIgnoreCase("CA")
               || atom.getAtomName().equalsIgnoreCase("P"))
       {
+        if (!atomValidated(atom, prevAtom, chainTerMap))
+        {
+          continue;
+        }
         Atom curAtom = new Atom(atom.x, atom.y, atom.z);
         curAtom.atomIndex = atom.getIndex();
         curAtom.chain = atom.getChainIDStr();
@@ -219,11 +220,57 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         curAtom.tfactor = atom.getBfactor100() / 100f;
         curAtom.type = 0;
         significantAtoms.add(curAtom);
+        prevAtom = atom;
       }
     }
     return significantAtoms;
   }
 
+  private boolean atomValidated(org.jmol.modelset.Atom curAtom,
+          org.jmol.modelset.Atom prevAtom,
+          HashMap<String, org.jmol.modelset.Atom> chainTerMap)
+  {
+    if (chainTerMap == null || prevAtom == null)
+    {
+      return true;
+    }
+    String curAtomChId = curAtom.getChainIDStr();
+    String prevAtomChId = prevAtom.getChainIDStr();
+    // new chain encoutered
+    if (!prevAtomChId.equals(curAtomChId))
+    {
+      // On chain switch add previous chain termination to xTerMap if not exists
+      if (!chainTerMap.containsKey(prevAtomChId))
+      {
+        chainTerMap.put(prevAtomChId, prevAtom);
+      }
+      // if current atom belongs to an already terminated chain and the resNum
+      // diff < 5 then mark as valid and update termination Atom
+      if (chainTerMap.containsKey(curAtomChId))
+      {
+        if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+        {
+          chainTerMap.put(curAtomChId, curAtom);
+          return true;
+        }
+        return false;
+      }
+    }
+    // atom with previously terminated chain encountered
+    else if (chainTerMap.containsKey(curAtomChId))
+    {
+      if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+      {
+        chainTerMap.put(curAtomChId, curAtom);
+        return true;
+      }
+      return false;
+    }
+    // HETATM with resNum jump > 2
+    return !(curAtom.isHetero() && ((curAtom.getResno() - prevAtom
+            .getResno()) > 2));
+  }
+
   private void createAnnotation(SequenceI sequence, PDBChain chain,
           org.jmol.modelset.Atom[] jmolAtoms)
   {

diff --git a/src/jalview/structure/StructureImportSettings.java b/src/jalview/structure/StructureImportSettings.java
index 4c06e0f..c49b141 100644 (file)
--- a/src/jalview/structure/StructureImportSettings.java
+++ b/src/jalview/structure/StructureImportSettings.java
@@ -24,8 +24,6 @@ public class StructureImportSettings
 
   private static boolean showSeqFeatures = true;
 
-  private static boolean processHETATMs = false;
-
   public static final String JMOL_PARSER = "JMolParser";
 
   public static final String JALVIEW_PARSER = "JalViewParser";
@@ -108,16 +106,6 @@ public class StructureImportSettings
     StructureImportSettings.defaultStructureFileFormat = defaultStructureFileFormat;
   }
 
-  public static boolean isProcessHETATMs()
-  {
-    return processHETATMs;
-  }
-
-  public static void setProcessHETATMs(boolean processHETATMs)
-  {
-    StructureImportSettings.processHETATMs = processHETATMs;
-  }
-
   public static String getDefaultPDBFileParser()
   {
     return defaultPDBFileParser;

diff --git a/test/jalview/ext/jmol/JmolParserTest.java b/test/jalview/ext/jmol/JmolParserTest.java
index 0010321..b0e0718 100644 (file)
--- a/test/jalview/ext/jmol/JmolParserTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@ -109,7 +109,6 @@ public class JmolParserTest
   @Test(groups = { "Functional" })
   public void testFileParser() throws Exception
   {
-    StructureImportSettings.setProcessHETATMs(false);
     for (String pdbStr : testFile)
     {
       PDBfile mctest = new PDBfile(false, false, false, pdbStr,
@@ -133,30 +132,7 @@ public class JmolParserTest
         validateSecStrRows(al);
       }
     }
-    StructureImportSettings.setProcessHETATMs(true);
-    for (String pdbStr : testFile)
-    {
-      PDBfile mctest = new PDBfile(false, false, false, pdbStr,
-              AppletFormatAdapter.FILE);
-      JmolParser jtest = new JmolParser(false, false, false, pdbStr,
-              jalview.io.AppletFormatAdapter.FILE);
-      Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
 
-      assertTrue(
-              "No sequences extracted from testfile\n"
-                      + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
-                              : "(No warnings raised)"), seqs != null
-                      && seqs.size() > 0);
-      for (SequenceI sq : seqs)
-      {
-        assertEquals("JMol didn't process " + pdbStr
-                + " to the same sequence as MCView",
-                sq.getSequenceAsString(), mcseqs.remove(0)
-                        .getSequenceAsString());
-        AlignmentI al = new Alignment(new SequenceI[] { sq });
-        validateSecStrRows(al);
-      }
-    }
   }
 
   private void validateSecStrRows(AlignmentI al)