JAL-1270 more fix for failing Functional test

[jalview.git] / src / MCview / PDBChain.java

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 6d5f9fe..3b84ee3 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -30,6 +30,7 @@ import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureMapping;
+import jalview.structure.StructureViewSettings;
 
 import java.awt.Color;
 import java.util.List;
@@ -147,6 +148,10 @@ public class PDBChain
 
       if (as.astr1.charAt(i) == as.astr2.charAt(i))
       {
+        if (pdbpos >= residues.size())
+        {
+          continue;
+        }
         Residue res = residues.elementAt(pdbpos);
         for (Atom atom : res.atoms)
         {
@@ -188,6 +193,10 @@ public class PDBChain
       status = PDBChain.IEASTATUS;
     }
     SequenceFeature[] features = sequence.getSequenceFeatures();
+    if (features == null)
+    {
+      return null;
+    }
     for (int i = 0; i < features.length; i++)
     {
       if (features[i].getFeatureGroup().equals(pdbid))
@@ -252,7 +261,7 @@ public class PDBChain
      * If > 99% 'P', flag as nucleotide; note the count doesn't include the last
      * residue
      */
-    if (residues.size() > 0 && (numNa / (residues.size() - 1) > 0.99))
+    if (residues.size() > 1 && (numNa / (residues.size() - 1) > 0.99))
     {
       isNa = true;
     }
@@ -295,11 +304,15 @@ public class PDBChain
     Vector<Annotation> resAnnotation = new Vector<Annotation>();
     int i, iSize = atoms.size() - 1;
     int resNumber = -1;
+    char insCode = ' ';
     for (i = 0; i <= iSize; i++)
     {
       Atom tmp = atoms.elementAt(i);
       resNumber = tmp.resNumber;
+      insCode = tmp.insCode;
+
       int res = resNumber;
+      char ins = insCode;
 
       if (i == 0)
       {
@@ -309,7 +322,7 @@ public class PDBChain
       Vector<Atom> resAtoms = new Vector<Atom>();
       // Add atoms to a vector while the residue number
       // remains the same as the first atom's resNumber (res)
-      while ((resNumber == res) && (i < atoms.size()))
+      while ((resNumber == res) && (ins == insCode) && (i < atoms.size()))
       {
         resAtoms.add(atoms.elementAt(i));
         i++;
@@ -317,6 +330,7 @@ public class PDBChain
         if (i < atoms.size())
         {
           resNumber = atoms.elementAt(i).resNumber;
+          insCode = atoms.elementAt(i).insCode;
         }
         else
         {
@@ -327,19 +341,48 @@ public class PDBChain
       // We need this to keep in step with the outer for i = loop
       i--;
 
+      // Add inserted residues as features to the base residue
+      Atom currAtom = resAtoms.get(0);
+      if (currAtom.insCode != ' '
+              && !residues.isEmpty()
+              && residues.lastElement().atoms.get(0).resNumber == currAtom.resNumber)
+      {
+        SequenceFeature sf = new SequenceFeature("INSERTION",
+                currAtom.resName + ":" + currAtom.resNumIns + " " + pdbid
+                        + id, "", offset + count - 1, offset + count - 1,
+                "PDB_INS");
+        resFeatures.addElement(sf);
+        residues.lastElement().atoms.addAll(resAtoms);
+      }
+      else
+      {
+
+        // boolean baseDetected = false;
+        // for (Atom resAtom : resAtoms)
+        // {
+        // if (resAtom.insCode == ' ')
+        // {
+        // baseDetected = true;
+        // }
+        // }
+        // if (!baseDetected)
+        // {
+        // continue;
+        // }
       // Make a new Residue object with the new atoms vector
       residues.addElement(new Residue(resAtoms, resNumber - 1, count));
 
       Residue tmpres = residues.lastElement();
       Atom tmpat = tmpres.atoms.get(0);
       // Make A new SequenceFeature for the current residue numbering
-      SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
+        SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
               + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
               + count, offset + count, pdbid);
       // MCview.PDBChain.PDBFILEFEATURE);
       resFeatures.addElement(sf);
       resAnnotation.addElement(new Annotation(tmpat.tfactor));
       // Keep totting up the sequence
+
       if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
       {
         String nucname = tmpat.resName.trim();
@@ -351,9 +394,12 @@ public class PDBChain
                 || ResidueProperties.nucleotideIndex[nucname
                         .charAt((deoxyn ? 1 : 0))] == -1)
         {
-          seq.append("X");
-          // System.err.println("PDBReader:Null aa3Hash for " +
-          // tmpat.resName);
+            char r = ResidueProperties
+                    .getSingleCharacterCode(ResidueProperties
+                            .getCanonicalAminoAcid(tmpat.resName));
+            seq.append(r == '0' ? 'X' : r);
+            // System.err.println("PDBReader:Null aa3Hash for " +
+            // tmpat.resName);
         }
         else
         {
@@ -371,7 +417,8 @@ public class PDBChain
         }
         seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
       }
-      count++;
+        count++;
+      }
     }
 
     if (id.length() < 1)
@@ -388,11 +435,15 @@ public class PDBChain
 
     // System.out.println("PDB Sequence is :\nSequence = " + seq);
     // System.out.println("No of residues = " + residues.size());
+
+    if (StructureViewSettings.isShowSeqFeatures())
+    {
     for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
     {
       sequence.addSequenceFeature(resFeatures.elementAt(i));
       resFeatures.setElementAt(null, i);
     }
+    }
     if (visibleChainAnnotation)
     {
       Annotation[] annots = new Annotation[resAnnotation.size()];