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 228eede..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))
@@ -335,6 +344,7 @@ public class PDBChain
       // 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",
@@ -347,6 +357,18 @@ public class PDBChain
       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));
 
@@ -360,6 +382,7 @@ public class PDBChain
       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();
@@ -371,9 +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
         {
@@ -409,11 +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()];