JAL-2418 source formatting

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

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 7fd0b25..f2dd3d0 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -31,6 +31,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureMapping;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.List;
@@ -38,6 +39,8 @@ import java.util.Vector;
 
 public class PDBChain
 {
+  public static final String RESNUM_FEATURE = "RESNUM";
+
   /**
    * SequenceFeature group for PDB File features added to sequences
    */
@@ -146,7 +149,9 @@ public class PDBChain
         pdbpos++;
       }
 
-      if (as.astr1.charAt(i) == as.astr2.charAt(i))
+      boolean sameResidue = Comparison.isSameResidue(as.astr1.charAt(i),
+              as.astr2.charAt(i), false);
+      if (sameResidue)
       {
         if (pdbpos >= residues.size())
         {
@@ -199,7 +204,8 @@ public class PDBChain
     }
     for (int i = 0; i < features.length; i++)
     {
-      if (features[i].getFeatureGroup().equals(pdbid))
+      if (features[i].getFeatureGroup() != null
+              && features[i].getFeatureGroup().equals(pdbid))
       {
         SequenceFeature tx = new SequenceFeature(features[i]);
         tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms
@@ -207,7 +213,8 @@ public class PDBChain
         tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms
                 .elementAt(0).alignmentMapping);
         tx.setStatus(status
-                + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
+                + ((tx.getStatus() == null || tx.getStatus().length() == 0)
+                        ? ""
                         : ":" + tx.getStatus()));
         if (tx.begin != 0 && tx.end != 0)
         {
@@ -343,14 +350,14 @@ 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)
+      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");
+                        + id,
+                "", offset + count - 1, offset + count - 1, "PDB_INS");
         resFeatures.addElement(sf);
         residues.lastElement().atoms.addAll(resAtoms);
       }
@@ -363,27 +370,28 @@ public class PDBChain
         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
-                + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
-                + count, offset + count, pdbid);
+        SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE,
+                tmpat.resName + ":" + tmpat.resNumIns + " " + pdbid + id,
+                "", offset + count, offset + count, pdbid);
         resFeatures.addElement(sf);
         resAnnotation.addElement(new Annotation(tmpat.tfactor));
         // Keep totting up the sequence
 
-        if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
+        if ((symbol = ResidueProperties.getAA3Hash()
+                .get(tmpat.resName)) == null)
         {
           String nucname = tmpat.resName.trim();
           // use the aaIndex rather than call 'toLower' - which would take a bit
           // more time.
           deoxyn = nucname.length() == 2
-                  && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D'];
+                  && ResidueProperties.aaIndex[nucname
+                          .charAt(0)] == ResidueProperties.aaIndex['D'];
           if (tmpat.name.equalsIgnoreCase("CA")
                   || ResidueProperties.nucleotideIndex[nucname
                           .charAt((deoxyn ? 1 : 0))] == -1)
           {
-            char r = ResidueProperties
-                    .getSingleCharacterCode(ResidueProperties
-                            .getCanonicalAminoAcid(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);
@@ -399,8 +407,8 @@ public class PDBChain
         {
           if (nucleotide)
           {
-            System.err
-                    .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
+            System.err.println(
+                    "Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
           }
           seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
         }
@@ -512,10 +520,12 @@ public class PDBChain
       try
       {
         index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
-        b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
+        b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0,
+                null, null, 0f);
 
         index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
-        b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
+        b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0,
+                null, null, 0f);
 
       } catch (Exception e)
       {
@@ -561,8 +571,8 @@ public class PDBChain
 
         for (AlignmentAnnotation ana : shadow.getAnnotation())
         {
-          List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
-                  ana.getCalcId(), ana.label);
+          List<AlignmentAnnotation> transfer = sq
+                  .getAlignmentAnnotations(ana.getCalcId(), ana.label);
           if (transfer == null || transfer.size() == 0)
           {
             ana = new AlignmentAnnotation(ana);
@@ -603,7 +613,8 @@ public class PDBChain
         // Useful for debugging mappings - adds annotation for mapped position
         float min = -1, max = 0;
         Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
-        for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++)
+        for (int i = sq.getStart(), j = sq
+                .getEnd(), k = 0; i <= j; i++, k++)
         {
           int prn = mapping.getPDBResNum(k + 1);