Merge branch 'bug/JAL-2920_uniprotvariantfeature' into releases/Release_2_10_4_Branch

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

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index f4bd31c..904a860 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -45,11 +45,11 @@ public class PDBChain
 
   public String id;
 
-  public Vector<Bond> bonds = new Vector<Bond>();
+  public Vector<Bond> bonds = new Vector<>();
 
-  public Vector<Atom> atoms = new Vector<Atom>();
+  public Vector<Atom> atoms = new Vector<>();
 
-  public Vector<Residue> residues = new Vector<Residue>();
+  public Vector<Residue> residues = new Vector<>();
 
   public int offset;
 
@@ -162,6 +162,50 @@ public class PDBChain
   }
 
   /**
+   * Annotate the residues with their corresponding positions in s1 using the
+   * alignment in as NOTE: This clears all atom.alignmentMapping values on the
+   * structure.
+   * 
+   * @param as
+   * @param s1
+   */
+  public void makeExactMapping(StructureMapping mapping, SequenceI s1)
+  {
+    // first clear out any old alignmentMapping values:
+    for (Atom atom : atoms)
+    {
+      atom.alignmentMapping = -1;
+    }
+    SequenceI ds = s1;
+    while (ds.getDatasetSequence() != null)
+    {
+      ds = ds.getDatasetSequence();
+    }
+    int pdboffset = 0;
+    for (Residue res : residues)
+    {
+      // res.number isn't set correctly for discontinuous/mismapped residues
+      int seqpos = mapping.getSeqPos(res.atoms.get(0).resNumber);
+      char strchar = sequence.getCharAt(pdboffset++);
+      if (seqpos == StructureMapping.UNASSIGNED_VALUE)
+      {
+        continue;
+      }
+      char seqchar = ds.getCharAt(seqpos - ds.getStart());
+
+      boolean sameResidue = Comparison.isSameResidue(
+              seqchar, strchar, false);
+      if (sameResidue)
+      {
+        for (Atom atom : res.atoms)
+        {
+          atom.alignmentMapping = seqpos - 1;
+        }
+      }
+    }
+  }
+
+  /**
    * Copies over the RESNUM seqfeatures from the internal chain sequence to the
    * mapped sequence
    * 
@@ -299,12 +343,13 @@ public class PDBChain
     boolean deoxyn = false;
     boolean nucleotide = false;
     StringBuilder seq = new StringBuilder(256);
-    Vector<SequenceFeature> resFeatures = new Vector<SequenceFeature>();
-    Vector<Annotation> resAnnotation = new Vector<Annotation>();
-    int i, iSize = atoms.size() - 1;
+    Vector<SequenceFeature> resFeatures = new Vector<>();
+    Vector<Annotation> resAnnotation = new Vector<>();
+    int iSize = atoms.size() - 1;
     int resNumber = -1;
     char insCode = ' ';
-    for (i = 0; i <= iSize; i++)
+
+    for (int i = 0; i <= iSize; i++)
     {
       Atom tmp = atoms.elementAt(i);
       resNumber = tmp.resNumber;
@@ -318,7 +363,7 @@ public class PDBChain
         offset = resNumber;
       }
 
-      Vector<Atom> resAtoms = new Vector<Atom>();
+      Vector<Atom> resAtoms = new Vector<>();
       // Add atoms to a vector while the residue number
       // remains the same as the first atom's resNumber (res)
       while ((resNumber == res) && (ins == insCode) && (i < atoms.size()))
@@ -425,7 +470,8 @@ public class PDBChain
 
     if (StructureImportSettings.isShowSeqFeatures())
     {
-      for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
+      iSize = resFeatures.size();
+      for (int i = 0; i < iSize; i++)
       {
         sequence.addSequenceFeature(resFeatures.elementAt(i));
         resFeatures.setElementAt(null, i);
@@ -434,20 +480,20 @@ public class PDBChain
     if (visibleChainAnnotation)
     {
       Annotation[] annots = new Annotation[resAnnotation.size()];
-      float max = 0;
-      for (i = 0, iSize = annots.length; i < iSize; i++)
+      float max = 0f;
+      float min = 0f;
+      iSize = annots.length;
+      for (int i = 0; i < iSize; i++)
       {
         annots[i] = resAnnotation.elementAt(i);
-        if (annots[i].value > max)
-        {
-          max = annots[i].value;
-        }
+        max = Math.max(max, annots[i].value);
+        min = Math.min(min, annots[i].value);
         resAnnotation.setElementAt(null, i);
       }
 
       AlignmentAnnotation tfactorann = new AlignmentAnnotation(
               "Temperature Factor", "Temperature Factor for " + pdbid + id,
-              annots, 0, max, AlignmentAnnotation.LINE_GRAPH);
+              annots, min, max, AlignmentAnnotation.LINE_GRAPH);
       tfactorann.setSequenceRef(sequence);
       sequence.addAlignmentAnnotation(tfactorann);
     }
@@ -550,6 +596,12 @@ public class PDBChain
   {
     SequenceI sq = mapping.getSequence();
     SequenceI dsq = sq;
+    if (sqmpping == null)
+    {
+      // SIFTS mappings are recorded in the StructureMapping object...
+
+      sqmpping = mapping.getSeqToPdbMapping();
+    }
     if (sq != null)
     {
       while (dsq.getDatasetSequence() != null)