/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
public int offset;
public Sequence sequence;
- public boolean isNa=false;
+
+ public boolean isNa = false;
+
public boolean isVisible = true;
public int pdbstart = 0;
- offset)).atoms.elementAt(0)).alignmentMapping);
tx.setEnd(1 + ((Atom) ((Residue) residues.elementAt(tx.getEnd()
- offset)).atoms.elementAt(0)).alignmentMapping);
- tx
- .setStatus(status
- + ((tx.getStatus() == null || tx.getStatus()
- .length() == 0) ? "" : ":" + tx.getStatus()));
+ tx.setStatus(status
+ + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
+ : ":" + tx.getStatus()));
if (tx.begin != 0 && tx.end != 0)
sq.addSequenceFeature(tx);
}
public void makeCaBondList()
{
- boolean na=false;
- int numNa=0;
+ boolean na = false;
+ int numNa = 0;
for (int i = 0; i < (residues.size() - 1); i++)
{
Residue tmpres = (Residue) residues.elementAt(i);
Residue tmpres2 = (Residue) residues.elementAt(i + 1);
Atom at1 = tmpres.findAtom("CA");
Atom at2 = tmpres2.findAtom("CA");
- na=false;
+ na = false;
if ((at1 == null) && (at2 == null))
{
- na=true;
+ na = true;
at1 = tmpres.findAtom("P");
at2 = tmpres2.findAtom("P");
}
System.out.println("not found " + i);
}
}
- if (numNa>0 && ((numNa/residues.size())>0.99))
+ if (numNa > 0 && ((numNa / residues.size()) > 0.99))
{
- isNa=true;
+ isNa = true;
}
}
// Keep totting up the sequence
if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
{
- String nucname=tmpat.resName.trim();
+ String nucname = tmpat.resName.trim();
if (ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
{
seq.append("X");
{
id = " ";
}
- isNa=nucleotide;
+ isNa = nucleotide;
sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
// resNumber-offset
// ~=
}
}
}
- sq
- .addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
- "PDB Residue Numbering for " + this.pdbid + ":"
- + this.id, an, (float) min, (float) max,
- AlignmentAnnotation.LINE_GRAPH));
+ sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
+ "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
+ an, (float) min, (float) max, AlignmentAnnotation.LINE_GRAPH));
}
}
}