/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
this.id = id;
}
+ /**
+ * character used to write newlines
+ */
+ protected String newline = System.getProperty("line.separator");
+
+ public void setNewlineString(String nl)
+ {
+ newline = nl;
+ }
+
+ public String getNewlineString()
+ {
+ return newline;
+ }
+
public String print()
{
String tmp = "";
{
tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " "
+ ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset
- + "\n";
+ + newline;
}
return tmp;
}
+ /**
+ * 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(AlignSeq as, SequenceI s1)
{
int pdbpos = as.getSeq2Start() - 2;
int alignpos = s1.getStart() + as.getSeq1Start() - 3;
-
+ // first clear out any old alignmentMapping values:
+ for (Atom atom: (Vector<Atom>) atoms) {
+ atom.alignmentMapping=-1;
+ }
+ // and now trace the alignment onto the atom set.
for (int i = 0; i < as.astr1.length(); i++)
{
if (as.astr1.charAt(i) != '-')
{
int count = 0;
Object symbol;
+ boolean deoxyn=false;
boolean nucleotide = false;
StringBuffer seq = new StringBuffer();
Vector resFeatures = new Vector();
if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
{
String nucname = tmpat.resName.trim();
- if (tmpat.name.equalsIgnoreCase("CA") || ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
+ // 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'];
+ if (tmpat.name.equalsIgnoreCase("CA")
+ || ResidueProperties.nucleotideIndex[nucname.charAt((deoxyn ? 1 : 0))] == -1)
{
seq.append("X");
// System.err.println("PDBReader:Null aa3Hash for " +
{
// nucleotide flag
nucleotide = true;
- seq.append(nucname.charAt(0));
+ seq.append(nucname.charAt((deoxyn ? 1 : 0)));
}
}
else