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apply version 2.7 copyright
[jalview.git]
/
src
/
MCview
/
PDBChain.java
diff --git
a/src/MCview/PDBChain.java
b/src/MCview/PDBChain.java
index
5176b15
..
0004308
100755
(executable)
--- a/
src/MCview/PDBChain.java
+++ b/
src/MCview/PDBChain.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * 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, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-99,7
+99,7
@@
public class PDBChain
/**
* Annotate the residues with their corresponding positions in s1 using the
* alignment in as
/**
* 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
*/
* @param as
* @param s1
*/
@@
-107,7
+107,11
@@
public class PDBChain
{
int pdbpos = as.getSeq2Start() - 2;
int alignpos = s1.getStart() + as.getSeq1Start() - 3;
{
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) != '-')
for (int i = 0; i < as.astr1.length(); i++)
{
if (as.astr1.charAt(i) != '-')
@@
-243,6
+247,7
@@
public class PDBChain
{
int count = 0;
Object symbol;
{
int count = 0;
Object symbol;
+ boolean deoxyn=false;
boolean nucleotide = false;
StringBuffer seq = new StringBuffer();
Vector resFeatures = new Vector();
boolean nucleotide = false;
StringBuffer seq = new StringBuffer();
Vector resFeatures = new Vector();
@@
-297,8
+302,10
@@
public class PDBChain
if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
{
String nucname = tmpat.resName.trim();
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'];
if (tmpat.name.equalsIgnoreCase("CA")
if (tmpat.name.equalsIgnoreCase("CA")
- || ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
+ || ResidueProperties.nucleotideIndex[nucname.charAt((deoxyn ? 1 : 0))] == -1)
{
seq.append("X");
// System.err.println("PDBReader:Null aa3Hash for " +
{
seq.append("X");
// System.err.println("PDBReader:Null aa3Hash for " +
@@
-308,7
+315,7
@@
public class PDBChain
{
// nucleotide flag
nucleotide = true;
{
// nucleotide flag
nucleotide = true;
- seq.append(nucname.charAt(0));
+ seq.append(nucname.charAt((deoxyn ? 1 : 0)));
}
}
else
}
}
else