X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2FMCview%2FPDBChain.java;h=4703a3c623cb891e05e024d828cfd2ece0f844eb;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=65504e4bdebcfec7077acedced1811dd6700c6a9;hpb=f5db0ff259cbb1132f6c061615d912b0668fd728;p=jalview.git
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 65504e4..4703a3c 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,19 +1,20 @@
/*
- * 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 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
@@ -98,8 +99,9 @@ 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.
+ * alignment in as NOTE: This clears all atom.alignmentMapping values on the
+ * structure.
+ *
* @param as
* @param s1
*/
@@ -108,8 +110,9 @@ public class PDBChain
int pdbpos = as.getSeq2Start() - 2;
int alignpos = s1.getStart() + as.getSeq1Start() - 3;
// first clear out any old alignmentMapping values:
- for (Atom atom: (Vector) atoms) {
- atom.alignmentMapping=-1;
+ for (Atom atom : (Vector) atoms)
+ {
+ atom.alignmentMapping = -1;
}
// and now trace the alignment onto the atom set.
for (int i = 0; i < as.astr1.length(); i++)
@@ -247,7 +250,7 @@ public class PDBChain
{
int count = 0;
Object symbol;
- boolean deoxyn=false;
+ boolean deoxyn = false;
boolean nucleotide = false;
StringBuffer seq = new StringBuffer();
Vector resFeatures = new Vector();
@@ -302,10 +305,13 @@ public class PDBChain
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'];
+ // 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)
+ || ResidueProperties.nucleotideIndex[nucname
+ .charAt((deoxyn ? 1 : 0))] == -1)
{
seq.append("X");
// System.err.println("PDBReader:Null aa3Hash for " +