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author
jprocter
<Jim Procter>
Tue, 18 Jan 2011 17:40:53 +0000
(17:40 +0000)
committer
jprocter
<Jim Procter>
Tue, 18 Jan 2011 17:40:53 +0000
(17:40 +0000)
src/MCview/PDBChain.java
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diff --git
a/src/MCview/PDBChain.java
b/src/MCview/PDBChain.java
index
779b4f0
..
92a573c
100755
(executable)
--- a/
src/MCview/PDBChain.java
+++ b/
src/MCview/PDBChain.java
@@
-66,18
+66,22
@@
public class PDBChain
this.pdbid = pdbid.toLowerCase();
this.id = id;
}
this.pdbid = pdbid.toLowerCase();
this.id = id;
}
+
/**
/**
- * character used to write newlines
+ * character used to write newlines
*/
protected String newline = System.getProperty("line.separator");
*/
protected String newline = System.getProperty("line.separator");
+
public void setNewlineString(String nl)
{
newline = nl;
}
public void setNewlineString(String nl)
{
newline = nl;
}
+
public String getNewlineString()
{
return newline;
}
public String getNewlineString()
{
return newline;
}
+
public String print()
{
String tmp = "";
public String print()
{
String tmp = "";
@@
-92,6
+96,14
@@
public class PDBChain
return tmp;
}
return tmp;
}
+ /**
+ * Annotate the residues with their corresponding positions in s1 using the
+ * alignment in as
+ *
+ * @param as
+ * @param s1
+ * @return last position in s1 for the last position in the chain
+ */
public void makeExactMapping(AlignSeq as, SequenceI s1)
{
int pdbpos = as.getSeq2Start() - 2;
public void makeExactMapping(AlignSeq as, SequenceI s1)
{
int pdbpos = as.getSeq2Start() - 2;
@@
-286,7
+298,8
@@
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();
- if (tmpat.name.equalsIgnoreCase("CA") || ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
+ if (tmpat.name.equalsIgnoreCase("CA")
+ || ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
{
seq.append("X");
// System.err.println("PDBReader:Null aa3Hash for " +
{
seq.append("X");
// System.err.println("PDBReader:Null aa3Hash for " +