git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Mapping now performed in PDBChain
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignSeq.java
diff --git
a/src/jalview/analysis/AlignSeq.java
b/src/jalview/analysis/AlignSeq.java
index
0e6f1bd
..
6b40e91
100755
(executable)
--- a/
src/jalview/analysis/AlignSeq.java
+++ b/
src/jalview/analysis/AlignSeq.java
@@
-69,8
+69,8
@@
public class AlignSeq
int maxj;
\r
int[] aseq1;
\r
int[] aseq2;
\r
int maxj;
\r
int[] aseq1;
\r
int[] aseq2;
\r
- String astr1 = "";
\r
- String astr2 = "";
\r
+ public String astr1 = "";
\r
+ public String astr2 = "";
\r
\r
/** DOCUMENT ME!! */
\r
public int seq1start;
\r
\r
/** DOCUMENT ME!! */
\r
public int seq1start;
\r
@@
-406,15
+406,15
@@
public class AlignSeq
public int [] getExactMapping()
\r
{
\r
// Print out the matching chars
\r
public int [] getExactMapping()
\r
{
\r
// Print out the matching chars
\r
- int size = s2.getLength();
\r
+ int size = s2.getLength()+1;
\r
int [] mapping = new int[size];
\r
for(int i=0; i<size; i++)
\r
mapping[i] = -1;
\r
\r
int [] mapping = new int[size];
\r
for(int i=0; i<size; i++)
\r
mapping[i] = -1;
\r
\r
- int pdbpos = seq2start-2;
\r
- int alignpos = seq1start-2;
\r
-
\r
+ int pdbpos = s2.getStart() + seq2start-3;
\r
+ int alignpos = s1.getStart() + seq1start-3;
\r
\r
\r
+System.out.println(pdbpos+" "+alignpos);
\r
for(int i=0; i<astr1.length(); i++)
\r
{
\r
if (astr1.charAt(i) != '-')
\r
for(int i=0; i<astr1.length(); i++)
\r
{
\r
if (astr1.charAt(i) != '-')
\r
@@
-432,16
+432,18
@@
public class AlignSeq
mapping[pdbpos] = alignpos;
\r
}
\r
}
\r
mapping[pdbpos] = alignpos;
\r
}
\r
}
\r
+System.out.println(s1.getStart()+" "+s2.getStart()+" "+seq1start+" "+seq2start+"\n"+
\r
+ s1.getSequence()+"\n"+s2.getSequence()+"\n"+astr1+"\n"+astr2);
\r
\r
\r
- /* for(int i=0; i<mapping.length; i++)
\r
+ for(int i=0; i<mapping.length; i++)
\r
{
\r
if(mapping[i]!=-1)
\r
System.out.println(i+" "+s2.getCharAt(i) + " " + mapping[i] + " " +
\r
{
\r
if(mapping[i]!=-1)
\r
System.out.println(i+" "+s2.getCharAt(i) + " " + mapping[i] + " " +
\r
- s1.findIndex(mapping[i])+" "+
\r
+ s1.findIndex(mapping[i]+1)+" "+
\r
s1.getCharAt(s1.findIndex(mapping[i])));
\r
else
\r
System.out.println(i+" "+"XX"+s2.getCharAt(i));
\r
s1.getCharAt(s1.findIndex(mapping[i])));
\r
else
\r
System.out.println(i+" "+"XX"+s2.getCharAt(i));
\r
- }*/
\r
+ }
\r
\r
return mapping;
\r
}
\r
\r
return mapping;
\r
}
\r