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Correct mapping for pdb file
author
amwaterhouse
<Andrew Waterhouse>
Fri, 25 Nov 2005 16:08:06 +0000
(16:08 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Fri, 25 Nov 2005 16:08:06 +0000
(16:08 +0000)
src/jalview/analysis/AlignSeq.java
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diff --git
a/src/jalview/analysis/AlignSeq.java
b/src/jalview/analysis/AlignSeq.java
index
1b7351b
..
3f3bab1
100755
(executable)
--- a/
src/jalview/analysis/AlignSeq.java
+++ b/
src/jalview/analysis/AlignSeq.java
@@
-406,31
+406,43
@@
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 [] mapping = new int[astr1.length()];
\r
- int agap=0, bgap=0;
\r
- boolean gap;
\r
+ int size = s2.getLength();
\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
+
\r
for(int i=0; i<astr1.length(); i++)
\r
{
\r
for(int i=0; i<astr1.length(); i++)
\r
{
\r
- mapping[i] = -1;
\r
- gap = false;
\r
-
\r
- if(astr1.charAt(i)=='-')
\r
- {
\r
- agap++;gap = true;
\r
- }
\r
- if(astr2.charAt(i)=='-')
\r
- {
\r
- bgap++;gap = true;
\r
- }
\r
-
\r
- if(!gap && astr1.charAt(i)==astr2.charAt(i))
\r
- {
\r
- mapping[i-agap] = i - bgap;
\r
- }
\r
-
\r
- System.out.println(astr1.charAt(i)+" "+i + " "+mapping[i-agap]+" "+astr2.charAt(i));
\r
+ if (astr1.charAt(i) != '-')
\r
+ {
\r
+ alignpos++;
\r
+ }
\r
+
\r
+ if (astr2.charAt(i) != '-')
\r
+ {
\r
+ pdbpos++;
\r
+ }
\r
+
\r
+ if (astr1.charAt(i) == astr2.charAt(i))
\r
+ {
\r
+ mapping[pdbpos] = alignpos;
\r
+ }
\r
}
\r
\r
}
\r
\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
+ s1.findIndex(mapping[i])+" "+
\r
+ s1.getCharAt(s1.findIndex(mapping[i])-1));
\r
+ else
\r
+ System.out.println(i+" "+"XX"+s2.getCharAt(i));
\r
+ }*/
\r
+
\r
return mapping;
\r
}
\r
\r
return mapping;
\r
}
\r
\r