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patch for JAL-556 - more robust mapping of sequence to structure sequence with correc...
[jalview.git]
/
src
/
MCview
/
AppletPDBCanvas.java
diff --git
a/src/MCview/AppletPDBCanvas.java
b/src/MCview/AppletPDBCanvas.java
index
6be8dd5
..
cdad671
100755
(executable)
--- a/
src/MCview/AppletPDBCanvas.java
+++ b/
src/MCview/AppletPDBCanvas.java
@@
-176,8
+176,9
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
// Now lets compare the sequences to get
// the start and end points.
// Align the sequence to the pdb
// Now lets compare the sequences to get
// the start and end points.
// Align the sequence to the pdb
+ // TODO: DNa/Pep switch
AlignSeq as = new AlignSeq(sequence, ((PDBChain) pdb.chains
AlignSeq as = new AlignSeq(sequence, ((PDBChain) pdb.chains
- .elementAt(i)).sequence, "pep");
+ .elementAt(i)).sequence, ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA : AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
as.calcScoreMatrix();
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)