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JAL-1483 cut and paste from SW score model to allow scores based on sequences to...
[jalview.git]
/
src
/
jalview
/
gui
/
Jalview2XML.java
diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
28ac886
..
ce42174
100644
(file)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-3737,6
+3737,20
@@
public class Jalview2XML
if (sq != dsq)
{ // make this dataset sequence sq's dataset sequence
sq.setDatasetSequence(dsq);
if (sq != dsq)
{ // make this dataset sequence sq's dataset sequence
sq.setDatasetSequence(dsq);
+ // and update the current dataset alignment
+ if (ds==null) {
+ if (dseqs!=null) {
+ if (!dseqs.contains(dsq))
+ {
+ dseqs.add(dsq);
+ }
+ } else {
+ if (ds.findIndex(dsq)<0)
+ {
+ ds.addSequence(dsq);
+ }
+ }
+ }
}
}
}
}
}
}
@@
-3763,11
+3777,11
@@
public class Jalview2XML
* sb.append(newres.substring(newres.length() - sq.getEnd() -
* dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
*/
* sb.append(newres.substring(newres.length() - sq.getEnd() -
* dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
*/
- dsq.setSequence(sb.toString());
+ dsq.setSequence(newres);
}
// TODO: merges will never happen if we 'know' we have the real dataset
// sequence - this should be detected when id==dssid
}
// TODO: merges will never happen if we 'know' we have the real dataset
// sequence - this should be detected when id==dssid
- System.err.println("DEBUG Notice: Merged dataset sequence"); // ("
+ System.err.println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
// + (pre ? "prepended" : "") + " "
// + (post ? "appended" : ""));
}
// + (pre ? "prepended" : "") + " "
// + (post ? "appended" : ""));
}