git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
5b697ed
)
JAL-674 test for presence of annotation derived from particular PDB file
author
Jim Procter
<j.procter@dundee.ac.uk>
Mon, 20 Oct 2014 12:46:05 +0000
(13:46 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Tue, 21 Oct 2014 10:34:53 +0000
(11:34 +0100)
src/MCview/PDBfile.java
patch
|
blob
|
history
diff --git
a/src/MCview/PDBfile.java
b/src/MCview/PDBfile.java
index
20b3171
..
ae2eb50
100755
(executable)
--- a/
src/MCview/PDBfile.java
+++ b/
src/MCview/PDBfile.java
@@
-269,8
+269,29
@@
public class PDBfile extends jalview.io.AlignFile
System.err.println(line);
}
}
System.err.println(line);
}
}
+ markCalcIds();
}
}
+ public static boolean isCalcIdForFile(String calcId, String pdbFile)
+ {
+ return (calcId != null && calcId.startsWith("JalviewPDB:" + pdbFile
+ + ":JalviewPDB:"));
+ }
+ private void markCalcIds()
+ {
+ for (SequenceI sq : seqs)
+ {
+ for (AlignmentAnnotation aa : sq.getAnnotation())
+ {
+ String oldId = aa.getCalcId();
+ if (oldId == null)
+ {
+ oldId = "";
+ }
+ aa.setCalcId("JalviewPDB:" + getDataName() + ":JalviewPDB:" + oldId);
+ }
+ }
+ }
private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
throws Exception
{
private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
throws Exception
{