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:
76bbf0a
)
JAL-2154 keep track of incomplete sequences and report if they weren’t resolved
author
Jim Procter
<jprocter@issues.jalview.org>
Sun, 24 Jul 2016 13:04:15 +0000
(14:04 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Sun, 24 Jul 2016 13:04:15 +0000
(14:04 +0100)
src/jalview/gui/Jalview2XML.java
patch
|
blob
|
history
diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
c0e1ebe
..
9b2b04a
100644
(file)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-165,6
+165,8
@@
public class Jalview2XML
*/
Map<String, SequenceI> seqRefIds = null;
*/
Map<String, SequenceI> seqRefIds = null;
+ Map<String, SequenceI> incompleteSeqs = null;
+
List<SeqFref> frefedSequence = null;
boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
List<SeqFref> frefedSequence = null;
boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
@@
-220,6
+222,10
@@
public class Jalview2XML
{
seqsToIds.clear();
}
{
seqsToIds.clear();
}
+ if (incompleteSeqs != null)
+ {
+ incompleteSeqs.clear();
+ }
// seqRefIds = null;
// seqsToIds = null;
}
// seqRefIds = null;
// seqsToIds = null;
}
@@
-242,6
+248,10
@@
public class Jalview2XML
{
seqRefIds = new HashMap<String, SequenceI>();
}
{
seqRefIds = new HashMap<String, SequenceI>();
}
+ if (incompleteSeqs == null)
+ {
+ incompleteSeqs = new HashMap<String, SequenceI>();
+ }
if (frefedSequence == null)
{
frefedSequence = new ArrayList<SeqFref>();
if (frefedSequence == null)
{
frefedSequence = new ArrayList<SeqFref>();
@@
-393,6
+403,24
@@
public class Jalview2XML
System.err.println("SERIOUS! " + failedtoresolve
+ " resolvable forward references failed to resolve.");
}
System.err.println("SERIOUS! " + failedtoresolve
+ " resolvable forward references failed to resolve.");
}
+ if (incompleteSeqs != null && incompleteSeqs.size() > 0)
+ {
+ System.err.println("Jalview Project Import: There are "
+ + incompleteSeqs.size()
+ + " sequences which may have incomplete metadata.");
+ if (incompleteSeqs.size() < 10)
+ {
+ for (SequenceI s : incompleteSeqs.values())
+ {
+ System.err.println(s.toString());
+ }
+ }
+ else
+ {
+ System.err
+ .println("Too many to report. Skipping output of incomplete sequences.");
+ }
+ }
}
/**
}
/**
@@
-2743,6
+2771,18
@@
public class Jalview2XML
SequenceI tmpSeq = seqRefIds.get(seqId);
if (tmpSeq != null)
{
SequenceI tmpSeq = seqRefIds.get(seqId);
if (tmpSeq != null)
{
+ if (!incompleteSeqs.containsKey(seqId))
+ {
+ // may not need this check, but keep it for at least 2.9,1 release
+ if (tmpSeq.getStart()!=jseqs[i].getStart() || tmpSeq.getEnd()!=jseqs[i].getEnd())
+ {
+ System.err
+ .println("Warning JAL-2154 regression: updating start/end for sequence "
+ + tmpSeq.toString());
+ }
+ } else {
+ incompleteSeqs.remove(seqId);
+ }
tmpSeq.setStart(jseqs[i].getStart());
tmpSeq.setEnd(jseqs[i].getEnd());
tmpseqs.add(tmpSeq);
tmpSeq.setStart(jseqs[i].getStart());
tmpSeq.setEnd(jseqs[i].getEnd());
tmpseqs.add(tmpSeq);
@@
-5103,6
+5143,7
@@
public class Jalview2XML
djs.setEnd(jmap.getMap().getToHighest());
djs.setVamsasId(uniqueSetSuffix + sqid);
jmap.setTo(djs);
djs.setEnd(jmap.getMap().getToHighest());
djs.setVamsasId(uniqueSetSuffix + sqid);
jmap.setTo(djs);
+ incompleteSeqs.put(sqid, djs);
seqRefIds.put(sqid, djs);
}
seqRefIds.put(sqid, djs);
}