git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
[jalview.git]
/
src
/
jalview
/
analysis
/
SeqsetUtils.java
diff --git
a/src/jalview/analysis/SeqsetUtils.java
b/src/jalview/analysis/SeqsetUtils.java
index
e2ed9b4
..
5a246f8
100755
(executable)
--- a/
src/jalview/analysis/SeqsetUtils.java
+++ b/
src/jalview/analysis/SeqsetUtils.java
@@
-21,6
+21,7
@@
package jalview.analysis;
import jalview.bin.Cache;
package jalview.analysis;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.PDBEntry;
@@
-121,7
+122,7
@@
public class SeqsetUtils
{
if (sqinfo.features.isPresent())
{
{
if (sqinfo.features.isPresent())
{
- Cache.log.warn("Setting dataset sequence for a sequence which has " +
+ Console.warn("Setting dataset sequence for a sequence which has " +
"sequence features. Dataset sequence features will not be visible.");
assert false;
}
"sequence features. Dataset sequence features will not be visible.");
assert false;
}
@@
-245,14
+246,14
@@
public class SeqsetUtils
{
if (!quiet)
{
{
if (!quiet)
{
- Cache.log.warn(format("Can't find '%s' in uniquified alignment",
+ Console.warn(format("Can't find '%s' in uniquified alignment",
key));
}
}
} catch (ClassCastException ccastex) {
if (!quiet)
{
key));
}
}
} catch (ClassCastException ccastex) {
if (!quiet)
{
- Cache.log.error("Unexpected object in SeqSet map : "+ key.getClass());
+ Console.error("Unexpected object in SeqSet map : "+ key.getClass());
}
}
}
}
}
}
@@
-265,7
+266,7
@@
public class SeqsetUtils
{
sb.append(", " + i.nextElement().getName());
}
{
sb.append(", " + i.nextElement().getName());
}
- Cache.log.warn(sb.toString());
+ Console.warn(sb.toString());
return false;
}
return false;
}