X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=5a246f8d84f83fd644cc6a03ebd1d8da250e8f01;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=e2ed9b451ca94bd64da7c0a675835ad4c1ab205c;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java index e2ed9b4..5a246f8 100755 --- a/src/jalview/analysis/SeqsetUtils.java +++ b/src/jalview/analysis/SeqsetUtils.java @@ -21,6 +21,7 @@ package jalview.analysis; import jalview.bin.Cache; +import jalview.bin.Console; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.HiddenMarkovModel; import jalview.datamodel.PDBEntry; @@ -121,7 +122,7 @@ public class SeqsetUtils { 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; } @@ -245,14 +246,14 @@ public class SeqsetUtils { 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) { - 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()); } - Cache.log.warn(sb.toString()); + Console.warn(sb.toString()); return false; }