X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;fp=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;h=7d57650aa8c920317c698e32ed84f8f602d0960e;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=00e4fbc97ce7334c5258f018a01e001af3a74103;hpb=c4e814d2930b175c789c2a004801b7b8a1dacd32;p=jalview.git diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java index 00e4fbc..7d57650 100644 --- a/src/jalview/io/vamsas/Tree.java +++ b/src/jalview/io/vamsas/Tree.java @@ -128,7 +128,7 @@ public class Tree extends DatastoreItem } } catch (Exception e) { - Cache.log.warn("Problems parsing treefile '" + Cache.warn("Problems parsing treefile '" + tree.getNewick(0).getContent() + "'", e); } } @@ -141,7 +141,7 @@ public class Tree extends DatastoreItem @Override public void conflict() { - Cache.log.info( + Cache.info( "Update (with conflict) from vamsas document to alignment associated tree not implemented yet."); } @@ -186,7 +186,7 @@ public class Tree extends DatastoreItem * idata[0] != null) { inputData = (AlignmentView) idata[0]; } ntree = * getNtree(); title = tree.getNewick(0).getTitle(); if (title == null || * title.length() == 0) { title = tree.getTitle(); // hack!!!! } } catch - * (Exception e) { Cache.log.warn("Problems parsing treefile '" + + * (Exception e) { Cache.warn("Problems parsing treefile '" + * tree.getNewick(0).getContent() + "'", e); } */ log.debug("Update the local tree in jalview from the document."); @@ -214,7 +214,7 @@ public class Tree extends DatastoreItem */ private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp) { - Cache.log.debug("Making Tree provenance for " + tp.getTitle()); + Cache.debug("Making Tree provenance for " + tp.getTitle()); Provenance prov = new Provenance(); prov.addEntry(new Entry()); prov.getEntry(0).setAction("imported " + tp.getTitle()); @@ -259,7 +259,7 @@ public class Tree extends DatastoreItem vInput.addSeg(visSeg); } } - Cache.log.debug("Finished Tree provenance for " + tp.getTitle()); + Cache.debug("Finished Tree provenance for " + tp.getTitle()); return prov; } @@ -297,7 +297,7 @@ public class Tree extends DatastoreItem } if (alsq.size() < sequences.length) { - Cache.log.warn( + Cache.warn( "Not recovered all alignment sequences for given set of input sequence CIGARS"); } return alsq; @@ -319,7 +319,7 @@ public class Tree extends DatastoreItem if (tp.getTree() == null) { - Cache.log.warn( + Cache.warn( "Not updating SequenceTreeMap for " + tree.getVorbaId()); return; } @@ -532,7 +532,7 @@ public class Tree extends DatastoreItem { if (tp.getEntry(pe).getInputCount() > 1) { - Cache.log.warn( + Cache.warn( "Ignoring additional input spec in provenance entry " + tp.getEntry(pe).toString()); } @@ -589,7 +589,7 @@ public class Tree extends DatastoreItem // bidirection alignments yet. if (to < se[1]) { - Cache.log.warn("Ignoring invalid segment in InputData spec."); + Cache.warn("Ignoring invalid segment in InputData spec."); } else { @@ -612,7 +612,7 @@ public class Tree extends DatastoreItem return new Object[] { new AlignmentView(view), jal }; } } - Cache.log.debug( + Cache.debug( "Returning null for input data recovery from provenance."); return null; } @@ -658,7 +658,7 @@ public class Tree extends DatastoreItem return true; } catch (Exception e) { - Cache.log.debug("Failed to parse newick tree string", e); + Cache.debug("Failed to parse newick tree string", e); } return false; }