X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;h=5ea97fbe12f9bcd30763a300098f701d90046d26;hb=faf491e024f9835435f5dd6c20a033250dd9297d;hp=1b7a8bf1d8d8765ebafbd8f50886259effcfe466;hpb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;p=jalview.git diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java index 1b7a8bf..5ea97fb 100644 --- a/src/jalview/io/vamsas/Tree.java +++ b/src/jalview/io/vamsas/Tree.java @@ -319,11 +319,10 @@ public class Tree extends DatastoreItem if (tp.getTree() == null) { - Console.warn( - "Not updating SequenceTreeMap for " + tree.getVorbaId()); + Console.warn("Not updating SequenceTreeMap for " + tree.getVorbaId()); return; } - Vector leaves = tp.getTree() + Vector leaves = tp.getTree() .findLeaves(tp.getTree().getTopNode()); Treenode[] tn = tree.getTreenode(); // todo: select nodes for this // particular tree @@ -359,7 +358,7 @@ public class Tree extends DatastoreItem } if (jvseq instanceof SequenceI) { - leaf.setElement(jvseq); + leaf.setElement((SequenceI) jvseq); leaf.setPlaceholder(false); } else @@ -382,7 +381,7 @@ public class Tree extends DatastoreItem */ public Treenode[] makeTreeNodes(TreeModel treeModel, Newick newick) { - Vector leaves = treeModel + Vector leaves = treeModel .findLeaves(treeModel.getTopNode()); Vector tnv = new Vector(); Enumeration l = leaves.elements(); @@ -395,8 +394,7 @@ public class Tree extends DatastoreItem { if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder()) { - Object assocseq = ((jalview.datamodel.SequenceNode) tnode) - .element(); + Object assocseq = ((BinaryNode) tnode).element(); if (assocseq instanceof SequenceI) { Vobject vobj = this.getjv2vObj(assocseq); @@ -417,11 +415,12 @@ public class Tree extends DatastoreItem } else { - System.err.println("WARNING: Unassociated treeNode " - + tnode.element().toString() + " " - + ((tnode.getName() != null) - ? " label " + tnode.getName() - : "")); + jalview.bin.Console + .errPrintln("WARNING: Unassociated treeNode " + + tnode.element().toString() + " " + + ((tnode.getName() != null) + ? " label " + tnode.getName() + : "")); } } } @@ -468,7 +467,7 @@ public class Tree extends DatastoreItem occurence = Integer.valueOf(oval).intValue(); } catch (Exception e) { - System.err.println("Invalid nodespec '" + nodespec + "'"); + jalview.bin.Console.errPrintln("Invalid nodespec '" + nodespec + "'"); return null; } jalview.datamodel.BinaryNode bn = null; @@ -532,9 +531,8 @@ public class Tree extends DatastoreItem { if (tp.getEntry(pe).getInputCount() > 1) { - Console.warn( - "Ignoring additional input spec in provenance entry " - + tp.getEntry(pe).toString()); + Console.warn("Ignoring additional input spec in provenance entry " + + tp.getEntry(pe).toString()); } // LATER: deal sensibly with multiple inputs Input vInput = tp.getEntry(pe).getInput(0);