From: jprocter Date: Thu, 17 Apr 2008 15:04:16 +0000 (+0000) Subject: todos X-Git-Tag: Release_2_4~115 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8299aae37669227dfa5468a51d922d38595ae7bf;p=jalview.git todos --- diff --git a/src/jalview/ws/MsaWSThread.java b/src/jalview/ws/MsaWSThread.java index 3be0c56..8d373ac 100644 --- a/src/jalview/ws/MsaWSThread.java +++ b/src/jalview/ws/MsaWSThread.java @@ -522,6 +522,7 @@ class MsaWSThread private jalview.datamodel.Sequence[] getVamsasAlignment( vamsas.objects.simple.Alignment valign) { + // TODO: refactor to helper class for vamsas.objects.simple objects vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs(); jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs. length]; @@ -606,7 +607,6 @@ class MsaWSThread Vector alorders = new Vector(); SequenceI[][] results = new SequenceI[jobs.length][]; AlignmentOrder[] orders = new AlignmentOrder[jobs.length]; - for (int j = 0; j < jobs.length; j++) { if (jobs[j].hasResults()) @@ -615,6 +615,7 @@ class MsaWSThread alorders.add(res[1]); results[j] = (SequenceI[]) res[0]; orders[j] = (AlignmentOrder) res[1]; + // SequenceI[] alignment = input.getUpdated } else @@ -632,7 +633,7 @@ class MsaWSThread SequenceI[] alignment = (SequenceI[]) newview[0]; ColumnSelection columnselection = (ColumnSelection) newview[1]; Alignment al = new Alignment(alignment); - + // TODO: add 'provenance' property to alignment from the method notes accompanying each subjob if (dataset != null) { al.setDataset(dataset); @@ -709,7 +710,7 @@ class MsaWSThread else { System.out.println("MERGE WITH OLD FRAME"); - + // TODO: modify alignment in original frame, replacing old for new alignment using the commands.EditCommand model to ensure the update can be undone } }