From: jprocter Date: Mon, 8 Jun 2009 10:53:26 +0000 (+0000) Subject: minor optimization. apply gpl development license X-Git-Tag: Release_2_5~292 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a8401d0452aac399083c1a89fb614adbfaa98ff8;p=jalview.git minor optimization. apply gpl development license --- diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java index 34219b4..fe971d9 100644 --- a/src/jalview/io/VamsasAppDatastore.java +++ b/src/jalview/io/VamsasAppDatastore.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -259,16 +259,19 @@ public class VamsasAppDatastore try { jalview.datamodel.AlignmentI jal = av.getAlignment(); + jalview.datamodel.AlignmentI jds = jal.getDataset(); boolean nw = false; VAMSAS root = null; // will be resolved based on Dataset Parent. // ///////////////////////////////////////// // SAVE THE DATASET DataSet dataset = null; - if (jal.getDataset() == null) + if (jds == null) { Cache.log.warn("Creating new dataset for an alignment."); jal.setDataset(null); + jds = jal.getDataset(); } + // try and get alignment and association for sequence set id Alignment alignment = (Alignment) getjv2vObj(av.getSequenceSetId()); @@ -277,7 +280,7 @@ public class VamsasAppDatastore dataset = (DataSet) alignment.getV_parent(); } else { // is the dataset already registered - dataset = (DataSet) getjv2vObj(jal.getDataset()); + dataset = (DataSet) getjv2vObj(jds); } if (dataset == null) @@ -285,8 +288,7 @@ public class VamsasAppDatastore // it might be that one of the dataset sequences does actually have a // binding, so search for it indirectly. If it does, then the local jalview dataset // must be merged with the existing vamsas dataset. - jalview.datamodel.SequenceI[] jdatset = jal.getDataset() - .getSequencesArray(); + jalview.datamodel.SequenceI[] jdatset = jds.getSequencesArray(); for (int i = 0; i < jdatset.length; i++) { Vobject vbound = getjv2vObj(jdatset[i]); @@ -321,7 +323,7 @@ public class VamsasAppDatastore root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying. dataset = new DataSet(); root.addDataSet(dataset); - bindjvvobj(jal.getDataset(), dataset); + bindjvvobj(jds, dataset); dataset.setProvenance(dummyProvenance()); // dataset.getProvenance().addEntry(provEntry); nw = true;