X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;h=eab51f00cbd3cc272e0b59edb5d70f81a2870ed2;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=fd9294b739b07e1388e4f5b413b8705b87e61fc9;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java index fd9294b..eab51f0 100644 --- a/src/jalview/io/vamsas/Tree.java +++ b/src/jalview/io/vamsas/Tree.java @@ -1,20 +1,19 @@ /* - * 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 (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, 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 - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.io.vamsas; @@ -71,46 +70,14 @@ public class Tree extends DatastoreItem uk.ac.vamsas.objects.core.Tree vtree) { Tree toTree = new Tree(datastore, alignFrame, vtree); - } public Tree(VamsasAppDatastore datastore, jalview.gui.AlignFrame alignFrame, uk.ac.vamsas.objects.core.Tree vtree) { - super(datastore); - tree = vtree; - TreePanel tp = (TreePanel) getvObj2jv(tree); - if (tp != null) - { - if (tree.isUpdated()) - { - Cache.log - .info("Update from vamsas document to alignment associated tree not implemented yet."); - } - } - else - { - // make a new tree - Object[] idata = recoverInputData(tree.getProvenance()); - try - { - if (idata != null && 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 '" - + tree.getNewick(0).getContent() + "'", e); - } - } + super(datastore, vtree, TreePanel.class); + doJvUpdate(); } private NewickFile getNtree() throws IOException @@ -121,30 +88,110 @@ public class Tree extends DatastoreItem public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2, uk.ac.vamsas.objects.core.Alignment alignment2) { - super(datastore); + super(datastore, tp2, uk.ac.vamsas.objects.core.Tree.class); jal = jal2; - tp = tp2; + tp = (TreePanel) jvobj; alignment = alignment2; - tree = (uk.ac.vamsas.objects.core.Tree) getjv2vObj(tp); - if (tree == null) - { - add(); - } - else + tree = (uk.ac.vamsas.objects.core.Tree) vobj; + doSync(); + } + + /* + * (non-Javadoc) + * + * @see jalview.io.vamsas.DatastoreItem#addFromDocument() + */ + public void addFromDocument() + { + tree = (uk.ac.vamsas.objects.core.Tree) vobj; // vtree; + TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree); + // make a new tree + Object[] idata = recoverInputData(tree.getProvenance()); + try { - if (isModifiable(tree.getModifiable())) + if (idata != null && idata[0] != null) { - // synchronize(); // update(); - // verify any changes. - System.out.println("Update tree in document."); + inputData = (AlignmentView) idata[0]; } - else + ntree = getNtree(); + title = tree.getNewick(0).getTitle(); + if (title == null || title.length() == 0) { - // handle conflict - System.out.println("Add modified tree as new tree in document."); + title = tree.getTitle(); // hack!!!! } + } catch (Exception e) + { + Cache.log.warn("Problems parsing treefile '" + + tree.getNewick(0).getContent() + "'", e); + } + } + + /* + * (non-Javadoc) + * + * @see jalview.io.vamsas.DatastoreItem#conflict() + */ + public void conflict() + { + Cache.log + .info("Update (with conflict) from vamsas document to alignment associated tree not implemented yet."); + } + + /* + * (non-Javadoc) + * + * @see jalview.io.vamsas.DatastoreItem#update() + */ + public void updateToDoc() + { + if (isModifiable(tree.getModifiable())) + { + // synchronize(); // update(); + // verify any changes. + log.info("TODO: Update tree in document from jalview."); + } + else + { + // handle conflict + log.info("TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged."); + } + } + + /* + * (non-Javadoc) + * + * @see jalview.io.vamsas.DatastoreItem#updateFromDoc() + */ + public void updateFromDoc() + { + // should probably just open a new tree panel in the same place as the old + // one + // TODO: Tree.updateFromDoc + /* + * TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree); + * + * // make a new tree Object[] idata = + * recoverInputData(tree.getProvenance()); try { if (idata != null && + * 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 '" + + * tree.getNewick(0).getContent() + "'", e); } + */ + log.debug("Update the local tree in jalview from the document."); + + if (isModifiable(tree.getModifiable())) + { + // synchronize(); // update(); + // verify any changes. + log.debug("Update tree in document from jalview."); + } + else + { + // handle conflict + log.debug("Add modified jalview tree as new tree in document."); } } @@ -172,8 +219,8 @@ public class Tree extends DatastoreItem // or just correctly resolve the tree's seqData to the correct alignment // in // the document. - Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal, tp - .getTree().seqData.getSequences())); + Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal, + tp.getTree().seqData.getSequences())); Object[] alsqs = new Object[alsqrefs.size()]; alsqrefs.copyInto(alsqs); vInput.setObjRef(alsqs); @@ -245,7 +292,7 @@ public class Tree extends DatastoreItem * Update jalview newick representation with TreeNode map * * @param tp - * the treepanel that this tree is bound to. + * the treepanel that this tree is bound to. */ public void UpdateSequenceTreeMap(TreePanel tp) { @@ -299,9 +346,7 @@ public class Tree extends DatastoreItem else { leaf.setPlaceholder(true); - leaf - .setElement(new Sequence(leaf.getName(), - "THISISAPLACEHLDER")); + leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER")); } } } @@ -390,7 +435,7 @@ public class Tree extends DatastoreItem * * @param nodespec * @param leaves - * as returned from NJTree.findLeaves( .., ..) .. + * as returned from NJTree.findLeaves( .., ..) .. * @return */ private jalview.datamodel.BinaryNode findNodeSpec(String nodespec, @@ -430,7 +475,7 @@ public class Tree extends DatastoreItem * add jalview object to vamsas document * */ - public void add() + public void addToDocument() { tree = new uk.ac.vamsas.objects.core.Tree(); bindjvvobj(tp, tree);