X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=45fc0df055332438c83276ef852bc688e13fbcb1;hb=c6016c2fdffb1f7f84e44fbc0a1c0630d89ca17e;hp=d179355ade6c4639d958677b22bb4ea5fa71b279;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index d179355..45fc0df 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.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 2.5) + * Copyright (C) 2010 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.gui; @@ -30,6 +29,7 @@ import javax.swing.*; import org.jibble.epsgraphics.*; import jalview.analysis.*; +import jalview.commands.OrderCommand; import jalview.datamodel.*; import jalview.io.*; import jalview.jbgui.*; @@ -56,17 +56,17 @@ public class TreePanel extends GTreePanel * Creates a new TreePanel object. * * @param av - * DOCUMENT ME! + * DOCUMENT ME! * @param seqVector - * DOCUMENT ME! + * DOCUMENT ME! * @param type - * DOCUMENT ME! + * DOCUMENT ME! * @param pwtype - * DOCUMENT ME! + * DOCUMENT ME! * @param s - * DOCUMENT ME! + * DOCUMENT ME! * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public TreePanel(AlignmentPanel ap, String type, String pwtype) { @@ -82,15 +82,15 @@ public class TreePanel extends GTreePanel * Creates a new TreePanel object. * * @param av - * DOCUMENT ME! + * DOCUMENT ME! * @param seqVector - * DOCUMENT ME! + * DOCUMENT ME! * @param newtree - * DOCUMENT ME! + * DOCUMENT ME! * @param type - * DOCUMENT ME! + * DOCUMENT ME! * @param pwtype - * DOCUMENT ME! + * DOCUMENT ME! */ public TreePanel(AlignmentPanel ap, String type, String pwtype, NewickFile newtree) @@ -140,6 +140,10 @@ public class TreePanel extends GTreePanel if (tree == null) { System.out.println("tree is null"); + // TODO: deal with case when a change event is received whilst a + // tree is still being calculated - should save reference for + // processing message later. + return; } if (evt.getNewValue() == null) { @@ -149,7 +153,7 @@ public class TreePanel extends GTreePanel tree.UpdatePlaceHolders((Vector) evt.getNewValue()); treeCanvas.nameHash.clear(); // reset the mapping between canvas - // rectangles and leafnodes + // rectangles and leafnodes repaint(); } } @@ -290,7 +294,10 @@ public class TreePanel extends GTreePanel treeCanvas.setTree(tree); treeCanvas.repaint(); av.setCurrentTree(tree); - + if (av.getSortByTree()) + { + sortByTree_actionPerformed(null); + } } } @@ -331,7 +338,7 @@ public class TreePanel extends GTreePanel * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void textbox_actionPerformed(ActionEvent e) { @@ -369,7 +376,7 @@ public class TreePanel extends GTreePanel * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void saveAsNewick_actionPerformed(ActionEvent e) { @@ -408,7 +415,7 @@ public class TreePanel extends GTreePanel * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void printMenu_actionPerformed(ActionEvent e) { @@ -479,7 +486,7 @@ public class TreePanel extends GTreePanel * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void fitToWindow_actionPerformed(ActionEvent e) { @@ -488,10 +495,28 @@ public class TreePanel extends GTreePanel } /** + * sort the associated alignment view by the current tree. + * + * @param e + */ + public void sortByTree_actionPerformed(ActionEvent e) + { + AlignmentPanel ap = av.getAlignPanel(); + SequenceI[] oldOrder = av.getAlignment().getSequencesArray(); + AlignmentSorter.sortByTree(av.getAlignment(), tree); + + ap.alignFrame.addHistoryItem(new OrderCommand("Tree Sort", oldOrder, + av.alignment)); + + ap.paintAlignment(true); + + } + + /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void font_actionPerformed(ActionEvent e) { @@ -520,7 +545,7 @@ public class TreePanel extends GTreePanel * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void distanceMenu_actionPerformed(ActionEvent e) { @@ -531,7 +556,7 @@ public class TreePanel extends GTreePanel * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void bootstrapMenu_actionPerformed(ActionEvent e) { @@ -542,7 +567,7 @@ public class TreePanel extends GTreePanel * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void placeholdersMenu_actionPerformed(ActionEvent e) { @@ -553,7 +578,7 @@ public class TreePanel extends GTreePanel * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void epsTree_actionPerformed(ActionEvent e) { @@ -625,7 +650,7 @@ public class TreePanel extends GTreePanel * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void pngTree_actionPerformed(ActionEvent e) { @@ -668,4 +693,75 @@ public class TreePanel extends GTreePanel ex.printStackTrace(); } } + + /** + * change node labels to the annotation referred to by labelClass TODO: + * promote to a datamodel modification that can be undone TODO: make argument + * one case of a generic transformation function ie { undoStep = apply(Tree, + * TransformFunction)}; + * + * @param labelClass + */ + public void changeNames(final String labelClass) + { + tree.applyToNodes(new NodeTransformI() + { + + public void transform(BinaryNode node) + { + if (node instanceof SequenceNode + && !((SequenceNode) node).isPlaceholder() + && !((SequenceNode) node).isDummy()) + { + String newname = null; + SequenceI sq = (SequenceI) ((SequenceNode) node).element(); + if (sq != null) + { + // search dbrefs, features and annotation + DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(sq + .getDBRef(), new String[] + { labelClass.toUpperCase() }); + if (refs != null) + { + for (int i = 0; i < refs.length; i++) + { + if (newname == null) + { + newname = new String(refs[i].getAccessionId()); + } + else + { + newname = newname + "; " + refs[i].getAccessionId(); + } + } + } + if (newname == null) + { + SequenceFeature sf[] = sq.getSequenceFeatures(); + for (int i = 0; sf != null && i < sf.length; i++) + { + if (sf[i].getType().equals(labelClass)) + { + if (newname == null) + { + newname = new String(sf[i].getDescription()); + } + else + { + newname = newname + "; " + sf[i].getDescription(); + } + } + } + } + } + if (newname != null) + { + String oldname = ((SequenceNode) node).getName(); + // TODO : save in the undo object for this modification. + ((SequenceNode) node).setName(newname); + } + } + } + }); + } }