From e2e2b85d7a8e3d7ed6926ef1bf55eb2328e744d1 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 27 Feb 2017 14:56:22 +0000 Subject: [PATCH] JAL-1632 similarity options on TreeChooser panel affect tree by PID --- src/jalview/analysis/NJTree.java | 3 +- .../analysis/scoremodels/SimilarityParams.java | 2 +- src/jalview/bin/Jalview.java | 10 +- src/jalview/gui/AlignFrame.java | 65 +++++----- src/jalview/gui/Jalview2XML.java | 2 +- src/jalview/gui/Jalview2XML_V1.java | 2 +- src/jalview/gui/TreeChooser.java | 104 ++++++++++++---- src/jalview/gui/TreePanel.java | 129 ++++++++------------ src/jalview/io/VamsasAppDatastore.java | 2 +- src/jalview/ws/jws1/SeqSearchWSThread.java | 2 +- 10 files changed, 170 insertions(+), 151 deletions(-) diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java index cc0e473..255d6df 100644 --- a/src/jalview/analysis/NJTree.java +++ b/src/jalview/analysis/NJTree.java @@ -20,7 +20,6 @@ */ package jalview.analysis; -import jalview.analysis.scoremodels.SimilarityParams; import jalview.api.analysis.DistanceScoreModelI; import jalview.api.analysis.ScoreModelI; import jalview.api.analysis.SimilarityParamsI; @@ -316,7 +315,7 @@ public class NJTree * compute similarity and invert it to give a distance measure */ MatrixI result = ((SimilarityScoreModelI) sm).findSimilarities( - seqData, SimilarityParams.Jalview); + seqData, scoreOptions); result.reverseRange(true); distances = result; } diff --git a/src/jalview/analysis/scoremodels/SimilarityParams.java b/src/jalview/analysis/scoremodels/SimilarityParams.java index 4cc5b1f..b6f2ba2 100644 --- a/src/jalview/analysis/scoremodels/SimilarityParams.java +++ b/src/jalview/analysis/scoremodels/SimilarityParams.java @@ -65,7 +65,7 @@ public class SimilarityParams implements SimilarityParamsI * if true, the denominator is the shorter sequence length (possibly * including gaps) */ - SimilarityParams(boolean includeGapGap, boolean matchGap, + public SimilarityParams(boolean includeGapGap, boolean matchGap, boolean includeGaps, boolean shortestLength) { includeGappedColumns = includeGapGap; diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 966e952..954bb34 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -578,18 +578,14 @@ public class Jalview data = aparser.getValue("tree", true); if (data != null) { - jalview.io.NewickFile fin = null; try { System.out.println("CMD [-tree " + data + "] executed successfully!"); - fin = new NewickFile(data, + NewickFile nf = new NewickFile(data, AppletFormatAdapter.checkProtocol(data)); - if (fin != null) - { - af.getViewport().setCurrentTree( - af.ShowNewickTree(fin, data).getTree()); - } + af.getViewport().setCurrentTree( + af.showNewickTree(nf, data).getTree()); } catch (IOException ex) { System.err.println("Couldn't add tree " + data); diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 4fd80b2..681a700 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -24,7 +24,6 @@ import jalview.analysis.AlignmentSorter; import jalview.analysis.AlignmentUtils; import jalview.analysis.CrossRef; import jalview.analysis.Dna; -import jalview.analysis.NJTree; import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; import jalview.api.AlignExportSettingI; @@ -36,6 +35,7 @@ import jalview.api.FeatureSettingsControllerI; import jalview.api.SplitContainerI; import jalview.api.ViewStyleI; import jalview.api.analysis.ScoreModelI; +import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.commands.CommandI; @@ -3588,17 +3588,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! + * Constructs a tree panel and adds it to the desktop * * @param type - * DOCUMENT ME! - * @param pwType - * DOCUMENT ME! - * @param title - * DOCUMENT ME! + * tree type (NJ or AV) + * @param sm + * distance or similarity score model used to compute the tree + * @param options + * parameters for the distance or similarity calculation */ - void newTreePanel(String type, String pwType, String title) + void newTreePanel(String type, ScoreModelI sm, SimilarityParamsI options) { + String frameTitle = ""; TreePanel tp; if (viewport.getSelectionGroup() != null @@ -3637,8 +3638,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - title = title + " on region"; - tp = new TreePanel(alignPanel, type, pwType); + tp = new TreePanel(alignPanel, type, sm, options); + frameTitle = tp.getPanelTitle() + " on region"; } else { @@ -3662,19 +3663,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - tp = new TreePanel(alignPanel, type, pwType); + tp = new TreePanel(alignPanel, type, sm, options); + frameTitle = tp.getPanelTitle(); } - title += " from "; + frameTitle += " from "; if (viewport.viewName != null) { - title += viewport.viewName + " of "; + frameTitle += viewport.viewName + " of "; } - title += this.title; + frameTitle += this.title; - Desktop.addInternalFrame(tp, title, 600, 500); + Desktop.addInternalFrame(tp, frameTitle, 600, 500); } /** @@ -3950,13 +3952,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (value == JalviewFileChooser.APPROVE_OPTION) { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - jalview.io.NewickFile fin = null; + String filePath = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", filePath); + NewickFile fin = null; try { - fin = new NewickFile(choice, DataSourceType.FILE); - viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); + fin = new NewickFile(filePath, DataSourceType.FILE); + viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); } catch (Exception ex) { JvOptionPane @@ -3978,19 +3980,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - public TreePanel ShowNewickTree(NewickFile nf, String title) + public TreePanel showNewickTree(NewickFile nf, String treeTitle) { - return ShowNewickTree(nf, title, 600, 500, 4, 5); + return showNewickTree(nf, treeTitle, 600, 500, 4, 5); } - public TreePanel ShowNewickTree(NewickFile nf, String title, int w, + public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w, int h, int x, int y) { - return ShowNewickTree(nf, title, null, w, h, x, y); + return showNewickTree(nf, treeTitle, null, w, h, x, y); } /** - * Add a treeviewer for the tree extracted from a newick file object to the + * Add a treeviewer for the tree extracted from a Newick file object to the * current alignment view * * @param nf @@ -4009,7 +4011,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * position * @return TreePanel handle */ - public TreePanel ShowNewickTree(NewickFile nf, String title, + public TreePanel showNewickTree(NewickFile nf, String treeTitle, AlignmentView input, int w, int h, int x, int y) { TreePanel tp = null; @@ -4020,7 +4022,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (nf.getTree() != null) { - tp = new TreePanel(alignPanel, NJTree.FROM_FILE, title, nf, input); + tp = new TreePanel(alignPanel, nf, treeTitle, input); tp.setSize(w, h); @@ -4029,7 +4031,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, tp.setLocation(x, y); } - Desktop.addInternalFrame(tp, title, w, h); + Desktop.addInternalFrame(tp, treeTitle, w, h); } } catch (Exception ex) { @@ -5631,13 +5633,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ColourMenuHelper.setColourSelected(colourMenu, schemeName); } - - public void newTreePanel(String treeType, ScoreModelI sm) - { - String scoreModelName = sm.getName(); - final String ttl = TreePanel.getPanelTitle(treeType, scoreModelName); - newTreePanel(treeType, scoreModelName, ttl); - } } class PrintThread extends Thread diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 3ac453f..68184e9 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -3666,7 +3666,7 @@ public class Jalview2XML TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId()); if (tp == null) { - tp = af.ShowNewickTree( + tp = af.showNewickTree( new jalview.io.NewickFile(tree.getNewick()), tree.getTitle(), tree.getWidth(), tree.getHeight(), tree.getXpos(), tree.getYpos()); diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java index e751a2c..70a341d 100755 --- a/src/jalview/gui/Jalview2XML_V1.java +++ b/src/jalview/gui/Jalview2XML_V1.java @@ -464,7 +464,7 @@ public class Jalview2XML_V1 Tree tree = jms.getTree(t); - TreePanel tp = af.ShowNewickTree( + TreePanel tp = af.showNewickTree( new jalview.io.NewickFile(tree.getNewick()), tree.getTitle(), tree.getWidth(), tree.getHeight(), tree.getXpos(), tree.getYpos()); diff --git a/src/jalview/gui/TreeChooser.java b/src/jalview/gui/TreeChooser.java index 8e2bff0..3542532 100644 --- a/src/jalview/gui/TreeChooser.java +++ b/src/jalview/gui/TreeChooser.java @@ -22,18 +22,24 @@ package jalview.gui; import jalview.analysis.NJTree; import jalview.analysis.scoremodels.ScoreModels; +import jalview.analysis.scoremodels.SimilarityParams; import jalview.api.analysis.ScoreModelI; +import jalview.api.analysis.SimilarityParamsI; import jalview.util.MessageManager; import java.awt.Color; import java.awt.FlowLayout; import java.awt.Font; +import java.awt.GridLayout; import java.awt.event.ActionEvent; +import java.beans.PropertyVetoException; import javax.swing.ButtonGroup; import javax.swing.JButton; +import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JInternalFrame; +import javax.swing.JLabel; import javax.swing.JLayeredPane; import javax.swing.JPanel; import javax.swing.JRadioButton; @@ -57,6 +63,14 @@ public class TreeChooser extends JPanel private ButtonGroup treeTypes; + private JCheckBox includeGaps; + + private JCheckBox matchGaps; + + private JCheckBox includeGappedColumns; + + private JCheckBox shorterSequence; + /** * Constructor * @@ -68,12 +82,22 @@ public class TreeChooser extends JPanel init(); } + /** + * Lays out the panel and adds it to the desktop + */ void init() { frame = new JInternalFrame(); frame.setContentPane(this); this.setBackground(Color.white); + /* + * Layout consists of 4 panels: + * - first with choice of tree method NJ or AV + * - second with choice of score model + * - third with score model parameter options + * - fourth with OK and Cancel + */ neighbourJoining = new JRadioButton( MessageManager.getString("label.tree_calc_nj")); neighbourJoining.setOpaque(false); @@ -83,7 +107,14 @@ public class TreeChooser extends JPanel treeTypes.add(neighbourJoining); treeTypes.add(averageDistance); neighbourJoining.setSelected(true); - + JPanel treeChoicePanel = new JPanel(); + treeChoicePanel.setOpaque(false); + treeChoicePanel.add(neighbourJoining); + treeChoicePanel.add(averageDistance); + + /* + * score model drop-down + */ matrixNames = new JComboBox(); ScoreModels scoreModels = ScoreModels.getInstance(); for (ScoreModelI sm : scoreModels.getModels()) @@ -94,7 +125,28 @@ public class TreeChooser extends JPanel matrixNames.addItem(sm.getName()); } } - + JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); + scoreModelPanel.setOpaque(false); + scoreModelPanel.add(matrixNames, FlowLayout.LEFT); + + /* + * score model parameters + */ + JPanel paramsPanel = new JPanel(new GridLayout(5, 1)); + paramsPanel.setOpaque(false); + includeGaps = new JCheckBox("Include gaps"); + matchGaps = new JCheckBox("Match gaps"); + includeGappedColumns = new JCheckBox("Include gapped columns"); + shorterSequence = new JCheckBox("Match on shorter sequence"); + paramsPanel.add(new JLabel("Pairwise sequence scoring options")); + paramsPanel.add(includeGaps); + paramsPanel.add(matchGaps); + paramsPanel.add(includeGappedColumns); + paramsPanel.add(shorterSequence); + + /* + * OK / Cancel buttons + */ JButton ok = new JButton(MessageManager.getString("action.ok")); ok.setFont(VERDANA_11PT); ok.addActionListener(new java.awt.event.ActionListener() @@ -105,7 +157,6 @@ public class TreeChooser extends JPanel ok_actionPerformed(e); } }); - JButton cancel = new JButton(MessageManager.getString("action.cancel")); cancel.setFont(VERDANA_11PT); cancel.addActionListener(new java.awt.event.ActionListener() @@ -116,25 +167,18 @@ public class TreeChooser extends JPanel cancel_actionPerformed(e); } }); + JPanel actionPanel = new JPanel(); + actionPanel.setOpaque(false); + actionPanel.add(ok); + actionPanel.add(cancel); - JPanel p1 = new JPanel(); - p1.setOpaque(false); - p1.add(neighbourJoining); - p1.add(averageDistance); - this.add(p1); - JPanel p2 = new JPanel(new FlowLayout(FlowLayout.LEFT)); - p2.setOpaque(false); - p2.add(matrixNames, FlowLayout.LEFT); - this.add(p2); - JPanel p3 = new JPanel(); - p3.setOpaque(false); - p3.add(ok); - p3.add(cancel); - this.add(p3); + this.add(treeChoicePanel); + this.add(scoreModelPanel); + this.add(paramsPanel); + this.add(actionPanel); Desktop.addInternalFrame(frame, - MessageManager.getString("label.choose_tree"), - 400, 200, false); + MessageManager.getString("label.choose_tree"), 400, 400, false); frame.setLayer(JLayeredPane.PALETTE_LAYER); } @@ -146,19 +190,29 @@ public class TreeChooser extends JPanel */ protected void ok_actionPerformed(ActionEvent e) { + String treeType = neighbourJoining.isSelected() ? NJTree.NEIGHBOUR_JOINING + : NJTree.AVERAGE_DISTANCE; + ScoreModelI sm = ScoreModels.getInstance().forName( + matrixNames.getSelectedItem().toString()); + SimilarityParamsI params = getSimilarityParameters(); + af.newTreePanel(treeType, sm, params); + try { frame.setClosed(true); - String treeType = neighbourJoining.isSelected() ? NJTree.NEIGHBOUR_JOINING - : NJTree.AVERAGE_DISTANCE; - ScoreModelI sm = ScoreModels.getInstance().forName( - matrixNames.getSelectedItem().toString()); - af.newTreePanel(treeType, sm); - } catch (Exception ex) + } catch (PropertyVetoException ex) { } } + private SimilarityParamsI getSimilarityParameters() + { + SimilarityParamsI params = new SimilarityParams( + includeGappedColumns.isSelected(), matchGaps.isSelected(), + includeGaps.isSelected(), shorterSequence.isSelected()); + return params; + } + /** * Closes dialog on cancel * diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 857e77c..9ac2872 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -22,9 +22,8 @@ package jalview.gui; import jalview.analysis.AlignmentSorter; import jalview.analysis.NJTree; -import jalview.analysis.scoremodels.ScoreModels; -import jalview.analysis.scoremodels.SimilarityParams; import jalview.api.analysis.ScoreModelI; +import jalview.api.analysis.SimilarityParamsI; import jalview.api.analysis.ViewBasedAnalysisI; import jalview.bin.Cache; import jalview.commands.CommandI; @@ -72,9 +71,13 @@ import org.jibble.epsgraphics.EpsGraphics2D; */ public class TreePanel extends GTreePanel { - String type; + String treeType; - String pwtype; + ScoreModelI scoreModel; // if tree computed + + String treeTitle; // if tree loaded + + SimilarityParamsI similarityParams; TreeCanvas treeCanvas; @@ -85,34 +88,29 @@ public class TreePanel extends GTreePanel /** * Creates a new TreePanel object. * - * @param av - * DOCUMENT ME! - * @param seqVector - * DOCUMENT ME! + * @param ap * @param type - * DOCUMENT ME! - * @param pwtype - * DOCUMENT ME! - * @param s - * DOCUMENT ME! - * @param e - * DOCUMENT ME! + * @param sm + * @param options */ - public TreePanel(AlignmentPanel ap, String type, String pwtype) + public TreePanel(AlignmentPanel ap, String type, ScoreModelI sm, + SimilarityParamsI options) { super(); - initTreePanel(ap, type, pwtype, null, null); + this.similarityParams = options; + initTreePanel(ap, type, sm, null, null); // We know this tree has distances. JBPNote TODO: prolly should add this as // a userdefined default // showDistances(true); } - public TreePanel(AlignmentPanel av, String type, String pwtype, - NewickFile newtree, AlignmentView inputData) + public TreePanel(AlignmentPanel alignPanel, NewickFile newtree, + String theTitle, AlignmentView inputData) { super(); - initTreePanel(av, type, pwtype, newtree, inputData); + this.treeTitle = theTitle; + initTreePanel(alignPanel, null, null, newtree, inputData); } public AlignmentI getAlignment() @@ -125,13 +123,13 @@ public class TreePanel extends GTreePanel return treeCanvas.av; } - void initTreePanel(AlignmentPanel ap, String type, String pwtype, + void initTreePanel(AlignmentPanel ap, String type, ScoreModelI sm, NewickFile newTree, AlignmentView inputData) { av = ap.av; - this.type = type; - this.pwtype = pwtype; + this.treeType = type; + this.scoreModel = sm; treeCanvas = new TreeCanvas(this, ap, scrollPane); scrollPane.setViewportView(treeCanvas); @@ -247,17 +245,17 @@ public class TreePanel extends GTreePanel { NewickFile newtree; - jalview.datamodel.AlignmentView odata = null; + AlignmentView odata = null; - public TreeLoader(NewickFile newtree) + public TreeLoader(NewickFile newickFile) { - this.newtree = newtree; - if (newtree != null) + this.newtree = newickFile; + if (newickFile != null) { // Must be outside run(), as Jalview2XML tries to // update distance/bootstrap visibility at the same time - showBootstrap(newtree.HasBootstrap()); - showDistances(newtree.HasDistances()); + showBootstrap(newickFile.HasBootstrap()); + showDistances(newickFile.HasDistances()); } } @@ -283,26 +281,8 @@ public class TreePanel extends GTreePanel } else { - int start, end; - SequenceI[] seqs; - boolean selview = av.getSelectionGroup() != null - && av.getSelectionGroup().getSize() > 1; - AlignmentView seqStrings = av.getAlignmentView(selview); - if (!selview) - { - start = 0; - end = av.getAlignment().getWidth(); - seqs = av.getAlignment().getSequencesArray(); - } - else - { - start = av.getSelectionGroup().getStartRes(); - end = av.getSelectionGroup().getEndRes() + 1; - seqs = av.getSelectionGroup().getSequencesInOrder( - av.getAlignment()); - } - ScoreModelI sm = configureScoreModel(pwtype); - tree = new NJTree(av, type, sm, SimilarityParams.Jalview); + ScoreModelI sm = configureScoreModel(); + tree = new NJTree(av, treeType, sm, similarityParams); showDistances(true); } @@ -362,7 +342,7 @@ public class TreePanel extends GTreePanel { CutAndPasteTransfer cap = new CutAndPasteTransfer(); - String newTitle = getPanelTitle(type, pwtype); + String newTitle = getPanelTitle(); NewickFile fout = new NewickFile(tree.getTopNode()); try @@ -575,11 +555,11 @@ public class TreePanel extends GTreePanel public CommandI sortAlignmentIn(AlignmentPanel ap) { - AlignmentViewport av = ap.av; - SequenceI[] oldOrder = av.getAlignment().getSequencesArray(); - AlignmentSorter.sortByTree(av.getAlignment(), tree); + AlignmentViewport viewport = ap.av; + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByTree(viewport.getAlignment(), tree); CommandI undo; - undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment()); + undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment()); ap.paintAlignment(true); return undo; @@ -607,11 +587,11 @@ public class TreePanel extends GTreePanel return treeCanvas.font; } - public void setTreeFont(Font font) + public void setTreeFont(Font f) { if (treeCanvas != null) { - treeCanvas.setFont(font); + treeCanvas.setFont(f); } } @@ -834,8 +814,8 @@ public class TreePanel extends GTreePanel } if (newname != null) { - String oldname = ((SequenceNode) node).getName(); - // TODO : save in the undo object for this modification. + // String oldname = ((SequenceNode) node).getName(); + // TODO : save oldname in the undo object for this modification. ((SequenceNode) node).setName(newname); } } @@ -849,17 +829,13 @@ public class TreePanel extends GTreePanel * Neighbour Joining Using BLOSUM62 *

* For a tree loaded from file, just uses the file name - * - * @param treeType - * NJ or AV or FromFile - * @param modelOrFileName * @return */ - public static String getPanelTitle(String treeType, String modelOrFileName) + public String getPanelTitle() { - if (NJTree.FROM_FILE.equals(treeType)) + if (treeTitle != null) { - return modelOrFileName; + return treeTitle; } /* @@ -869,10 +845,10 @@ public class TreePanel extends GTreePanel + treeType.toLowerCase()); /* - * i18n description (if any) of score model used + * i18n description (if available) of score model used */ String smn = MessageManager.getStringOrReturn("label.score_model_", - modelOrFileName); + scoreModel.getName()); /* * put them together as Using @@ -883,27 +859,26 @@ public class TreePanel extends GTreePanel } /** - * Gets the score model for the given name. If the score model is one that - * requires to get state data from the current view, allow it to do so + * If the score model is one that requires to get state data from the current + * view, create and configure a new instance of it * - * @param sm * @return */ - protected ScoreModelI configureScoreModel(String modelName) + protected ScoreModelI configureScoreModel() { - ScoreModelI sm = ScoreModels.getInstance().forName(modelName); - if (sm instanceof ViewBasedAnalysisI) + if (scoreModel instanceof ViewBasedAnalysisI) { try { - sm = sm.getClass().newInstance(); - ((ViewBasedAnalysisI) sm).configureFromAlignmentView(treeCanvas.ap); + scoreModel = scoreModel.getClass().newInstance(); + ((ViewBasedAnalysisI) scoreModel) + .configureFromAlignmentView(treeCanvas.ap); } catch (Exception q) { Cache.log.error("Couldn't create a scoremodel instance for " - + sm.getName()); + + scoreModel.getName()); } } - return sm; + return scoreModel; } } diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java index 2c35547..1cab8ca 100644 --- a/src/jalview/io/VamsasAppDatastore.java +++ b/src/jalview/io/VamsasAppDatastore.java @@ -1942,7 +1942,7 @@ public class VamsasAppDatastore TreePanel tp = null; if (vstree.isValidTree()) { - tp = alignFrame.ShowNewickTree(vstree.getNewickTree(), + tp = alignFrame.showNewickTree(vstree.getNewickTree(), vstree.getTitle(), vstree.getInputData(), 600, 500, t * 20 + 50, t * 20 + 50); diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java index b14917e..edc9ae8 100644 --- a/src/jalview/ws/jws1/SeqSearchWSThread.java +++ b/src/jalview/ws/jws1/SeqSearchWSThread.java @@ -666,7 +666,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); if (nf != null) { - af.ShowNewickTree(nf, MessageManager.formatMessage( + af.showNewickTree(nf, MessageManager.formatMessage( "label.tree_from", new String[] { this.alTitle })); } // initialise with same renderer settings as in parent alignframe. -- 1.7.10.2