X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=30e4305eec3291ac6bcfe5aeb8b25e47743a5dd5;hb=5d5099b75d2653cedf49bb98308dcb94202ed16e;hp=2d8e729c2c54833082ed5f8366e8b408d15f46ec;hpb=9a20ebe6844fd13b704e5b73fe752bd00230aba6;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 2d8e729..30e4305 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -20,6 +20,26 @@ */ package jalview.gui; +import java.awt.Font; +import java.awt.Graphics; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.beans.PropertyChangeEvent; +import java.beans.PropertyChangeListener; +import java.io.File; +import java.io.FileOutputStream; +import java.util.ArrayList; +import java.util.List; +import java.util.Locale; + +import javax.swing.ButtonGroup; +import javax.swing.JMenuItem; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; + +import org.jibble.epsgraphics.EpsGraphics2D; + import jalview.analysis.AlignmentSorter; import jalview.analysis.AverageDistanceTree; import jalview.analysis.NJTree; @@ -28,9 +48,12 @@ import jalview.analysis.TreeModel; import jalview.analysis.scoremodels.ScoreModels; import jalview.api.analysis.ScoreModelI; import jalview.api.analysis.SimilarityParamsI; +import jalview.bin.Cache; +import jalview.bin.Console; import jalview.commands.CommandI; import jalview.commands.OrderCommand; import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.BinaryNode; @@ -49,25 +72,6 @@ import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; -import java.awt.Font; -import java.awt.Graphics; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.beans.PropertyChangeEvent; -import java.beans.PropertyChangeListener; -import java.io.File; -import java.io.FileOutputStream; -import java.util.ArrayList; -import java.util.List; - -import javax.swing.ButtonGroup; -import javax.swing.JMenuItem; -import javax.swing.JRadioButtonMenuItem; -import javax.swing.event.InternalFrameAdapter; -import javax.swing.event.InternalFrameEvent; - -import org.jibble.epsgraphics.EpsGraphics2D; - /** * DOCUMENT ME! * @@ -102,6 +106,7 @@ public class TreePanel extends GTreePanel SimilarityParamsI options) { super(); + this.setFrameIcon(null); this.similarityParams = options; initTreePanel(ap, type, modelName, null, null); @@ -114,10 +119,40 @@ public class TreePanel extends GTreePanel String theTitle, AlignmentView inputData) { super(); + this.setFrameIcon(null); this.treeTitle = theTitle; initTreePanel(alignPanel, null, null, newtree, inputData); } + /** + * columnwise tree associated with positions in aa + * + * @param alignPanel + * @param fin + * @param title + * @param aa + */ + public TreePanel(AlignmentPanel alignPanel, NewickFile fin, + AlignmentAnnotation aa, String title) + { + super(); + columnWise=true; + assocAnnotation = aa; + this.setFrameIcon(null); + this.treeTitle = title; + initTreePanel(alignPanel, null, null, fin, null); + } + + boolean columnWise=false; + AlignmentAnnotation assocAnnotation=null; + public boolean isColumnWise() + { + return columnWise; + } + public AlignmentAnnotation getAssocAnnotation() { + return assocAnnotation; + } + public AlignmentI getAlignment() { return getTreeCanvas().getViewport().getAlignment(); @@ -137,6 +172,15 @@ public class TreePanel extends GTreePanel this.treeType = type; this.scoreModelName = modelName; + if (columnWise) + { + bootstrapMenu.setVisible(false); + placeholdersMenu.setSelected(false); + placeholdersMenu.setVisible(false); + fitToWindow.setSelected(false); + sortAssocViews.setVisible(false); + } + treeCanvas = new TreeCanvas(this, ap, scrollPane); scrollPane.setViewportView(treeCanvas); @@ -318,9 +362,8 @@ public class TreePanel extends GTreePanel } else { - ScoreModelI sm = ScoreModels.getInstance() - .getScoreModel(scoreModelName, - treeCanvas.getAssociatedPanel()); + ScoreModelI sm = ScoreModels.getInstance().getScoreModel( + scoreModelName, treeCanvas.getAssociatedPanel()); TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(av, sm, similarityParams) : new AverageDistanceTree(av, sm, similarityParams); @@ -406,7 +449,7 @@ public class TreePanel extends GTreePanel { // TODO: JAL-3048 save newick file for Jalview-JS JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.save_tree_as_newick")); @@ -417,7 +460,7 @@ public class TreePanel extends GTreePanel if (value == JalviewFileChooser.APPROVE_OPTION) { String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", + Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent()); try @@ -456,7 +499,7 @@ public class TreePanel extends GTreePanel AlignmentView originalData = tree.getOriginalData(); if (originalData == null) { - jalview.bin.Cache.log.info( + Console.info( "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); return; } @@ -586,9 +629,8 @@ public class TreePanel extends GTreePanel } else { - treeCanvas.getAssociatedPanel().alignFrame - .addHistoryItem( - sortAlignmentIn(treeCanvas.getAssociatedPanel())); + treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem( + sortAlignmentIn(treeCanvas.getAssociatedPanel())); } } @@ -693,7 +735,8 @@ public class TreePanel extends GTreePanel String tree = MessageManager.getString("label.tree"); ImageExporter exporter = new ImageExporter(writer, null, imageFormat, tree); - exporter.doExport(null, this, width, height, tree.toLowerCase()); + exporter.doExport(null, this, width, height, + tree.toLowerCase(Locale.ROOT)); } /** @@ -717,13 +760,13 @@ public class TreePanel extends GTreePanel && !((SequenceNode) node).isDummy()) { String newname = null; - SequenceI sq = (SequenceI) ((SequenceNode) node).element(); + SequenceI sq = (SequenceI) ((BinaryNode) node).element(); if (sq != null) { // search dbrefs, features and annotation List refs = jalview.util.DBRefUtils .selectRefs(sq.getDBRefs(), new String[] - { labelClass.toUpperCase() }); + { labelClass.toUpperCase(Locale.ROOT) }); if (refs != null) { for (int i = 0, ni = refs.size(); i < ni; i++) @@ -759,7 +802,7 @@ public class TreePanel extends GTreePanel { // String oldname = ((SequenceNode) node).getName(); // TODO : save oldname in the undo object for this modification. - ((SequenceNode) node).setName(newname); + ((BinaryNode) node).setName(newname); } } } @@ -785,8 +828,8 @@ public class TreePanel extends GTreePanel /* * i18n description of Neighbour Joining or Average Distance method */ - String treecalcnm = MessageManager - .getString("label.tree_calc_" + treeType.toLowerCase()); + String treecalcnm = MessageManager.getString( + "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT)); /* * short score model name (long description can be too long) @@ -815,8 +858,7 @@ public class TreePanel extends GTreePanel int width = treeCanvas.getWidth(); int height = treeCanvas.getHeight(); - FileOutputStream out = new FileOutputStream( - outFile); + FileOutputStream out = new FileOutputStream(outFile); EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height); pg.setAccurateTextMode(!textOption); @@ -830,7 +872,7 @@ public class TreePanel extends GTreePanel ex.printStackTrace(); } } - + public AlignViewport getViewport() { return av;