X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=0e1fd42b071e7b99399eb8cc930c073a83980fbb;hb=4b7d3640209c4434d569c746672cf9eed4250ace;hp=5795a9fc90249b1499ed420a763a0ccf8fd914d0;hpb=7534e6f358b2bba0db179cb2f496bd2e5a4da43d;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 5795a9f..0e1fd42 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; @@ -29,9 +49,11 @@ 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; @@ -41,34 +63,15 @@ import jalview.datamodel.NodeTransformI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.datamodel.SequenceNode; +import jalview.gui.ImageExporter.ImageWriterI; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.io.NewickFile; import jalview.jbgui.GTreePanel; -import jalview.util.ImageMaker; +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.awt.image.BufferedImage; -import java.beans.PropertyChangeEvent; -import java.beans.PropertyChangeListener; -import java.io.FileOutputStream; -import java.util.ArrayList; -import java.util.List; - -import javax.imageio.ImageIO; -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! * @@ -85,11 +88,11 @@ public class TreePanel extends GTreePanel SimilarityParamsI similarityParams; - TreeCanvas treeCanvas; + private TreeCanvas treeCanvas; TreeModel tree; - AlignViewport av; + private AlignViewport av; /** * Creates a new TreePanel object. @@ -103,6 +106,7 @@ public class TreePanel extends GTreePanel SimilarityParamsI options) { super(); + this.setFrameIcon(null); this.similarityParams = options; initTreePanel(ap, type, modelName, null, null); @@ -115,18 +119,53 @@ 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 treeCanvas.av.getAlignment(); + return getTreeCanvas().getViewport().getAlignment(); } public AlignmentViewport getViewPort() { - return treeCanvas.av; + // @Mungo - Why don't we return our own viewport ??? + return getTreeCanvas().getViewport(); } void initTreePanel(AlignmentPanel ap, String type, String modelName, @@ -137,6 +176,15 @@ 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); @@ -159,6 +207,7 @@ public class TreePanel extends GTreePanel { av.removePropertyChangeListener(listener); } + releaseReferences(); } }); @@ -168,6 +217,17 @@ public class TreePanel extends GTreePanel } /** + * Ensure any potentially large object references are nulled + */ + public void releaseReferences() + { + this.tree = null; + this.treeCanvas.tree = null; + this.treeCanvas.nodeHash = null; + this.treeCanvas.nameHash = null; + } + + /** * @return */ protected PropertyChangeListener addAlignmentListener() @@ -214,7 +274,7 @@ public class TreePanel extends GTreePanel { AlignmentPanel[] aps = PaintRefresher .getAssociatedPanels(av.getSequenceSetId()); - if (aps.length == 1 && treeCanvas.ap == aps[0]) + if (aps.length == 1 && getTreeCanvas().getAssociatedPanel() == aps[0]) { associateLeavesMenu.setVisible(false); return; @@ -237,7 +297,8 @@ public class TreePanel extends GTreePanel for (i = 0; i < iSize; i++) { final AlignmentPanel ap = aps[i]; - item = new JRadioButtonMenuItem(ap.av.viewName, ap == treeCanvas.ap); + item = new JRadioButtonMenuItem(ap.av.getViewName(), + ap == treeCanvas.getAssociatedPanel()); buttonGroup.add(item); item.addActionListener(new ActionListener() { @@ -245,8 +306,8 @@ public class TreePanel extends GTreePanel public void actionPerformed(ActionEvent evt) { treeCanvas.applyToAllViews = false; - treeCanvas.ap = ap; - treeCanvas.av = ap.av; + treeCanvas.setAssociatedPanel(ap); + treeCanvas.setViewport(ap.av); PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId()); } }); @@ -305,8 +366,8 @@ public class TreePanel extends GTreePanel } else { - ScoreModelI sm = ScoreModels.getInstance() - .getScoreModel(scoreModelName, treeCanvas.ap); + 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); @@ -392,7 +453,7 @@ 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")); @@ -403,7 +464,7 @@ 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 @@ -442,7 +503,7 @@ 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; } @@ -572,8 +633,8 @@ public class TreePanel extends GTreePanel } else { - treeCanvas.ap.alignFrame - .addHistoryItem(sortAlignmentIn(treeCanvas.ap)); + treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem( + sortAlignmentIn(treeCanvas.getAssociatedPanel())); } } @@ -658,128 +719,28 @@ public class TreePanel extends GTreePanel } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void epsTree_actionPerformed(ActionEvent e) - { - boolean accurateText = true; - - String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING", - "Prompt each time"); - - // If we need to prompt, and if the GUI is visible then - // Prompt for EPS rendering style - if (renderStyle.equalsIgnoreCase("Prompt each time") - && !(System.getProperty("java.awt.headless") != null && System - .getProperty("java.awt.headless").equals("true"))) - { - EPSOptions eps = new EPSOptions(); - renderStyle = eps.getValue(); - - if (renderStyle == null || eps.cancelled) - { - return; - } - - } - - if (renderStyle.equalsIgnoreCase("text")) - { - accurateText = false; - } - - int width = treeCanvas.getWidth(); - int height = treeCanvas.getHeight(); - - try - { - // TODO: JAL-3048 not needed for Jalview-JS - Requires EpsGraphics2D dependency - JalviewFileChooser chooser = new JalviewFileChooser( - ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION); - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle( - MessageManager.getString("label.create_eps_from_tree")); - chooser.setToolTipText(MessageManager.getString("action.save")); - - int value = chooser.showSaveDialog(this); - - if (value != JalviewFileChooser.APPROVE_OPTION) - { - return; - } - - Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); - - FileOutputStream out = new FileOutputStream( - chooser.getSelectedFile()); - EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, - height); - - pg.setAccurateTextMode(accurateText); - - treeCanvas.draw(pg, width, height); - - pg.flush(); - pg.close(); - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Outputs the Tree in image format (currently EPS or PNG). The user is + * prompted for the file to save to, and for EPS (unless a preference is + * already set) for the choice of Text or Lineart for character rendering. */ @Override - public void pngTree_actionPerformed(ActionEvent e) + public void writeTreeImage(TYPE imageFormat) { - // TODO: JAL-3048 image export supported in JalviewJS ? int width = treeCanvas.getWidth(); int height = treeCanvas.getHeight(); - - try + ImageWriterI writer = new ImageWriterI() { - JalviewFileChooser chooser = new JalviewFileChooser( - ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION); - - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle( - MessageManager.getString("label.create_png_from_tree")); - chooser.setToolTipText(MessageManager.getString("action.save")); - - int value = chooser.showSaveDialog(this); - - if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION) + @Override + public void exportImage(Graphics g) throws Exception { - return; + treeCanvas.draw(g, width, height); } - - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); - - FileOutputStream out = new FileOutputStream( - chooser.getSelectedFile()); - - BufferedImage bi = new BufferedImage(width, height, - BufferedImage.TYPE_INT_RGB); - Graphics png = bi.getGraphics(); - - treeCanvas.draw(png, width, height); - - ImageIO.write(bi, "png", out); - out.close(); - } catch (Exception ex) - { - ex.printStackTrace(); - } + }; + String tree = MessageManager.getString("label.tree"); + ImageExporter exporter = new ImageExporter(writer, null, imageFormat, + tree); + exporter.doExport(null, this, width, height, + tree.toLowerCase(Locale.ROOT)); } /** @@ -803,24 +764,24 @@ 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 - DBRefEntry[] refs = jalview.util.DBRefUtils + List refs = jalview.util.DBRefUtils .selectRefs(sq.getDBRefs(), new String[] - { labelClass.toUpperCase() }); + { labelClass.toUpperCase(Locale.ROOT) }); if (refs != null) { - for (int i = 0; i < refs.length; i++) + for (int i = 0, ni = refs.size(); i < ni; i++) { if (newname == null) { - newname = new String(refs[i].getAccessionId()); + newname = new String(refs.get(i).getAccessionId()); } else { - newname = newname + "; " + refs[i].getAccessionId(); + newname += "; " + refs.get(i).getAccessionId(); } } } @@ -845,7 +806,7 @@ 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); } } } @@ -871,8 +832,8 @@ 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) @@ -882,8 +843,52 @@ public class TreePanel extends GTreePanel /* * put them together as Using */ - final String ttl = MessageManager.formatMessage("label.treecalc_title", + final String ttl = MessageManager.formatMessage("label.calc_title", treecalcnm, smn); return ttl; } + + /** + * Builds an EPS image and writes it to the specified file. + * + * @param outFile + * @param textOption + * true for Text character rendering, false for Lineart + */ + protected void writeEpsFile(File outFile, boolean textOption) + { + try + { + int width = treeCanvas.getWidth(); + int height = treeCanvas.getHeight(); + + FileOutputStream out = new FileOutputStream(outFile); + EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, + height); + pg.setAccurateTextMode(!textOption); + treeCanvas.draw(pg, width, height); + + pg.flush(); + pg.close(); + } catch (Exception ex) + { + System.err.println("Error writing tree as EPS"); + ex.printStackTrace(); + } + } + + public AlignViewport getViewport() + { + return av; + } + + public void setViewport(AlignViewport av) + { + this.av = av; + } + + public TreeCanvas getTreeCanvas() + { + return treeCanvas; + } }