X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=190f15cf811164411174a79b2044c7c7d54acf0e;hb=623d576bab61337289656eab9e4e26cf63e0afc0;hp=ff02d49ec487eef6189d2acba088ca4b4267e9bf;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index ff02d49..190f15c 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -38,7 +38,7 @@ import java.util.*; import javax.imageio.*; -import javax.swing.*; +import java.beans.PropertyChangeEvent; /** @@ -49,13 +49,11 @@ import javax.swing.*; */ public class TreePanel extends GTreePanel { - SequenceI[] seq; String type; String pwtype; - int start; - int end; TreeCanvas treeCanvas; NJTree tree; + AlignViewport av; /** * Creates a new TreePanel object. @@ -67,38 +65,13 @@ public class TreePanel extends GTreePanel * @param s DOCUMENT ME! * @param e DOCUMENT ME! */ - public TreePanel(AlignViewport av, Vector seqVector, String type, - String pwtype, int s, int e) + public TreePanel(AlignViewport av, String type, String pwtype) { - super(); + super(); + initTreePanel(av, type, pwtype, null); - this.type = type; - this.pwtype = pwtype; - - start = s; - end = e; - - String longestName = ""; - seq = new Sequence[seqVector.size()]; - - for (int i = 0; i < seqVector.size(); i++) - { - seq[i] = (Sequence) seqVector.elementAt(i); - - if (seq[i].getName().length() > longestName.length()) - { - longestName = seq[i].getName(); - } - } - - tree = new NJTree(seq, type, pwtype, start, end); - - treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName); - treeCanvas.setShowDistances(true); // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default - setViewStateFromTreeCanvas(treeCanvas); - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); - scrollPane.setViewportView(treeCanvas); + // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default + showDistances(true); } /** @@ -110,99 +83,149 @@ public class TreePanel extends GTreePanel * @param type DOCUMENT ME! * @param pwtype DOCUMENT ME! */ - public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree, - String type, String pwtype) + public TreePanel(AlignViewport av, + String type, + String pwtype, + NewickFile newtree) + { + super(); + initTreePanel(av, type, pwtype, newtree); + } + + public AlignmentI getAlignment() { - super(); + return treeCanvas.av.getAlignment(); + } + - // These are probably only arbitrary strings reflecting source of tree - this.type = type; - this.pwtype = pwtype; + void initTreePanel(AlignViewport av, String type, String pwtype, + NewickFile newTree) + { - start = 0; - end = seqVector.size(); + this.type = type; + this.pwtype = pwtype; - String longestName = ""; - seq = new Sequence[seqVector.size()]; + treeCanvas = new TreeCanvas(av, scrollPane); + scrollPane.setViewportView(treeCanvas); - for (int i = 0; i < seqVector.size(); i++) + av.addPropertyChangeListener(new java.beans.PropertyChangeListener() + { + public void propertyChange(PropertyChangeEvent evt) { - seq[i] = (Sequence) seqVector.elementAt(i); + if (evt.getPropertyName().equals("alignment")) + { + if(tree==null) + System.out.println("tree is null"); + if(evt.getNewValue()==null) + System.out.println("new value is null"); + + tree.UpdatePlaceHolders( (Vector) evt.getNewValue()); + + repaint(); + } } + }); - // This constructor matches sequence names to treenodes and sets up the tree layouts. - tree = new NJTree(seq, newtree); + this.av = av; - // Now have to calculate longest name based on the leaves - Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector()); - boolean has_placeholders = false; - for (int i = 0; i < leaves.size(); i++) + TreeLoader tl = new TreeLoader(newTree); + tl.start(); + + } + + class TreeLoader extends Thread + { + NewickFile newtree; + + public TreeLoader(NewickFile newtree) + { + this.newtree = newtree; + if (newtree != null) { - SequenceNode lf = (SequenceNode) leaves.elementAt(i); + // Must be outside run(), as Jalview2XML tries to + // update distance/bootstrap visibility at the same time + showBootstrap(newtree.HasBootstrap()); + showDistances(newtree.HasDistances()); + } + } - if (lf.isPlaceholder()) - { - has_placeholders = true; - } + public void run() + { - if (longestName.length() < ((Sequence) lf.element()).getName() - .length()) - { - longestName = TreeCanvas.PLACEHOLDER + - ((Sequence) lf.element()).getName(); - } + if(newtree!=null) + tree = new NJTree(av.alignment.getSequencesArray(), + newtree); + else + { + int start, end; + SequenceI [] seqs; + String [] seqStrings = null; + if (av.hasHiddenColumns) + { + seqStrings = av.getSelectionAsString(); + } + + if(av.getSelectionGroup()==null) + { + start = 0; + end = av.alignment.getWidth(); + seqs = av.alignment.getSequencesArray(); + } + else + { + start = av.getSelectionGroup().getStartRes(); + end = av.getSelectionGroup().getEndRes()+1; + seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); + } + + tree = new NJTree(seqs, seqStrings, type, pwtype, start, end); } + tree.reCount(tree.getTopNode()); tree.findHeight(tree.getTopNode()); + treeCanvas.setTree(tree); - treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName); - treeCanvas.setShowBootstrap(newtree.HasBootstrap()); - treeCanvas.setShowDistances(newtree.HasDistances()); - scrollPane.setViewportView(treeCanvas); - treeCanvas.setMarkPlaceholders(has_placeholders); - setViewStateFromTreeCanvas(treeCanvas); + treeCanvas.repaint(); - // JBPNote TODO: preference for always marking placeholders in new associated tree + av.setCurrentTree(tree); + + } } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public NJTree getTree() + public void showDistances(boolean b) { - return tree; + treeCanvas.setShowDistances(b); + distanceMenu.setSelected(b); } - /** - * DOCUMENT ME! - * - * @param tree DOCUMENT ME! - */ - private void setViewStateFromTreeCanvas(TreeCanvas tree) + public void showBootstrap(boolean b) { - // update view menu state from treeCanvas render state - distanceMenu.setSelected(tree.showDistances); - bootstrapMenu.setSelected(tree.showBootstrap); - placeholdersMenu.setSelected(tree.markPlaceholders); + treeCanvas.setShowBootstrap(b); + bootstrapMenu.setSelected(b); } + public void showPlaceholders(boolean b) + { + placeholdersMenu.setState(b); + treeCanvas.setMarkPlaceholders(b); + } + + + + /** * DOCUMENT ME! * - * @param tree DOCUMENT ME! + * @return DOCUMENT ME! */ - private void setTreeCanvasFromViewState(TreeCanvas tree) + public NJTree getTree() { - // update view menu state from treeCanvas render state - tree.showDistances = distanceMenu.isSelected(); - tree.showBootstrap = bootstrapMenu.isSelected(); - tree.markPlaceholders = placeholdersMenu.isSelected(); + return tree; } + /** * DOCUMENT ME! * @@ -235,7 +258,7 @@ public class TreePanel extends GTreePanel Desktop.addInternalFrame(cap, buffer.toString(), 500, 100); jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode()); - cap.setText(fout.print(false, true)); + cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance())); } /** @@ -262,7 +285,7 @@ public class TreePanel extends GTreePanel try { jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode()); - String output = fout.print(false, true); // distances only + String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()); java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter( choice)); out.println(output); @@ -286,6 +309,16 @@ public class TreePanel extends GTreePanel treeCanvas.startPrinting(); } + + public void originalSeqData_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setText(tree.printOriginalSequenceData()); + Desktop.addInternalFrame(cap, "Original Data", + 400, 400); + } + + /** * DOCUMENT ME! * @@ -302,33 +335,25 @@ public class TreePanel extends GTreePanel * * @param e DOCUMENT ME! */ - public void fontSize_actionPerformed(ActionEvent e) + public void font_actionPerformed(ActionEvent e) { if (treeCanvas == null) { return; } - String size = fontSize.getText().substring(fontSize.getText().indexOf("-") + - 1); - - Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop, - "Select font size", "Font size", JOptionPane.QUESTION_MESSAGE, - null, - new String[] - { - "1", "2", "4", "6", "8", "10", "12", "14", "16", "18", "20" - }, "Font Size - " + size); - - if (selection != null) - { - fontSize.setText("Font Size - " + selection); + new FontChooser(this); + } - int i = Integer.parseInt(selection.toString()); - treeCanvas.setFontSize(i); - } + public Font getTreeFont() + { + return treeCanvas.font; + } - scrollPane.setViewportView(treeCanvas); + public void setTreeFont(Font font) + { + if(treeCanvas!=null) + treeCanvas.setFont(font); } /** @@ -368,6 +393,32 @@ public class TreePanel extends GTreePanel */ 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(); @@ -389,11 +440,13 @@ public class TreePanel extends GTreePanel } jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); + chooser.getSelectedFile().getParent()); FileOutputStream out = new FileOutputStream(chooser.getSelectedFile()); EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, - height); + height); + + pg.setAccurateTextMode(accurateText); treeCanvas.draw(pg, width, height);