X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=3fa7643b497f141e0c9e3afb11d61c99db93d3c0;hb=559b96a91b710f3f2e116790c9cf7e3aa6c76766;hp=8d13e93c2c591dd1f453c4b9c671e5e202e6c3ad;hpb=8a5c39442bced20fc95272efe6d3176719ca3f15;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 8d13e93..3fa7643 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. @@ -67,14 +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(); - initTreePanel(av, seqVector, type, pwtype, s, e, null); + initTreePanel(av, type, pwtype, null); // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default - treeCanvas.setShowDistances(true); + // showDistances(true); } /** @@ -86,30 +83,51 @@ 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, seqVector, type, pwtype, 0, seqVector.size(), newtree); + initTreePanel(av, type, pwtype, newtree); + } + + public AlignmentI getAlignment() + { + return treeCanvas.av.getAlignment(); } - void initTreePanel(AlignViewport av, Vector seqVector, String type, - String pwtype, int s, int e, NewickFile newTree) + void initTreePanel(AlignViewport av, String type, String pwtype, + NewickFile newTree) { this.type = type; this.pwtype = pwtype; - start = s; - end = e; + treeCanvas = new TreeCanvas(av, scrollPane); + scrollPane.setViewportView(treeCanvas); - seq = new Sequence[seqVector.size()]; - seqVector.toArray(seq); + av.addPropertyChangeListener(new java.beans.PropertyChangeListener() + { + public void propertyChange(PropertyChangeEvent evt) + { + 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.av = av; - treeCanvas = new TreeCanvas(av, scrollPane); - scrollPane.setViewportView(treeCanvas); TreeLoader tl = new TreeLoader(newTree); tl.start(); @@ -119,73 +137,100 @@ public class TreePanel extends GTreePanel class TreeLoader extends Thread { NewickFile newtree; - + jalview.datamodel.AlignmentView odata=null; public TreeLoader(NewickFile newtree) { this.newtree = newtree; + if (newtree != null) + { + // Must be outside run(), as Jalview2XML tries to + // update distance/bootstrap visibility at the same time + showBootstrap(newtree.HasBootstrap()); + showDistances(newtree.HasDistances()); + } } public void run() { - NJTree tree; - if(newtree!=null) - tree = new NJTree(seq, newtree); - else - tree = new NJTree(seq, type, pwtype, start, end); - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); - treeCanvas.setTree(tree); if(newtree!=null) { - treeCanvas.setShowBootstrap(newtree.HasBootstrap()); - treeCanvas.setShowDistances(newtree.HasDistances()); + if (odata==null) { + tree = new NJTree(av.alignment.getSequencesArray(), + newtree); + } else { + tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree); + } + if (!tree.hasOriginalSequenceData()) + allowOriginalSeqData(false); + } + else + { + int start, end; + SequenceI [] seqs; + AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null); + 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); + showDistances(true); } - setViewStateFromTreeCanvas(treeCanvas); + tree.reCount(tree.getTopNode()); + tree.findHeight(tree.getTopNode()); + treeCanvas.setTree(tree); treeCanvas.repaint(); + av.setCurrentTree(tree); } } + public void showDistances(boolean b) + { + treeCanvas.setShowDistances(b); + distanceMenu.setSelected(b); + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public NJTree getTree() + public void showBootstrap(boolean b) { - return tree; + treeCanvas.setShowBootstrap(b); + bootstrapMenu.setSelected(b); } - /** - * DOCUMENT ME! - * - * @param tree DOCUMENT ME! - */ - private void setViewStateFromTreeCanvas(TreeCanvas tree) + public void showPlaceholders(boolean b) { - // update view menu state from treeCanvas render state - distanceMenu.setSelected(tree.showDistances); - bootstrapMenu.setSelected(tree.showBootstrap); - placeholdersMenu.setSelected(tree.markPlaceholders); + placeholdersMenu.setState(b); + treeCanvas.setMarkPlaceholders(b); + } + + private void allowOriginalSeqData(boolean b) { + originalSeqData.setVisible(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! * @@ -218,7 +263,7 @@ 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())); } /** @@ -245,7 +290,7 @@ 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); @@ -269,6 +314,52 @@ public class TreePanel extends GTreePanel treeCanvas.startPrinting(); } + + public void originalSeqData_actionPerformed(ActionEvent e) + { + if (!tree.hasOriginalSequenceData()) + { + jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); + return; + } + // decide if av alignment is sufficiently different to original data to warrant a new window to be created + // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs) + // or create a selection box around columns in alignment view + // test Alignment(SeqCigar[]) + Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av. + getGapCharacter()); + + + if (alAndColsel != null && alAndColsel[0]!=null) + { + // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); + + Alignment al = new Alignment((SequenceI[]) alAndColsel[0]); + Alignment dataset = av.getAlignment().getDataset(); + if (dataset != null) + { + al.setDataset(dataset); + } + + if (true) + { + // make a new frame! + AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1]); + + //>>>This is a fix for the moment, until a better solution is found!!<<< + // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer()); + + // af.addSortByOrderMenuItem(ServiceName + " Ordering", + // msaorder); + + Desktop.addInternalFrame(af, "Original Data for " + this.title, + AlignFrame.NEW_WINDOW_WIDTH, + AlignFrame.NEW_WINDOW_HEIGHT); + } + } + } + + /** * DOCUMENT ME! * @@ -285,33 +376,25 @@ 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); } /** @@ -351,6 +434,32 @@ 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(); @@ -372,11 +481,13 @@ 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);