X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=05f01cf9558fb5774934fdf585e165e0922e1215;hb=3eddd392a6b8d30279aba258ca90c52c39af9420;hp=c6c9b5342c5e7e6a1a05f20e855261657b8094ae;hpb=e3cad17c5dba620dafc8459295ecc959cbe52938;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index c6c9b53..05f01cf 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -38,7 +38,6 @@ import java.util.*; import javax.imageio.*; -import javax.swing.*; import java.beans.PropertyChangeEvent; @@ -50,13 +49,11 @@ import java.beans.PropertyChangeEvent; */ 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. @@ -68,15 +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); - distanceMenu.setSelected(true); + // showDistances(true); } /** @@ -88,28 +83,28 @@ 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; - - seq = new Sequence[seqVector.size()]; - seqVector.toArray(seq); - - treeCanvas = new TreeCanvas(av, scrollPane); scrollPane.setViewportView(treeCanvas); @@ -131,6 +126,8 @@ public class TreePanel extends GTreePanel } }); + this.av = av; + TreeLoader tl = new TreeLoader(newTree); tl.start(); @@ -140,7 +137,7 @@ public class TreePanel extends GTreePanel class TreeLoader extends Thread { NewickFile newtree; - + jalview.datamodel.AlignmentView odata=null; public TreeLoader(NewickFile newtree) { this.newtree = newtree; @@ -148,30 +145,80 @@ public class TreePanel extends GTreePanel { // Must be outside run(), as Jalview2XML tries to // update distance/bootstrap visibility at the same time - treeCanvas.setShowBootstrap(newtree.HasBootstrap()); - bootstrapMenu.setSelected(newtree.HasBootstrap()); - - treeCanvas.setShowDistances(newtree.HasDistances()); - distanceMenu.setSelected(newtree.HasDistances()); + showBootstrap(newtree.HasBootstrap()); + showDistances(newtree.HasDistances()); } } public void run() { + if(newtree!=null) - tree = new NJTree(seq, newtree); + { + 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 - tree = new NJTree(seq, type, pwtype, start, end); + { + 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); + } + 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); + } + + public void showBootstrap(boolean b) + { + treeCanvas.setShowBootstrap(b); + bootstrapMenu.setSelected(b); + } + + public void showPlaceholders(boolean b) + { + placeholdersMenu.setState(b); + treeCanvas.setMarkPlaceholders(b); + } + + private void allowOriginalSeqData(boolean b) { + originalSeqData.setVisible(b); + } + + /** * DOCUMENT ME! @@ -216,7 +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())); } /** @@ -243,7 +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); @@ -267,6 +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! *