From 6813ed412a7820a1695905e9d7608d520b9f45ac Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Wed, 25 May 2005 16:32:04 +0000 Subject: [PATCH] formatting changes --- src/jalview/appletgui/TreePanel.java | 316 +++++++++++++++++----------------- 1 file changed, 158 insertions(+), 158 deletions(-) diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java index 99d0328..d6ee70e 100755 --- a/src/jalview/appletgui/TreePanel.java +++ b/src/jalview/appletgui/TreePanel.java @@ -1,158 +1,158 @@ -package jalview.appletgui; - -import jalview.datamodel.*; -import jalview.io.NewickFile; -import jalview.analysis.*; -import jalview.jbappletgui.GTreePanel; -import java.awt.event.*; -import java.util.*; -import jalview.io.NewickFile; - - -public class TreePanel extends GTreePanel -{ - SequenceI[] seq; - String type; - String pwtype; - AlignViewport av; - int start; - int end; - TreeCanvas treeCanvas; - NJTree tree; - - public NJTree getTree() - { - return tree; - } - - public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e) - { - super(); - - 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); - - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); - scrollPane.add(treeCanvas); - - } - public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree, - String type, String pwtype) - { - super(); - // These are probably only arbitrary strings reflecting source of tree - this.type = type; - this.pwtype = pwtype; - - start = 0; - end = seqVector.size(); - - String longestName = ""; - seq = new Sequence [seqVector.size()]; - for (int i=0;i < seqVector.size();i++) - { - seq[i] = (Sequence) seqVector.elementAt(i); - } - // This constructor matches sequence names to treenodes and sets up the tree layouts. - tree = new NJTree(seq, newtree); - // Now have to calculate longest name based on the leaves - Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector()); - - for (int i=0;i < leaves.size();i++) - if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length()) - longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName(); - - tree.reCount(tree.getTopNode()); - tree.findHeight(tree.getTopNode()); - - treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName); - treeCanvas.setShowBootstrap(newtree.HasBootstrap()); - treeCanvas.setShowDistances(newtree.HasDistances()); - distanceMenu.setState(newtree.HasDistances()); - bootstrapMenu.setState(newtree.HasBootstrap()); - if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree - placeholdersMenu.setState(treeCanvas.markPlaceholders); - scrollPane.add(treeCanvas); - - } - -public String getText(String format) { - return null; -} - - protected void fitToWindow_actionPerformed(ActionEvent e) - { - treeCanvas.fitToWindow = fitToWindow.getState(); - repaint(); - } - - public void newickOutput_actionPerformed(ActionEvent actionEvent) - { - jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode()); - String output = fout.print(false, true); - CutAndPasteTransfer cap = new CutAndPasteTransfer(false); - cap.setText(output); - java.awt.Frame frame = new java.awt.Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,500); - } - - - - protected void fontSize_actionPerformed(ActionEvent e) - { - /* if( treeCanvas==null ) - return; - - String size = fontSize.getLabel().substring( fontSize.getLabel().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); - - int i = Integer.parseInt(selection.toString()); - treeCanvas.setFontSize(i); - } - scrollPane.setViewportView(treeCanvas); -*/ - } - - protected void distanceMenu_actionPerformed(ActionEvent e) - { - treeCanvas.setShowDistances(distanceMenu.getState()); - } - - protected void bootstrapMenu_actionPerformed(ActionEvent e) - { - treeCanvas.setShowBootstrap(bootstrapMenu.getState()); - } - - protected void placeholdersMenu_actionPerformed(ActionEvent e) - { - treeCanvas.setMarkPlaceholders(placeholdersMenu.getState()); - } - -} +package jalview.appletgui; + +import jalview.datamodel.*; +import jalview.io.NewickFile; +import jalview.analysis.*; +import jalview.jbappletgui.GTreePanel; +import java.awt.event.*; +import java.util.*; +import jalview.io.NewickFile; + + +public class TreePanel extends GTreePanel +{ + SequenceI[] seq; + String type; + String pwtype; + AlignViewport av; + int start; + int end; + TreeCanvas treeCanvas; + NJTree tree; + + public NJTree getTree() + { + return tree; + } + + public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e) + { + super(); + + 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); + + tree.reCount(tree.getTopNode()); + tree.findHeight(tree.getTopNode()); + scrollPane.add(treeCanvas); + + } + public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree, + String type, String pwtype) + { + super(); + // These are probably only arbitrary strings reflecting source of tree + this.type = type; + this.pwtype = pwtype; + + start = 0; + end = seqVector.size(); + + String longestName = ""; + seq = new Sequence [seqVector.size()]; + for (int i=0;i < seqVector.size();i++) + { + seq[i] = (Sequence) seqVector.elementAt(i); + } + // This constructor matches sequence names to treenodes and sets up the tree layouts. + tree = new NJTree(seq, newtree); + // Now have to calculate longest name based on the leaves + Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector()); + + for (int i=0;i < leaves.size();i++) + if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length()) + longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName(); + + tree.reCount(tree.getTopNode()); + tree.findHeight(tree.getTopNode()); + + treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName); + treeCanvas.setShowBootstrap(newtree.HasBootstrap()); + treeCanvas.setShowDistances(newtree.HasDistances()); + distanceMenu.setState(newtree.HasDistances()); + bootstrapMenu.setState(newtree.HasBootstrap()); + if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree + placeholdersMenu.setState(treeCanvas.markPlaceholders); + scrollPane.add(treeCanvas); + + } + +public String getText(String format) { + return null; +} + + protected void fitToWindow_actionPerformed(ActionEvent e) + { + treeCanvas.fitToWindow = fitToWindow.getState(); + repaint(); + } + + public void newickOutput_actionPerformed(ActionEvent actionEvent) + { + jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode()); + String output = fout.print(false, true); + CutAndPasteTransfer cap = new CutAndPasteTransfer(false); + cap.setText(output); + java.awt.Frame frame = new java.awt.Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,100); + } + + + + protected void fontSize_actionPerformed(ActionEvent e) + { + /* if( treeCanvas==null ) + return; + + String size = fontSize.getLabel().substring( fontSize.getLabel().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); + + int i = Integer.parseInt(selection.toString()); + treeCanvas.setFontSize(i); + } + scrollPane.setViewportView(treeCanvas); +*/ + } + + protected void distanceMenu_actionPerformed(ActionEvent e) + { + treeCanvas.setShowDistances(distanceMenu.getState()); + } + + protected void bootstrapMenu_actionPerformed(ActionEvent e) + { + treeCanvas.setShowBootstrap(bootstrapMenu.getState()); + } + + protected void placeholdersMenu_actionPerformed(ActionEvent e) + { + treeCanvas.setMarkPlaceholders(placeholdersMenu.getState()); + } + +} -- 1.7.10.2