From 4308c9d432a2e0a1acc23020c0450ec519fdad6f Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 19 Feb 2026 18:13:54 +0000
Subject: [PATCH 1/3] Initial plan
From 830c5ccbb9d91ad3e69d14398c4e69c3f48c6930 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 19 Feb 2026 18:18:11 +0000
Subject: [PATCH 2/3] Remove deprecated Java applet code
(AppletInteractionController comments and BeanTree files)
Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
---
.../lib/docs/mesquite/BeanTree/BeanTree.html | 1 -
.../lib/docs/mesquite/BeanTree/BeanTree.java | 1 -
.../mesquite/BeanTree/BeanTree/BeanTree.class | Bin 1759 -> 0 bytes
.../BeanTree/BeanTree/BeanTreeControls.class | Bin 1456 -> 0 bytes
.../docs/mesquite/BeanTree/BeanTree/Branch.class | Bin 928 -> 0 bytes
.../mesquite/BeanTree/BeanTree/TreeCanvas.class | Bin 6044 -> 0 bytes
.../mesquite/BeanTree/BeanTree/TreeClass.class | Bin 2374 -> 0 bytes
.../BeanTree/com/metrowerks/AppletFrame.class | Bin 1680 -> 0 bytes
.../src/main/webapp/WEB-INF/treebase-servlet.xml | 8 +-------
9 files changed, 1 insertion(+), 9 deletions(-)
delete mode 100755 treebase-core/lib/docs/mesquite/BeanTree/BeanTree.html
delete mode 100755 treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java
delete mode 100755 treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTree.class
delete mode 100755 treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTreeControls.class
delete mode 100755 treebase-core/lib/docs/mesquite/BeanTree/BeanTree/Branch.class
delete mode 100755 treebase-core/lib/docs/mesquite/BeanTree/BeanTree/TreeCanvas.class
delete mode 100755 treebase-core/lib/docs/mesquite/BeanTree/BeanTree/TreeClass.class
delete mode 100755 treebase-core/lib/docs/mesquite/BeanTree/BeanTree/com/metrowerks/AppletFrame.class
diff --git a/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.html b/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.html
deleted file mode 100755
index ad060a139..000000000
--- a/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.html
+++ /dev/null
@@ -1 +0,0 @@
-BeanTree
BeanTree
It all started yesterday because I thought that perhaps I should try out some object oriented programming in case I wanted to teach an object oriented language to the students in my class next spring....
Much faster as stand alone application.
Taxon names must be one character only (actually, they can all be the same character).
\ No newline at end of file
diff --git a/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java b/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java
deleted file mode 100755
index 106f0adbe..000000000
--- a/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java
+++ /dev/null
@@ -1 +0,0 @@
-//package wpm;
import java.awt.*;
import java.applet.Applet;
public class BeanTree extends Applet
{
static TreeCanvas TreeDisplay;
static BeanTreeControls controls;
public void init()
{
setLayout( new BorderLayout() );
resize(300, 300);
TreeDisplay = new TreeCanvas(10, 10, 400, 400);
add( "Center", TreeDisplay );
add("North", controls = new BeanTreeControls(TreeDisplay));
TreeDisplay.Tree = new TreeClass();
TreeDisplay.controls = controls;
TreeDisplay.Tree.SubRoot = new Branch(null, false);
TreeDisplay.Tree.Root = new Branch(TreeDisplay.Tree.SubRoot, false);
TreeDisplay.edgewidth = 10;
TreeDisplay.needsUpdating = false;
TreeDisplay.highlightedBranch = null;
TreeDisplay.Tree.exists = false;
repaint();
}
public void start() {
controls.enable();
}
public void stop() {
controls.disable();
}
public static void main(String args[])
{
com.metrowerks.AppletFrame.startApplet("BeanTree", "BeanTree", args);
}
}
/** ======================================================================== */
class TreeCanvas extends Canvas {
TreeClass Tree;
int x_max, y_max;
int edgewidth;
Branch highlightedBranch, branchFrom;
int xFrom, yFrom, xTo, yTo;
boolean needsUpdating;
String treeDescription;
BeanTreeControls controls;
private int lastleft;
private int taxspacing;
private Branch foundBranch;
public TreeCanvas( int x_max, int y_max, int x_size, int y_size )
{
this.x_max = x_max;
this.y_max = y_max;
resize( x_size, y_size );
repaint();
}
/*_________________________________________________*/
private void WriteTreeDescription(Branch N) {
if (N.left!=null)
{
treeDescription+='(';
WriteTreeDescription(N.left);
treeDescription+=',';
WriteTreeDescription(N.right);
treeDescription+=')';
}
else
{
treeDescription+='*';
}
}
public String Describe() {
treeDescription="";
WriteTreeDescription(Tree.Root);
treeDescription+=';';
return treeDescription;
}
/*_________________________________________________*/
private void CalcInternalLocs(Branch N)
{
if (N.left != null) //internal
{
CalcInternalLocs(N.left);
CalcInternalLocs(N.right);
N.y = (-N.left.x + N.right.x+N.left.y + N.right.y) / 2;
N.x =(N.left.x + N.right.x - N.left.y + N.right.y) / 2;
}
}
/*_________________________________________________*/
private void CalcTerminalLocs(Branch N)
{
if (N.left == null) //terminal
{
lastleft+= taxspacing;
N.y = 90;
N.x = lastleft;
}
else
{
CalcTerminalLocs(N.left);
CalcTerminalLocs(N.right);
}
}
/*_________________________________________________*/
private void CalcBranchPolys(Branch N)
{
if (N.left != null) //terminal
{
CalcBranchPolys(N.left);
CalcBranchPolys(N.right);
N.branchPoly.npoints=0;
N.branchPoly.addPoint(N.x, N.y);
N.branchPoly.addPoint(N.x+edgewidth/2, N.y-edgewidth/2);
N.branchPoly.addPoint(N.x+edgewidth, N.y);
N.branchPoly.addPoint(N.ancestor.x+edgewidth, N.ancestor.y);
N.branchPoly.addPoint(N.ancestor.x, N.ancestor.y);
N.branchPoly.npoints=5;
}
else
{
N.branchPoly.npoints=0;
N.branchPoly.addPoint(N.x, N.y);
N.branchPoly.addPoint(N.x+edgewidth, N.y);
N.branchPoly.addPoint(N.ancestor.x+edgewidth, N.ancestor.y);
N.branchPoly.addPoint(N.ancestor.x, N.ancestor.y);
N.branchPoly.npoints=4;
}
}
/*_________________________________________________*/
private void calcBranches() {
lastleft = 0;
taxspacing = (bounds().width - 10) / Tree.numTaxa;
CalcTerminalLocs(Tree.Root);
CalcInternalLocs(Tree.Root);
Tree.SubRoot.y = (Tree.Root.y)+20;
Tree.SubRoot.x = (Tree.Root.x)-20;
CalcBranchPolys(Tree.Root);
}
/*_________________________________________________*/
private void drawBranch(Graphics g, Branch N) {
g.setColor(N.color);
g.fillPolygon(N.branchPoly);
if (N.left != null)
drawBranch(g, N.left);
if (N.right != null)
drawBranch(g, N.right);
}
/*_________________________________________________*/
public void drawTree(Graphics g) {
if (Tree.exists)
{
calcBranches();
drawBranch(g, Tree.Root);
}
}
/*_________________________________________________*/
public void paint(Graphics g) {
drawTree(g);
needsUpdating = false;
}
/*_________________________________________________*/
public void InvertBranch(Graphics g, Branch N) {
// N.color=Color.white;
highlightedBranch=N;
g.setColor(Color.white);
g.fillPolygon(N.branchPoly);
// needsUpdating=true;
}
/*_________________________________________________*/
public void RevertBranch(Graphics g, Branch N) {
// N.color=Color.black;
highlightedBranch=null;
g.setColor(Color.black);
g.fillPolygon(N.branchPoly);
// needsUpdating=true;
}
/*_________________________________________________*/
private void ScanBranches(Branch N, int x, int y)
{
if (foundBranch==null) {
if (N.branchPoly.inside(x, y))
foundBranch = N;
if (N.left != null) //terminal
{
ScanBranches(N.left, x, y);
ScanBranches(N.right, x, y);
}
}
}
/*_________________________________________________*/
public Branch FindBranch(int x, int y) {
foundBranch=null;
ScanBranches(Tree.Root, x, y);
return foundBranch;
}
/*_________________________________________________*/
public void ScanTouch(Graphics g, int x, int y) {
Branch branchFound=FindBranch( x, y);
if (branchFound!=null)
{
branchFrom=branchFound;
xFrom=x;
yFrom=y;
xTo=x;
yTo=y;
g.setXORMode(Color.gray);
g.setColor(Color.black);
g.drawLine(xFrom,yFrom,xTo,yTo);
}
}
/*_________________________________________________*/
public void ScanFlash(Graphics g, int x, int y) {
Branch branchFound=FindBranch( x, y);
if (highlightedBranch != null)
{if (branchFound==null)
RevertBranch(g, highlightedBranch);
else if (branchFound!=highlightedBranch)
{
RevertBranch(g, highlightedBranch);
InvertBranch(g, branchFound);
}
}
else if (branchFound!=null)
InvertBranch(g, branchFound);
}
/*_________________________________________________*/
public void ScanDrop(Graphics g, int x, int y) {
Branch branchTo=FindBranch( x, y);
if (branchTo != null)
{if (branchFrom==branchTo)
{
}
else
{
Tree.MoveBranch(branchFrom, branchTo);
controls.RedescribeTree();
}
};
needsUpdating=true;
branchFrom = null;
}
/*_________________________________________________*/
public boolean mouseMove(Event e, int x, int y) {
Graphics g = getGraphics();
ScanFlash(g, x, y);
return true;
}
/*_________________________________________________*/
public boolean mouseDown(Event e, int x, int y) {
Graphics g = getGraphics();
ScanTouch(g, x, y);
if (needsUpdating)
repaint();
return true;
}
/*_________________________________________________*/
public boolean mouseDrag(Event e, int x, int y) {
if (branchFrom!=null)
{
Graphics g = getGraphics();
g.setColor(Color.black);
g.setXORMode(Color.gray);
g.drawLine(xFrom,yFrom,xTo,yTo);
xTo=x;
yTo=y;
g.drawLine(xFrom,yFrom,xTo,yTo);
}
return true;
}
/*_________________________________________________*/
public boolean mouseUp(Event e, int x, int y) {
Graphics g = getGraphics();
if (branchFrom!=null) {
ScanDrop( g, x, y);
repaint();
}
branchFrom=null;
g.setXORMode(g.getColor());
return true;
}
}
/** ======================================================================== */
public class TreeClass {
Branch Root, SubRoot;
int numTaxa;
boolean exists;
private int stringloc;
/** ________________ read tree ________________ */
private void ParseTreeDescription(String TreeDescription, Branch Ancestor) {
if (TreeDescription.charAt(stringloc) == '(')
{
stringloc++;
Ancestor.sprout();
ParseTreeDescription(TreeDescription, Ancestor.left);
stringloc++; //skip comma
ParseTreeDescription(TreeDescription, Ancestor.right);
stringloc++; //skip parensu
}
else
{
stringloc++; //skip tt name
numTaxa++;
}
}
public void ReadTree(String TreeDescription) {
stringloc=0;
numTaxa=0;
ParseTreeDescription(TreeDescription, Root);
exists=true;
}
/** ______________________________________________ */
private boolean DescendantOf(Branch branchD, Branch branchA) {
return false;
}
private boolean NodeSlantsRight(Branch N) {
if (N.ancestor.right==N)
return true;
else
return false;
}
private Branch Sister(Branch N) {
if (N.ancestor.right==N)
return N.ancestor.left;
else
return N.ancestor.right;
}
/** ______________________________________________ */
public void MoveBranch(Branch branchFrom, Branch branchTo) {
Branch sideN,C, G, F, H, NCAnc;
boolean fromancslantRight, fromslantRight, toslantRight, NCslantRight, fromroot, toroot;
if ((branchFrom.ancestor.ancestor == branchTo) & (branchTo == Root))
{
branchFrom = Sister(branchFrom);
branchTo = Sister(branchFrom.ancestor);
}
if ((branchFrom.ancestor == Root) & (branchTo.ancestor.ancestor == Root))
{
sideN = branchFrom;
branchFrom = branchTo;
branchTo = sideN;
}
fromroot = false;
toroot = false;
fromslantRight = NodeSlantsRight(branchFrom);
fromancslantRight = NodeSlantsRight(branchFrom.ancestor);
toslantRight = NodeSlantsRight(branchTo);
G = Sister(branchFrom);
H = branchFrom.ancestor.ancestor;
C = branchTo.ancestor;
F = branchFrom.ancestor;
if (F == Root)
fromroot = true;
else if (branchTo == Root )
toroot = true;
if (fromslantRight == toslantRight)
{
sideN = F.left;
F.left = F.right;
F.right = sideN;
}
G.ancestor = H;
F.ancestor = C;
branchTo.ancestor = F;
if (fromancslantRight)
H.right = G;
else
H.left = G;
if (toslantRight)
{
F.right = branchTo;
C.right = F;
}
else
{
F.left = branchTo;
C.left = F;
}
sideN = Sister(G);
if (fromroot)
{
sideN = Root;
Root = G;
G = sideN;
}
if (toroot)
{
sideN = Root;
Root = F;
F = sideN;
}
if (!NodeSlantsRight(Root))
{
SubRoot.right = Root;
}
}
}
/** ======================================================================== */
public class Branch {
Branch left, right, ancestor;
int x;
int y;
Polygon branchPoly;
Color color;
Branch(Branch Ancestor, boolean isFirstDescendant) {
this.ancestor = Ancestor;
this.color=Color.black;
branchPoly= new Polygon();
branchPoly.xpoints = new int[5];
branchPoly.ypoints = new int[5];
branchPoly.npoints=5;
}
public boolean sprout() {
this.left = new Branch(this, true);
this.right = new Branch(this, false);
return true;
}
}
class BeanTreeControls extends Panel {
TextField tf;
TreeCanvas TreeDisplay;
public BeanTreeControls(TreeCanvas TreeDisplay) {
this.TreeDisplay = TreeDisplay;
add(tf = new TextField("(((*,*),(*,*)),(((*,*),*),*));", 40));
add(new Button("Show"));
}
public boolean action(Event ev, Object arg) {
if (ev.target instanceof Button) {
/* destroy current tree if present */
/*Display.startApplet("BeanTree.html", "BeanTree.html", args);*/
TreeDisplay.treeDescription=tf.getText();
TreeDisplay.Tree.ReadTree(TreeDisplay.treeDescription);
TreeDisplay.repaint();
return true;
}
return false;
}
public void RedescribeTree() {
TreeDisplay.treeDescription = TreeDisplay.Describe();
tf.setText(TreeDisplay.treeDescription);
repaint();
}
}
\ No newline at end of file
diff --git a/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTree.class b/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTree.class
deleted file mode 100755
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diff --git a/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/com/metrowerks/AppletFrame.class b/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/com/metrowerks/AppletFrame.class
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BeanTree
It all started yesterday because I thought that perhaps I should try out some object oriented programming in case I wanted to teach an object oriented language to the students in my class next spring....
Much faster as stand alone application.
Taxon names must be one character only (actually, they can all be the same character).
\ No newline at end of file
diff --git a/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java b/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java
new file mode 100755
index 000000000..106f0adbe
--- /dev/null
+++ b/treebase-core/lib/docs/mesquite/BeanTree/BeanTree.java
@@ -0,0 +1 @@
+//package wpm;
import java.awt.*;
import java.applet.Applet;
public class BeanTree extends Applet
{
static TreeCanvas TreeDisplay;
static BeanTreeControls controls;
public void init()
{
setLayout( new BorderLayout() );
resize(300, 300);
TreeDisplay = new TreeCanvas(10, 10, 400, 400);
add( "Center", TreeDisplay );
add("North", controls = new BeanTreeControls(TreeDisplay));
TreeDisplay.Tree = new TreeClass();
TreeDisplay.controls = controls;
TreeDisplay.Tree.SubRoot = new Branch(null, false);
TreeDisplay.Tree.Root = new Branch(TreeDisplay.Tree.SubRoot, false);
TreeDisplay.edgewidth = 10;
TreeDisplay.needsUpdating = false;
TreeDisplay.highlightedBranch = null;
TreeDisplay.Tree.exists = false;
repaint();
}
public void start() {
controls.enable();
}
public void stop() {
controls.disable();
}
public static void main(String args[])
{
com.metrowerks.AppletFrame.startApplet("BeanTree", "BeanTree", args);
}
}
/** ======================================================================== */
class TreeCanvas extends Canvas {
TreeClass Tree;
int x_max, y_max;
int edgewidth;
Branch highlightedBranch, branchFrom;
int xFrom, yFrom, xTo, yTo;
boolean needsUpdating;
String treeDescription;
BeanTreeControls controls;
private int lastleft;
private int taxspacing;
private Branch foundBranch;
public TreeCanvas( int x_max, int y_max, int x_size, int y_size )
{
this.x_max = x_max;
this.y_max = y_max;
resize( x_size, y_size );
repaint();
}
/*_________________________________________________*/
private void WriteTreeDescription(Branch N) {
if (N.left!=null)
{
treeDescription+='(';
WriteTreeDescription(N.left);
treeDescription+=',';
WriteTreeDescription(N.right);
treeDescription+=')';
}
else
{
treeDescription+='*';
}
}
public String Describe() {
treeDescription="";
WriteTreeDescription(Tree.Root);
treeDescription+=';';
return treeDescription;
}
/*_________________________________________________*/
private void CalcInternalLocs(Branch N)
{
if (N.left != null) //internal
{
CalcInternalLocs(N.left);
CalcInternalLocs(N.right);
N.y = (-N.left.x + N.right.x+N.left.y + N.right.y) / 2;
N.x =(N.left.x + N.right.x - N.left.y + N.right.y) / 2;
}
}
/*_________________________________________________*/
private void CalcTerminalLocs(Branch N)
{
if (N.left == null) //terminal
{
lastleft+= taxspacing;
N.y = 90;
N.x = lastleft;
}
else
{
CalcTerminalLocs(N.left);
CalcTerminalLocs(N.right);
}
}
/*_________________________________________________*/
private void CalcBranchPolys(Branch N)
{
if (N.left != null) //terminal
{
CalcBranchPolys(N.left);
CalcBranchPolys(N.right);
N.branchPoly.npoints=0;
N.branchPoly.addPoint(N.x, N.y);
N.branchPoly.addPoint(N.x+edgewidth/2, N.y-edgewidth/2);
N.branchPoly.addPoint(N.x+edgewidth, N.y);
N.branchPoly.addPoint(N.ancestor.x+edgewidth, N.ancestor.y);
N.branchPoly.addPoint(N.ancestor.x, N.ancestor.y);
N.branchPoly.npoints=5;
}
else
{
N.branchPoly.npoints=0;
N.branchPoly.addPoint(N.x, N.y);
N.branchPoly.addPoint(N.x+edgewidth, N.y);
N.branchPoly.addPoint(N.ancestor.x+edgewidth, N.ancestor.y);
N.branchPoly.addPoint(N.ancestor.x, N.ancestor.y);
N.branchPoly.npoints=4;
}
}
/*_________________________________________________*/
private void calcBranches() {
lastleft = 0;
taxspacing = (bounds().width - 10) / Tree.numTaxa;
CalcTerminalLocs(Tree.Root);
CalcInternalLocs(Tree.Root);
Tree.SubRoot.y = (Tree.Root.y)+20;
Tree.SubRoot.x = (Tree.Root.x)-20;
CalcBranchPolys(Tree.Root);
}
/*_________________________________________________*/
private void drawBranch(Graphics g, Branch N) {
g.setColor(N.color);
g.fillPolygon(N.branchPoly);
if (N.left != null)
drawBranch(g, N.left);
if (N.right != null)
drawBranch(g, N.right);
}
/*_________________________________________________*/
public void drawTree(Graphics g) {
if (Tree.exists)
{
calcBranches();
drawBranch(g, Tree.Root);
}
}
/*_________________________________________________*/
public void paint(Graphics g) {
drawTree(g);
needsUpdating = false;
}
/*_________________________________________________*/
public void InvertBranch(Graphics g, Branch N) {
// N.color=Color.white;
highlightedBranch=N;
g.setColor(Color.white);
g.fillPolygon(N.branchPoly);
// needsUpdating=true;
}
/*_________________________________________________*/
public void RevertBranch(Graphics g, Branch N) {
// N.color=Color.black;
highlightedBranch=null;
g.setColor(Color.black);
g.fillPolygon(N.branchPoly);
// needsUpdating=true;
}
/*_________________________________________________*/
private void ScanBranches(Branch N, int x, int y)
{
if (foundBranch==null) {
if (N.branchPoly.inside(x, y))
foundBranch = N;
if (N.left != null) //terminal
{
ScanBranches(N.left, x, y);
ScanBranches(N.right, x, y);
}
}
}
/*_________________________________________________*/
public Branch FindBranch(int x, int y) {
foundBranch=null;
ScanBranches(Tree.Root, x, y);
return foundBranch;
}
/*_________________________________________________*/
public void ScanTouch(Graphics g, int x, int y) {
Branch branchFound=FindBranch( x, y);
if (branchFound!=null)
{
branchFrom=branchFound;
xFrom=x;
yFrom=y;
xTo=x;
yTo=y;
g.setXORMode(Color.gray);
g.setColor(Color.black);
g.drawLine(xFrom,yFrom,xTo,yTo);
}
}
/*_________________________________________________*/
public void ScanFlash(Graphics g, int x, int y) {
Branch branchFound=FindBranch( x, y);
if (highlightedBranch != null)
{if (branchFound==null)
RevertBranch(g, highlightedBranch);
else if (branchFound!=highlightedBranch)
{
RevertBranch(g, highlightedBranch);
InvertBranch(g, branchFound);
}
}
else if (branchFound!=null)
InvertBranch(g, branchFound);
}
/*_________________________________________________*/
public void ScanDrop(Graphics g, int x, int y) {
Branch branchTo=FindBranch( x, y);
if (branchTo != null)
{if (branchFrom==branchTo)
{
}
else
{
Tree.MoveBranch(branchFrom, branchTo);
controls.RedescribeTree();
}
};
needsUpdating=true;
branchFrom = null;
}
/*_________________________________________________*/
public boolean mouseMove(Event e, int x, int y) {
Graphics g = getGraphics();
ScanFlash(g, x, y);
return true;
}
/*_________________________________________________*/
public boolean mouseDown(Event e, int x, int y) {
Graphics g = getGraphics();
ScanTouch(g, x, y);
if (needsUpdating)
repaint();
return true;
}
/*_________________________________________________*/
public boolean mouseDrag(Event e, int x, int y) {
if (branchFrom!=null)
{
Graphics g = getGraphics();
g.setColor(Color.black);
g.setXORMode(Color.gray);
g.drawLine(xFrom,yFrom,xTo,yTo);
xTo=x;
yTo=y;
g.drawLine(xFrom,yFrom,xTo,yTo);
}
return true;
}
/*_________________________________________________*/
public boolean mouseUp(Event e, int x, int y) {
Graphics g = getGraphics();
if (branchFrom!=null) {
ScanDrop( g, x, y);
repaint();
}
branchFrom=null;
g.setXORMode(g.getColor());
return true;
}
}
/** ======================================================================== */
public class TreeClass {
Branch Root, SubRoot;
int numTaxa;
boolean exists;
private int stringloc;
/** ________________ read tree ________________ */
private void ParseTreeDescription(String TreeDescription, Branch Ancestor) {
if (TreeDescription.charAt(stringloc) == '(')
{
stringloc++;
Ancestor.sprout();
ParseTreeDescription(TreeDescription, Ancestor.left);
stringloc++; //skip comma
ParseTreeDescription(TreeDescription, Ancestor.right);
stringloc++; //skip parensu
}
else
{
stringloc++; //skip tt name
numTaxa++;
}
}
public void ReadTree(String TreeDescription) {
stringloc=0;
numTaxa=0;
ParseTreeDescription(TreeDescription, Root);
exists=true;
}
/** ______________________________________________ */
private boolean DescendantOf(Branch branchD, Branch branchA) {
return false;
}
private boolean NodeSlantsRight(Branch N) {
if (N.ancestor.right==N)
return true;
else
return false;
}
private Branch Sister(Branch N) {
if (N.ancestor.right==N)
return N.ancestor.left;
else
return N.ancestor.right;
}
/** ______________________________________________ */
public void MoveBranch(Branch branchFrom, Branch branchTo) {
Branch sideN,C, G, F, H, NCAnc;
boolean fromancslantRight, fromslantRight, toslantRight, NCslantRight, fromroot, toroot;
if ((branchFrom.ancestor.ancestor == branchTo) & (branchTo == Root))
{
branchFrom = Sister(branchFrom);
branchTo = Sister(branchFrom.ancestor);
}
if ((branchFrom.ancestor == Root) & (branchTo.ancestor.ancestor == Root))
{
sideN = branchFrom;
branchFrom = branchTo;
branchTo = sideN;
}
fromroot = false;
toroot = false;
fromslantRight = NodeSlantsRight(branchFrom);
fromancslantRight = NodeSlantsRight(branchFrom.ancestor);
toslantRight = NodeSlantsRight(branchTo);
G = Sister(branchFrom);
H = branchFrom.ancestor.ancestor;
C = branchTo.ancestor;
F = branchFrom.ancestor;
if (F == Root)
fromroot = true;
else if (branchTo == Root )
toroot = true;
if (fromslantRight == toslantRight)
{
sideN = F.left;
F.left = F.right;
F.right = sideN;
}
G.ancestor = H;
F.ancestor = C;
branchTo.ancestor = F;
if (fromancslantRight)
H.right = G;
else
H.left = G;
if (toslantRight)
{
F.right = branchTo;
C.right = F;
}
else
{
F.left = branchTo;
C.left = F;
}
sideN = Sister(G);
if (fromroot)
{
sideN = Root;
Root = G;
G = sideN;
}
if (toroot)
{
sideN = Root;
Root = F;
F = sideN;
}
if (!NodeSlantsRight(Root))
{
SubRoot.right = Root;
}
}
}
/** ======================================================================== */
public class Branch {
Branch left, right, ancestor;
int x;
int y;
Polygon branchPoly;
Color color;
Branch(Branch Ancestor, boolean isFirstDescendant) {
this.ancestor = Ancestor;
this.color=Color.black;
branchPoly= new Polygon();
branchPoly.xpoints = new int[5];
branchPoly.ypoints = new int[5];
branchPoly.npoints=5;
}
public boolean sprout() {
this.left = new Branch(this, true);
this.right = new Branch(this, false);
return true;
}
}
class BeanTreeControls extends Panel {
TextField tf;
TreeCanvas TreeDisplay;
public BeanTreeControls(TreeCanvas TreeDisplay) {
this.TreeDisplay = TreeDisplay;
add(tf = new TextField("(((*,*),(*,*)),(((*,*),*),*));", 40));
add(new Button("Show"));
}
public boolean action(Event ev, Object arg) {
if (ev.target instanceof Button) {
/* destroy current tree if present */
/*Display.startApplet("BeanTree.html", "BeanTree.html", args);*/
TreeDisplay.treeDescription=tf.getText();
TreeDisplay.Tree.ReadTree(TreeDisplay.treeDescription);
TreeDisplay.repaint();
return true;
}
return false;
}
public void RedescribeTree() {
TreeDisplay.treeDescription = TreeDisplay.Describe();
tf.setText(TreeDisplay.treeDescription);
repaint();
}
}
\ No newline at end of file
diff --git a/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTree.class b/treebase-core/lib/docs/mesquite/BeanTree/BeanTree/BeanTree.class
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