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java.lang.Objectjava.awt.Component
java.awt.Container
java.awt.Window
java.awt.Frame
javax.swing.JFrame
net.sourceforge.olduvai.treejuxtaposer.TreeWriter
public class TreeWriter
Static utility class to write a tree to a file. Does not create an object, no constructor. Newick files are created, but the functions here could be used to create a Nexus file writer.
Nested Class Summary |
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Nested classes/interfaces inherited from class javax.swing.JFrame |
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javax.swing.JFrame.AccessibleJFrame |
Nested classes/interfaces inherited from class java.awt.Frame |
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java.awt.Frame.AccessibleAWTFrame |
Nested classes/interfaces inherited from class java.awt.Window |
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java.awt.Window.AccessibleAWTWindow |
Nested classes/interfaces inherited from class java.awt.Container |
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java.awt.Container.AccessibleAWTContainer |
Nested classes/interfaces inherited from class java.awt.Component |
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java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
Field Summary | |
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private javax.swing.JButton |
CancelButton
Cancel button that does not change the node and does not reset differences. |
private static char |
childSeparator
Place between children of a subtree root. |
private static char |
closeBracket
Close bracket to wrap children of a subtree root. |
private javax.swing.JLabel |
dialogLabel
Label for the text field. |
private static char |
doubleQuote
Quote object to wrap node names. |
private static char |
infoSeparator
UNUSED separator for placing more information after the node name. |
private static char |
lineTerminator
End of tree character. |
private javax.swing.JTextField |
newLabel
Text area to read new label name. |
private javax.swing.JButton |
OkButton
OK button that resets the differences and search dialog. |
private static char |
openBracket
Open bracket to wrap children of a subtree root. |
private static char |
quote
UNUSED single quote character. |
private TreeNode |
renameNode
Node that is being renamed. |
private TreeJuxtaposer |
tj
TreeJuxtaposer used to reset the differences and search dialog with TreeJuxtaposer.postDeleteTrees() . |
private static char |
treeTerminator
End of tree character. |
Fields inherited from class javax.swing.JFrame |
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accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled |
Fields inherited from class java.awt.Frame |
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CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR |
Fields inherited from class java.awt.Component |
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BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT |
Fields inherited from interface javax.swing.WindowConstants |
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DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE |
Fields inherited from interface java.awt.image.ImageObserver |
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ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
Constructor Summary | |
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TreeWriter(TreeNode renameNode,
TreeJuxtaposer tj)
Start a tree writer dialog that allows a user to enter a new name for a node. |
Method Summary | |
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void |
actionPerformed(java.awt.event.ActionEvent arg0)
Capture button press for newly renamed node. |
private void |
initGUI()
Initialize the GUI for changing the label of a node. |
private static void |
nodeWriter(TreeNode currNode,
java.io.BufferedWriter writer)
Write a single node to the writer object, after calling the subtree writer on each child. |
private static void |
subtreeWriter(TreeNode subtreeRoot,
java.io.BufferedWriter writer)
Wrap a series of nodes in brackets, then call the node writer on each child of the input subtree root. |
static void |
writeTree(Tree t,
java.lang.String fileName)
Writes Tree to file by name of fileName. |
Methods inherited from class javax.swing.JFrame |
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addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, repaint, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, update |
Methods inherited from class java.awt.Frame |
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addNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated |
Methods inherited from class java.awt.Window |
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addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOwnedWindows, getOwner, getOwnerlessWindows, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setVisible, show, toBack, toFront |
Methods inherited from class java.awt.Container |
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add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusBackward, transferFocusDownCycle, validate, validateTree |
Methods inherited from class java.awt.Component |
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action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, setBackground, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusUpCycle |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface java.awt.MenuContainer |
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getFont, postEvent |
Field Detail |
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private static final char lineTerminator
private static final char treeTerminator
private static final char openBracket
private static final char closeBracket
private static final char childSeparator
private static final char doubleQuote
private static final char infoSeparator
private static final char quote
private TreeJuxtaposer tj
TreeJuxtaposer.postDeleteTrees()
.
private TreeNode renameNode
private javax.swing.JButton OkButton
private javax.swing.JButton CancelButton
private javax.swing.JLabel dialogLabel
private javax.swing.JTextField newLabel
Constructor Detail |
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public TreeWriter(TreeNode renameNode, TreeJuxtaposer tj)
renameNode
- Node that is being renamed, does not know it's own tree.tj
- TreeJuxtaposer object, for referencing the search dialog.Method Detail |
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public static void writeTree(Tree t, java.lang.String fileName)
t
- Tree to be written to file.fileName
- output file name.private static void nodeWriter(TreeNode currNode, java.io.BufferedWriter writer) throws java.io.IOException
doubleQuote
.
currNode
- Node to write.writer
- Writer object used to send the node and its subtree to file.
java.io.IOException
private static void subtreeWriter(TreeNode subtreeRoot, java.io.BufferedWriter writer) throws java.io.IOException
subtreeRoot
- Root of the subtree to write. This node itself is not written by this function.writer
- Writer object used to send the subtree to file.
java.io.IOException
private void initGUI()
public void actionPerformed(java.awt.event.ActionEvent arg0)
actionPerformed
in interface java.awt.event.ActionListener
arg0
- Button press, either OK or cancel.
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