pl.krakow.cmuj.bioinformatics.jellipse
Class PdbFetcher

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Frame
                  javax.swing.JFrame
                      pl.krakow.cmuj.bioinformatics.jellipse.PdbFetcher

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class PdbFetcher
extends javax.swing.JFrame

Loads PDB file content via http protocol from RCSB or from a local file. Assumption is made that filess retrieved from the server are gzipped and local ones are not.

See Also:

PdbFile, Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JFrame

javax.swing.JFrame.AccessibleJFrame

Nested classes/interfaces inherited from class java.awt.Frame

java.awt.Frame.AccessibleAWTFrame

Nested classes/interfaces inherited from class java.awt.Window

java.awt.Window.AccessibleAWTWindow

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

private javax.swing.JButton	jButtonFtpPdbRetrieve
private javax.swing.JButton	jButtonPdbFileChoose
private javax.swing.JFileChooser	jFileChooserSelectPdb
private javax.swing.JLabel	jLabel1
private javax.swing.JLabel	jLabelFtpPdbId
private javax.swing.JPanel	jPanelGetPdbViaFtp
private javax.swing.JPanel	jPanelGetPdbViaLocal
private javax.swing.JTextField	jTextFieldFtpPdbId
private PdbFile	pdb
private java.lang.StringBuffer	pdbContent
private java.lang.String	pdbid
private int	pdbsize

Fields inherited from class javax.swing.JFrame

accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Frame

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

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

PdbFetcher()
Creates new PdbFetcher and displays as a JFrame

Method Summary

private void	centerWindow(java.awt.Component frame) Displays any component in the center of the screen.
PdbFile	getPdbFile() Get pdb file read by the PdbFetcher.
private void	getPdbFtp(java.lang.String pdbid) Retrieve peptide structure as a gzipped PDB file via http protocol.
java.lang.String	getPdbId() Allows to read PDB ID of the PdbFetcher.
private void	getPdbLoad(java.lang.String pdbpath) Load the structure from a non-compressed PDB file on the local filesystem.
private void	initComponents() This method is called from within the constructor to initialize the form.
private void	jButtonFtpPdbRetrieveActionPerformed(java.awt.event.ActionEvent evt) Starts PDB file retrieval.
private void	jButtonPdbFileChooseActionPerformed(java.awt.event.ActionEvent evt) Handles dialog window allowing to choose PDB file form a local filesystem.
private void	jTextFieldFtpPdbIdActionPerformed(java.awt.event.ActionEvent evt)
private void	jTextFieldFtpPdbIdKeyReleased(java.awt.event.KeyEvent evt) Sets jTextFieldFtpPdbId's backgroung pink if PDB ID given is supposed to be incorrect (with length not equal to 4).
private void	setPdbId(java.lang.String pdbid) Sets PdbFetcher's PDB ID in uppercase.
private void	waitForRetrieval() Serves as a lock (should be invoked from the constructor).

Methods inherited from class javax.swing.JFrame

addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update

Methods inherited from class java.awt.Frame

addNotify, finalize, 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

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setAlwaysOnTop, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationByPlatform, setLocationRelativeTo, show, toBack, toFront

Methods inherited from class java.awt.Container

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

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, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, 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, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Field Detail

pdbid

private java.lang.String pdbid

pdbContent

private java.lang.StringBuffer pdbContent

pdb

private PdbFile pdb

pdbsize

private int pdbsize

jButtonFtpPdbRetrieve

private javax.swing.JButton jButtonFtpPdbRetrieve

jButtonPdbFileChoose

private javax.swing.JButton jButtonPdbFileChoose

jFileChooserSelectPdb

private javax.swing.JFileChooser jFileChooserSelectPdb

jLabel1

private javax.swing.JLabel jLabel1

jLabelFtpPdbId

private javax.swing.JLabel jLabelFtpPdbId

jPanelGetPdbViaFtp

private javax.swing.JPanel jPanelGetPdbViaFtp

jPanelGetPdbViaLocal

private javax.swing.JPanel jPanelGetPdbViaLocal

jTextFieldFtpPdbId

private javax.swing.JTextField jTextFieldFtpPdbId

Constructor Detail

PdbFetcher

public PdbFetcher()

Creates new PdbFetcher and displays as a JFrame

Method Detail

centerWindow

private void centerWindow(java.awt.Component frame)

Displays any component in the center of the screen.

Parameters:

frame - usually a window

waitForRetrieval

private void waitForRetrieval()

Serves as a lock (should be invoked from the constructor). After JFrame appears, it's cruicial to have the complete PDB file read.

getPdbFtp

private void getPdbFtp(java.lang.String pdbid)

Retrieve peptide structure as a gzipped PDB file via http protocol. Performs getting from a location like http://www.rcsb.org/pdb/cgi/export.cgi/ZZZZ.pdb.gz?format=PDB&pdbId=ZZZZ&compression=gz where ZZZZ is the PDB id.

Parameters:

pdbid - a PDB ID in uppercase

See Also:

setPdbId(java.lang.String), getPdbId()

getPdbLoad

private void getPdbLoad(java.lang.String pdbpath)

Load the structure from a non-compressed PDB file on the local filesystem.

Parameters:

pdbpath - path to a local file containing PDB-formatted structure.

See Also:

getPdbFtp(java.lang.String), waitForRetrieval()

getPdbFile

public PdbFile getPdbFile()

Get pdb file read by the PdbFetcher.

Returns:

pdb PDB file read by a current instance of PdbFetcher

setPdbId

private void setPdbId(java.lang.String pdbid)

Sets PdbFetcher's PDB ID in uppercase. For retrieval from the RCSB server uppercase is essential.

getPdbId

public java.lang.String getPdbId()

Allows to read PDB ID of the PdbFetcher.

Returns:

four character, uppercase PDB ID

initComponents

private void initComponents()

This method is called from within the constructor to initialize the form. The content of this method is always regenerated by the Form Editor.

jTextFieldFtpPdbIdActionPerformed

private void jTextFieldFtpPdbIdActionPerformed(java.awt.event.ActionEvent evt)

jTextFieldFtpPdbIdKeyReleased

private void jTextFieldFtpPdbIdKeyReleased(java.awt.event.KeyEvent evt)

Sets jTextFieldFtpPdbId's backgroung pink if PDB ID given is supposed to be incorrect (with length not equal to 4).

Parameters:

evt - when a key is released

jButtonFtpPdbRetrieveActionPerformed

private void jButtonFtpPdbRetrieveActionPerformed(java.awt.event.ActionEvent evt)

Starts PDB file retrieval.

jButtonPdbFileChooseActionPerformed

private void jButtonPdbFileChooseActionPerformed(java.awt.event.ActionEvent evt)

Handles dialog window allowing to choose PDB file form a local filesystem.