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'STRAP:multiple sequence alignments ' | ||||||||
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java.lang.Object java.awt.Component java.awt.Container javax.swing.JComponent javax.swing.JTabbedPane charite.christo.strap.AbstractDialogJTabbedPane charite.christo.strap.DialogAlign
public final class DialogAlign
HELP
The Dialog is used to align a
number of selected proteins (see WIKI:Sequence_alignment).
The user selects an alignment method COMBO:charite.christo.strap.extensions.MultipleAlignerClustalW.
By pressing the button LABEL:ChButton#BUTTON_GO the alignment
computation is started. It takes some seconds to minutes, before the
computation the result is shown in a preview panel.
To accept the alignment in the preview and to infer the alignment into
the working alignment panel
BUTTON:DialogAlignResult#BUT_LAB_Apply needs to be pressed to.
Types of alignment procedures:
So-called local alignment procedures identify local matches
whereas global alignment algorithms align the entire sequences.
Some alignment programs align two sequences only. The derived multiple
alignments are not as good as those from methods that
natively support multiple alignments.
3D-superposition programs consider only the 3D-structure and do not
regard the residue type.
Profiles: ClustalW and T-coffee can use pre-aligned
sequences as a so-called sequence profile. For more information
see the manual of T-coffee.
SEE_DIALOG:DialogAlignOneToAll
Nested Class Summary |
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Nested classes/interfaces inherited from class javax.swing.JComponent |
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javax.swing.JComponent.AccessibleJComponent |
Nested classes/interfaces inherited from class java.awt.Component |
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java.awt.Component.BaselineResizeBehavior |
Field Summary | |
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static java.lang.String |
RADIO_REGION
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static java.lang.String |
RADIO_SELECTION
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Fields inherited from class javax.swing.JTabbedPane |
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SCROLL_TAB_LAYOUT, WRAP_TAB_LAYOUT |
Fields inherited from class javax.swing.JComponent |
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TOOL_TIP_TEXT_KEY, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW |
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 charite.christo.ChRunnable |
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APPEND, COLUMN_TITLE, DOWNLOAD_FINISHED, GET_PANEL, ICON, INTERPRET_LINE, IS_DRAG4XY, ITEM_TEXT, MODIFY_RENDERER_COMPONENT, PROGRESS, REPAINT_CURSOR, SAY_DOWNLOADING, SET_ICON_IMAGE, SET_TREE_VALUE, SHOW_IN_FRAME, TAB_TEXT, TIP_TEXT |
Fields inherited from interface charite.christo.Disposable |
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NONE |
Fields inherited from interface javax.swing.SwingConstants |
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BOTTOM, CENTER, EAST, HORIZONTAL, LEADING, LEFT, NEXT, NORTH, NORTH_EAST, NORTH_WEST, PREVIOUS, RIGHT, SOUTH, SOUTH_EAST, SOUTH_WEST, TOP, TRAILING, VERTICAL, WEST |
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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DialogAlign()
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Method Summary | |
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void |
actionPerformed(java.awt.event.ActionEvent ev)
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void |
addProfiles(SequenceAligner aligner)
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void |
handleEvent(StrapEvent e)
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java.lang.Object |
run(java.lang.String id,
java.lang.Object arg)
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Methods inherited from class charite.christo.strap.AbstractDialogJTabbedPane |
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dispose, fireStateChanged, isDisposed |
Methods inherited from class javax.swing.JTabbedPane |
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add, add, add, add, add, addChangeListener, addTab, addTab, addTab, getAccessibleContext, getBackgroundAt, getBoundsAt, getChangeListeners, getComponentAt, getDisabledIconAt, getDisplayedMnemonicIndexAt, getForegroundAt, getIconAt, getMnemonicAt, getModel, getSelectedComponent, getSelectedIndex, getTabComponentAt, getTabCount, getTabLayoutPolicy, getTabPlacement, getTabRunCount, getTitleAt, getToolTipText, getToolTipTextAt, getUI, getUIClassID, indexAtLocation, indexOfComponent, indexOfTab, indexOfTab, indexOfTabComponent, insertTab, isEnabledAt, remove, remove, removeAll, removeChangeListener, removeTabAt, setBackgroundAt, setComponentAt, setDisabledIconAt, setDisplayedMnemonicIndexAt, setEnabledAt, setForegroundAt, setIconAt, setMnemonicAt, setModel, setSelectedComponent, setSelectedIndex, setTabComponentAt, setTabLayoutPolicy, setTabPlacement, setTitleAt, setToolTipTextAt, setUI, updateUI |
Methods inherited from class javax.swing.JComponent |
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addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintImmediately, paintImmediately, print, printAll, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update |
Methods inherited from class java.awt.Container |
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addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusBackward, transferFocusDownCycle, validate |
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, contains, createImage, createImage, createVolatileImage, createVolatileImage, dispatchEvent, enable, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public static final java.lang.String RADIO_REGION
public static final java.lang.String RADIO_SELECTION
Constructor Detail |
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public DialogAlign()
Method Detail |
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public void addProfiles(SequenceAligner aligner)
public void actionPerformed(java.awt.event.ActionEvent ev)
actionPerformed
in interface java.awt.event.ActionListener
public void handleEvent(StrapEvent e)
handleEvent
in interface StrapListener
public java.lang.Object run(java.lang.String id, java.lang.Object arg)
run
in interface ChRunnable
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