ResidueAnnotationView

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'STRAP:multiple sequence alignments '

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charite.christo.strap
Class ResidueAnnotationView

java.lang.Object
  javax.swing.table.AbstractTableModel
      javax.swing.table.DefaultTableModel
          charite.christo.strap.ResidueAnnotationView

All Implemented Interfaces:: ChRunnable, Disposable, HasPanel, ProcessEv, StrapListener, java.io.Serializable, javax.swing.CellEditor, javax.swing.ListCellRenderer, javax.swing.table.TableCellEditor, javax.swing.table.TableCellRenderer, javax.swing.table.TableModel

public final class ResidueAnnotationView
extends javax.swing.table.DefaultTableModel
implements HasPanel, ProcessEv, Disposable, StrapListener, javax.swing.ListCellRenderer, javax.swing.table.TableCellEditor, javax.swing.table.TableCellRenderer, ChRunnable
extends javax.swing.table.DefaultTableModel
implements HasPanel, ProcessEv, Disposable, StrapListener, javax.swing.ListCellRenderer, javax.swing.table.TableCellEditor, javax.swing.table.TableCellRenderer, ChRunnable

HELP PACKAGE:charite.christo.strap.extensions. PACKAGE:charite.christo.protein. To edit a CLASS_REF:ResidueAnnotationresidue annotation The item BUTTON:ResidueSelectionPopup#ACTION_edit of the context menu must be activated. The annotation view contains a table. Each row is one annotation entry.

**Figure:** Residue annotation panel. The annotated text is displayed as a table. The left column contains the category and the right column the free text. Each row has a toggle button to activate and inactivate the entry. The user can type into the table and add new table rows.
JCOMPONENT:ResidueAnnotationView#docuView()

These entries can be modified and are saved when the alignment is saved. Four obligatory fields STRING_ARRAY:ResidueAnnotation#MAIN_KEYS are unique and mandatory whereas the fields Note, Remark, CLASSICON_CLASSNAME:Texshade and CLASSICON_CLASSNAME:Pymol may occur zero to several times.

The most important field is "STRING:ResidueAnnotation#POS" because it defines the indices of the selected residues. Here are some examples of valid entries
1. The expression "1,3,4,6,101-103,110-112" selects the residue indices 1,3,4,6,101,102,103,110,111,112. Instead of the kommas spaces can by used.
2. The expression "+2 1 3 4" selects the residues 3,5, and 6 because the preceding +2 adds an offset of 2 to all positions. The "+"-sign is the first character in this expression. For the user interface the first residue has the index "1" whereas internally STRAP starts counting at zero. A negative offset of "2" is achieved by a leading "+-2".
3. The expression "1:G-3:G 5:G" selects the residues with the pdb-numbers 1,2, 3 and 5 of the chain G. If the protein has only one chain the chain identifier can be ommited like "1:-3: 5:"
4. Refering to nucleotide positions: When the toggle button is pressed (default state) the indices refer to amino acid positions. Otherwise the positions indicate nucleotides in case the protein is translated from a nucleotide sequence.
5. To any group an atom specification can be appended. This allows to select certain atoms before changing their style in the 3D-viewers. Even though protein 3D viewers usually have a specific language for atom selection, the atom expression used here is defined by STRAP and works for all 3D-viewers.
  for example "10:-20:.CA.CB" narrows the selection to the atoms CA and CB for the residues 10 to 20. A later command such as "3D_spheres" would affect only c-alpha and c-beta atoms. There may be more than one "Atoms"-entries. Each "Atoms" specification take effect only on the following 3D-style commands but not on the previous. Asterisk can be used as a wild card like "*.CA" or "10:-20:.C". For the proper atom identifiers have a look at the PDB file.
STRING:ResidueAnnotation#ATOMS Certain Atoms can be specified by an expression like ".CB.CA" which means only Cα and Cβ atoms. The next 3D-command will act on these rather than on all atoms of the amino acid. When sending the commands to a 3D-program, the rows are processed sequentially. If there comes yet another STRING:ResidueAnnotation#ATOMS-row, the previous atom-specification is replaced by the new one.
STRING:ResidueAnnotation#NAME Each selection has a name. Un-checking the check box deactivates the residue annotation.
STRING:ResidueAnnotation#GROUP Several selections may be bundled in one group e.g. "active site"
CLASSICON_CLASSNAME:Texshade: TeXshade is a LaTeX-extension for exporting an alignment as PDF or PostScript. This field is for TeXshade rendering commands. Active when the check-box is selected.
CLASSICON_CLASSNAME:ChJmolPROXY and CLASSICON_CLASSNAME:Pymol: Rasmol, VMD, Pymol and Jmol are protein structure viewers. 3D-rendering commands can be typed. On pressing the icon-buttons the commands are send to the viewers.
Note, Remark: Free text can be typed here. Clicking on the hyperlink icon opens the specified URLs in the Web-browser. There are two ways to specify an URL:
1. By typing an URL directly
2. By using a database prefix and a key as for example PDB:1ryp, PUBMED:0815. The list of databases can be changed if the CTRL key is hold while the mouse is clicked.
ICON:IC_EDITNote: free text
ICON:IC_EDITRemark:free text

SEE_DIALOG:DialogResidueAnnotationChanges SEE_DIALOG:DialogResidueAnnotationList SEE_CLASS:ResidueAnnotation SEE_CLASS:ResidueSelection

See Also:: Serialized Form

Field Summary
`static java.lang.String`	`BUT_INS_VAR`
`static java.lang.String`	`BUT_LAB_VARIABLES`
`static java.lang.String`	`POS_AA`
`static java.lang.String`	`POS_NUCL`

Fields inherited from interface charite.christo.HasPanel
`NEW_PANEL, NO_NEW_PANEL`

Fields inherited from interface charite.christo.Disposable
`NONE`

Fields inherited from interface charite.christo.ChRunnable
`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`

Constructor Summary
`ResidueAnnotationView(ResidueAnnotation a)`

Method Summary
`void`	`addCellEditorListener(javax.swing.event.CellEditorListener li)`
`void`	`cancelCellEditing()`
`void`	`dispose()`
`static javax.swing.JComponent`	`docuView()`
`java.lang.Object`	`getCellEditorValue()`
`java.awt.Component`	`getListCellRendererComponent(javax.swing.JList l, java.lang.Object o, int idx, boolean isSelected, boolean hasFocus)`
`java.awt.Component`	`getPanel(int mode)`
`int`	`getRowCount()`
`java.awt.Component`	`getTableCellEditorComponent(javax.swing.JTable table, java.lang.Object value, boolean hasFocus, int row, int column)`
`java.awt.Component`	`getTableCellRendererComponent(javax.swing.JTable table, java.lang.Object value, boolean isSelected, boolean hasFocus, int row, int column)`
`java.lang.Object`	`getValueAt(int row, int col)`
`void`	`handleEvent(StrapEvent ev)`
`boolean`	`isCellEditable(java.util.EventObject ev)`
`boolean`	`isCellEditable(int row, int col)`
`void`	`processEv(java.awt.AWTEvent ev)`
`void`	`removeCellEditorListener(javax.swing.event.CellEditorListener li)`
`java.lang.Object`	`run(java.lang.String id, java.lang.Object arg)`
`void`	`setValueAt(java.lang.Object o, int row, int col)`
`boolean`	`shouldSelectCell(java.util.EventObject ev)`
`boolean`	`stopCellEditing()`

Methods inherited from class javax.swing.table.DefaultTableModel
`addColumn, addColumn, addColumn, addRow, addRow, getColumnCount, getColumnName, getDataVector, insertRow, insertRow, moveRow, newDataAvailable, newRowsAdded, removeRow, rowsRemoved, setColumnCount, setColumnIdentifiers, setColumnIdentifiers, setDataVector, setDataVector, setNumRows, setRowCount`

Methods inherited from class javax.swing.table.AbstractTableModel
`addTableModelListener, findColumn, fireTableCellUpdated, fireTableChanged, fireTableDataChanged, fireTableRowsDeleted, fireTableRowsInserted, fireTableRowsUpdated, fireTableStructureChanged, getColumnClass, getListeners, getTableModelListeners, removeTableModelListener`

Methods inherited from class java.lang.Object
`equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Field Detail

POS_AA

public static final java.lang.String POS_AA

POS_NUCL

public static final java.lang.String POS_NUCL

BUT_INS_VAR

public static final java.lang.String BUT_INS_VAR

See Also:: Constant Field Values

BUT_LAB_VARIABLES

public static final java.lang.String BUT_LAB_VARIABLES

See Also:: Constant Field Values

Constructor Detail