charite.christo.strap
Class SequenceFeatures

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

All Implemented Interfaces:

ChRunnable, ProcessEv, TooltipProvider, java.io.Serializable, java.util.Comparator, javax.swing.table.TableModel

public class SequenceFeatures
extends javax.swing.table.DefaultTableModel
implements java.util.Comparator, ChRunnable, ProcessEv, TooltipProvider

HELP

Sequence Features

Sequence features are annotations of sequence positions indicating for example signal peptides, disulfide bonds, glycosylated or phosphorylated amino acids. In Strap they are loaded from the protein file, from BioDAS* servers, from Expasy or from the Catalytic Site Atlas at the EBI. They are underlined in the alignment panel and in the alignment output. They have a context menu (right-click), a balloon message and they can be dragged to other proteins or 3D-views.

Downloading sequence features

The button "Load and underline sequence features" loads a selection of sequence features. For more control expand "Options" and open "BioDas".

The Table

The table lists the sequence features of all or of all selected proteins. Each table row gives the color, the type such as "Metal binding", and the number of features. With check-boxes the user can control where the sequence feature is displayed. The following explains the table columns in detail:

• Feature: This column tells the type of sequence feature. Left click selects all features of this type. In the alignment panel the selected sequence features will be indicated by WIKI:Marching_ants. Right click opens the context menu for the sequence features. Drag-and-drop copies all sequence features of this type to the target such as a 3D-structure.
• # The number of entries found.
• Checkbox Sequence: This check-box controls whether the residues are shown in the alignment panel or not. If overview display of the horizontal scroll-bar is activated, then the annotated residues are also highlighted in the scroll-bar which acts as an overview.
• Checkbox 3D-backbone: In the 3D-backbone view, the one letter code of hte selected amino acids is written at the C-alpha position. Find the tool button "3D" above the alignment panel.
• Checkbox MS-Word, HTML: The MS-Word export is opened with the tool-button W. Underlining of sequence features works well in MS-Word, but not yet in Abiword or OpenOffice.
• Checkbox Jalview-Export: The Jalview-Export option is also found in the export dialog in the tab "More options" of the export dialog.
• Button "ICON:IC_WWW16": Clicking these buttons opens the source of information in the Web browser.
• Jump to the first selected residue in the alignment panel.
• Jump to the previous selected residue in the alignment panel.
• Jump to the next selected residue in the alignment panel.
• Jump to the last selected residue in the alignment panel.

Colors

Each feature type has a color for black background (screen), and one for white background (paper). These colors can be customized in the context menu.

Mouse-control

The following mouse actions apply to the sequence features in the sequence feature table and in the alignment panel.

• Right click opens a context menu for the feature.
• CTRL left-click selects and deselects the sequence features.
• Dragging the mouse copies sequence features to other proteins or to 3D-views (See WIKI:Drag_and_drop).
• Double clicking a feature opens a table with detailed data.
• Moving the mouse provides a balloon text with information on the sequence feature under the mouse.

Deactivated Features

Deactivated features are hidden unless it is explicitely selected in the choice-menu at the top of the sequence feature panel. Reasons why features are deaktivated:

• Poor alignment with the homologous sequence, where the feature is indirectly inferred from.
• The Sequence positions do not fall into the shown sequence fragment. This is often the case for N-terminal signal sequences in Pfam alignments showing only the conserved part.
• Secondary structure when the the structure information is already obtained from the protein file. Files with secondary structure information: PDB, Pfam (Stockholm-Format), DSSP.
• Phospho-tyrosine falling on a non-'Y' residue. This is controlled by the third column of the color table which contains a set of allowed letters or a dash if all letters are allowed. This table appears when opening the menu item Edit > Color of the context menu.

Examples

The following Swissprot entries have many sequence features and can be used for testing/demonstration: SWISS:Q9Y4K3 SWISS:Q9H9D4 SWISS:Q05516 SWISS:P28825 SWISS:P08045 SWISS:Q13105
However, for many other protein files no sequence features is recorded yet.

See Also:

Serialized Form

Field Summary

static java.util.Map<java.lang.String,java.lang.String>

_lCase

Fields inherited from interface charite.christo.ChRunnable

APPEND, COLUMN_TITLE, DOWNLOAD_FINISHED, GET_PANEL, ICON, INTERPRET_LINE, IS_DRAG4XY, ITEM_TEXT, MODIFY_RENDERER_COMPONENT, REPAINT_CURSOR, SAY_DOWNLOADING, SET_ICON_IMAGE, SET_TREE_VALUE, SHOW_IN_FRAME, TAB_TEXT, TIP_TEXT

Constructor Summary

SequenceFeatures()

Method Summary

int	compare(java.lang.Object o1, java.lang.Object o2)
static void	cssColors(Protein[] pp, BA ba)
static charite.christo.strap.SequenceFeatures.FeatureColor	featureName2color(java.lang.String f)
java.lang.Object	getValueAt(int row, int col)
static SequenceFeatures	instance()
boolean	isCellEditable(int row, int col)
static void	loadFeaturesBG(long options, Protein[] pp, java.lang.Runnable run)
static ChRunnable	logR()
static java.lang.String	mapSynonyms(java.lang.String fn, boolean[] found)
void	processEv(java.awt.AWTEvent ev)
java.lang.String	provideTip(java.lang.Object objOrEv)
java.lang.Object	run(java.lang.String id, java.lang.Object arg)
void	setValueAt(java.lang.Object o, int row, int col)
void	showPanel()
static ResidueAnnotation	summarizeRelated(ResidueAnnotation a, Protein p)
static void	toSpiceViewer(Protein p)
static void	updateNames()

Methods inherited from class javax.swing.table.DefaultTableModel

addColumn, addColumn, addColumn, addRow, addRow, getColumnCount, getColumnName, getDataVector, getRowCount, 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

Methods inherited from interface java.util.Comparator

equals

Field Detail

_lCase

public static final java.util.Map<java.lang.String,java.lang.String> _lCase

Constructor Detail

SequenceFeatures

public SequenceFeatures()

Method Detail

instance

public static SequenceFeatures instance()

isCellEditable

public boolean isCellEditable(int row,
                              int col)

Specified by:

isCellEditable in interface javax.swing.table.TableModel

Overrides:

isCellEditable in class javax.swing.table.DefaultTableModel

getValueAt

public java.lang.Object getValueAt(int row,
                                   int col)

Specified by:

getValueAt in interface javax.swing.table.TableModel

Overrides:

getValueAt in class javax.swing.table.DefaultTableModel

setValueAt

public void setValueAt(java.lang.Object o,
                       int row,
                       int col)

Specified by:

setValueAt in interface javax.swing.table.TableModel

Overrides:

setValueAt in class javax.swing.table.DefaultTableModel

provideTip

public java.lang.String provideTip(java.lang.Object objOrEv)

Specified by:

provideTip in interface TooltipProvider

showPanel

public void showPanel()

compare

public int compare(java.lang.Object o1,
                   java.lang.Object o2)

Specified by:

compare in interface java.util.Comparator

processEv

public void processEv(java.awt.AWTEvent ev)

Specified by:

processEv in interface ProcessEv

See Also:

EvAdapter

cssColors

public static void cssColors(Protein[] pp,
                             BA ba)

featureName2color

public static charite.christo.strap.SequenceFeatures.FeatureColor featureName2color(java.lang.String f)

updateNames

public static void updateNames()

run

public java.lang.Object run(java.lang.String id,
                            java.lang.Object arg)

Specified by:

run in interface ChRunnable

loadFeaturesBG

public static void loadFeaturesBG(long options,
                                  Protein[] pp,
                                  java.lang.Runnable run)

summarizeRelated

public static ResidueAnnotation summarizeRelated(ResidueAnnotation a,
                                                 Protein p)

mapSynonyms

public static java.lang.String mapSynonyms(java.lang.String fn,
                                           boolean[] found)

toSpiceViewer

public static void toSpiceViewer(Protein p)

logR

public static ChRunnable logR()