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:
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 |
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 |
_lCase
public static final java.util.Map<java.lang.String,java.lang.String> _lCase
SequenceFeatures
public SequenceFeatures()
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()
'The most important classes are StrapAlign, Protein and StrapEvent.'