charite.christo.strap
Class StrapDAS

java.lang.Object
  javax.swing.border.AbstractBorder
      charite.christo.ChRenderer
          charite.christo.strap.StrapDAS

All Implemented Interfaces:

ChRunnable, PaintHook, ProcessEv, java.io.Serializable, javax.swing.border.Border, javax.swing.CellEditor, javax.swing.ListCellRenderer, javax.swing.table.TableCellEditor, javax.swing.table.TableCellRenderer, javax.swing.tree.TreeCellRenderer

public class StrapDAS
extends ChRenderer
implements ChRunnable, ProcessEv

HELP BioDAS* services provide residue specific annotations for proteins. BioDAS* services are listed in STRING:DAS#URL_REGISTRY (http://www.dasregistry.org/). STRAP reads this BioDAS* registry file and sorts the services according to the authority. The most important authority is "UniProt" which is displayed in the first tab. The user can select one or several DAS services in the table and one or several proteins. When LABEL:ChButton#BUTTON_GO is pressed, the DAS features are read from the selected Services. For this purpose, the database references stored in the protein files are used. The database references of proteins can be seen in the balloon text over the protein labels of the alignment. If a services from the "UniProt" tab is used, then only those proteins can be processed, that have a "UniProt" reference.

Cache: The downloaded files are cached in STRING:ChUtils#dirWeb() and are valid for STRING:DAS#DAYS_VALID days.

Example XML output: Press BUTTON:StrapDAS#docButExamble()! to get a list of example XML files for each DAS service. These XML files are basis for the table column "Example".

See Also:

Serialized Form

Field Summary

static long

STOP_ON_CLOSED_FRAME

Fields inherited from class charite.christo.ChRenderer

_value, BUT_WIDTH, CLASS_NAMES, CMD_FOND_NAME, KEY_CB_SELECTED, KEY_EDITED_COL, KEY_EDITED_ROW, KEY_EDITOR_COMPONENT, KEY_NOT_EDITABLE_BG, KEY_RENDERER_COMPONENT, KEY_TO_CLOSE, KEY_TOGGLE_SELECTED, KOPT_FULL_FILE_PATH, KOPT_NO_CHANGE_FG_AND_BG_IF_SELECTED, LAST_PATH_COMPONENT_DOT, LAST_PATH_COMPONENT_SLASH, SMALL_CLOSE, SMALL_MAXIM, STRIKE_THROUGH_THICK, STRIKE_THROUGH_V

Fields inherited from interface charite.christo.ChRunnable

APPEND, 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

StrapDAS()

Method Summary

static void	_loadFeatures(long option, java.lang.Object[] row, Protein p, ChRunnable globalLog)
static ChButton	docButExamble()
java.awt.Component	getTableCellRendererComponent(javax.swing.JTable t, java.lang.Object value0, boolean selected, boolean focus, int row0, int col)
static void	load(long option, java.lang.String[] titles, Protein[] pp, ChRunnable log)
static void	loadFeaturesInRows(long options, java.lang.Object[][] rows, Protein[] pp, ChRunnable log)
static ChRunnable	logR()
void	processEv(java.awt.AWTEvent ev)
java.lang.Object	run(java.lang.String id, java.lang.Object arg)
static void	show(boolean downloadExamples)
static java.lang.Thread	thread_load(long option, java.lang.String[] title, Protein[] pp, ChRunnable log)
static java.lang.Thread	thread_loadFeatures(long option, java.lang.Object[] row, Protein p, ChRunnable globalLog)
static java.lang.Thread	thread_loadFeaturesInRows(long options, java.lang.Object[][] rows, Protein[] pp, ChRunnable log)

Methods inherited from class charite.christo.ChRenderer

addCellEditorListener, cancelCellEditing, drawSmallButtons, editedCol, editedRow, getBorderInsets, getCellEditorValue, getListCellRendererComponent, getTableCellEditorComponent, getTreeCellRendererComponent, inButClose, isCellEditable, label, options, options, paint, paintBorder, paintHook, process, randomStrikeThrough, removeCellEditorListener, setEnabled, setOrigRenderer, setRendererText, setRendererTextWeak, setSmallButtonX, setSmallButtonXc, shouldSelectCell, stopCellEditing, textField

Methods inherited from class javax.swing.border.AbstractBorder

getBaseline, getBaselineResizeBehavior, getBorderInsets, getInteriorRectangle, getInteriorRectangle, isBorderOpaque

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

STOP_ON_CLOSED_FRAME

public static final long STOP_ON_CLOSED_FRAME

See Also:

Constant Field Values

Constructor Detail

StrapDAS

public StrapDAS()

Method Detail

docButExamble

public static ChButton docButExamble()

logR

public static ChRunnable logR()

thread_load

public static java.lang.Thread thread_load(long option,
                                           java.lang.String[] title,
                                           Protein[] pp,
                                           ChRunnable log)

load

public static void load(long option,
                        java.lang.String[] titles,
                        Protein[] pp,
                        ChRunnable log)

thread_loadFeaturesInRows

public static java.lang.Thread thread_loadFeaturesInRows(long options,
                                                         java.lang.Object[][] rows,
                                                         Protein[] pp,
                                                         ChRunnable log)

loadFeaturesInRows

public static void loadFeaturesInRows(long options,
                                      java.lang.Object[][] rows,
                                      Protein[] pp,
                                      ChRunnable log)

thread_loadFeatures

public static java.lang.Thread thread_loadFeatures(long option,
                                                   java.lang.Object[] row,
                                                   Protein p,
                                                   ChRunnable globalLog)

_loadFeatures

public static void _loadFeatures(long option,
                                 java.lang.Object[] row,
                                 Protein p,
                                 ChRunnable globalLog)

show

public static void show(boolean downloadExamples)

getTableCellRendererComponent

public java.awt.Component getTableCellRendererComponent(javax.swing.JTable t,
                                                        java.lang.Object value0,
                                                        boolean selected,
                                                        boolean focus,
                                                        int row0,
                                                        int col)

Specified by:

getTableCellRendererComponent in interface javax.swing.table.TableCellRenderer

Overrides:

getTableCellRendererComponent in class ChRenderer

run

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

Specified by:

run in interface ChRunnable

processEv

public void processEv(java.awt.AWTEvent ev)

Specified by:

processEv in interface ProcessEv

Overrides:

processEv in class ChRenderer

See Also:

EvAdapter