number and chain code ([RES]Num:Chain). Moving the mouse over an
associated residue in an alignment window highlights the associated
atoms in the displayed structures. When residues are selected in the
- Chimera window, they are highlighted on the alignment. For
- comprehensive details of Chimera's commands, refer to the tool's
- Help menu.
-
+ Chimera window, they are highlighted on the alignment.
+ <p>For comprehensive details of Chimera's commands, refer to the
+ tool's Help menu.</p>
<p>
<strong>Selecting residues in Jalview from Chimera</strong><br />
- When a selection is highlighted in a Jalview window, use the <em>Select→Select
- Highlighted Region</em> function to create a column selection for the
- mapped positions in the sequence alignment.
+ When a selection is highlighted in a Jalview window, use the
+ <em>Select→Select Highlighted Region</em> or press <em>B</em>
+ to add the mapped positions to the alignment window's column
+ selection.
</p>
<p>
Basic screen operations (see <a
based structure superposition was added in Jalview 2.6</em>
</p>
<p>
- <strong>Controls</strong><br> The structure is by default
- rendered as a ribbon diagram. Moving the mouse over the structure
- brings up tooltips giving the residue name, PDB residue number and
- chain code, atom name and number
- ([RES]Num:Chain.AtomName#AtomNumber). If a mapping exists to a
- residue in any associated sequences, then this will be highlighted
- in each one's alignment window. The converse also occurs - moving
- the mouse over an associated residue in an alignment window
- highlights the associated atoms in the displayed structures.
+ <strong>Controls</strong><br> The structure is by default rendered
+ as a ribbon diagram. Moving the mouse over the structure brings up
+ tooltips giving the residue name, PDB residue number and chain code,
+ atom name and number ([RES]Num:Chain.AtomName#AtomNumber). If a
+ mapping exists to a residue in any associated sequences, then this
+ will be highlighted in each one's alignment window. The converse
+ also occurs - moving the mouse over an associated residue in an
+ alignment window highlights the associated atoms in the displayed
+ structures. Press B or use
+ <em>Select→Select Highlighted columns</em> from any linked
+ alignment window to mark the columns highlighted after mousing over
+ the structure.
</p>
<p>Selecting a residue highlights its associated sequence residue
and alpha carbon location. Double clicking an atom allows distances
Settings" under the "View" menu to change the
visibility and colour of the new sequence feature.</p>
<p>
+ <p>
+ <strong>Selecting regions from Search Results</strong>
+ </p>
+ <p>
+ Press 'B' or select the <em>Select Highlighted Columns</em> option
+ from the alignment window's select menu to add columns containing
+ highlighted search results to the alignment window's column
+ selection.
+ </p>
+ <p>
+
<strong>A quick Regular Expression Guide</strong>
</p>
<p>A regular expression is not just a simple text query - although
<td>Both</td>
<td>Launches the search window</td>
</tr>
+ <tr><td><strong>B</strong></td>
+ <td>Both</td>
+ <td>Mark the currently highlighted columns</td>
+ </tr>
+ <tr><td><strong>Alt 'B'</strong></td>
+ <td>Both</td>
+ <td>Mark all but the currently highlighted columns</td>
+ </tr>
+ <tr><td><strong>Control 'B'</strong></td>
+ <td>Both</td>
+ <td>Toggle the marks on the currently highlighted
+ columns (or all others if Alt is pressed)</td>
+ </tr>
<tr>
<td><strong>H</strong></td>
<td>Both</td>
columns in the alignment according to secondary structure,
labels and values shown in alignment annotation rows. </em></li>
<li><strong>Select Highlighted Columns</strong> <br /> <em>Selects
- the columns currently highlighted as a result of a find, mouse
- over, or selection event from a linked structure viewer or other
- application. Modifiers will work on some platforms: SHIFT will
- add columns to selection, ALT will invert the highlighted set
- before selection, and CTRL (or META) will toggle the selection.
- </em></li>
+ the columns currently highlighted as a result of a find, mouse
+ over, or selection event from a linked structure viewer or other
+ application. Modifiers will work on some platforms: ALT will add
+ all but the highlighted set to the column selection, and CTRL
+ (or META) will toggle the selection. </em></li>
</ul></li>
<li><strong>View</strong>
<ul>
<li><strong>Select Highlighted Columns</strong> <br /> <em>Selects
the columns currently highlighted as a result of a find, mouse
over, or selection event from a linked structure viewer or other
- application. Modifiers will work on some platforms: SHIFT will
- add columns to selection, ALT will invert the highlighted set
- before selection, and CTRL (or META) will toggle the selection.
- </em></li>
+ application. Modifiers will work on some platforms: ALT will add
+ all but the highlighted set to the column selection, and CTRL
+ (or META) will toggle the selection. </em></li>
</ul>
</body>
</html>
action.calculate = Calculate
action.select_all = Select all
action.select_highlighted_columns = Select Highlighted Columns
+tooltip.select_highlighted_columns = Press B to mark highlighted columns, Ctrl-B to toggle, and Alt-B to mark all but highlighted columns
action.deselect_all = Deselect all
action.invert_selection = Invert selection
action.using_jmol = Using Jmol
toggleHiddenRegions(toggleSeqs, toggleCols);
break;
}
+ case KeyEvent.VK_B:
+ {
+ boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
+ boolean modifyExisting = true; // always modify, don't clear
+ // evt.isShiftDown();
+ boolean invertHighlighted = evt.isAltDown();
+ avc.markHighlightedColumns(invertHighlighted, modifyExisting,
+ toggleSel);
+ break;
+ }
case KeyEvent.VK_PAGE_UP:
if (viewport.getWrapAlignment())
{
protected void selectHighlightedColumns_actionPerformed(
ActionEvent actionEvent)
{
+ // include key modifier check in case user selects from menu
avc.markHighlightedColumns(
(actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
- (actionEvent.getModifiers() & ActionEvent.SHIFT_MASK) != 0,
- (actionEvent.getModifiers() & ActionEvent.CTRL_MASK) != 0);
+ true,
+ (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
}
}
}
});
JMenuItem selectHighlighted = new JMenuItem(
- MessageManager.getString("label.select_highlighted_columns"));
- keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ MessageManager.getString("action.select_highlighted_columns"));
+ selectHighlighted.setToolTipText(MessageManager
+ .getString("tooltip.select_highlighted_columns"));
al = new ActionListener()
{
@Override
selectHighlightedColumns_actionPerformed(actionEvent);
}
};
- addMenuActionAndAccelerator(keyStroke, selectHighlighted, al);
-
+ selectHighlighted.addActionListener(al);
JMenu tooltipSettingsMenu = new JMenu(
MessageManager.getString("label.sequence_id_tooltip"));
JMenu autoAnnMenu = new JMenu(
git://source.jalview.org / jalview.git / commitdiff