<p>The red box indicates the currently viewed region of the
alignment, this may be moved by clicking and dragging with the
mouse.</p>
- <p><strong>Right-click</strong> (or CMD-Click) to open the
- overview's popup menu. This provides an option to include hidden
- regions in the overview (shown as dark-grey rows and columns). <br/><br/>
- <em>The option to include/exclude hidden regions in the
- overview was introduced in Jalview 2.10.2</em>.
+ <p>Click anywhere else in the overview to centre the view on that
+ position</p>
+ <p></p>
+ <p>
+ <strong>Hiding hidden regions in the overview</strong>
+ </p>
+ <p>
+ Hidden sequences and columns are by default shown as dark-grey rows
+ and columns in the overview. Hidden regions can also be omitted
+ entirely (to make the Overview 'WYSIWIG') by <strong>Right-clicking</strong>
+ (or CMD-Clicking) to open the overview's popup menu.<br />
+ <br /> <em>The option to include/exclude hidden regions in the
+ overview was introduced in Jalview 2.10.2</em>.
+
<p>
<img src="overview.gif" width="407" height="137">
</p>
<!-- JAL-384 -->Custom shading schemes created via groovy
scripts
</li>
- <li>
- <!-- JAL-2491 -->linked scrolling of CDS/Protein views
- via Overview or sequence motif search operations
- </li>
- <li>
- <!-- JAL-2526 -->Efficiency improvements for interacting
- with alignment and overview windows
- </li>
- <li>
- <!-- JAL-2388 -->Hidden columns and sequences can be
- omitted in Overview
+ <li>Improved overview window
+ <ul>
+ <li>
+ <!-- JAL-2526 -->Efficiency improvements for
+ interacting with alignment and overview windows
+ </li>
+ <li>
+ <!-- JAL-2491 -->Linked scrolling of CDS/Protein
+ views via Overview or sequence motif search operations
+ </li>
+ <li>
+ <!-- JAL-2514 -->Scrolling of wrapped alignment views
+ via overview
+ </li>
+ <li>
+ <!-- JAL-2388 -->Hidden columns and sequences can be
+ omitted in Overview
+ </li>
+ <li>
+ <!-- JAL-2611 -->Click-drag in visible area allows
+ fine adjustment of visible position
+ </li>
+ </ul>
</li>
<li>
<!-- JAL-2535 -->Posterior probability annotation from
due to 'null' string rather than empty string used for
residues with no corresponding PDB mapping).
</li>
+ <li><!-- JAL-2592 -->User defined colourschemes called 'User Defined' don't appear in Colours menu</li>
+ <li>
</ul>
public void setWrapAlignment(boolean wrap)
{
- vpRanges.setStartSeq(0);
+ vpRanges.setStartEndSeq(0, vpRanges.getVisibleAlignmentHeight());
vpRanges.setStartRes(0);
scalePanelHolder.setVisible(!wrap);
public void fastPaint(int horizontal)
{
- if (horizontal == 0
+ if (horizontal == 0 || gg == null
|| av.getAlignment().getAlignmentAnnotation() == null
|| av.getAlignment().getAlignmentAnnotation().length < 1)
{
/**
* serves a search condition for finding the first feature whose end
- * position follows a given target location
+ * position is at or follows a given target location
*
* @param target
* @return
protected void findNonNestedFeatures(long from, long to,
List<SequenceFeature> result)
{
+ /*
+ * find the first feature whose end position is
+ * after the target range start
+ */
int startIndex = binarySearch(nonNestedFeatures,
SearchCriterion.byEnd(from));
- findNonNestedFeatures(startIndex, from, to, result);
- }
-
- /**
- * Scans the list of non-nested features, starting from startIndex, to find
- * those that overlap the from-to range, and adds them to the result list.
- * Returns the index of the first feature whose start position is after the
- * target range (or the length of the whole list if no such feature exists).
- *
- * @param startIndex
- * @param from
- * @param to
- * @param result
- * @return
- */
- protected int findNonNestedFeatures(final int startIndex, long from,
- long to, List<SequenceFeature> result)
- {
- int i = startIndex;
+ final int startIndex1 = startIndex;
+ int i = startIndex1;
while (i < nonNestedFeatures.size())
{
SequenceFeature sf = nonNestedFeatures.get(i);
}
i++;
}
- return i;
}
/**
* 'User Defined' opens a panel to configure or load a
* user-defined colour scheme
*/
- if (ResidueColourScheme.USER_DEFINED.equals(name))
+ if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
{
new UserDefinedColours(alignPanel);
return;
final String label = MessageManager.getString("action.user_defined");
JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(
label);
- userDefinedColour.setName(ResidueColourScheme.USER_DEFINED);
+ userDefinedColour.setName(ResidueColourScheme.USER_DEFINED_MENU);
userDefinedColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- client.changeColour_actionPerformed(ResidueColourScheme.USER_DEFINED);
+ client.changeColour_actionPerformed(ResidueColourScheme.USER_DEFINED_MENU);
}
});
colourMenu.add(userDefinedColour);
{
none = radioButton;
}
- if (ResidueColourScheme.USER_DEFINED.equals(buttonName))
+ if (ResidueColourScheme.USER_DEFINED_MENU.equals(buttonName))
{
userDefined = radioButton;
}
{
public static final String NONE = "None";
+ /*
+ * default display name for a user defined colour scheme
+ */
public static final String USER_DEFINED = "User Defined";
/*
+ * name for (new) "User Defined.." colour scheme menu item
+ */
+ public static final String USER_DEFINED_MENU = "*User Defined*";
+
+ /*
* lookup up by character value e.g. 'G' to the colors array index
* e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K
*/
{
return schemeName;
}
- return "User Defined";
+ return ResidueColourScheme.USER_DEFINED;
}
/**
git://source.jalview.org / jalview.git / commitdiff