<strong>Structure Viewers in the Jalview Desktop</strong><br /> The
<a href="jmol.html">Jmol viewer</a> has been included since Jalview
2.3. Jalview 2.8.2 included support for <a href="chimera.html">Chimera</a>,
- provided it is installed and can be launched by Jalview. ChimeraX and PyMOL
+ provided it is installed and can be launched by Jalview. ChimeraX and <a href="pymol.html">PyMOL</a>
support is included from Jalview 2.11.2. The default
viewer can be configured in the <a href="preferences.html#structure">Structure
tab</a> in the <strong>Tools→Preferences</strong> dialog box.
un-tick the <strong>Superpose Structures</strong> checkbox.
</p>
- <p>
- <em>Superposing structures</em><br/>Jalview superposes structures using
- the visible portions of any associated sequence alignments. A
- message in the structure viewer's status bar will be shown if not
- enough aligned columns were available to perform a superposition.
- </p>
- <p>
- See the <a href="jmol.html">Jmol
- </a> and <a href="chimera.html">Chimera</a> help pages for
- more information about their capabilities.</p>
-
-
- <p>
+ <p>
+ <em>Superposing structures</em><br />Jalview superposes structures
+ using the currently selected columns (if more than 3 columns are
+ selected), or the visible portions of any associated sequence
+ alignments. Depending on the viewer, Root Mean Squared Deviation (RMS
+ or RMSD) for each pair of superpositions may be output in the
+ structure viewer's console.
+ </p>
+ <p>A message in the structure viewer's status bar will be shown if
+ not enough aligned columns were available to perform a superposition.
+ </p>
+ <p>
+ See the <a href="jmol.html">Jmol</a>, <a href="chimera.html">Chimera/X</a>
+ and <a href="pymol.html">Pymol</a> help pages for more information
+ about their individual capabilities.
+ </p>
+ <p>
<strong>Retrieving sequences from the PDB</strong><br>You can
retrieve sequences from the PDB using the <a
href="pdbsequencefetcher.html">Sequence Fetcher</a>. The sequences
- <!-- JAL-2910 --> HeadlessException in console in headless mode (actually fixed in 2.11.{0,1,2))
## New Known defects
+- <!-- JAL-4303 --> EBI-AlphaFold PLDDT colours cannot be overlaid on alignment via 'Colour by annotation' unless the alignment's colourscheme has been set to 'None' via the Colours menu.
+- <!-- JAL-4302 --> Tree renderer doesn't show bottom-most leaves of tree when Fit-To-Window is enabled.
- <!-- JAL-4178 --> Cannot cancel structure view open action once it has been started via the structure chooser dialog
- <!-- JAL-4142 --> Example project's multiple views do not open in distinct locations when eXpand views is used to show them all separately
- <!-- JAL-4127 --> 'Reload' for a jalview project results in all windows being duplicated
if ((nd.left() == null) && (nd.right() == null))
{
+ // TODO FIX FOR COLUMN TREES
jalview.bin.Console.outPrintln("Leaf = " + ((SequenceI) nd.element()).getName());
jalview.bin.Console.outPrintln("Dist " + nd.dist);
jalview.bin.Console.outPrintln("Boot " + nd.getBootstrap());
if ((nd.left() == null) && (nd.right() == null))
{
- nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
+ nd.height = nd.parent().height + nd.dist;
if (nd.height > maxheight)
{
{
if (nd.parent() != null)
{
- nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
+ nd.height = nd.parent().height + nd.dist;
}
else
{
}
else if (bootstrapArgs.contains(Arg.DEBUG))
{
- logLevel = "DEBUG";
+ logLevel = bootstrapArgs.getBoolean(Arg.DEBUG) ? "DEBUG" : "INFO";
}
if (logLevel == null && !(bootstrapProperties == null))
{
/**
* Returns a read-only view of the (possibly empty) list of selected columns
+ * (base 1)
* <p>
- * The list contains no duplicates but is not necessarily ordered. It also may
- * include columns hidden from the current view. To modify (for example sort)
- * the list, you should first make a copy.
+ * The list contains no duplicates but is not necessarily ordered. Columns are
+ * reported in alignment coordinates (base 1), so may also include columns
+ * hidden from the current view. To modify (for example sort) the list, you
+ * should first make a copy.
* <p>
* The list is not thread-safe: iterating over it could result in
* ConcurrentModificationException if it is modified by another thread.
{
if (atoms != null)
{
- boolean useScriptWait = atoms.size() > 1;
if (resetLastRes.length() > 0)
{
- jmolScript(resetLastRes.toString(), useScriptWait);
+ jmolScript(resetLastRes.toString());
resetLastRes.setLength(0);
}
+ StringBuilder highlightCommands=null;
for (AtomSpec atom : atoms)
{
- highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
- atom.getChain(), atom.getPdbFile(), useScriptWait);
+ StringBuilder thisAtom = highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
+ atom.getChain(), atom.getPdbFile());
+ if (thisAtom!=null) {
+ if (highlightCommands==null)
+ {
+ highlightCommands=thisAtom;
+ } else {
+ highlightCommands.append(thisAtom);
+ }
+ }
+ }
+ if (highlightCommands!=null)
+ {
+ jmolHistory(false);
+ jmolScript(highlightCommands.toString());
+ jmolHistory(true);
}
// Highlight distances between atoms with a 'measure' command - not yet
// working
}
// jmol/ssm only
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile, boolean useScriptWait)
+ private StringBuilder highlightAtom(int atomIndex, int pdbResNum, String chain,
+ String pdbfile)
{
String modelId = getModelIdForFile(pdbfile);
if (modelId.isEmpty())
{
- return;
+ return null;
}
- jmolHistory(false, useScriptWait);
-
StringBuilder selection = new StringBuilder(32);
StringBuilder cmd = new StringBuilder(64);
selection.append("select ").append(String.valueOf(pdbResNum));
resetLastRes.append(selection).append(";wireframe 0;").append(selection)
.append(" and not hetero; spacefill 0;");
- jmolScript(cmd.toString(), useScriptWait);
- jmolHistory(true, useScriptWait);
+ return cmd;
}
private boolean debug = true;
// logLevelCombo.addItem(LogLevel.ERROR);
// logLevelCombo.addItem(LogLevel.OFF);
// set startingLogLevel
- if (jalview.bin.Console.log == null)
+
+ if (jalview.bin.Console.getLogger() == null)
{
- try
- {
- startingLogLevel = LogLevel
- .valueOf(Cache.getDefault(Cache.JALVIEWLOGLEVEL, null));
- } catch (IllegalArgumentException e1)
- {
- jalview.bin.Console.debug(
- "Invalid value for preference " + Cache.JALVIEWLOGLEVEL);
- } catch (NullPointerException e2)
- {
- // no value in preferences
- } finally
- {
- if (startingLogLevel == null)
- {
- startingLogLevel = LogLevel.INFO;
- }
- }
+ startingLogLevel = jalview.bin.Console.getCachedLogLevel();
}
else
{
- startingLogLevel = jalview.bin.Console.log.getLevel();
+ startingLogLevel = jalview.bin.Console.getLogger().getLevel();
}
setChosenLogLevelCombo();
logLevelCombo.addActionListener(new ActionListener()
{
try
{
- this.wait(100);
+ this.wait(100); // ##### implicated BLOCKED
if (pin.available() == 0)
{
trimBuffer(false);
{
try
{
- this.wait(100);
+ this.wait(100); // ##### implicated BLOCKED
if (pin2.available() == 0)
{
trimBuffer(false);
displayPipe = tmp;
}
// simply append whole buffer
- textArea.append(replace.toString());
- count += replace.length();
- if (count > byteslim)
+ synchronized (textArea.getDocument())
{
- trimBuffer(false);
+ textArea.append(replace.toString()); // ##### implicated BLOCKED
+ count += replace.length();
+ if (count > byteslim)
+ {
+ trimBuffer(false);
+ }
}
+
}
if (displayPipe.length() == 0)
{
// A better hack which works is to create a new JFrame parent with
// setAlwaysOnTop(true)
+ boolean parentOnTop = dialogParent.isAlwaysOnTop();
dialogParent.setAlwaysOnTop(true);
parentComponent = dialogParent;
JOPTIONPANE_MESSAGETYPE, icon, options, initialValue, modal,
buttons);
+ dialogParent.setAlwaysOnTop(parentOnTop);
+
if (dispose)
{
dialogParent.setAlwaysOnTop(false);
try
{
- iframe.setClosed(true);
+ iframe.setClosed(true); // ##### implicated BLOCKED
} catch (Exception ex)
{
}
}
int ystart = (node.left() == null ? 0
- : (int) (((BinaryNode) node.left()).ycount * chunk)) + offy;
+ : (int) (node.left().ycount * chunk)) + offy;
int yend = (node.right() == null ? 0
- : (int) (((BinaryNode) node.right()).ycount * chunk)) + offy;
+ : (int) (node.right().ycount * chunk)) + offy;
Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
nodeHash.put(node, pos);
if (top.count == 0)
{
- top.count = ((BinaryNode) top.left()).count
- + ((BinaryNode) top.right()).count;
+ top.count = top.left().count
+ + top.right().count;
}
- double chunk = (double) (height - (offy)) / (double)top.count;
+ float chunk = (float) (height - (offy)) / top.count;
drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);
{
for (int s : cs.getSelected())
{
- if (hiddenCols == null)
- {
matched.set(s);
- }
- else
- {
- matched.set(hiddenCols.visibleToAbsoluteColumn(s));
- }
}
}
else
git://source.jalview.org / jalview.git / commitdiff