--- /dev/null
+<!DOCTYPE html>
+<html>
+<head>
+<meta charset="UTF-8">
+<title>mmCIF File Format</title>
+</head>
+<body>
+ <strong>mmCIF File Format</strong>
+ <p>The mmCIF file format (macromolecular Crystallographic
+ Information) was developed under the auspices of the International Union of Crystallography (IUCr) to extend the Crystallographic Information
+ File (CIF) data representation used for describing small molecule
+ structures and associated diffraction experiments.</p>
+ <strong>Merits of mmCIF file format</strong>
+ <ul>
+ <li>Large structures (containing >62 chains and/or 99999 ATOM
+ records) that cannot be fully represented in the PDB file format are
+ available in the PDB archive as single PDBx/mmCIF files.</li>
+ <li>PDBx/mmCIF file format provides richer data annotation</li>
+ <li>PDBx/mmCIF became the standard PDB archive format in 2014.
+ Since 2016 the PDB File Format is no longer being modified or
+ extended to support new content.
+ </li>
+ </ul>
+
+ <em>mmCIF file format support for importing 3D structure data from
+ flat file and EMBL-PDBe via mmCIF was added in Jalview 2.9.1</em>
+</body>
+</html>
\ No newline at end of file
retrieved by the <a href="seqfetch.html">Sequence Fetcher</a>, and
allows sequence features to be mapped directly from Uniprot das
sources to their coding region on EMBL sequence records.
+ </p>
+ <p>In Jalview 2.9.1 <a href="siftsmapping.html">SIFTS Mapping</a> was added as a better means for explicitly identifying the coordinates corresponding to a displayed sequence when viewing a PDB structure associated with a sequence </p>
</body>
</html>
--- /dev/null
+<!DOCTYPE html>
+<html>
+<head>
+<meta charset="UTF-8">
+<title>SIFTS Mapping</title>
+</head>
+<body>
+
+ <p><strong>SIFTS Mapping</strong></p>
+
+ <p>
+ SIFTS (Structure integration with function, taxonomy
+ and sequences) provides an up-to-date resource for residue-level
+ mapping between Uniprot and PDB entries. The information is updated and
+ released weekly simultaneously with the release of new PDB entries.
+ SIFTS Entries are published as XML files and made publicly available via an FTP
+ site hosted at the European Bioinformatics Institute.
+ </p>
+
+ <p>
+ At the point of viewing a PDB structure, Jalview downloads a SIFTS file
+ for the target entry and uses it to accurately map the sequence residues with the
+ structure residue. Prior to SIFTS integration, Jalview uses Needleman and Wunsch
+ Alignment algorithm to map sequence residues to structure residues, and that may not
+ always result to a correct mapping since it is computational determined.
+ </p>
+
+ <p>
+ The default method for 'Sequence ↔ Structure' mapping can be configured
+ in the Structure tab in the <strong>Tools → Preferences</strong> dialog box. When 'SIFTS'
+ is enabled as the default, all mappings between 'Sequence ↔ Structure' is
+ performed via SIFTS provided that there is a valid SIFTS entry for PDB structure. If no
+ valid SIFTS resource is available, then the 'Sequence ↔ Structure' mapping falls
+ back to Needleman and Wunsch Alignment algorithm.
+ </p>
+
+ <p>To verify the mapping method used, you can view the mapping output via the structure viewer menu <strong>File → View mapping.</strong> A sample mapping output can be seen in the screenshot below. The highlighted position shows the method used. </p>
+ <p>
+ <img src="sifts_mapping_output.png" align="left" alt="SIFTS mapping output" />
+ </p>
+
+ <p><em>SIFTS Mapping integration was added in Jalview 2.9.1</em></p>
+
+</body>
+</html>
\ No newline at end of file
</p>
<p>
+ <strong>Importing PDB Entries or files in mmCIF format</strong><br>
+ <a href="mmcif.html">mmCIF file format</a> provides an alternative means for
+ importing 3D structure data from flat file and EMBL-PDBe
+ web-service. To enable mmCIF as the default format for
+ importing PBD sequences from the PDB sequence fetcher, add or modify the
+ property
+ <code>DEFAULT_STRUCTURE_FORMAT=mmCIF</code> in Jalview properties file.
+ Once this is done, the steps followed in retrieving PDB format files above can
+ be followed to obtain the same data with mmCIF. <em>mmCIF format file support was added in Jalview 2.9.1.</em></p>
+
+
+
+ <p>
<strong>Associating a large number of PDB files to
sequences in an alignment</strong><br /> It is often the case when working
with structure alignments that you will have a directory of PDB
System.out
.println("Jalview Version: " + codeVersion + codeInstallation);
- Pdb.setCurrentDefaultFomart(jalview.bin.Cache.getDefault(
+ Pdb.setCurrentDefaultFormat(jalview.bin.Cache.getDefault(
"DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT));
// jnlpVersion will be null if we're using InstallAnywhere
// Dont do this check if running in headless mode
"text/uri-list;class=java.lang.String");
if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
{
+ Cache.log.debug("Drop handled as javaFileListFlavor");
// Works on Windows and MacOSX
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
files = (java.util.List) t
}
else if (t.isDataFlavorSupported(uriListFlavor))
{
+ Cache.log.debug("Drop handled as uriListFlavor");
// This is used by Unix drag system
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
String data = (String) t.getTransferData(uriListFlavor);
if (data == null)
{
+ Cache.log.debug("standard URIListFlavor (" + uriListFlavor
+ + ") doesn't resolve. trying others.");
// try 'best' dataflavor
data = (String) t.getTransferData(DataFlavor
.selectBestTextFlavor(t.getTransferDataFlavors()));
+ Cache.log.debug("Dataflavor "
+ + DataFlavor.selectBestTextFlavor(t
+ .getTransferDataFlavors()) + " returned " + data);
}
files = new java.util.ArrayList(1);
for (java.util.StringTokenizer st = new java.util.StringTokenizer(
files.add(file.toString());
}
}
+ if (files.size() < 1)
+ {
+ Cache.log
+ .debug("Couldn't resolve drop data with 'best text'. Here are the supported flavors:");
+ if (data == null && Cache.log.isDebugEnabled())
+ {
+ for (DataFlavor fl : t.getTransferDataFlavors())
+ {
+ Cache.log.debug("Supported transfer dataflavor: "
+ + fl.toString());
+ Object df = t.getTransferData(fl);
+ if (df != null)
+ {
+ Cache.log.debug("Retrieves: " + df);
+ }
+ }
+ }
+ }
}
} catch (Exception e)
{
* Set Output tab defaults
*/
epsRendering
- .addItem(MessageManager.getString("label.prompt_each_time"));
+.addItem("Prompt each time");
epsRendering.addItem(MessageManager.getString("label.lineart"));
epsRendering.addItem(MessageManager.getString("action.text"));
epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (evt.getPropertyName().equals("alignment"))
}
+ @Override
public void viewMenu_menuSelected()
{
buildAssociatedViewMenu();
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
treeCanvas.applyToAllViews = false;
itemf.setSelected(treeCanvas.applyToAllViews);
itemf.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
treeCanvas.applyToAllViews = itemf.isSelected();
}
}
+ @Override
public void run()
{
* @param e
* DOCUMENT ME!
*/
+ @Override
public void textbox_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
* @param e
* DOCUMENT ME!
*/
+ @Override
public void saveAsNewick_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
* @param e
* DOCUMENT ME!
*/
+ @Override
public void printMenu_actionPerformed(ActionEvent e)
{
// Putting in a thread avoids Swing painting problems
treeCanvas.startPrinting();
}
+ @Override
public void originalSeqData_actionPerformed(ActionEvent e)
{
if (!tree.hasOriginalSequenceData())
* @param e
* DOCUMENT ME!
*/
+ @Override
public void fitToWindow_actionPerformed(ActionEvent e)
{
treeCanvas.fitToWindow = fitToWindow.isSelected();
* @param e
* DOCUMENT ME!
*/
+ @Override
public void font_actionPerformed(ActionEvent e)
{
if (treeCanvas == null)
* @param e
* DOCUMENT ME!
*/
+ @Override
public void distanceMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setShowDistances(distanceMenu.isSelected());
* @param e
* DOCUMENT ME!
*/
+ @Override
public void bootstrapMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
* @param e
* DOCUMENT ME!
*/
+ @Override
public void placeholdersMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
* @param e
* DOCUMENT ME!
*/
+ @Override
public void epsTree_actionPerformed(ActionEvent e)
{
boolean accurateText = true;
// If we need to prompt, and if the GUI is visible then
// Prompt for EPS rendering style
- if (renderStyle.equalsIgnoreCase("Prompt each time")
+ if (renderStyle.equalsIgnoreCase(MessageManager
+ .getString("label.prompt_each_time"))
&& !(System.getProperty("java.awt.headless") != null && System
.getProperty("java.awt.headless").equals("true")))
{
* @param e
* DOCUMENT ME!
*/
+ @Override
public void pngTree_actionPerformed(ActionEvent e)
{
int width = treeCanvas.getWidth();
tree.applyToNodes(new NodeTransformI()
{
+ @Override
public void transform(BinaryNode node)
{
if (node instanceof SequenceNode
}
}
- if (renderStyle.equalsIgnoreCase("lineart"))
+ if (renderStyle.equalsIgnoreCase(MessageManager
+ .getString("label.lineart")))
{
g1.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
}
}
- if (renderStyle.equalsIgnoreCase("lineart"))
+ if (renderStyle.equalsIgnoreCase(MessageManager
+ .getString("label.lineart")))
{
ig2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
stopQuery();
return null;
}
- String ext = getCurrentDefaultFomart().equalsIgnoreCase("mmcif") ? ".cif"
+ String ext = getCurrentDefaultFormat().equalsIgnoreCase("mmcif") ? ".cif"
: ".xml";
EBIFetchClient ebi = new EBIFetchClient();
file = ebi.fetchDataAsFile("pdb:" + id,
- getCurrentDefaultFomart().toLowerCase(), "raw", ext)
+ getCurrentDefaultFormat().toLowerCase(), "raw", ext)
.getAbsolutePath();
stopQuery();
if (file == null)
pdbAlignment = new FormatAdapter().readFile(file,
jalview.io.AppletFormatAdapter.FILE,
- getCurrentDefaultFomart());
+ getCurrentDefaultFormat());
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
return 0;
}
- public static String getCurrentDefaultFomart()
+ public static String getCurrentDefaultFormat()
{
return currentDefaultFomart;
}
- public static void setCurrentDefaultFomart(String currentDefaultFomart)
+ public static void setCurrentDefaultFormat(String currentDefaultFomart)
{
Pdb.currentDefaultFomart = currentDefaultFomart;
}
git://source.jalview.org / jalview.git / commitdiff
