</tr>
<tr>
<td>
+ <div align="center">-nonews</div>
+ <td>
+ <div align="left">Disable check for <a href="../webServices/newsreader.html">Jalview news</a> on startup (not recommended other than for classroom / demo usage)</div>
+ </td>
+ </tr>
+ <tr>
+ <td>
<div align="center">-nousagestats</div>
<td>
<div align="left">Turn off google analytics usage tracking</div>
</p>
<p>
Jalview includes a client for retrieving sequences and their
- features via the <a href="http://www.biodas.org">Distributed
- Annotation System</a>.
+ features via the Distributed Annotation System.
</p>
<ol>
<li>Open the Feature Settings panel by selecting "View
<p>
<em>DAS support was introduced in Jalview Version 2.1.</em>
</p>
+ <br/>
+ <p>
+ <em>The DAS registry at http://www.dasregistry.org was decommissioned early in 2015. An unmaintained mirror is currently hosted at http://www.ebi.ac.uk/das-srv/registry/.</em>
+ </p>
<p>
</body>
</html>
<strong>The VARNA RNA Viewer</strong>
</p>
<p>
- <a href="http://varna.lri.fr/index.html">VARNA</a> was integrated
+ <a href="http://varna.lri.fr">VARNA</a> was integrated
into Jalview 2.8 to allow interactive viewing of RNA secondary
structure annotation. It is opened by selecting the <strong>"Structure→View
Structure:"</strong> option in the <a href="../menus/popupMenu.html">sequence
NBRF/PIR (including MODELLER variant), Pfam/Stockholm</em>
</p>
<p>
- The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a>
- of these file formats.
- </p>
- <p>
Additionally, whole sets of coloured and annotated alignments and
trees can be read from a <a href="../features/jalarchive.html">Jalview
(jar) format</a> file using <strong>Desktop→Load
annotation.</li>
<li><em>Clustal files</em> - certain RNA alignment programs,
such as <a
- href="http://rna.informatik.uni-freiburg.de:8080/LocARNA.jsp"
+ href="http://rna.informatik.uni-freiburg.de/LocARNA"
>LocaRNA</a> output consensus RNA secondary structure lines in the
line normally reserved for the Clustal consensus line in a clustal
file.</li>
services were maintained by the Barton group at the University of
Dundee, and ran programs on the Life Sciences High-performance
Computing Cluster. With the advent of <a
- href="http://www.compbio.dundee.ac.uk/JABAWS"
+ href="http://www.compbio.dundee.ac.uk/jabaws"
>JABAWS</a>, however, it is possible for anyone to host Jalview web
services.
</p>
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
-<head>Jalview Desktop RSS News Reader
+<head>
</head>
<body>
<p>
<p>The news reader will be launched automatically when you start
the Desktop if new items are available. Should you want to browse
older items, however, you can open it manually from the 'Jalview
- news reader' option in the Desktop's 'Tools' menu.</p>
- <img src="jalviewrssreader.gif" align="center" width="513"
- height="337" alt="Snapshot of the Jalview Desktop's RSS reader"
- />
- <p>
+ news reader' option in the Desktop's <a href="../menus/desktopMenu.html">'Tools' menu</a>.</p><br/>
+ <div style="text-align: center;"><img src="jalviewrssreader.gif" width="513"
+ height="337" alt="Snapshot of the Jalview Desktop's RSS reader"/></div>
+
+ <br/><p>
The <em>Jalview news reader</em> was introduced in <a
href="http://www.jalview.org/releaseHistory.html#Jalview2.7"
>Jalview version 2.7</a>. Its implementation is based on <a
href="http://jswingreader.sourceforge.net/"
>JSwingReader</a>.
</p>
+ <br/><em>From Jalview 2.10.0, check for news on startup can be disabled with <a href="../features/clarguments.html">command-line parameter</a> '-nonews'.
+ This is not recommended for normal use, but may be useful to avoid interruptions when teaching, demonstrating, recording etc.</em>
</body>
</html>
status.obtaining_mapping_with_sifts = Obtaining mapping with SIFTS
status.obtaining_mapping_with_nw_alignment = Obtaining mapping with NW alignment
status.exporting_alignment_as_x_file = Exporting alignment as {0} file
+label.column = Column
+label.sequence = Sequence
label.edit_sequence = Editar secuencia
label.edit_sequences = Editar secuencias
label.sequence_details = Detalles de la secuencia
-label.jmol_help = Ayuda de Jmol
-label.all = Todo
+label.jmol_help = Ayuda de Jmol
+# Todos/Todas is gender-sensitive, but currently only used for feminine (cadena / anotación)!
+label.all = Todas
label.sort_by = Ordenar por
label.sort_by_score = Ordenar por puntuación
label.sort_by_density = Ordenar por densidad
status.fetching_dbrefs_for_sequences_without_valid_refs=Buscando referencias para {0} secuencia(s) sin referencia válida necesaria para mapeado SIFTS
status.obtaining_mapping_with_nw_alignment=Obteniendo mapeo por alineamiento Needleman y Wunsch
status.exporting_alignment_as_x_file = Exportando alineamiento como fichero tipo {0}
+label.column = Columna
+label.sequence = Secuencia
public class APopupMenu extends java.awt.PopupMenu implements
ActionListener, ItemListener
{
- private static final String ALL_ANNOTATIONS = "All";
-
Menu groupMenu = new Menu();
MenuItem editGroupName = new MenuItem();
showMenu.removeAll();
hideMenu.removeAll();
- final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+ final List<String> all = Arrays.asList(new String[] { MessageManager
+ .getString("label.all") });
addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
false);
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
+import jalview.util.Comparison;
import jalview.util.MessageManager;
import java.awt.Color;
}
}
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+ int column = evt.getX() / av.getCharWidth() + av.getStartRes();
if (av.hasHiddenColumns())
{
- res = av.getColumnSelection().adjustForHiddenColumns(res);
+ column = av.getColumnSelection().adjustForHiddenColumns(column);
}
- if (row > -1 && res < aa[row].annotations.length
- && aa[row].annotations[res] != null)
+ if (row > -1 && column < aa[row].annotations.length
+ && aa[row].annotations[column] != null)
{
- StringBuffer text = new StringBuffer("Sequence position " + (res + 1));
- if (aa[row].annotations[res].description != null)
+ StringBuilder text = new StringBuilder();
+ text.append(MessageManager.getString("label.column")).append(" ")
+ .append(column + 1);
+ if (aa[row].annotations[column].description != null)
{
- text.append(" " + aa[row].annotations[res].description);
+ text.append(" ").append(aa[row].annotations[column].description);
}
+
+ /*
+ * if the annotation is sequence-specific, show the sequence number
+ * in the alignment, and (if not a gap) the residue and position
+ */
+ SequenceI seqref = aa[row].sequenceRef;
+ if (seqref != null)
+ {
+ int seqIndex = av.getAlignment().findIndex(seqref);
+ if (seqIndex != -1)
+ {
+ text.append(", ")
+ .append(MessageManager.getString("label.sequence"))
+ .append(" ").append(seqIndex + 1);
+ char residue = seqref.getCharAt(column);
+ if (!Comparison.isGap(residue))
+ {
+ int residuePos = seqref.findPosition(column);
+ text.append(": ").append(residue).append(" (")
+ .append(residuePos).append(")");
+ }
+ }
+ }
+
ap.alignFrame.statusBar.setText(text.toString());
}
}
Cache.log.debug("Starting questionnaire with default url: "
+ defurl);
desktop.checkForQuestionnaire(defurl);
-
}
}
}
{
System.err.println("CMD [-noquestionnaire] executed successfully!");
}
+
if (!aparser.contains("nonews"))
{
desktop.checkForNews();
}
- }
- if (!isHeadlessMode())
- {
BioJsHTMLOutput.updateBioJS();
}
+ "-eps FILE\tCreate EPS file FILE from alignment.\n"
+ "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
+ "-noquestionnaire\tTurn off questionnaire check.\n"
+ + "-nonews\tTurn off check for Jalview news.\n"
+ "-nousagestats\tTurn off google analytics tracking for this session.\n"
+ "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
// +
import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
+import jalview.util.Comparison;
import jalview.util.MessageManager;
import java.awt.AlphaComposite;
}
}
else
- // HELIX OR SHEET
+ // HELIX, SHEET or STEM
{
char type = 0;
String symbol = "\u03B1";
}
}
+
av.getAlignment().validateAnnotation(aa[activeRow]);
ap.alignmentChanged();
-
+ ap.alignFrame.setMenusForViewport();
adjustPanelHeight();
repaint();
}
/**
- * DOCUMENT ME!
+ * Constructs the tooltip, and constructs and displays a status message, for
+ * the current mouse position
*
* @param evt
- * DOCUMENT ME!
*/
@Override
public void mouseMoved(MouseEvent evt)
if (evt.getY() < height)
{
row = i;
-
break;
}
}
return;
}
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+ int column = (evt.getX() / av.getCharWidth()) + av.getStartRes();
if (av.hasHiddenColumns())
{
- res = av.getColumnSelection().adjustForHiddenColumns(res);
+ column = av.getColumnSelection().adjustForHiddenColumns(column);
+ }
+
+ AlignmentAnnotation ann = aa[row];
+ if (row > -1 && ann.annotations != null
+ && column < ann.annotations.length)
+ {
+ buildToolTip(ann, column, aa);
+ setStatusMessage(column, ann);
+ }
+ else
+ {
+ this.setToolTipText(null);
+ ap.alignFrame.statusBar.setText(" ");
}
+ }
- if (row > -1 && aa[row].annotations != null
- && res < aa[row].annotations.length)
+ /**
+ * Builds a tooltip for the annotation at the current mouse position.
+ *
+ * @param ann
+ * @param column
+ * @param anns
+ */
+ void buildToolTip(AlignmentAnnotation ann, int column,
+ AlignmentAnnotation[] anns)
+ {
+ if (ann.graphGroup > -1)
{
- if (aa[row].graphGroup > -1)
+ StringBuilder tip = new StringBuilder(32);
+ tip.append("<html>");
+ for (int i = 0; i < anns.length; i++)
{
- StringBuffer tip = new StringBuffer("<html>");
- for (int gg = 0; gg < aa.length; gg++)
+ if (anns[i].graphGroup == ann.graphGroup
+ && anns[i].annotations[column] != null)
{
- if (aa[gg].graphGroup == aa[row].graphGroup
- && aa[gg].annotations[res] != null)
+ tip.append(anns[i].label);
+ String description = anns[i].annotations[column].description;
+ if (description != null && description.length() > 0)
{
- tip.append(aa[gg].label + " "
- + aa[gg].annotations[res].description + "<br>");
+ tip.append(" ").append(description);
}
- }
- if (tip.length() != 6)
- {
- tip.setLength(tip.length() - 4);
- this.setToolTipText(tip.toString() + "</html>");
+ tip.append("<br>");
}
}
- else if (aa[row].annotations[res] != null
- && aa[row].annotations[res].description != null
- && aa[row].annotations[res].description.length() > 0)
+ if (tip.length() != 6)
{
- this.setToolTipText(JvSwingUtils.wrapTooltip(true,
- aa[row].annotations[res].description));
+ tip.setLength(tip.length() - 4);
+ this.setToolTipText(tip.toString() + "</html>");
}
- else
+ }
+ else if (ann.annotations[column] != null)
+ {
+ String description = ann.annotations[column].description;
+ if (description != null && description.length() > 0)
{
- // clear the tooltip.
- this.setToolTipText(null);
+ this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
}
+ }
+ else
+ {
+ // clear the tooltip.
+ this.setToolTipText(null);
+ }
+ }
- if (aa[row].annotations[res] != null)
+ /**
+ * Constructs and displays the status bar message
+ *
+ * @param column
+ * @param ann
+ */
+ void setStatusMessage(int column, AlignmentAnnotation ann)
+ {
+ /*
+ * show alignment column and annotation description if any
+ */
+ StringBuilder text = new StringBuilder(32);
+ text.append(MessageManager.getString("label.column")).append(" ")
+ .append(column + 1);
+
+ if (ann.annotations[column] != null)
+ {
+ String description = ann.annotations[column].description;
+ if (description != null && description.trim().length() > 0)
{
- StringBuffer text = new StringBuffer("Sequence position "
- + (res + 1));
+ text.append(" ").append(description);
+ }
+ }
- if (aa[row].annotations[res].description != null)
+ /*
+ * if the annotation is sequence-specific, show the sequence number
+ * in the alignment, and (if not a gap) the residue and position
+ */
+ SequenceI seqref = ann.sequenceRef;
+ if (seqref != null)
+ {
+ int seqIndex = av.getAlignment().findIndex(seqref);
+ if (seqIndex != -1)
+ {
+ text.append(", ")
+ .append(MessageManager.getString("label.sequence"))
+ .append(" ")
+ .append(seqIndex + 1);
+ char residue = seqref.getCharAt(column);
+ if (!Comparison.isGap(residue))
{
- text.append(" " + aa[row].annotations[res].description);
+ int residuePos = seqref.findPosition(column);
+ text.append(": ").append(residue).append(" (")
+ .append(residuePos).append(")");
}
-
- ap.alignFrame.statusBar.setText(text.toString());
}
}
- else
- {
- this.setToolTipText(null);
- }
+
+ ap.alignFrame.statusBar.setText(text.toString());
}
/**
*/
public class PopupMenu extends JPopupMenu
{
- private static final String ALL_ANNOTATIONS = "All";
-
JMenu groupMenu = new JMenu();
JMenuItem groupName = new JMenuItem();
showMenu.removeAll();
hideMenu.removeAll();
- final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+ final List<String> all = Arrays.asList(new String[] { MessageManager
+ .getString("label.all") });
addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
false);
* Sequence number (if known), and sequence name.
*/
String seqno = seq == -1 ? "" : " " + (seq + 1);
- text.append("Sequence" + seqno + " ID: " + sequence.getName());
+ text.append("Sequence").append(seqno).append(" ID: ")
+ .append(sequence.getName());
String residue = null;
/*
return;
}
- internetAvailable &= connectToUrl("http://www.example.com");
+ internetAvailable &= connectToUrl("http://www.example.org");
Map<String, String> tocTargets = checkHelpMappings(helpFolder);
git://source.jalview.org / jalview.git / commitdiff