<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
<ul>
<li>Ensure that you have TestNG plugin correctly install for eclipse</li>
<li>Ensure that your test classes are error free and properly annotated</li>
- <li>Create a lunch configuration "Select the Run / Run... (or Run / Debug...) menu and create a new TestNG configuration"</li>
+ <li>Create a launch configuration "Select the Run / Run... (or Run / Debug...) menu and create a new TestNG configuration"</li>
<li>Run the tests by executing the configuration target created above</li>
</ul>
A more detailed guide for installing and executing TestNG in eclipse is available at <a href=http://testng.org/doc/eclipse.html>testng.org/doc/eclipse.html</a> <br>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
<li>BioJS MSA - A JavaScript based multiple sequence alignment
viewer. <br> <em>For interactive alignment data
visualisation in a web browser.<br />Get more info about the
- BioJS MSA viewer at a
- href="http://msa.biojs.net/">http://msa.biojs.net/</a>
+ BioJS MSA viewer at <a href="http://msa.biojs.net/">http://msa.biojs.net/</a>
</em>
</li>
<p>
In Jalview 2.9, new HTML exporting options were introduced. The
standard HTML export option displays alignments as SVG documents
- embedded as scollable panes. Exported pages can optionally also
+ embedded as scrollable panes. Exported pages can optionally also
include <a href="../features/bioJsonFormat.html">BioJSON</a> data,
which allows Jalview to extract the original data used to create the
page. Jalview can also generate HTML pages which embed BioJSON data
and the BioJS MSA viewer, a pure javascript alignment viewer that
- provides a range of interactive analysis capabiltiies.
+ provides a range of interactive analysis capabilities.
</p>
<p>
<p>
<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
</td>
</tr>
<tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
+ <em>29/09/2015</em></strong>
+ </div>
+ </td>
+ <td>
+ <div align="center"></div>
+ </td>
+ <td>
+ <div align="left">
+ <ul>
+ <li>Mapping of cDNA to protein in split frames incorrect when sequence start > 1</li>
+ <li>Split frame example added to applet examples page</li>
+ <li>Applet with Jmol examples not loading correctly</li>
+ <li>Incorrect warning on deleting selected columns</li>
+ <li>Annotations incorrectly rendered after BioJS export and reimport</li>
+ <li>Incorrect sequence limits after Fetch DB References with 'trim retrieved sequences'</li>
+ <li>Spanish translations of localized text - updates needed for 2.9</li>
+ <li>Provide signed OSX InstallAnywhere installer</li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
<td><div align="center">
<strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
</div></td>
</td>
</tr>
<tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.8.2b1">2.8.2b1</a><br />
- <em>15/12/2014</em></strong>
- </div>
- </td>
- <td>
- <div align="center"></div>
- </td>
- <td>
- <div align="center">
- <ul>
- <li>Reinstated the display of default example file on
- startup</li>
- <li>All pairs shown in Jalview window when viewing
- result of pairwise alignment</li>
- </ul>
- </div>
- </td>
- </tr>
- <tr>
<td><div align="center">
<strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
</div></td>
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
import java.awt.Canvas;
import java.awt.CheckboxMenuItem;
import java.awt.Color;
+ import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Frame;
import java.awt.Menu;
import java.awt.MenuBar;
import java.awt.MenuItem;
+ import java.awt.Panel;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusEvent;
import java.util.StringTokenizer;
import java.util.Vector;
- import javax.swing.JOptionPane;
-
import org.jmol.viewer.Viewer;
public class AlignFrame extends EmbmenuFrame implements ActionListener,
normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
annotationPanelMenuItem.setState(viewport.isShowAnnotation());
- showAlignmentAnnotations.setState(viewport.isShowAnnotation());
- showSequenceAnnotations.setState(viewport.isShowAnnotation());
+ showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showAlignmentAnnotations.setState(true);
+ showSequenceAnnotations.setState(false);
seqLimits.setState(viewport.getShowJVSuffix());
}
else if (source == annotationPanelMenuItem)
{
- viewport.setShowAnnotation(annotationPanelMenuItem.getState());
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
+ boolean showAnnotations = annotationPanelMenuItem.getState();
+ showAlignmentAnnotations.setEnabled(showAnnotations);
+ showSequenceAnnotations.setEnabled(showAnnotations);
+ viewport.setShowAnnotation(showAnnotations);
+ alignPanel.setAnnotationVisible(showAnnotations);
}
else if (source == sequenceFeatures)
{
/*
* If the cut affects all sequences, warn, remove highlighted columns
- */if (sg.getSize() == viewport.getAlignment().getHeight())
+ */
+ if (sg.getSize() == viewport.getAlignment().getHeight())
{
boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
.getAlignment().getWidth()) ? true : false;
if (isEntireAlignWidth)
{
- int confirm = JOptionPane.showConfirmDialog(this,
- MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
- MessageManager.getString("label.delete_all"), // $NON-NLS-1$
- JOptionPane.OK_CANCEL_OPTION);
+ String title = MessageManager.getString("label.delete_all");
+ Panel infoPanel = new Panel();
+ infoPanel.setLayout(new FlowLayout());
+ infoPanel
+ .add(new Label(MessageManager.getString("warn.delete_all")));
+
+ final JVDialog dialog = new JVDialog(this, title, true, 400,
+ 200);
+ dialog.setMainPanel(infoPanel);
+ dialog.ok.setLabel(MessageManager.getString("action.ok"));
+ dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
+ dialog.setVisible(true);
- if (confirm == JOptionPane.CANCEL_OPTION
- || confirm == JOptionPane.CLOSED_OPTION)
+ if (!dialog.accept)
{
return;
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
import java.util.Iterator;
import java.util.Vector;
- import javax.swing.JPanel;
+ //import javax.swing.JPanel;
//import net.miginfocom.swing.MigLayout;
actionPanel.add(ok);
actionPanel.add(cancel);
- JPanel staticPanel = new JPanel();
+ Panel staticPanel = new Panel();
staticPanel.setLayout(new BorderLayout());
staticPanel.setBackground(Color.white);
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
import java.awt.Panel;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+ import java.awt.event.WindowAdapter;
+ import java.awt.event.WindowEvent;
public class JVDialog extends Dialog implements ActionListener
{
width, height);
}
+ public JVDialog(Frame owner, Panel mainPanel, String title,
+ boolean modal, int width, int height)
+ {
+ super(owner, title, modal);
+ this.owner = owner;
+
+ height += owner.getInsets().top + getInsets().bottom;
+
+ setBounds(owner.getBounds().x + (owner.getSize().width - width) / 2,
+ owner.getBounds().y + (owner.getSize().height - height) / 2,
+ width, height);
+ setMainPanel(mainPanel);
+ }
+
void setMainPanel(Panel panel)
{
add(panel, BorderLayout.NORTH);
buttonPanel.add(cancel);
ok.addActionListener(this);
cancel.addActionListener(this);
-
add(buttonPanel, BorderLayout.SOUTH);
+ addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent ev)
+ {
+ setVisible(false);
+ dispose();
+ }
+ });
+
pack();
}
}
setVisible(false);
+ dispose();
}
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
URL localref)
{
String resolvedPath = "";
+ if (targetPath.startsWith("/"))
+ {
+ String codebase = localref.toString();
+ String localfile = localref.getFile();
+ resolvedPath = codebase.substring(0,
+ codebase.length() - localfile.length())
+ + targetPath;
+ return resolvedPath;
+ }
/*
* get URL path and strip off any trailing file e.g.
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
annotationScroller.setPreferredSize(new Dimension(annotationScroller
.getWidth(), annotationHeight));
+ Dimension e = idPanel.getSize();
+ alabels.setSize(new Dimension(e.width, annotationHeight));
+
annotationSpaceFillerHolder.setPreferredSize(new Dimension(
annotationSpaceFillerHolder.getWidth(), annotationHeight));
annotationScroller.validate();
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
// pin down annotation sort order for test
Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
SequenceAnnotationOrder.NONE.name());
- final String True = Boolean.TRUE.toString();
+ final String TRUE = Boolean.TRUE.toString();
Cache.applicationProperties.setProperty(
- Preferences.SHOW_AUTOCALC_ABOVE, True);
- Cache.applicationProperties.setProperty("SHOW_QUALITY", True);
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION", True);
- Cache.applicationProperties.setProperty("SHOW_IDENTITY", True);
+ Preferences.SHOW_AUTOCALC_ABOVE, TRUE);
+ Cache.applicationProperties.setProperty("SHOW_QUALITY", TRUE);
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE);
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY", TRUE);
AlignmentI al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
AppletFormatAdapter.PASTE, "FASTA");
assertTrue(i + "'th sequence not visible", anns[i].visible);
}
+ /*
+ * check options to hide JMol and IUPRED annotations for all sequences
+ */
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
setSelected(hideCheckbox, true);
assertTrue(anns[0].visible); // Conservation
assertTrue(anns[1].visible); // Quality
assertTrue(anns[2].visible); // Consensus
- assertTrue(anns[3].visible); // Beauty (not seq-related)
- assertFalse(anns[4].visible); // IUPRED
+ assertFalse(anns[3].visible); // IUPRED
+ assertTrue(anns[4].visible); // Beauty (not seq-related)
assertFalse(anns[5].visible); // JMol
assertFalse(anns[6].visible); // IUPRED
assertFalse(anns[7].visible); // JMol
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* available, plain) fonts and point sizes that would be rejected by Jalview's
* FontChooser as having an I-width of less than 1.0.
*/
- @Test(groups = { "Functional" })
+ @Test(groups = { "Functional" }, enabled = false)
public void dumpInvalidFonts()
{
String[] fonts = java.awt.GraphicsEnvironment
git://source.jalview.org / jalview.git / commitdiff