<mapID target="pdbmcviewer" url="html/features/pdbviewer.html"/>
<mapID target="pdbjmol" url="html/features/jmol.html"/>
<mapID target="chimera" url="html/features/chimera.html"/>
+ <mapID target="chimera.annotxfer" url="html/features/chimera.html#annotxfer"/>
<mapID target="varna" url="html/features/varna.html"/>
<mapID target="xsspannotation" url="html/features/xsspannotation.html"/>
<mapID target="preferences" url="html/features/preferences.html"/>
<tocitem text="Jalview Documentation" target="home" expand="true">
<tocitem text="What's new" target="new" expand="true">
<tocitem text="Latest Release Notes" target="release"/>
+ <tocitem text="Structure Chooser" target="pdbchooser"/>
+ <tocitem text="Chimera Annotation Exchange" target="chimera.annotxfer"/>
</tocitem>
<tocitem text="Editing Alignments" target="edit" />
structure in the alignment. The regions used to calculate
the superposition will be highlighted using the 'Cartoon'
rendering style, and the remaining data shown as a chain
- trace.<br/><br/>
+ trace.<br />
+ <br />
</em></li>
- <li><strong><a name="experimental">EXPERIMENTAL FEATURES</a></strong><br/>
- <em>
- These are only available if the <strong>Tools→Enable
- Experimental Features</strong> option is enabled. (Since Jalview 2.10.2)</em>
- <ul>
- <li><strong>Write Jalview features</strong><br /> <em>Selecting
- this option will create new residue attributes for any
- features currently visible in the associated alignment
- views, allowing those positions to be selected and
- analysed with via Chimera's 'Render by Attribute' tool
- (found in the Tools submenu called Structure Analysis).<br />
- <br />If you use this option, please remember to select
- the <em>Refresh Menus</em> option in Chimera's Render by
- Attribute dialog box in order to see the attributes
- derived from Jalview sequence features.
- </em><br />
- <a href="https://issues.jalview.org/browse/JAL-2295">View
- this function's issue in Jalview's bug tracker</a></li>
- <li><strong>Fetch Chimera Attributes</strong><br /> <em>This
- submenu lists available Chimera residue attributes that
- can be imported as Jalview features on associated
- sequences.<br />This is particularly useful for
- transferring quantitative positional annotation. For
- example, structure similarity for an alignment can be
- visualised by transferring the local RMSD attributes
- generated by Chimera's Match->Align tool onto aligned
- sequences and displayed with a <a
- href="featureschemes.html">Graduated feature colour
- scheme</a>.
- </em><a href="https://issues.jalview.org/browse/JAL-2296">View
- this function's issue in Jalview's bug tracker</a></li>
- </ul></li>
- <li><strong>Help<br>
+ <li><a name="annotxfer"><strong>Write Jalview
+ features</strong></a><br /> <em>Selecting this option will create
+ new residue attributes for any features currently visible in
+ the associated alignment views, allowing those positions to
+ be selected and analysed with via Chimera's 'Render by
+ Attribute' tool (found in the Tools submenu called Structure
+ Analysis).<br /> <br />If you use this option, please
+ remember to select the <em>Refresh Menus</em> option in
+ Chimera's Render by Attribute dialog box in order to see the
+ attributes derived from Jalview sequence features.
+ </em></li>
+ <li><strong>Fetch Chimera Attributes</strong><br /> <em>This
+ submenu lists available Chimera residue attributes that can
+ be imported as Jalview features on associated sequences.<br />This
+ is particularly useful for transferring quantitative
+ positional annotation. For example, structure similarity for
+ an alignment can be visualised by transferring the local
+ RMSD attributes generated by Chimera's Match->Align tool
+ onto aligned sequences and displayed with a <a
+ href="featureschemes.html">Graduated feature colour
+ scheme</a>. </li>
+ </ul></li>
+ <li><strong>Help<br>
</strong>
<ul>
<li><strong>Chimera Help<br>
the <a href="../features/groovy.html">Groovy Console</a> for
interactive scripting.
</em><strong><br></strong></li>
- <li><strong>Enable Experimental Features</strong> <em>Enable or disable <a href="../whatsNew.html#experimental">features still under development</a> in Jalview's user interface. This setting is remembered in your preferences.</em>
+ <!-- <li><strong>Enable Experimental Features</strong> <em>Enable or disable <a href="../whatsNew.html#experimental">features still under development</a> in Jalview's user interface. This setting is remembered in your preferences.</em> -->
</ul></li>
<li><strong>Vamsas</strong> <em>For more details, read the
<tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>1/05/2018</em></strong>
+ <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>8/05/2018</em></strong>
</div>
</td>
<td><div align="left">
<em></em>
<ul>
<li>
- <!-- JAL-1847 JAL-2944 -->Structure Chooser controls to
- control superposition of multiple structures and open
- structures in existing views
+ <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
+ for disabling automatic superposition of multiple
+ structures and open structures in existing views
</li>
<li>
<!-- JAL-984 -->Mouse cursor changes to indicate Sequence
</li>
<li>
<!-- JAL-2593 -->Improved performance when rendering lots
- of features
+ of features (particularly when transparency is disabled)
</li>
</ul>
</div>
overlapping alignment panel
</li>
<li>
+ <!-- JAL-2929 -->overview doesn't show end of unpadded
+ sequence as gaps
+ </li>
+ <li>
+ <!-- JAL-2789, JAL-2893 -->Cross-reference handling improved: CDS not handled correctly if transcript has no UTR
+ </li>
+ <li>
+ <!-- JAL-2321 -->Secondary structure and temperature
+ factor annotation not added to sequence when local PDB
+ file associated with it by drag'n'drop or structure
+ chooser
+ </li>
+ <li>
<!-- JAL-2666 -->Linked scrolling via protein horizontal
scroll bar doesn't work for some CDS/Protein views
</li>
as generated by CONSURF)
</li>
<li>
+ <!-- JAL-2922 -->Invert displayed features very slow when
+ structure and/or overview windows are also shown
+ </li>
+ <li>
<!-- JAL-2954 -->Selecting columns from highlighted regions
very slow for alignments with large numbers of sequences
</li>
- <li><!-- JAL-2925 -->Copy Consensus fails for group consensus with 'StringIndexOutOfBounds'</li>
- <li><em>New Defects</em>
- <ul>
- <li>
- <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
- structures for protein subsequence (if 'Trim Retrieved
- Sequences' enabled) or Ensembl isoforms (Workaround in
- 2.10.4 is to fail back to N&W mapping)
- </li>
- </ul>
+ <li>
+ <!-- JAL-2925 -->Copy Consensus fails for group consensus
+ with 'StringIndexOutOfBounds'
+ </li>
+ <li>
+ <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
+ platforms running Java 10
+ </li>
+ <li>
+ <!-- JAL-2960 -->Adding a structure to existing structure
+ view appears to do nothing because the view is hidden behind the alignment view
+ </li>
</ul>
<em>Applet</em>
<ul>
<!-- JAL-2926 -->Copy consensus sequence option in applet
should copy the group consensus when popup is opened on it
</li>
-
+ </ul>
+ <em>Batch Mode</em>
+ <ul>
+ <li>
+ <!-- JAL-2913 -->Fixed ID width preference is not respected
+ </li>
</ul>
<em>New Known Defects</em>
<ul>
repeatedly after a series of edits even when the overview
is no longer reflecting updates
</li>
+ <li>
+ <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
+ structures for protein subsequence (if 'Trim Retrieved
+ Sequences' enabled) or Ensembl isoforms (Workaround in
+ 2.10.4 is to fail back to N&W mapping)
+ </li>
</ul>
</div>
</td>
<strong>What's new in Jalview 2.10.4 ?</strong>
</p>
<p>
- This is the February 2018 release of Jalview, with several minor bug fixes and enhanvements.
- The full list bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.4">2.10.4
- Release Notes</a>. In addition, Jalview 2.10.4 provides:
+ This is the May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes:
</p>
<ul>
- <li></li>
+ <li>Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns</li>
+ <li>Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services</li>
+ <li>Critical patches for running Jalview on OSX with Java 10</li>
+ <li>Easier adjustment of the Alignment ID panel and Annotation panel</li>
+ <li>Improved support for mapping between 3D Structures and Uniprot Protein Sequences</li>
+ <li>Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs</li>
+ <li>New buttons on the Structure Chooser for adding structures
+ to an existing view, and disabling automatic superposition
+ according to linked alignments</li>
+ <li>Annotation transfer between Chimera and Jalview <em>(formerly only
+ available in 'Experimental' mode)</em></li>
</ul>
<p>
- <strong><a name="experimental">Experimental Features</a></strong>
+ The full list of bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.4">2.10.4
+ Release Notes</a>.
</p>
- <p>
- Remember, please enable the <em>Experimental Features</em> option in
- the Jalview Desktop's <em>Tools</em> menu, and then restart Jalview
- if you want to try out features below:
- </p>
- <ul>
- <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
- <a href="features/chimera.html#experimental">new entries in
- the Chimera viewer's Chimera menu</a> allow positional annotation to
- be exchanged between Chimera and Jalview.</li>
- </ul>
-
</body>
</html>
*/
void setAlignAddedStructures(boolean alignAdded);
+ /**
+ * Raise the panel to the top of the stack...
+ */
+ void raiseViewer();
+
}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
public final class HiddenCursorPosition
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
import java.util.Iterator;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
import java.util.ArrayList;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
import java.util.ArrayList;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
import java.util.ArrayList;
import java.util.Map;
import java.util.Vector;
-import javax.swing.SwingUtilities;
-
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolSelectionListener;
lastCommand = command;
}
+ Thread colourby = null;
/**
* Sends a set of colour commands to the structure viewer
*
protected void colourBySequence(
final StructureMappingcommandSet[] colourBySequenceCommands)
{
- SwingUtilities.invokeLater(new Runnable()
+ if (colourby != null)
+ {
+ colourby.interrupt();
+ colourby = null;
+ }
+ colourby = new Thread(new Runnable()
{
@Override
public void run()
}
}
});
+ colourby.start();
}
/**
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureImportSettings;
import jalview.util.Format;
import jalview.util.MessageManager;
{
Viewer viewer = null;
+ public JmolParser(boolean immediate, String inFile,
+ DataSourceType sourceType) throws IOException
+ {
+ super(immediate, inFile, sourceType);
+ }
+
public JmolParser(String inFile, DataSourceType sourceType)
throws IOException
{
}
lastID = tmpatom.resNumIns.trim();
}
- xferSettings();
+ if (isParseImmediately())
+ {
+ // configure parsing settings from the static singleton
+ xferSettings();
+ }
makeResidueList();
makeCaBondList();
prot.add(chainseq);
}
- if (StructureImportSettings.isProcessSecondaryStructure())
+ // look at local setting for adding secondary tructure
+ if (predictSecondaryStructure)
{
createAnnotation(chainseq, chain, ms.at);
}
public boolean equals(Object otherObject)
{
FTSDataColumnI that = (FTSDataColumnI) otherObject;
- return this.getCode().equals(that.getCode())
+ return otherObject == null ? false
+ : this.getCode().equals(that.getCode())
&& this.getName().equals(that.getName())
&& this.getGroup().equals(that.getGroup());
}
savemenu.setVisible(false); // not yet implemented
viewMenu.add(fitToWindow);
- /*
- * exchange of Jalview features and Chimera attributes is for now
- * an optionally enabled experimental feature
- */
- if (Desktop.instance.showExperimental())
+ JMenuItem writeFeatures = new JMenuItem(
+ MessageManager.getString("label.create_chimera_attributes"));
+ writeFeatures.setToolTipText(MessageManager
+ .getString("label.create_chimera_attributes_tip"));
+ writeFeatures.addActionListener(new ActionListener()
{
- JMenuItem writeFeatures = new JMenuItem(
- MessageManager.getString("label.create_chimera_attributes"));
- writeFeatures.setToolTipText(MessageManager
- .getString("label.create_chimera_attributes_tip"));
- writeFeatures.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- sendFeaturesToChimera();
- }
- });
- viewerActionMenu.add(writeFeatures);
-
- final JMenu fetchAttributes = new JMenu(
- MessageManager.getString("label.fetch_chimera_attributes"));
- fetchAttributes.setToolTipText(MessageManager
- .getString("label.fetch_chimera_attributes_tip"));
- fetchAttributes.addMouseListener(new MouseAdapter()
+ @Override
+ public void actionPerformed(ActionEvent e)
{
+ sendFeaturesToChimera();
+ }
+ });
+ viewerActionMenu.add(writeFeatures);
- @Override
- public void mouseEntered(MouseEvent e)
- {
- buildAttributesMenu(fetchAttributes);
- }
- });
- viewerActionMenu.add(fetchAttributes);
- }
+ final JMenu fetchAttributes = new JMenu(
+ MessageManager.getString("label.fetch_chimera_attributes"));
+ fetchAttributes.setToolTipText(
+ MessageManager.getString("label.fetch_chimera_attributes_tip"));
+ fetchAttributes.addMouseListener(new MouseAdapter()
+ {
+
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ buildAttributesMenu(fetchAttributes);
+ }
+ });
+ viewerActionMenu.add(fetchAttributes);
}
/**
sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdbId);
}
sview.updateTitleAndMenus();
+ sview.raiseViewer();
return sview;
}
ViewerType viewerType = getViewerType();
return seqColoursApplied;
}
+ @Override
+ public void raiseViewer()
+ {
+ toFront();
+ }
+
}
long end;
- private boolean parseCalled;
+ /**
+ * true if parse() has been called
+ */
+ private boolean parseCalled = false;
+
+ private boolean parseImmediately = true;
+
+ /**
+ * @return if doParse() was called at construction time
+ */
+ protected boolean isParseImmediately()
+ {
+ return parseImmediately;
+ }
/**
* Creates a new AlignFile object.
{
super(source);
initData();
+
+ // stash flag in case parse needs to know if it has to autoconfigure or was
+ // configured after construction
+ this.parseImmediately = parseImmediately;
+
if (parseImmediately)
{
doParse();
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
{
// FIXME if sourceType is not null, we've lost data here
sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
- pdb = new JmolParser(pdbFile, sourceType);
-
+ pdb = new JmolParser(false, pdbFile, sourceType);
+ pdb.addSettings(parseSecStr && processSecondaryStructure,
+ parseSecStr && addTempFacAnnot,
+ parseSecStr && secStructServices);
+ pdb.doParse();
if (pdb.getId() != null && pdb.getId().trim().length() > 0
&& DataSourceType.FILE == sourceType)
{
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.gui;
import static org.testng.Assert.assertEquals;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.renderer;
import static org.testng.Assert.assertEquals;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.renderer.seqfeatures;
import static org.testng.Assert.assertEquals;
@Test(groups = { "Functional" })
public void compareTransferredToRefPDBAnnot() throws Exception
{
+ StructureImportSettings.setProcessSecondaryStructure(true);
+ StructureImportSettings.setVisibleChainAnnotation(true);
StructureImportSettings.setShowSeqFeatures(true);
AlignFrame ref = new FileLoader(false)
.LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.structure;
import static org.testng.Assert.assertEquals;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.dbsources;
import static org.testng.Assert.assertEquals;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.dbsources;
import static org.testng.Assert.assertEquals;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.dbsources;
import static org.testng.Assert.assertEquals;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.dbsources;
import static org.testng.Assert.assertEquals;
<string><![CDATA[664]]></string>
</property>
<property name="sourceName">
- <string><![CDATA[Vaqua4.jar]]></string>
+ <string><![CDATA[VAqua4.jar]]></string>
</property>
<property name="overrideUnixPermissions">
<boolean>false</boolean>
<boolean>true</boolean>
</property>
<property name="destinationName">
- <string><![CDATA[Vaqua4.jar]]></string>
+ <string><![CDATA[VAqua4.jar]]></string>
</property>
<property name="fileSize">
<long>1355141</long>
git://source.jalview.org / jalview.git / commitdiff