<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="pymol" url="html/features/pymol.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"/>
<tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
<tocitem text="PDB & 3D-Beacons Structure Chooser" target="pdbchooser" />
<tocitem text="Jmol Viewer" target="pdbjmol" />
- <tocitem text="Chimera Viewer" target="chimera" />
+ <tocitem text="Chimera Viewer" target="chimera" />
+ <tocitem text="Pymol Viewer" target="pymol" />
</tocitem>
<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
<tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
</head>
<body>
<p>
- <strong>The Chimera Viewer</strong>
+ <strong>The Chimera and ChimeraX Viewers</strong>
</p>
<p>
Since Jalview 2.8.2, <a href="http://www.cgl.ucsf.edu/chimera/">Chimera</a>
(http://www.cgl.ucsf.edu/chimera/) can be used for viewing
structures opened via the <a href="structurechooser.html"><strong>"View
- Structure Data.."</strong> dialog</a>.
+ Structure Data.."</strong> dialog</a>. In Jalview 2.11.2, support
+ was also added for ChimeraX.
</p>
<p>
You can set a default choice of Jmol or Chimera structure viewer in
--- /dev/null
+<html>
+<!--
+ * 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.
+ -->
+<head>
+<title>The Pymol PDB Viewer</title>
+</head>
+<body>
+ <p>
+ <strong>The Pymol Viewer</strong>
+ </p>
+ <p>
+ In Jalview 2.11.2, support was added for <a href="https://pymol.org/2/">Pymol</a>
+ (https://pymol.org/2/) to be used for viewing
+ structures opened via the <a href="structurechooser.html"><strong>"View
+ Structure Data.."</strong> dialog</a>.
+ </p>
+ <p>
+ You can configure Pymol as your preferred structure viewer in
+ <a href="preferences.html#structure"> Preferences</a>. You can also
+ optionally specify the path to the Pymol program here (if it differs
+ from the standard paths searched by Jalview).<br /> <strong>Jalview
+ requires Pymol's RPC interface, which is not available in older
+ versions of the Pymol community edition.<br />Please make sure your
+ version of Pymol is up to date.
+ </strong>
+ </p>
+ <p>
+ If you save your Jalview session as a project file, the state of any
+ open Pymol windows will also be saved, and can be reopened by
+ loading the project file on any machine with Pymol installed.
+ </p>
+ <p>
+ <strong>Known Limitations</strong><br /> Jalview provides an easy way
+ to employ Pymol for linked analysis of sequences and structures in the
+ same way as <a href="chimera.html">Chimera and ChimeraX</a>. There are
+ some limitations, however:
+ </p>
+ <ul>
+ <li>Pymol does not support some forms of legacy structural data
+ (e.g. the 1A70 C-alpha only PDB file included in the Jalview example
+ project).</li>
+ <li>Pymol to Jalview communication does not support transfer of
+ properties or highlighting sequence regions corresponding to
+ structure selections or mouse-overs in Pymol.</li>
+ </ul>
+ <p>
+ Basic screen operations (see <a
+ href="https://pymol.org/dokuwiki/doku.php?id=mouse">Pymol Wiki</a> at
+ https://pymol.org/dokuwiki/doku.php?id=mouse
+ for full details).
+ <table border="1">
+ <tr>
+ <td><strong>Action</strong></td>
+ <td><strong>Windows</strong></td>
+ <td><strong>Unix</strong></td>
+ <td><strong>Mac/OSX</strong></td>
+ </tr>
+ <tr>
+ <td>Rotate View</td>
+ <td>Left Click and Drag</td>
+ <td>Left Click and Drag</td>
+ <td>Left Click and Drag</td>
+ </tr>
+ <tr>
+ <td>Zoom</td>
+ <td>Right Click<br> drag mouse up or down
+ </td>
+ <td>Right Click<br>drag mouse up or down
+ </td>
+ <td>cmd or Right + Click and drag mouse up or down, <br>or
+ use mouse scroll button
+ </td>
+ </tr>
+ <tr>
+ <td>Move Origin</td>
+ <td>Middle Button + Drag</td>
+ <td>Middle Button and drag</td>
+ <td>alt + Click<br> and drag
+ </td>
+ </tr>
+ <tr>
+ <td>Select Residues</td>
+ <td>Ctrl + Click (and drag to select a region)</td>
+ <td>Ctrl + Click (and drag)</td>
+ <td>Ctrl + Click (and drag)</td>
+ </tr>
+ </table>
+ </p>
+ <p>
+ <strong>Jalview Controls</strong>
+ <p>The Jalview Pymol View window has up to five menus:</p>
+ <ul>
+ <li><Strong>File<br>
+ </strong>
+ <ul>
+ <li><strong>View Mapping<br>
+ </strong><em> Opens a text window showing the alignment between the
+ residues corresponding to alpha-carbon atoms in the PDB
+ structure and the residues in the associated sequence.</em></li>
+ </ul></li>
+ <li><strong>View</strong>
+ <ul>
+ <li><strong>Show Chains<br>
+ </strong><em>Select which of the PDB file's chains (if more than
+ one) are to be displayed.</em></li>
+ <li><strong>Colour by ..<br></strong><em>Submenu
+ allowing specific alignment views to be selected for
+ colouring associated chains in the structure display. This
+ menu contains all the alignment views associated with the
+ structure view, with those used to colour the view indicated
+ by ticks. Addditionally, it contains the following menu
+ entries:</em>
+ <ul>
+ <li><strong>Select many views<br></strong><em>When
+ this option is enabled, selecting an alignment view adds
+ it to the set used to colour the structures. Use this
+ when colouring structures related to a number of
+ alignments involving different domains or chains which
+ are shown in the same structure view.</em></li>
+ <li><strong>Select all views<br></strong><em>This
+ is only enabled when </em><strong>Select many views</strong><em>
+ is also enabled, and will add all associated views to
+ the set used to colour the structure display.</em></li>
+ <li><strong>Invert selection<br></strong><em>This
+ is only enabled when </em><strong>Select many views</strong><em>
+ is also enabled, and will replace the current set of
+ views with any remaining views not currently used to
+ colour the structure display.</em></li>
+ </ul></li>
+ </ul>
+ <li><strong>Colours<br>
+ </strong>
+ <ul>
+ <li><strong>By Sequence<br>
+ </strong><em> Colours each residue in the structure with the colour
+ of its corresponding residue in the associated sequence as
+ rendered in the associated alignment views, including any
+ UniProt sequence features or region colourings.<br />Pick
+ which of the associated alignment views are used to colour
+ the structures using the <strong>View→Colour
+ by ..</strong> sub menu.
+ </em><br> Residues which only exist in the PDB structure are
+ coloured white if they are insertions (relative to the
+ associated sequence in the alignment) and grey if they are N
+ or C terminal flanks outside the region mapped to the
+ alignment window's sequence.</em></li>
+ <li><strong>By Chain<br>
+ </strong><em>Uses Pymol's 'spectrum(chain)' command to apply a
+ different colour to each chain.</em></li>
+ <li><strong>Charge & Cysteine<br>
+ </strong><em> Highlights cysteines in yellow, anionic (Aspartic Acid
+ or Glutamic Acid) residues in red, and cationic (Lysine or
+ Arginine) residues in blue.</em></li>
+ <li><strong>Colour with Pymol<br></strong><em>Defers
+ any colouring operations to Pymol. Select this if you want
+ to use the Pymol scripting interface or menu to modify the
+ view directly.</em></li>
+ <li><strong>Standard and User Defined Jalview
+ colourschemes.<br>
+ </strong><em>The remaining entries apply the colourschemes available
+ from the standard and user defined <a
+ href="../colourSchemes/index.html">amino acid
+ colours</a>.
+ </em></li>
+ </ul></li>
+ <li><strong>Pymol<br>
+ </strong><em>This pulldown menu provides access to Pymol's capabilities from Jalview.</em>
+ <ul>
+ <li><strong><a name="sAlign">Align</a> <br> </strong><em>
+ When selected, the associated alignment will be used to
+ superimpose all the structures in the view onto the first
+ 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 />
+ </em></li>
+ <li><a name="annotxfer"><strong>Write Jalview
+ features</strong></a><br /> <em>Selecting this option will create
+ new atom properties for any features currently visible in
+ the associated alignment views. This allows those atoms to
+ be selected and analysed in Pymol directly.
+ </em><br>
+ <ul><li>Feature transfer in Pymol is experimental.</li><li>To select by a particular feature use the string matching syntax:<br>
+ select foo,p.jv_helix in helix
+ </li>
+ <li>To view transferred properties use Pymol's Properties Inspector</li><li>
+ For more information see <a href="https://pymol.org/dokuwiki/doku.php?id=properties#selection_language">Property based selection in Pymol's Documentation</a>.
+ </li>
+ </ul>
+ </li>
+ </ul></li>
+ <li><strong>Help<br>
+ </strong>
+ <ul>
+ <li><strong>Pymol Help<br>
+ </strong><em>Access the Pymol Help documentation in a new browser window.
+ window.</em></li>
+ </ul></li>
+ </ul>
+ <p>
+ <strong>Pymol and Windows Firewall</strong>
+ </p>
+ Jalview and Pymol communicate using the <a href="https://pymolwiki.org/index.php/RPC">Pymol's XML-RPC over HTTP interface</a>(https://pymolwiki.org/index.php/RPC).
+
+<br> Technically this requires both Pymol and Jalview to open
+ ports on the local network, and this may be blocked by Windows
+ Firewall with a warning message such as
+ <br /> "Windows Firewall has blocked some features of this program"
+ (where the program may be java.exe or javaw.exe).
+ <br /> To allow Jalview and Pymol to interact, you may need to add
+ permission for the program to communicate over the network. This can
+ be done from the warning dialogue, or in Control Panel, Firewall
+ settings.
+</body>
+</html>
label.web_services = Web Services
label.right_click_to_edit_currently_selected_parameter = Right click to edit currently selected parameter.
label.let_jmol_manage_structure_colours = Let Jmol manage structure colours
-label.fetch_chimera_attributes = Fetch Chimera attributes
-label.fetch_chimera_attributes_tip = Copy Chimera attribute to Jalview feature
+label.fetch_viewer_attributes = Fetch {0} attributes
+label.fetch_viewer_attributes_tip = Copy {0} attribute to Jalview feature
label.marks_leaves_tree_not_associated_with_sequence = Marks leaves of tree not associated with a sequence
label.index_web_services_menu_by_host_site = Index web services in menu by the host site
label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up = Check this option if you want to be informed<br>when a web service URL cannot be accessed by Jalview<br>when it starts up
label.insufficient_residues = Not enough aligned residues ({0}) to perform superposition
label.create_viewer_attributes = Write Jalview features
label.create_viewer_attributes_tip = Set structure residue attributes for Jalview features
-label.attributes_set = {0} attribute values set on Chimera
+label.attributes_set = {0} attribute values set on {1}
label.sort_alignment_by_tree = Sort Alignment By Tree
label.mark_unlinked_leaves = Mark Unlinked Leaves
label.associate_leaves_with = Associate Leaves With
{
out.close();
}
+ if (Cache.log.isTraceEnabled())
+ {
+ Cache.log.trace("Sent: " + command.toString());
+ if (result != null)
+ {
+ Cache.log.trace("Received: " + result);
+ }
+ }
}
return result;
}
btn_autosearch.setText(MessageManager.getString("option.autosearch"));
btn_autosearch.setToolTipText(
MessageManager.getString("option.enable_disable_autosearch"));
+ // disable autosearch by default
btn_autosearch.setSelected(!Platform.isJS()
- && Cache.getDefault(getAutosearchPreference(), true));
+ && Cache.getDefault(getAutosearchPreference(), false));
btn_autosearch.addActionListener(new java.awt.event.ActionListener()
{
@Override
} catch (Exception ex)
{
}
-
if (b)
{
- alignFrame.setDisplayedView(this);
+ setAlignFrameView();
}
}
-
+ public void setAlignFrameView()
+ {
+ alignFrame.setDisplayedView(this);
+ }
+
@Override
public StructureSelectionManager getStructureSelectionManager()
{
viewerActionMenu.add(writeFeatures);
fetchAttributes = new JMenu(
- MessageManager.getString("label.fetch_chimera_attributes"));
+ MessageManager.formatMessage("label.fetch_viewer_attributes",getViewerName()));
fetchAttributes.setToolTipText(
- MessageManager.getString("label.fetch_chimera_attributes_tip"));
+ MessageManager.formatMessage("label.fetch_viewer_attributes_tip",getViewerName()));
fetchAttributes.addMouseListener(new MouseAdapter()
{
// todo pull up?
int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
statusBar.setText(
- MessageManager.formatMessage("label.attributes_set", count));
+ MessageManager.formatMessage("label.attributes_set", count, getViewerName()));
}
/**
* a second parameter sets the pdbid as the loaded PyMOL object name
*/
String pdbId = pe.getId();
+ try {
+ String safePDBId = java.net.URLEncoder.encode(pdbId,"UTF-8");
+ pdbId = safePDBId.replace('%', '_');
+ pdbId = pdbId.replace("-", "__");
+ char fc = pdbId.charAt(0);
+ // put an 's' before any numerics
+ if (fc>='0' && fc<='9')
+ {
+ pdbId = 's'+pdbId;
+ }
+// pdbId.replace('-', 0)
+ } catch (Exception x)
+ {
+ Cache.log.error("Unxpected encoding exception for '"+pdbId+"'",x);
+ }
cmd.addParameter(pdbId);
executeCommand(cmd, false);
{
int count = binding.sendFeaturesToViewer(getAlignmentPanel());
statusBar.setText(
- MessageManager.formatMessage("label.attributes_set", count));
+ MessageManager.formatMessage("label.attributes_set", count, getViewerName()));
}
}
} else {
if (processingEntry.hasRetrievalUrl())
{
+ String safePDBId = java.net.URLEncoder.encode(pdbid,"UTF-8");
+
// retrieve from URL to new local tmpfile
- File tmpFile = File.createTempFile(pdbid,
+ File tmpFile = File.createTempFile(safePDBId,
"." + (PDBEntry.Type.MMCIF.toString().equals(
processingEntry.getType().toString()) ? "cif"
: "pdb"));
import jalview.api.AlignmentViewPanel;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.awt.Component;
import java.awt.event.ActionEvent;
}
}
});
+ final ViewSelectionMenu us=this;
checkBox.addMouseListener(new MouseAdapter()
{
@Override
{
try
{
- ap.setSelected(false);
} catch (Exception ex)
{
}
{
try
{
- ap.setSelected(true);
+ ap.setAlignFrameView();
} catch (Exception ex)
{
}
import java.util.HashMap;
import java.util.IdentityHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Vector;
pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
seqToStrucMapping.add(siftsMapping);
maxChain.makeExactMapping(siftsMapping, seq);
- maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");
+ maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId().toLowerCase(Locale.ROOT));
maxChain.transferResidueAnnotation(siftsMapping, null);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
targetChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, "IEA:Jalview"); // FIXME: is
+ maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is
// this
// "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
siftsClient);
foundSiftsMappings.add(siftsMapping);
chain.makeExactMapping(siftsMapping, seq);
- chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
+ chain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId().toLowerCase(Locale.ROOT));// FIXME: is this
// "IEA:SIFTS" ?
chain.transferResidueAnnotation(siftsMapping, null);
} catch (SiftsException e)
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
maxChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
- maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+ maxChain.transferRESNUMFeatures(seq, null,pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is this
// "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
maxChain.makeExactMapping(maxAlignseq, seq);
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
- maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferRESNUMFeatures(seq, null, pdb.getId().toLowerCase(Locale.ROOT));
HashMap<Integer, int[]> mapping = new HashMap<>();
int resNum = -10000;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeaturesI;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
dbVersion, (chid == null ? id : id + chid));
// dbentry.setMap()
pdbcs.addDBRef(dbentry);
+ // update any feature groups
+ List<SequenceFeature> allsf = pdbcs.getFeatures().getAllFeatures();
+ List<SequenceFeature> newsf = new ArrayList<SequenceFeature>();
+ if (allsf!=null && allsf.size()>0)
+ {
+ for (SequenceFeature f:allsf)
+ {
+ if (file.equals(f.getFeatureGroup()))
+ {
+ f = new SequenceFeature(f, f.type, f.begin, f.end, id, f.score);
+ }
+ newsf.add(f);
+ }
+ pdbcs.setSequenceFeatures(newsf);
+ }
}
}
else
* @param seq
* @param status
* The Status of the transferred annotation
+ *
+ * @param altPDBID the group id for the features on the destination sequence (e.g. the official accession ID)
*/
public void transferRESNUMFeatures(SequenceI seq,
- String status)
+ String status, String altPDBID)
{
+ if (altPDBID==null)
+ {
+ altPDBID = pdbid;
+ }
SequenceI sq = seq;
while (sq != null && sq.getDatasetSequence() != null)
{
int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
.elementAt(0).alignmentMapping;
SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
- feature.getFeatureGroup(), feature.getScore());
+ altPDBID, feature.getScore());
tx.setStatus(status
+ ((tx.getStatus() == null || tx.getStatus().length() == 0)
? ""
xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
- width="210mm"
- height="297mm"
- viewBox="0 0 210 297"
+ width="132.29233mm"
+ height="132.29326mm"
+ viewBox="0 0 132.29233 132.29326"
version="1.1"
id="svg8"
- inkscape:version="1.0.1 (0767f8302a, 2020-10-17)"
- sodipodi:docname="JalviewDevelopLogo2.svg">
+ inkscape:version="0.92.5 (2060ec1f9f, 2020-04-08)"
+ sodipodi:docname="jalview_develop_logo.svg">
<defs
id="defs2">
<linearGradient
clipPathUnits="userSpaceOnUse"
id="clipPath1000">
<path
- style="fill:none;stroke:#000000;stroke-width:0.264583px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ style="fill:none;stroke:#000000;stroke-width:0.26458299px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
d="M 87.312506,136.26042 162.71876,190.5 133.61459,206.375 H 107.15626 L 84.666668,186.53125 80.697918,158.75 Z"
- id="path1002" />
+ id="path1002"
+ inkscape:connector-curvature="0" />
</clipPath>
<clipPath
clipPathUnits="userSpaceOnUse"
id="clipPath1093-1">
<rect
- style="fill:#256c7a;fill-opacity:1;stroke:#000000;stroke-width:0.850394;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="fill:#256c7a;fill-opacity:1;stroke:#000000;stroke-width:0.85039401;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="rect1095-8"
width="105"
height="229.99998"
clipPathUnits="userSpaceOnUse"
id="clipPath1281">
<rect
- style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.256539;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.25653899;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="rect1283"
width="34.395832"
height="74.083336"
clipPathUnits="userSpaceOnUse"
id="clipPath1285">
<rect
- style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.256539;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.25653899;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="rect1287"
width="34.395832"
height="74.083336"
clipPathUnits="userSpaceOnUse"
id="clipPath1333">
<rect
- style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.225;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.22499999;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="rect1335"
width="62.177082"
height="54.239582"
clipPathUnits="userSpaceOnUse"
id="clipPath1375">
<rect
- style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.225;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.22499999;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="rect1377"
width="64.822914"
height="64.822914"
clipPathUnits="userSpaceOnUse"
id="clipPath1675">
<rect
- style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.204471;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.20447101;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="rect1677"
width="33.037834"
height="66.145836"
clipPathUnits="userSpaceOnUse"
id="clipPath1680">
<rect
- style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.515557;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:0.51555699;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="rect1682"
width="68.626167"
height="129.34053"
clipPathUnits="userSpaceOnUse"
id="clipPath1692">
<path
- style="fill:none;stroke:#000000;stroke-width:0.989976px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ style="fill:none;stroke:#000000;stroke-width:0.98997599px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
d="m 162.06065,485.50479 v 69.97715 l 53.92055,4.99839 24.50939,39.98694 14.70561,4.99839 h 14.70561 V 480.5064 H 162.06065 Z"
- id="path1694" />
+ id="path1694"
+ inkscape:connector-curvature="0" />
</clipPath>
<clipPath
clipPathUnits="userSpaceOnUse"
<path
id="mask-powermask-path-effect945_box"
style="fill:#ffffff;fill-opacity:1"
- d="M 43.979163,54.562507 H 167.06656 V 178.27083 H 43.979163 Z" />
+ d="M 43.979163,54.562507 H 167.06656 V 178.27083 H 43.979163 Z"
+ inkscape:connector-curvature="0" />
<g
id="g943"
style="fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.5;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
transform="matrix(0.91530618,0,0,0.91999994,3.6852506,4.2711328)">
<path
- style="color:#000000;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:medium;line-height:normal;font-family:sans-serif;font-variant-ligatures:normal;font-variant-position:normal;font-variant-caps:normal;font-variant-numeric:normal;font-variant-alternates:normal;font-variant-east-asian:normal;font-feature-settings:normal;font-variation-settings:normal;text-indent:0;text-align:start;text-decoration:none;text-decoration-line:none;text-decoration-style:solid;text-decoration-color:#000000;letter-spacing:normal;word-spacing:normal;text-transform:none;writing-mode:lr-tb;direction:ltr;text-orientation:mixed;dominant-baseline:auto;baseline-shift:baseline;text-anchor:start;white-space:normal;shape-padding:0;shape-margin:0;inline-size:0;clip-rule:nonzero;display:inline;overflow:visible;visibility:visible;opacity:1;isolation:auto;mix-blend-mode:normal;color-interpolation:sRGB;color-interpolation-filters:linearRGB;solid-color:#000000;solid-opacity:1;vector-effect:none;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;stroke-width:0.5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;color-rendering:auto;image-rendering:auto;shape-rendering:auto;text-rendering:auto;enable-background:accumulate;stop-color:#000000;stop-opacity:1"
+ style="color:#000000;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:medium;line-height:normal;font-family:sans-serif;font-variant-ligatures:normal;font-variant-position:normal;font-variant-caps:normal;font-variant-numeric:normal;font-variant-alternates:normal;font-feature-settings:normal;text-indent:0;text-align:start;text-decoration:none;text-decoration-line:none;text-decoration-style:solid;text-decoration-color:#000000;letter-spacing:normal;word-spacing:normal;text-transform:none;writing-mode:lr-tb;direction:ltr;text-orientation:mixed;dominant-baseline:auto;baseline-shift:baseline;text-anchor:start;white-space:normal;shape-padding:0;clip-rule:nonzero;display:inline;overflow:visible;visibility:visible;opacity:1;isolation:auto;mix-blend-mode:normal;color-interpolation:sRGB;color-interpolation-filters:linearRGB;solid-color:#000000;solid-opacity:1;vector-effect:none;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;stroke-width:0.5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;color-rendering:auto;image-rendering:auto;shape-rendering:auto;text-rendering:auto;enable-background:accumulate"
d="m 67.791016,78.375 v 62.85352 h 25.8125 V 104.1875 h 58.855464 v 58.85352 H 44.978516 v 1 l -0.707032,0.70703 24.105469,24.10547 H 178.27148 V 78.375 Z m 2,2 H 176.27148 V 186.85352 H 69.205078 l -21.8125,-21.8125 H 154.45898 V 102.1875 H 91.603516 v 37.04102 h -21.8125 z"
- id="path939" />
+ id="path939"
+ inkscape:connector-curvature="0" />
<path
- style="color:#000000;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:medium;line-height:normal;font-family:sans-serif;font-variant-ligatures:normal;font-variant-position:normal;font-variant-caps:normal;font-variant-numeric:normal;font-variant-alternates:normal;font-variant-east-asian:normal;font-feature-settings:normal;font-variation-settings:normal;text-indent:0;text-align:start;text-decoration:none;text-decoration-line:none;text-decoration-style:solid;text-decoration-color:#000000;letter-spacing:normal;word-spacing:normal;text-transform:none;writing-mode:lr-tb;direction:ltr;text-orientation:mixed;dominant-baseline:auto;baseline-shift:baseline;text-anchor:start;white-space:normal;shape-padding:0;shape-margin:0;inline-size:0;clip-rule:nonzero;display:inline;overflow:visible;visibility:visible;opacity:1;isolation:auto;mix-blend-mode:normal;color-interpolation:sRGB;color-interpolation-filters:linearRGB;solid-color:#000000;solid-opacity:1;vector-effect:none;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;stroke-width:0.5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;paint-order:fill markers stroke;color-rendering:auto;image-rendering:auto;shape-rendering:auto;text-rendering:auto;enable-background:accumulate;stop-color:#000000;stop-opacity:1"
+ style="color:#000000;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:medium;line-height:normal;font-family:sans-serif;font-variant-ligatures:normal;font-variant-position:normal;font-variant-caps:normal;font-variant-numeric:normal;font-variant-alternates:normal;font-feature-settings:normal;text-indent:0;text-align:start;text-decoration:none;text-decoration-line:none;text-decoration-style:solid;text-decoration-color:#000000;letter-spacing:normal;word-spacing:normal;text-transform:none;writing-mode:lr-tb;direction:ltr;text-orientation:mixed;dominant-baseline:auto;baseline-shift:baseline;text-anchor:start;white-space:normal;shape-padding:0;clip-rule:nonzero;display:inline;overflow:visible;visibility:visible;opacity:1;isolation:auto;mix-blend-mode:normal;color-interpolation:sRGB;color-interpolation-filters:linearRGB;solid-color:#000000;solid-opacity:1;vector-effect:none;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;stroke-width:0.5;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;paint-order:fill markers stroke;color-rendering:auto;image-rendering:auto;shape-rendering:auto;text-rendering:auto;enable-background:accumulate"
d="M 43.978516,54.5625 V 165.04102 H 154.45898 V 102.1875 h -25.8125 v 37.04102 H 69.791016 V 80.375 H 177.27148 v -1 L 177.97852,78.667969 153.87305,54.5625 Z m 2,2 H 153.04492 l 21.8125,21.8125 H 67.791016 v 62.85352 H 130.64648 V 104.1875 h 21.8125 v 58.85352 H 45.978516 Z"
- id="path941" />
+ id="path941"
+ inkscape:connector-curvature="0" />
</g>
</mask>
<filter
borderopacity="1.0"
inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
- inkscape:zoom="1.63"
- inkscape:cx="357.63388"
- inkscape:cy="452.52787"
+ inkscape:zoom="4.6103362"
+ inkscape:cx="237.96116"
+ inkscape:cy="274.8671"
inkscape:document-units="mm"
inkscape:current-layer="layer1"
inkscape:document-rotation="0"
showgrid="true"
inkscape:window-width="3840"
- inkscape:window-height="1989"
+ inkscape:window-height="1997"
inkscape:window-x="0"
inkscape:window-y="0"
- inkscape:window-maximized="1">
+ inkscape:window-maximized="1"
+ fit-margin-top="0"
+ fit-margin-left="0"
+ fit-margin-right="0"
+ fit-margin-bottom="0">
<inkscape:grid
type="xygrid"
- id="grid10" />
+ id="grid10"
+ originx="-42.332674"
+ originy="-109.80208" />
</sodipodi:namedview>
<metadata
id="metadata5">
</rdf:RDF>
</metadata>
<g
+ inkscape:groupmode="layer"
+ id="layer4"
+ inkscape:label="underneath"
+ transform="translate(0.01538153)" />
+ <g
inkscape:label="Layer 1"
inkscape:groupmode="layer"
- id="layer1">
+ id="layer1"
+ transform="translate(-42.332673,-54.904652)">
<g
- id="g1189"
- transform="matrix(1.0925306,0,0,1.0869566,-4.026249,-4.642536)"
- style="stroke:none"
- mask="url(#mask-powermask-path-effect945)"
- inkscape:path-effect="#path-effect945"
- inkscape:export-xdpi="1.54"
- inkscape:export-ydpi="1.54">
+ id="g1000">
<path
- style="fill:#a8008c;fill-opacity:1;stroke:none;stroke-width:0.62096px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
- d="m 44.979174,55.562507 h 99.353746 l 21.73364,21.733639 H 66.712812 V 133.1826 H 44.979174 Z"
+ style="fill:#a8008c;fill-opacity:1;stroke:none;stroke-width:0.67668498px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ d="M 42.348072,54.904652 H 150.89508 l 21.08409,21.168255 H 63.5 V 142.21874 H 42.333333 Z"
id="path12-7-3"
sodipodi:nodetypes="ccccccc"
- inkscape:original-d="m 44.979174,55.562507 h 99.353746 l 21.73364,21.733639 H 66.712812 V 133.1826 H 44.979174 Z" />
+ inkscape:connector-curvature="0" />
<path
- style="fill:#ff7200;fill-opacity:1;stroke:none;stroke-width:0.62096px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
- d="m 66.712812,77.296146 h 99.353748 l -2e-5,21.733614 H 88.446427 V 133.1826 H 66.712812 Z"
+ style="fill:#ff7200;fill-opacity:1;stroke:none;stroke-width:0.67668498px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ d="M 66.145833,78.718741 H 174.625 v 21.166666 l -87.31255,-3e-6 5e-5,39.687506 H 66.145833 Z"
id="path12-3-5-1"
sodipodi:nodetypes="ccccccc"
- inkscape:original-d="m 66.712812,77.296146 h 99.353748 l -2e-5,21.733614 H 88.446427 V 133.1826 H 66.712812 Z" />
+ inkscape:connector-curvature="0" />
<path
- style="fill:#0064b4;fill-opacity:1;stroke:none;stroke-width:0.62096px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
- d="M 166.06654,177.27083 66.712789,176.64985 44.979174,154.91624 H 144.33292 V 99.02976 h 21.73362 z"
+ style="fill:#0064b4;fill-opacity:1;stroke:none;stroke-width:0.67668498px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ d="M 174.625,187.19791 H 66.145833 L 44.979167,166.03124 153.45834,165.76666 V 103.58958 H 174.625 Z"
id="path12-6-9-9"
sodipodi:nodetypes="ccccccc"
- inkscape:original-d="M 166.06654,177.27083 66.712789,176.64985 44.979174,154.91624 H 144.33292 V 99.02976 h 21.73362 z" />
+ inkscape:connector-curvature="0" />
<path
- style="fill:#54c800;fill-opacity:1;stroke:none;stroke-width:0.62096px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
- d="M 144.33292,154.91624 H 44.979174 V 133.1826 H 122.59928 V 99.02976 h 21.73364 z"
+ style="fill:#54c800;fill-opacity:1;stroke:none;stroke-width:0.67668498px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ d="M 150.8125,163.38541 H 42.333333 v -21.16667 h 87.312497 v -39.6875 h 21.16667 z"
id="path12-3-7-2-4"
sodipodi:nodetypes="ccccccc"
- inkscape:original-d="M 144.33292,154.91624 H 44.979174 V 133.1826 H 122.59928 V 99.02976 h 21.73364 z" />
+ inkscape:connector-curvature="0" />
<path
- style="fill:url(#linearGradient1484);fill-opacity:1;stroke:none;stroke-width:0.264583px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
- d="m 111.125,148.16666 v 30.42709 h 33.07292 v -9.26042 h -23.8125 v -21.16667 z"
+ style="fill:url(#linearGradient1484);fill-opacity:1;stroke:none;stroke-width:0.26458299px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ d="m 111.125,148.16666 -0.006,30.61821 h 34.05188 v -8.29733 h -25.79662 l -2.6e-4,-22.29908 z"
id="path1329-7"
sodipodi:nodetypes="ccccccc"
clip-path="url(#clipPath1466)"
- transform="matrix(2.3469387,0,0,2.3469387,-215.8244,-264.23234)"
- inkscape:original-d="m 111.125,148.16666 v 30.42709 h 33.07292 v -9.26042 h -23.8125 v -21.16667 z" />
+ transform="matrix(2.5641023,0,0,2.5510205,-242.58781,-292.69847)"
+ inkscape:connector-curvature="0" />
<path
- style="fill:url(#linearGradient1486);fill-opacity:1;stroke:none;stroke-width:0.264583px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
- d="m 129.64583,145.52083 33.07292,1e-5 v 33.07291 h -9.26042 l 1e-5,-23.8125 h -23.81251 v -9.26042"
+ style="fill:url(#linearGradient1486);fill-opacity:1;stroke:none;stroke-width:0.26458299px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+ d="m 128.66113,145.59554 h 34.05188 v 34.2265 h -8.255 v -25.92918 h -25.79687 v -8.29733"
id="path1363-8"
clip-path="url(#clipPath1471)"
- transform="matrix(2.3469387,0,0,2.3469387,-215.8244,-264.23234)"
+ transform="matrix(2.5641023,0,0,2.5510205,-242.58781,-292.69847)"
sodipodi:nodetypes="ccccccc"
- inkscape:original-d="m 129.64583,145.52083 33.07292,1e-5 v 33.07291 h -9.26042 l 1e-5,-23.8125 h -23.81251 v -9.26042" />
+ inkscape:connector-curvature="0" />
</g>
</g>
<g
inkscape:groupmode="layer"
id="layer2"
inkscape:label="Layer 2"
- style="display:inline;mix-blend-mode:lighten" />
+ style="display:inline;mix-blend-mode:lighten"
+ transform="translate(-42.332673,-54.904652)" />
<g
inkscape:groupmode="layer"
id="layer3"
inkscape:label="Layer 3"
- style="display:inline;mix-blend-mode:normal" />
+ style="display:inline;mix-blend-mode:normal"
+ transform="translate(-42.332673,-54.904652)" />
</svg>
<serializedBean>
<property name="description" type="string">Jalview File</property>
<property name="extension" type="string">jvp</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Jalview Launch File</property>
<property name="extension" type="string">jvl</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-Launch.icns</string>
<serializedBean>
<property name="description" type="string">CIF File</property>
<property name="extension" type="string">cif</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">mmCIF File</property>
<property name="extension" type="string">mcif,mmcif</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">PDB File</property>
<property name="extension" type="string">ent,pdb</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">AMSA File</property>
<property name="extension" type="string">amsa</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Jalview Annotations File</property>
<property name="extension" type="string">annotations,jvannotations</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">BioJSON File</property>
<property name="extension" type="string">biojson</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">BLC File</property>
<property name="extension" type="string">blc</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Clustal File</property>
<property name="extension" type="string">aln</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">ENA Flatfile File</property>
<property name="extension" type="string">txt</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Fasta File</property>
<property name="extension" type="string">fa,fasta</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Jalview Features File</property>
<property name="extension" type="string">features,jvfeatures</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">GenBank Flatfile File</property>
<property name="extension" type="string">gb,gbk</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Generic Features Format v2 File</property>
<property name="extension" type="string">gff2</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Generic Features Format v3 File</property>
<property name="extension" type="string">gff3</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">JnetFile File</property>
<property name="extension" type="string">concise,jnet</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">MSF File</property>
<property name="extension" type="string">msf</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">PFAM File</property>
<property name="extension" type="string">pfam</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">PHYLIP File</property>
<property name="extension" type="string">phy</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">PileUp File</property>
<property name="extension" type="string">pileup</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">PIR File</property>
<property name="extension" type="string">pir</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">RNAML File</property>
<property name="extension" type="string">rnaml</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Substitution Matrix File</property>
<property name="extension" type="string">mat</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">Stockholm File</property>
<property name="extension" type="string">stk,sto</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>Jalview-File.icns</string>
<serializedBean>
<property name="description" type="string">$$NAME$$ File</property>
<property name="extension" type="string">$$EXTENSION$$</property>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="macIconFile">
<object class="com.install4j.api.beans.ExternalFile">
<string>$$ICONFILE$$.icns</string>
</components>
</files>
<launchers>
- <launcher name="Jalview Launcher" id="737" menuName="${compiler:JALVIEW_APPLICATION_NAME}" icnsFile="${compiler:JALVIEW_DIR}/${compiler:MAC_ICONS_FILE}" customMacBundleIdentifier="true" macBundleIdentifier="${compiler:BUNDLE_ID}" fileset="734" useCustomMacosExecutableName="true" customMacosExecutableName="${compiler:JALVIEW_APPLICATION_NAME}">
+ <launcher name="Jalview Launcher" id="737" customizedId="JALVIEW" menuName="${compiler:JALVIEW_APPLICATION_NAME}" icnsFile="${compiler:JALVIEW_DIR}/${compiler:MAC_ICONS_FILE}" customMacBundleIdentifier="true" macBundleIdentifier="${compiler:BUNDLE_ID}" fileset="734" useCustomMacosExecutableName="true" customMacosExecutableName="${compiler:JALVIEW_APPLICATION_NAME}">
<executable name="${compiler:EXECUTABLE_NAME}" iconSet="true" iconFile="${compiler:JALVIEW_DIR}/${compiler:WINDOWS_ICONS_FILE}" redirectStdout="true" executableMode="gui" changeWorkingDirectory="false" singleInstance="true" checkConsoleParameter="true">
<versionInfo include="true" fileDescription="${compiler:sys.fullName}" legalCopyright="${compiler:COPYRIGHT_MESSAGE}" internalName="${compiler:INTERNAL_ID}" productName="${compiler:sys.fullName}" />
</executable>
</group>
<action id="2350" beanClass="com.install4j.runtime.beans.actions.desktop.UrlHandlerAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="scheme" type="string">jalview</property>
</serializedBean>
</action>
<action id="2450" beanClass="com.install4j.runtime.beans.actions.desktop.UrlHandlerAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="scheme" type="string">jalviews</property>
</serializedBean>
</action>
<action id="2641" beanClass="com.install4j.runtime.beans.actions.desktop.UrlHandlerAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="launcherId" type="string">737</property>
+ <property name="launcherId" type="string">JALVIEW</property>
<property name="scheme" type="string">${compiler:EXTRA_SCHEME}</property>
</serializedBean>
</action>
git://source.jalview.org / jalview.git / commitdiff
