4 <title>SwingJS test Jalview</title>
5 <meta charset="utf-8" />
6 <script src="swingjs/swingjs2.js"></script>
7 <script src="swingjs/JalviewApplet.js"></script>
9 if (!self.SwingJS)alert('swingjs2.js was not found. It needs to be in swingjs folder in the same directory as ' + document.location.href)
12 main: "jalview.bin.Jalview",
15 resourcePath: "examples",
17 serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php',
18 j2sPath: 'swingjs/j2s',
20 startButton:'Start Jalview',
22 embedInternalFrames:false,
29 <!-- content template start
30 JalviewApplet.js will add divs such as these:
31 <div id="jalview0-desktop-div" style="width:0px;display:none"></div>
32 <div id="jalview0-alignment-div" style="width:0px;display:none"></div>
35 <h2>JalviewJS Button Examples</h2>
36 Try out JalviewJS by pressing one of the buttons below.
37 <a target="_blank" href="http://www.jalview.org/examples/applets.html">Original Java</a> (requires SeaMonkey browser)
39 <p> </p><div align="center">
41 <h2>Ferredoxins, chloroplast precursor related UniRef50
43 <br /> (15 sequences x 150 residues)
47 <td width="10%" valign="center">
49 code="jalview.bin.JalviewLite" width="140" height="35"
50 archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
51 <param name="permissions" value="sandbox"/>
52 <param name="file" value="uniref50.fa"/>
53 <param name="treeFile" value="ferredoxin.nw"/>
54 <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
55 <param name="sortByTree" value="True"/>
56 <param name="showSequenceLogo" value="true"/>
57 <param name="showGroupConsensus" value="true"/>
58 <param name="showFullId" value="false"/>
59 <param name="linkLabel_1" value="Uniprot"/>
60 <param name="linkUrl_1" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
61 <param name="linkLabel_2" value="EMBL-EBI Search"/>
62 <param name="linkUrl_2" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
63 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
66 <td valign="center">User Defined Colours, loads an associated
67 Newick format tree file which is used to sort the alignment, and
68 group consensus and sequence logos are shown below the alignment.</td>
71 <td width="10%" valign="center"><applet
72 code="jalview.bin.JalviewLite" width="140" height="35"
73 archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
74 <param name="permissions" value="sandbox"/>
75 <param name="file" value="uniref50.fa"/>
76 <param name="features" value="exampleFeatures.txt"/>
77 <param name="showFullId" value="false"/>
78 <param name="windowHeight" value="500"/>
79 <param name="windowWidth" value="650"/>
80 <param name="showFeatureSettings" value="true"/>
81 <param name="wrap" value="true"/>
82 <param name="showAnnotation" value="false"/>
83 <param name="linkLabel_1" value="Uniprot"/>
84 <param name="linkUrl_1"
85 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
86 <param name="linkLabel_2" value="EMBL-EBI Search"/>
87 <param name="linkUrl_2"
88 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
89 <param name="APPLICATION_URL"
90 value="http://www.jalview.org/services/launchApp"/>
93 <td valign="center">Displays a features file on the alignment</td>
96 <td width="10%" valign="center"><applet
97 code="jalview.bin.JalviewLite" width="140" height="35"
98 archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
99 <param name="permissions" value="sandbox"/>
100 <param name="file" value="uniref50.fa"/>
101 <param name="showFullId" value="false"/>
102 <param name="windowHeight" value="500"/>
103 <param name="windowWidth" value="650"/>
104 <param name="wrap" value="true"/>
105 <param name="debug" value="true"/>
106 <param name="showAnnotation" value="false"/>
107 <param name="defaultColour" value="Strand Propensity"/>
108 <param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
109 <param name="linkLabel_1" value="Uniprot"/>
110 <param name="linkUrl_1"
111 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
112 <param name="linkLabel_2" value="EMBL-EBI Search"/>
113 <param name="linkUrl_2"
114 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
115 <param name="APPLICATION_URL"
116 value="http://www.jalview.org/services/launchApp"/>
119 <td valign="center">Associates PDB file 1GAQ with sequence
123 <td width="10%" valign="center"><applet
124 code="jalview.bin.JalviewLite" width="140" height="35"
125 archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
126 <param name="permissions" value="sandbox"/>
127 <param name="file" value="jpred_msa.fasta"/>
128 <param name="jnetfile" value="jpred_msa.seq.concise"/>
129 <param name="showFullId" value="false"/>
130 <param name="windowHeight" value="515"/>
131 <param name="windowWidth" value="650"/>
132 <param name="showAnnotation" value="true"/>
133 <param name="defaultColour" value="Clustal"/>
134 <param name="linkLabel_1" value="Uniprot"/>
135 <param name="linkUrl_1"
136 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
137 <param name="linkLabel_2" value="EMBL-EBI Search"/>
138 <param name="linkUrl_2"
139 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
140 <param name="APPLICATION_URL"
141 value="http://www.jalview.org/services/launchApp"/>
144 <td valign="middle">Displays a Multiple Sequence Alignment
145 Based JPred Prediction for a Sequence</td>
149 <h2>RF00031 RFAM Alignment with per sequence secondary
154 <td width="10%" valign="center"><applet
155 code="jalview.bin.JalviewLite" width="140" height="35"
156 archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
157 <param name="permissions" value="sandbox"/>
158 <param name="file" value="RF00031_folded.stk"/>
159 <param name="showFullId" value="false"/>
160 <param name="windowHeight" value="515"/>
161 <param name="windowWidth" value="650"/>
162 <param name="showAnnotation" value="true"/>
163 <param name="defaultColour" value="Purine/Pyrimidine"/>
164 <param name="APPLICATION_URL"
165 value="http://www.jalview.org/services/launchApp"/>
168 <td valign="center">Displays an RFAM RNA fold family with
169 secondary structure annotation</td>
173 <h2>Linked Protein and cDNA alignments for a family of Steroid Receptors</h2>
177 <td width="10%" valign="center">
179 code="jalview.bin.JalviewLite" width="140" height="35"
180 archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
181 <param name="permissions" value="sandbox"/>
182 <param name="file2" value="estrogenReceptorCdna_frag.fa"/>
183 <param name="file" value="estrogenReceptorProtein_frag.fa"/>
184 <param name="enableSplitFrame" value="true"/>
185 <param name="scaleProteinAsCdna" value="true"/>
186 <param name="showFullId" value="false"/>
187 <param name="windowHeight" value="300"/>
188 <param name="windowWidth" value="800"/>
189 <param name="showAnnotation" value="true"/>
190 <param name="showSequenceLogo" value="true"/>
191 <param name="defaultColourNuc" value="Purine/Pyrimidine"/>
192 <param name="defaultColourProt" value="Clustal"/>
193 <param name="APPLICATION_URL"
194 value="http://www.jalview.org/services/launchApp"/>
197 <td valign="center">Displays a split window view showing aligned protein
198 and a reconstructed cDNA alignment.<br />Proteins were aligned with <a
199 href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31,
200 via the Jalview Desktop).<br />Data retrieved from Uniprot and
201 ENA, after Thornton, Need and Crews, <a
202 href="http://dx.doi.org/10.1126/science.1086185">Science 19
203 September 2003: 301 (5640), 1714-1717</a>
208 <div id="sysout" style="width:500px;height:300px;background:yellow;overflow:auto"></div>
213 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
214 * Copyright (C) $$Year-Rel$$ The Jalview Authors
216 * This file is part of Jalview.
218 * Jalview is free software: you can redistribute it and/or
219 * modify it under the terms of the GNU General Public License
220 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
222 * Jalview is distributed in the hope that it will be useful, but
223 * WITHOUT ANY WARRANTY; without even the implied warranty
224 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
225 * PURPOSE. See the GNU General Public License for more details.
227 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
228 * The Jalview Authors are detailed in the 'AUTHORS' file.