2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
20 <!-- boiler plate link to alternate demopage -->
21 <div style="width: 100%">
22 <div style="width:35%; align:left; float:right;">
23 <div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
24 <p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
29 <!-- content template start -->
32 <h2>JalviewLite Button Examples</h2>
33 Try out JalviewLite by pressing one of the buttons below.<br/>
34 For more information on how to use the applet in your website, see the <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
35 <p> </p><div align="center">
37 <h2>Ferredoxins, chloroplast precursor related UniRef50
39 <br /> (15 sequences x 150 residues)
43 <td width="10%" valign="center">
45 code="jalview.bin.JalviewLite" width="140" height="35"
46 archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
47 <param name="permissions" value="sandbox"/>
48 <param name="file" value="uniref50.fa"/>
49 <param name="treeFile" value="ferredoxin.nw"/>
50 <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
51 <param name="sortByTree" value="True"/>
52 <param name="showSequenceLogo" value="true"/>
53 <param name="showGroupConsensus" value="true"/>
54 <param name="showFullId" value="false"/>
55 <param name="linkLabel_1" value="Uniprot"/>
56 <param name="linkUrl_1" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
57 <param name="linkLabel_2" value="EMBL-EBI Search"/>
58 <param name="linkUrl_2" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
59 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
62 <td valign="center">User Defined Colours, loads an associated
63 Newick format tree file which is used to sort the alignment, and
64 group consensus and sequence logos are shown below the alignment.</td>
67 <td width="10%" valign="center"><applet
68 code="jalview.bin.JalviewLite" width="140" height="35"
69 archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
70 <param name="permissions" value="sandbox"/>
71 <param name="file" value="uniref50.fa"/>
72 <param name="features" value="exampleFeatures.txt"/>
73 <param name="showFullId" value="false"/>
74 <param name="windowHeight" value="500"/>
75 <param name="windowWidth" value="650"/>
76 <param name="showFeatureSettings" value="true"/>
77 <param name="wrap" value="true"/>
78 <param name="showAnnotation" value="false"/>
79 <param name="linkLabel_1" value="Uniprot"/>
80 <param name="linkUrl_1"
81 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
82 <param name="linkLabel_2" value="EMBL-EBI Search"/>
83 <param name="linkUrl_2"
84 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
85 <param name="APPLICATION_URL"
86 value="http://www.jalview.org/services/launchApp"/>
89 <td valign="center">Displays a features file on the alignment</td>
92 <td width="10%" valign="center"><applet
93 code="jalview.bin.JalviewLite" width="140" height="35"
94 archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
95 <param name="permissions" value="sandbox"/>
96 <param name="file" value="uniref50.fa"/>
97 <param name="showFullId" value="false"/>
98 <param name="windowHeight" value="500"/>
99 <param name="windowWidth" value="650"/>
100 <param name="wrap" value="true"/>
101 <param name="showAnnotation" value="false"/>
102 <param name="defaultColour" value="Strand Propensity"/>
103 <param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
104 <param name="linkLabel_1" value="Uniprot"/>
105 <param name="linkUrl_1"
106 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
107 <param name="linkLabel_2" value="EMBL-EBI Search"/>
108 <param name="linkUrl_2"
109 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
110 <param name="APPLICATION_URL"
111 value="http://www.jalview.org/services/launchApp"/>
114 <td valign="center">Associates PDB file 1GAQ with sequence
118 <td width="10%" valign="center"><applet
119 code="jalview.bin.JalviewLite" width="140" height="35"
120 archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
121 <param name="permissions" value="sandbox"/>
122 <param name="file" value="jpred_msa.fasta"/>
123 <param name="jnetfile" value="jpred_msa.seq.concise"/>
124 <param name="showFullId" value="false"/>
125 <param name="windowHeight" value="515"/>
126 <param name="windowWidth" value="650"/>
127 <param name="showAnnotation" value="true"/>
128 <param name="defaultColour" value="Clustal"/>
129 <param name="linkLabel_1" value="Uniprot"/>
130 <param name="linkUrl_1"
131 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
132 <param name="linkLabel_2" value="EMBL-EBI Search"/>
133 <param name="linkUrl_2"
134 value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
135 <param name="APPLICATION_URL"
136 value="http://www.jalview.org/services/launchApp"/>
139 <td valign="middle">Displays a Multiple Sequence Alignment
140 Based JNet Prediction for a Sequence</td>
144 <h2>RF00031 RFAM Alignment with per sequence secondary
149 <td width="10%" valign="center"><applet
150 code="jalview.bin.JalviewLite" width="140" height="35"
151 archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
152 <param name="permissions" value="sandbox"/>
153 <param name="file" value="RF00031_folded.stk"/>
154 <param name="showFullId" value="false"/>
155 <param name="windowHeight" value="515"/>
156 <param name="windowWidth" value="650"/>
157 <param name="showAnnotation" value="true"/>
158 <param name="defaultColour" value="Purine/Pyrimidine"/>
159 <param name="APPLICATION_URL"
160 value="http://www.jalview.org/services/launchApp"/>
163 <td valign="center">Displays an RFAM RNA fold family with
164 secondary structure annotation</td>
168 <h2>Linked amino acid and cDNA alignments for homologous proteins</h2>
172 <td width="10%" valign="center">
174 code="jalview.bin.JalviewLite" width="140" height="35"
175 archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
176 <param name="permissions" value="sandbox"/>
177 <param name="file" value="estrogenReceptorCdna.fa"/>
178 <param name="file2" value="estrogenReceptorProtein.fa"/>
179 <param name="enableSplitFrame" value="true"/>
180 <param name="scaleProteinAsCdna" value="true"/>
181 <param name="showFullId" value="false"/>
182 <param name="windowHeight" value="300"/>
183 <param name="windowWidth" value="800"/>
184 <param name="showAnnotation" value="true"/>
185 <param name="showSequenceLogo" value="true"/>
186 <param name="defaultColour" value="Purine/Pyrimidine"/>
187 <param name="APPLICATION_URL"
188 value="http://www.jalview.org/services/launchApp"/>
191 <td valign="center">Displays a split window view of protein and its related cDNA</td>