JAL-2428 pass AlignmentView to TreeModel so Show Input Data works
[jalview.git] / examples / applets.html
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21 <div id="view_decorated" name="view_decorated"  style="margin:8px; padding:10px; border: 2px solid red; text-align:center; display:none;"><b>Click <a href="index.html#applets"> here</a> to view decorated page</b></div>
22
23 <!-- boiler plate link to alternate demopage -->
24 <div style="width: 100%">
25 </div>
26 <!-- content template start -->
27
28 <p align="left">
29 <h2>JalviewLite Button Examples</h2>
30 Try out JalviewLite by pressing one of the buttons below. 
31   <a href="view-source:http://www.jalview.org/builds/develop/examples/applets.html" target="_blank">View the source for the examples below here</a> (If the link doesn't work on your browser try going to <a href="http://www.jalview.org/builds/develop/examples/applets.html">this page</a> and viewing the page source manually).<br/>
32  For more information on how to use the applet in your website, see the <a href="javascript:doSubmit('appletDeployment')"><strong>applet deployment,</strong></a> <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters,</strong></a> and other documentation in the links to the left.</p>
33 <p>&nbsp;</p><div align="center">
34   <p align="center">
35     <h2>Ferredoxins, chloroplast precursor related UniRef50
36       cluster</h2>
37     <br /> (15 sequences x 150 residues)
38   </p>
39   <table width="90%">
40     <tr>
41       <td width="10%" valign="center">
42       <applet
43         code="jalview.bin.JalviewLite" width="140" height="35"
44         archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">  
45         <param name="permissions" value="sandbox"/>
46         <param name="file" value="uniref50.fa"/>
47         <param name="treeFile" value="ferredoxin.nw"/>
48         <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
49         <param name="sortByTree" value="True"/>
50         <param name="showSequenceLogo" value="true"/>
51         <param name="showGroupConsensus" value="true"/>
52         <param name="showFullId" value="false"/>
53         <param name="linkLabel_1" value="Uniprot"/>
54         <param name="linkUrl_1" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
55         <param name="linkLabel_2" value="EMBL-EBI Search"/>
56         <param name="linkUrl_2" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
57         <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
58      </applet>
59 </td>
60       <td valign="center">User Defined Colours, loads an associated
61         Newick format tree file which is used to sort the alignment, and
62         group consensus and sequence logos are shown below the alignment.</td>
63     </tr>
64     <tr>
65       <td width="10%" valign="center"><applet
66    code="jalview.bin.JalviewLite" width="140" height="35"
67    archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
68 <param name="permissions" value="sandbox"/>
69 <param name="file" value="uniref50.fa"/>
70 <param name="features" value="exampleFeatures.txt"/>
71 <param name="showFullId" value="false"/>
72 <param name="windowHeight" value="500"/>
73 <param name="windowWidth" value="650"/>
74 <param name="showFeatureSettings" value="true"/>
75 <param name="wrap" value="true"/>
76 <param name="showAnnotation" value="false"/>
77    <param name="linkLabel_1" value="Uniprot"/>
78    <param name="linkUrl_1"
79      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
80    <param name="linkLabel_2" value="EMBL-EBI Search"/>
81    <param name="linkUrl_2"
82      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
83    <param name="APPLICATION_URL"
84      value="http://www.jalview.org/services/launchApp"/>
85 </applet>
86 </td>
87       <td valign="center">Displays a features file on the alignment</td>
88     </tr>
89     <tr>
90       <td width="10%" valign="center"><applet
91    code="jalview.bin.JalviewLite" width="140" height="35"
92    archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
93 <param name="permissions" value="sandbox"/>
94 <param name="file" value="uniref50.fa"/>
95 <param name="showFullId" value="false"/>
96 <param name="windowHeight" value="500"/>
97 <param name="windowWidth" value="650"/>
98 <param name="wrap" value="true"/>
99 <param name="debug" value="true"/>
100 <param name="showAnnotation" value="false"/>
101 <param name="defaultColour" value="Strand Propensity"/>
102 <param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
103    <param name="linkLabel_1" value="Uniprot"/>
104    <param name="linkUrl_1"
105      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
106    <param name="linkLabel_2" value="EMBL-EBI Search"/>
107    <param name="linkUrl_2"
108      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
109    <param name="APPLICATION_URL"
110      value="http://www.jalview.org/services/launchApp"/>
111 </applet>
112 </td>
113       <td valign="center">Associates PDB file 1GAQ with sequence
114         FER1_MAIZE</td>
115     </tr>
116     <tr>
117       <td width="10%" valign="center"><applet
118    code="jalview.bin.JalviewLite" width="140" height="35"
119    archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
120 <param name="permissions" value="sandbox"/>
121 <param name="file" value="jpred_msa.fasta"/>
122 <param name="jnetfile" value="jpred_msa.seq.concise"/>
123 <param name="showFullId" value="false"/>
124 <param name="windowHeight" value="515"/>
125 <param name="windowWidth" value="650"/>
126 <param name="showAnnotation" value="true"/>
127 <param name="defaultColour" value="Clustal"/>
128    <param name="linkLabel_1" value="Uniprot"/>
129    <param name="linkUrl_1"
130      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
131    <param name="linkLabel_2" value="EMBL-EBI Search"/>
132    <param name="linkUrl_2"
133      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
134    <param name="APPLICATION_URL"
135      value="http://www.jalview.org/services/launchApp"/>
136 </applet>
137                                                        </td>
138       <td valign="middle">Displays a Multiple Sequence Alignment
139         Based JPred Prediction for a Sequence</td>
140     </tr>
141   </table>
142   <p>
143     <h2>RF00031 RFAM Alignment with per sequence secondary
144       structure</h2>
145   </p>
146   <table width="90%">
147     <tr>
148       <td width="10%" valign="center"><applet
149    code="jalview.bin.JalviewLite" width="140" height="35"
150    archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
151 <param name="permissions" value="sandbox"/>
152 <param name="file" value="RF00031_folded.stk"/>
153 <param name="showFullId" value="false"/>
154 <param name="windowHeight" value="515"/>
155 <param name="windowWidth" value="650"/>
156 <param name="showAnnotation" value="true"/>
157 <param name="defaultColour" value="Purine/Pyrimidine"/>
158    <param name="APPLICATION_URL"
159      value="http://www.jalview.org/services/launchApp"/>
160 </applet>
161 </td>
162       <td valign="center">Displays an RFAM RNA fold family with
163         secondary structure annotation</td>
164     </tr>
165   </table>
166   <p>
167     <h2>Linked Protein and cDNA alignments for a family of Steroid Receptors</h2>
168   </p>
169   <table width="90%">
170     <tr>
171       <td width="10%" valign="center">
172 <applet
173    code="jalview.bin.JalviewLite" width="140" height="35"
174    archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
175 <param name="permissions" value="sandbox"/>
176 <param name="file2" value="estrogenReceptorCdna_frag.fa"/>
177 <param name="file" value="estrogenReceptorProtein_frag.fa"/>
178 <param name="enableSplitFrame" value="true"/>
179 <param name="scaleProteinAsCdna" value="true"/>
180 <param name="showFullId" value="false"/>
181 <param name="windowHeight" value="300"/>
182 <param name="windowWidth" value="800"/>
183 <param name="showAnnotation" value="true"/>
184 <param name="showSequenceLogo" value="true"/>
185 <param name="defaultColourNuc" value="Purine/Pyrimidine"/>
186 <param name="defaultColourProt" value="Clustal"/>
187    <param name="APPLICATION_URL"
188      value="http://www.jalview.org/services/launchApp"/>
189 </applet>
190 </td>
191       <td valign="center">Displays a split window view showing aligned protein
192         and a reconstructed cDNA alignment.<br />Proteins were aligned with <a
193         href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31,
194         via the Jalview Desktop).<br />Data retrieved from Uniprot and
195         ENA, after Thornton, Need and Crews, <a
196         href="http://dx.doi.org/10.1126/science.1086185">Science 19
197           September 2003: 301 (5640), 1714-1717</a>
198       </td>
199     </tr>
200   </table>