Jmol visualiser

client/gulpfile.js

@@ -23,6 +23,7 @@ const STATIC_PLUGIN_BUILD_IDS = [
     "h5web",
     "heatmap/heatmap_default",
     "hyphyvision",
+    "jmol",
     "jqplot/jqplot_bar",
     "media_player",
     "mvpapp",

config/plugins/visualizations/jmol/README.md

@@ -0,0 +1,14 @@
+## Jmol Visualizer Plugin for Galaxy
+
+This plugin allows you to visualize molecular structures within the Galaxy platform using [JSmol](http://wiki.jmol.org/index.php/JSmol), a powerful JavaScript library for molecular visualization.
+
+**Usage:**
+
+1. In your Galaxy workflow, select a dataset containing a supported molecular format (e.g., cif file).
+2. Choose the "jmol Visualization" tool from the available tools.
+3. The molecule will be rendered within the visualization panel. You can interact with the molecule using the controls provided by JSmol.
+
+**Additional Notes:**
+
+* For detailed information on JSmol and supported features, refer to the JSmol documentation: [https://sourceforge.net/projects/jmol/](https://sourceforge.net/projects/jmol/)
+

config/plugins/visualizations/jmol/config/jmol.xml

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
+<visualization name="jmol">
+    <description>This is a visualiser for molecular structures using Jmol</description>
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
+    </data_sources>
+    <params>
+        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+    </params>
+    <template>jmol.mako</template>
+</visualization>

config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/cif/BCIFDataParser.js

@@ -0,0 +1,138 @@
+Clazz.declarePackage("J.adapter.readers.cif");
+Clazz.load(["JU.CifDataParser"], "J.adapter.readers.cif.BCIFDataParser", ["java.io.BufferedInputStream", "$.FileInputStream", "JU.BinaryDocument", "$.MessagePackReader", "J.adapter.readers.cif.BCIFDecoder"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.rdr = null;
+this.categoryName = null;
+this.rowCount = 0;
+this.columnMaps = null;
+this.columnDecoders = null;
+this.rowPt = 0;
+this.ifield = 0;
+this.dfield = 0;
+this.fieldStr = null;
+this.fieldIsValid = false;
+this.cifMap = null;
+this.header = null;
+Clazz.instantialize(this, arguments);}, J.adapter.readers.cif, "BCIFDataParser", JU.CifDataParser);
+Clazz.makeConstructor(c$, 
+function(bcifReader, debugging){
+Clazz.superConstructor (this, J.adapter.readers.cif.BCIFDataParser, []);
+this.rdr = bcifReader;
+this.debugging = debugging;
+}, "J.adapter.readers.cif.BCIFReader,~B");
+Clazz.defineMethod(c$, "getDecoder", 
+function(key, col, rowCount, catName){
+var sb = null;
+var d =  new J.adapter.readers.cif.BCIFDecoder(sb, key, col).setRowCount(rowCount, catName).finalizeDecoding(null);
+return (d == null || d.dataType == 0 ? null : d);
+}, "~S,java.util.Map,~N,~S");
+Clazz.defineMethod(c$, "initializeCategory", 
+function(catName, rowCount, columns){
+this.columnMaps = columns;
+this.rowCount = rowCount;
+this.categoryName = catName;
+var n = this.columnCount = columns.length;
+if (this.columnNames == null || this.columnNames.length < n) this.columnNames =  new Array(n);
+for (var i = 0; i < n; i++) {
+this.columnNames[i] = (catName + "_" + (columns[i]).get("name")).toLowerCase();
+}
+}, "~S,~N,~A");
+Clazz.overrideMethod(c$, "parseDataBlockParameters", 
+function(fieldNames, key, data, key2col, col2key){
+this.haveData = false;
+this.rowPt = -1;
+for (var i = 100; --i >= 0; ) {
+col2key[i] = key2col[i] = -1;
+}
+if (!JU.CifDataParser.htFields.containsKey(fieldNames[0])) {
+for (var i = fieldNames.length; --i >= 0; ) JU.CifDataParser.htFields.put(fieldNames[i], Integer.$valueOf(i));
+
+}this.columnDecoders =  new Array(this.columnCount);
+for (var pt = 0; pt < this.columnCount; pt++) {
+var s = this.columnNames[pt];
+var iField = JU.CifDataParser.htFields.get(s);
+var keyIndex = col2key[pt] = (iField == null ? -1 : iField.intValue());
+var d = (keyIndex == -1 ? null : this.getDecoder(s, this.getDataColumn(pt), this.rowCount, this.categoryName));
+if (d == null) {
+if (keyIndex >= 0) key2col[keyIndex] = -2;
+} else {
+this.columnDecoders[pt] = d;
+key2col[keyIndex] = pt;
+this.haveData = true;
+}}
+}, "~A,~S,~S,~A,~A");
+Clazz.defineMethod(c$, "decodeAndGetData", 
+function(icol){
+this.columnDecoders =  Clazz.newArray(-1, [this.getDecoder(null, this.getDataColumn(icol), this.rowCount, this.categoryName)]);
+this.getColumnData(0);
+this.columnDecoders = null;
+}, "~N");
+Clazz.overrideMethod(c$, "getData", 
+function(){
+this.rowPt++;
+var done = this.rowPt >= this.rowCount;
+if (done) {
+for (var i = this.columnDecoders.length; --i >= 0; ) this.columnDecoders[i] = null;
+
+}return !done;
+});
+Clazz.overrideMethod(c$, "getColumnData", 
+function(colPt){
+this.rdr.key = this.getColumnName(colPt);
+this.ifield = -2147483648;
+this.dfield = NaN;
+if (colPt >= this.columnDecoders.length) System.out.println("???");
+if (this.columnDecoders[colPt] == null) {
+this.fieldIsValid = false;
+return this.fieldStr = this.nullString;
+}switch (this.columnDecoders[colPt].dataType) {
+case 1:
+this.ifield = this.columnDecoders[colPt].getIntValue(this.rowPt);
+this.fieldStr = (this.ifield == -2147483648 ? this.nullString : "_");
+break;
+case 2:
+this.dfield = this.columnDecoders[colPt].getFixedPtValue(this.rowPt);
+this.fieldStr = (Double.isNaN(this.dfield) ? this.nullString : "_");
+break;
+case 3:
+this.fieldStr = this.columnDecoders[colPt].getStringValue(this.rowPt);
+break;
+}
+this.fieldIsValid = (this.fieldStr !== this.nullString);
+return this.fieldStr;
+}, "~N");
+Clazz.defineMethod(c$, "isFieldValid", 
+function(){
+return this.fieldIsValid;
+});
+Clazz.defineMethod(c$, "getDataColumn", 
+function(icol){
+return (icol >= 0 && icol < this.columnCount ? this.columnMaps[icol] : null);
+}, "~N");
+Clazz.overrideMethod(c$, "getAllCifData", 
+function(){
+return null;
+});
+c$.main = Clazz.defineMethod(c$, "main", 
+function(args){
+try {
+var testFile = (args.length == 0 ? "c:/temp/1cbs.bcif" : args[0]);
+var binaryDoc =  new JU.BinaryDocument();
+var bis =  new java.io.BufferedInputStream( new java.io.FileInputStream(testFile));
+binaryDoc.setStream(bis, true);
+var msgMap;
+msgMap = ( new JU.MessagePackReader(binaryDoc, false)).readMap();
+var parser =  new J.adapter.readers.cif.BCIFDataParser(null, true);
+parser.debugConstructCifMap(msgMap);
+binaryDoc.close();
+System.out.println("OK - DONE");
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+e.printStackTrace();
+} else {
+throw e;
+}
+}
+}, "~A");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024