X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fext%2Fjmol%2FJmolCommands.js;fp=site%2Fj2s%2Fjalview%2Fext%2Fjmol%2FJmolCommands.js;h=b08a4e34313f5c05724e55a3a8c9119f967f9464;hp=495572c79c023ed986b47b61cff1f6001722c0f8;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/ext/jmol/JmolCommands.js b/site/j2s/jalview/ext/jmol/JmolCommands.js
index 495572c..b08a4e3 100644
--- a/site/j2s/jalview/ext/jmol/JmolCommands.js
+++ b/site/j2s/jalview/ext/jmol/JmolCommands.js
@@ -1,69 +1,69 @@
-Clazz.declarePackage ("jalview.ext.jmol");
-Clazz.load (null, "jalview.ext.jmol.JmolCommands", ["jalview.structure.StructureMappingcommandSet", "jalview.util.Comparison", "java.lang.StringBuffer", "java.util.ArrayList"], function () {
-c$ = Clazz.declareType (jalview.ext.jmol, "JmolCommands");
-c$.getColourBySequenceCommand = Clazz.defineMethod (c$, "getColourBySequenceCommand", 
-function (ssm, files, sequence, sr, fr, alignment) {
-var cset =  new java.util.ArrayList ();
-for (var pdbfnum = 0; pdbfnum < files.length; pdbfnum++) {
-var mapping = ssm.getMapping (files[pdbfnum]);
-var command =  new StringBuffer ();
-var smc;
-var str =  new java.util.ArrayList ();
-if (mapping == null || mapping.length < 1) {
-continue;
-}var lastPos = -1;
-for (var s = 0; s < sequence[pdbfnum].length; s++) {
-for (var sp, m = 0; m < mapping.length; m++) {
-if (mapping[m].getSequence () === sequence[pdbfnum][s] && (sp = alignment.findIndex (sequence[pdbfnum][s])) > -1) {
-var asp = alignment.getSequenceAt (sp);
-for (var r = 0; r < asp.getLength (); r++) {
-if (jalview.util.Comparison.isGap (asp.getCharAt (r))) {
-continue;
-}var pos = mapping[m].getPDBResNum (asp.findPosition (r));
-if (pos < 1 || pos == lastPos) {
-continue;
-}lastPos = pos;
-var col = sr.getResidueBoxColour (sequence[pdbfnum][s], r);
-if (fr != null) {
-col = fr.findFeatureColour (col, sequence[pdbfnum][s], r);
-}var newSelcom = (mapping[m].getChain () !== " " ? ":" + mapping[m].getChain () : "") + "/" + (pdbfnum + 1) + ".1" + ";color[" + col.getRed () + "," + col.getGreen () + "," + col.getBlue () + "]";
-if (command.length () > newSelcom.length && command.substring (command.length () - newSelcom.length).equals (newSelcom)) {
-command = jalview.ext.jmol.JmolCommands.condenseCommand (command, pos);
-continue;
-}command.append (";");
-if (command.length () > 51200) {
-str.add (command.toString ());
-command.setLength (0);
-}command.append ("select " + pos);
-command.append (newSelcom);
-}
-break;
-}}
-}
-{
-str.add (command.toString ());
-command.setLength (0);
-}cset.add ( new jalview.structure.StructureMappingcommandSet (jalview.ext.jmol.JmolCommands, files[pdbfnum], str.toArray ( new Array (str.size ()))));
-}
-return cset.toArray ( new Array (cset.size ()));
-}, "jalview.structure.StructureSelectionManager,~A,~A,jalview.api.SequenceRenderer,jalview.api.FeatureRenderer,jalview.datamodel.AlignmentI");
-c$.condenseCommand = Clazz.defineMethod (c$, "condenseCommand", 
-function (command, pos) {
-var p = command.length ();
-var q = p;
-do {
-p -= 6;
-if (p < 1) {
-p = 0;
-};} while ((q = command.indexOf ("select", p)) == -1 && p > 0);
-var sb =  new StringBuffer (command.substring (0, q + 7));
-command = command.$delete (0, q + 7);
-var start;
-if (command.indexOf ("-") > -1) {
-start = command.substring (0, command.indexOf ("-"));
-} else {
-start = command.substring (0, command.indexOf (":"));
-}sb.append (start + "-" + pos + command.substring (command.indexOf (":")));
-return sb;
-}, "StringBuffer,~N");
-});
+Clazz.declarePackage ("jalview.ext.jmol");
+Clazz.load (null, "jalview.ext.jmol.JmolCommands", ["jalview.structure.StructureMappingcommandSet", "jalview.util.Comparison", "java.lang.StringBuffer", "java.util.ArrayList"], function () {
+c$ = Clazz.declareType (jalview.ext.jmol, "JmolCommands");
+c$.getColourBySequenceCommand = Clazz.defineMethod (c$, "getColourBySequenceCommand", 
+function (ssm, files, sequence, sr, fr, alignment) {
+var cset =  new java.util.ArrayList ();
+for (var pdbfnum = 0; pdbfnum < files.length; pdbfnum++) {
+var mapping = ssm.getMapping (files[pdbfnum]);
+var command =  new StringBuffer ();
+var smc;
+var str =  new java.util.ArrayList ();
+if (mapping == null || mapping.length < 1) {
+continue;
+}var lastPos = -1;
+for (var s = 0; s < sequence[pdbfnum].length; s++) {
+for (var sp, m = 0; m < mapping.length; m++) {
+if (mapping[m].getSequence () === sequence[pdbfnum][s] && (sp = alignment.findIndex (sequence[pdbfnum][s])) > -1) {
+var asp = alignment.getSequenceAt (sp);
+for (var r = 0; r < asp.getLength (); r++) {
+if (jalview.util.Comparison.isGap (asp.getCharAt (r))) {
+continue;
+}var pos = mapping[m].getPDBResNum (asp.findPosition (r));
+if (pos < 1 || pos == lastPos) {
+continue;
+}lastPos = pos;
+var col = sr.getResidueBoxColour (sequence[pdbfnum][s], r);
+if (fr != null) {
+col = fr.findFeatureColour (col, sequence[pdbfnum][s], r);
+}var newSelcom = (mapping[m].getChain () !== " " ? ":" + mapping[m].getChain () : "") + "/" + (pdbfnum + 1) + ".1" + ";color[" + col.getRed () + "," + col.getGreen () + "," + col.getBlue () + "]";
+if (command.length () > newSelcom.length && command.substring (command.length () - newSelcom.length).equals (newSelcom)) {
+command = jalview.ext.jmol.JmolCommands.condenseCommand (command, pos);
+continue;
+}command.append (";");
+if (command.length () > 51200) {
+str.add (command.toString ());
+command.setLength (0);
+}command.append ("select " + pos);
+command.append (newSelcom);
+}
+break;
+}}
+}
+{
+str.add (command.toString ());
+command.setLength (0);
+}cset.add ( new jalview.structure.StructureMappingcommandSet (jalview.ext.jmol.JmolCommands, files[pdbfnum], str.toArray ( new Array (str.size ()))));
+}
+return cset.toArray ( new Array (cset.size ()));
+}, "jalview.structure.StructureSelectionManager,~A,~A,jalview.api.SequenceRenderer,jalview.api.FeatureRenderer,jalview.datamodel.AlignmentI");
+c$.condenseCommand = Clazz.defineMethod (c$, "condenseCommand", 
+function (command, pos) {
+var p = command.length ();
+var q = p;
+do {
+p -= 6;
+if (p < 1) {
+p = 0;
+};} while ((q = command.indexOf ("select", p)) == -1 && p > 0);
+var sb =  new StringBuffer (command.substring (0, q + 7));
+command = command.$delete (0, q + 7);
+var start;
+if (command.indexOf ("-") > -1) {
+start = command.substring (0, command.indexOf ("-"));
+} else {
+start = command.substring (0, command.indexOf (":"));
+}sb.append (start + "-" + pos + command.substring (command.indexOf (":")));
+return sb;
+}, "StringBuffer,~N");
+});