X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fext%2Fvarna%2FVarnaCommands.js;h=6562f804f948f247b8589293b4d66c4b5a7ba008;hp=b609d095e1e6144895cb7d8396966c1c045668b8;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/ext/varna/VarnaCommands.js b/bin/jalview/ext/varna/VarnaCommands.js
index b609d09..6562f80 100644
--- a/bin/jalview/ext/varna/VarnaCommands.js
+++ b/bin/jalview/ext/varna/VarnaCommands.js
@@ -1,66 +1,66 @@
-Clazz.declarePackage ("jalview.ext.varna");
-Clazz.load (null, "jalview.ext.varna.VarnaCommands", ["jalview.util.Comparison", "java.lang.StringBuffer", "java.util.ArrayList"], function () {
-c$ = Clazz.declareType (jalview.ext.varna, "VarnaCommands");
-c$.getColourBySequenceCommand = Clazz.defineMethod (c$, "getColourBySequenceCommand", 
-function (ssm, files, sequence, sr, fr, alignment) {
-var str =  new java.util.ArrayList ();
-var command =  new StringBuffer ();
-for (var pdbfnum = 0; pdbfnum < files.length; pdbfnum++) {
-var mapping = ssm.getMapping (files[pdbfnum]);
-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.varna.VarnaCommands.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);
-}return str.toArray ( new Array (str.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.$delete (0, q + 7);
-var start;
-if (command.indexOf ("-") > -1) {
-start = command.substring (0, command.indexOf ("-"));
-} else {
-start = command.substring (0, command.indexOf (":"));
-}sb.append (start + "-" + pos + command.substring (command.indexOf (":")));
-return sb;
-}, "StringBuffer,~N");
-});
+Clazz.declarePackage ("jalview.ext.varna");
+Clazz.load (null, "jalview.ext.varna.VarnaCommands", ["jalview.util.Comparison", "java.lang.StringBuffer", "java.util.ArrayList"], function () {
+c$ = Clazz.declareType (jalview.ext.varna, "VarnaCommands");
+c$.getColourBySequenceCommand = Clazz.defineMethod (c$, "getColourBySequenceCommand", 
+function (ssm, files, sequence, sr, fr, alignment) {
+var str =  new java.util.ArrayList ();
+var command =  new StringBuffer ();
+for (var pdbfnum = 0; pdbfnum < files.length; pdbfnum++) {
+var mapping = ssm.getMapping (files[pdbfnum]);
+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.varna.VarnaCommands.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);
+}return str.toArray ( new Array (str.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");
+});