X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=bin%2Fjalview%2Fio%2FSequenceAnnotationReport.js;fp=bin%2Fjalview%2Fio%2FSequenceAnnotationReport.js;h=889211be7b883434adc3e6a66ca380a800802014;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hp=4ab2aa6f6c648bd49573cb67218d15e7b626dbb4;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921;p=jalviewjs.git
diff --git a/bin/jalview/io/SequenceAnnotationReport.js b/bin/jalview/io/SequenceAnnotationReport.js
index 4ab2aa6..889211b 100644
--- a/bin/jalview/io/SequenceAnnotationReport.js
+++ b/bin/jalview/io/SequenceAnnotationReport.js
@@ -1,181 +1,181 @@
-Clazz.declarePackage ("jalview.io");
-Clazz.load (null, "jalview.io.SequenceAnnotationReport", ["jalview.util.DBRefUtils", "$.UrlLink", "java.lang.Float", "java.util.ArrayList"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.linkImageURL = null;
-Clazz.instantialize (this, arguments);
-}, jalview.io, "SequenceAnnotationReport");
-Clazz.makeConstructor (c$,
-function (linkImageURL) {
-this.linkImageURL = linkImageURL;
-}, "~S");
-Clazz.defineMethod (c$, "appendFeatures",
-function (tooltipText2, rpos, features) {
-this.appendFeatures (tooltipText2, rpos, features, null);
-}, "StringBuffer,~N,java.util.List");
-Clazz.defineMethod (c$, "appendFeatures",
-function (tooltipText2, rpos, features, minmax) {
-var tmpString;
-if (features != null) {
-for (var feature, $feature = features.iterator (); $feature.hasNext () && ((feature = $feature.next ()) || true);) {
-if (feature.getType ().equals ("disulfide bond")) {
-if (feature.getBegin () == rpos || feature.getEnd () == rpos) {
-if (tooltipText2.length () > 6) {
-tooltipText2.append ("
");
-}tooltipText2.append ("disulfide bond " + feature.getBegin () + ":" + feature.getEnd ());
-}} else {
-if (tooltipText2.length () > 6) {
-tooltipText2.append ("
");
-}var linkOnly = feature.getValue ("linkonly") != null;
-if (!linkOnly) {
-tooltipText2.append (feature.getType () + " ");
-if (rpos != 0) {
-tooltipText2.append (feature.begin);
-}if (feature.begin != feature.end) {
-tooltipText2.append (" " + feature.end);
-}if (feature.getDescription () != null && !feature.description.equals (feature.getType ())) {
-tmpString = feature.getDescription ();
-var tmp2up = tmpString.toUpperCase ();
-var startTag = tmp2up.indexOf ("");
-if (startTag > -1) {
-tmpString = tmpString.substring (startTag + 6);
-tmp2up = tmp2up.substring (startTag + 6);
-}var endTag = tmp2up.indexOf ("");
-if (endTag > -1) {
-tmpString = tmpString.substring (0, endTag);
-tmp2up = tmp2up.substring (0, endTag);
-}endTag = tmp2up.indexOf ("