X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fio%2FJnetAnnotationMaker.js;h=e2f51a55524112f56bca41b6424b865f6d3c9bb5;hp=f39d55b539dc090ac7c877488fdb00ec4d66ec44;hb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/io/JnetAnnotationMaker.js b/bin/jalview/io/JnetAnnotationMaker.js
index f39d55b..e2f51a5 100644
--- a/bin/jalview/io/JnetAnnotationMaker.js
+++ b/bin/jalview/io/JnetAnnotationMaker.js
@@ -1,90 +1,90 @@
-Clazz.declarePackage ("jalview.io");
-Clazz.load (null, "jalview.io.JnetAnnotationMaker", ["jalview.datamodel.AlignmentAnnotation", "$.Annotation", "jalview.util.MessageManager", "java.lang.Exception", "$.Float"], function () {
-c$ = Clazz.declareType (jalview.io, "JnetAnnotationMaker");
-c$.add_annotation = Clazz.defineMethod (c$, "add_annotation", 
-function (prediction, al, firstSeq, noMsa) {
-jalview.io.JnetAnnotationMaker.add_annotation (prediction, al, firstSeq, noMsa, Clazz.castNullAs ("Array"));
-}, "jalview.io.AlignFile,jalview.datamodel.AlignmentI,~N,~B");
-c$.add_annotation = Clazz.defineMethod (c$, "add_annotation", 
-function (prediction, al, firstSeq, noMsa, delMap) {
-var i = 0;
-var preds = prediction.getSeqsAsArray ();
-var seqRef = al.getSequenceAt (firstSeq);
-var width = preds[0].getSequence ().length;
-var gapmap = al.getSequenceAt (firstSeq).gapMap ();
-if ((delMap != null && delMap.length > width) || (delMap == null && gapmap.length != width)) {
-throw ( new Exception (jalview.util.MessageManager.formatMessage ("exception.number_of_residues_in_query_sequence_differ_from_prediction",  Clazz.newArray (-1, [(delMap == null ? "" : jalview.util.MessageManager.getString ("label.mapped")), al.getSequenceAt (firstSeq).getName (), al.getSequenceAt (firstSeq).getSequenceAsString (), Integer.$valueOf (width).toString ()]))));
-}var annot;
-var annotations = null;
-var existingAnnotations = 0;
-if (al.getAlignmentAnnotation () != null) {
-existingAnnotations = al.getAlignmentAnnotation ().length;
-}var sol =  new Array (al.getWidth ());
-var firstsol = true;
-while (i < preds.length) {
-var id = preds[i].getName ().toUpperCase ();
-if (id.startsWith ("LUPAS") || id.startsWith ("JNET") || id.startsWith ("JPRED")) {
-if (id.startsWith ("JNETSOL")) {
-var amnt = (id.endsWith ("25") ? 3 : id.endsWith ("5") ? 6 : 9);
-for (var spos = 0; spos < width; spos++) {
-var sposw = (delMap == null) ? gapmap[spos] : gapmap[delMap[spos]];
-if (firstsol) {
-sol[sposw] =  new jalview.datamodel.Annotation (0);
-}if (preds[i].getCharAt (spos) == 'B' && (sol[sposw].value == 0 || sol[sposw].value < amnt)) {
-sol[sposw].value = amnt;
-}}
-firstsol = false;
-} else {
-annotations =  new Array (al.getWidth ());
-if (id.equals ("JNETPRED") || id.equals ("JNETPSSM") || id.equals ("JNETFREQ") || id.equals ("JNETHMM") || id.equals ("JNETALIGN") || id.equals ("JPRED")) {
-if (delMap == null) {
-for (var j = 0; j < width; j++) {
-annotations[gapmap[j]] =  new jalview.datamodel.Annotation ("", "", preds[i].getCharAt (j), 0);
-}
-} else {
-for (var j = 0; j < width; j++) {
-annotations[gapmap[delMap[j]]] =  new jalview.datamodel.Annotation ("", "", preds[i].getCharAt (j), 0);
-}
-}} else if (id.equals ("JNETCONF")) {
-if (delMap == null) {
-for (var j = 0; j < width; j++) {
-var value =  new Float (preds[i].getCharAt (j) + "").floatValue ();
-annotations[gapmap[j]] =  new jalview.datamodel.Annotation (preds[i].getCharAt (j) + "", "", preds[i].getCharAt (j), value);
-}
-} else {
-for (var j = 0; j < width; j++) {
-var value =  new Float (preds[i].getCharAt (j) + "").floatValue ();
-annotations[gapmap[delMap[j]]] =  new jalview.datamodel.Annotation (preds[i].getCharAt (j) + "", "", preds[i].getCharAt (j), value);
-}
-}} else {
-if (delMap == null) {
-for (var j = 0; j < width; j++) {
-annotations[gapmap[j]] =  new jalview.datamodel.Annotation (preds[i].getCharAt (j) + "", "", ' ', 0);
-}
-} else {
-for (var j = 0; j < width; j++) {
-annotations[gapmap[delMap[j]]] =  new jalview.datamodel.Annotation (preds[i].getCharAt (j) + "", "", ' ', 0);
-}
-}}if (id.equals ("JNETCONF")) {
-annot =  new jalview.datamodel.AlignmentAnnotation (preds[i].getName (), "JNet Output", annotations, 0, 10, 1);
-} else {
-annot =  new jalview.datamodel.AlignmentAnnotation (preds[i].getName (), "JNet Output", annotations);
-}if (seqRef != null) {
-annot.createSequenceMapping (seqRef, 1, true);
-seqRef.addAlignmentAnnotation (annot);
-}al.addAnnotation (annot);
-al.setAnnotationIndex (annot, al.getAlignmentAnnotation ().length - existingAnnotations - 1);
-}if (noMsa) {
-al.deleteSequence (preds[i]);
-}}i++;
-}
-if (!firstsol) {
-annot =  new jalview.datamodel.AlignmentAnnotation ("Jnet Burial", "<html>Prediction of Solvent Accessibility<br/>levels are<ul><li>0 - Exposed</li><li>3 - 25% or more S.A. accessible</li><li>6 - 5% or more S.A. accessible</li><li>9 - Buried (<5% exposed)</li></ul>", sol, 0, 9, 1);
-annot.validateRangeAndDisplay ();
-if (seqRef != null) {
-annot.createSequenceMapping (seqRef, 1, true);
-seqRef.addAlignmentAnnotation (annot);
-}al.addAnnotation (annot);
-al.setAnnotationIndex (annot, al.getAlignmentAnnotation ().length - existingAnnotations - 1);
-}}, "jalview.io.AlignFile,jalview.datamodel.AlignmentI,~N,~B,~A");
-});
+Clazz.declarePackage ("jalview.io");
+Clazz.load (null, "jalview.io.JnetAnnotationMaker", ["jalview.datamodel.AlignmentAnnotation", "$.Annotation", "jalview.util.MessageManager", "java.lang.Exception", "$.Float"], function () {
+c$ = Clazz.declareType (jalview.io, "JnetAnnotationMaker");
+c$.add_annotation = Clazz.defineMethod (c$, "add_annotation", 
+function (prediction, al, firstSeq, noMsa) {
+jalview.io.JnetAnnotationMaker.add_annotation (prediction, al, firstSeq, noMsa, Clazz.castNullAs ("Array"));
+}, "jalview.io.AlignFile,jalview.datamodel.AlignmentI,~N,~B");
+c$.add_annotation = Clazz.defineMethod (c$, "add_annotation", 
+function (prediction, al, firstSeq, noMsa, delMap) {
+var i = 0;
+var preds = prediction.getSeqsAsArray ();
+var seqRef = al.getSequenceAt (firstSeq);
+var width = preds[0].getSequence ().length;
+var gapmap = al.getSequenceAt (firstSeq).gapMap ();
+if ((delMap != null && delMap.length > width) || (delMap == null && gapmap.length != width)) {
+throw ( new Exception (jalview.util.MessageManager.formatMessage ("exception.number_of_residues_in_query_sequence_differ_from_prediction",  Clazz.newArray (-1, [(delMap == null ? "" : jalview.util.MessageManager.getString ("label.mapped")), al.getSequenceAt (firstSeq).getName (), al.getSequenceAt (firstSeq).getSequenceAsString (), Integer.$valueOf (width).toString ()]))));
+}var annot;
+var annotations = null;
+var existingAnnotations = 0;
+if (al.getAlignmentAnnotation () != null) {
+existingAnnotations = al.getAlignmentAnnotation ().length;
+}var sol =  new Array (al.getWidth ());
+var firstsol = true;
+while (i < preds.length) {
+var id = preds[i].getName ().toUpperCase ();
+if (id.startsWith ("LUPAS") || id.startsWith ("JNET") || id.startsWith ("JPRED")) {
+if (id.startsWith ("JNETSOL")) {
+var amnt = (id.endsWith ("25") ? 3 : id.endsWith ("5") ? 6 : 9);
+for (var spos = 0; spos < width; spos++) {
+var sposw = (delMap == null) ? gapmap[spos] : gapmap[delMap[spos]];
+if (firstsol) {
+sol[sposw] =  new jalview.datamodel.Annotation (0);
+}if (preds[i].getCharAt (spos) == 'B' && (sol[sposw].value == 0 || sol[sposw].value < amnt)) {
+sol[sposw].value = amnt;
+}}
+firstsol = false;
+} else {
+annotations =  new Array (al.getWidth ());
+if (id.equals ("JNETPRED") || id.equals ("JNETPSSM") || id.equals ("JNETFREQ") || id.equals ("JNETHMM") || id.equals ("JNETALIGN") || id.equals ("JPRED")) {
+if (delMap == null) {
+for (var j = 0; j < width; j++) {
+annotations[gapmap[j]] =  new jalview.datamodel.Annotation ("", "", preds[i].getCharAt (j), 0);
+}
+} else {
+for (var j = 0; j < width; j++) {
+annotations[gapmap[delMap[j]]] =  new jalview.datamodel.Annotation ("", "", preds[i].getCharAt (j), 0);
+}
+}} else if (id.equals ("JNETCONF")) {
+if (delMap == null) {
+for (var j = 0; j < width; j++) {
+var value =  new Float (preds[i].getCharAt (j) + "").floatValue ();
+annotations[gapmap[j]] =  new jalview.datamodel.Annotation (preds[i].getCharAt (j) + "", "", preds[i].getCharAt (j), value);
+}
+} else {
+for (var j = 0; j < width; j++) {
+var value =  new Float (preds[i].getCharAt (j) + "").floatValue ();
+annotations[gapmap[delMap[j]]] =  new jalview.datamodel.Annotation (preds[i].getCharAt (j) + "", "", preds[i].getCharAt (j), value);
+}
+}} else {
+if (delMap == null) {
+for (var j = 0; j < width; j++) {
+annotations[gapmap[j]] =  new jalview.datamodel.Annotation (preds[i].getCharAt (j) + "", "", ' ', 0);
+}
+} else {
+for (var j = 0; j < width; j++) {
+annotations[gapmap[delMap[j]]] =  new jalview.datamodel.Annotation (preds[i].getCharAt (j) + "", "", ' ', 0);
+}
+}}if (id.equals ("JNETCONF")) {
+annot =  new jalview.datamodel.AlignmentAnnotation (preds[i].getName (), "JNet Output", annotations, 0, 10, 1);
+} else {
+annot =  new jalview.datamodel.AlignmentAnnotation (preds[i].getName (), "JNet Output", annotations);
+}if (seqRef != null) {
+annot.createSequenceMapping (seqRef, 1, true);
+seqRef.addAlignmentAnnotation (annot);
+}al.addAnnotation (annot);
+al.setAnnotationIndex (annot, al.getAlignmentAnnotation ().length - existingAnnotations - 1);
+}if (noMsa) {
+al.deleteSequence (preds[i]);
+}}i++;
+}
+if (!firstsol) {
+annot =  new jalview.datamodel.AlignmentAnnotation ("Jnet Burial", "<html>Prediction of Solvent Accessibility<br/>levels are<ul><li>0 - Exposed</li><li>3 - 25% or more S.A. accessible</li><li>6 - 5% or more S.A. accessible</li><li>9 - Buried (<5% exposed)</li></ul>", sol, 0, 9, 1);
+annot.validateRangeAndDisplay ();
+if (seqRef != null) {
+annot.createSequenceMapping (seqRef, 1, true);
+seqRef.addAlignmentAnnotation (annot);
+}al.addAnnotation (annot);
+al.setAnnotationIndex (annot, al.getAlignmentAnnotation ().length - existingAnnotations - 1);
+}}, "jalview.io.AlignFile,jalview.datamodel.AlignmentI,~N,~B,~A");
+});