Clazz.declarePackage ("JSV.source");
Clazz.load (null, "JSV.source.BrukerReader", ["java.io.BufferedInputStream", "$.ByteArrayInputStream", "$.File", "$.FileInputStream", "java.lang.Double", "java.util.Hashtable", "java.util.zip.ZipInputStream", "JU.BinaryDocument", "$.Lst", "$.Rdr", "JSV.common.Coordinate", "$.Spectrum", "JSV.source.JDXReader", "$.JDXSource"], function () {
c$ = Clazz.decorateAsClass (function () {
this.allowPhasing = false;
Clazz.instantialize (this, arguments);
}, JSV.source, "BrukerReader");
Clazz.makeConstructor (c$, 
function () {
});
Clazz.defineMethod (c$, "readBrukerZip", 
function (bytes, fullPath) {
try {
var zis =  new java.util.zip.ZipInputStream (bytes == null ?  new java.io.FileInputStream (fullPath) :  new java.io.ByteArrayInputStream (bytes));
var ze;
var map =  new java.util.Hashtable ();
var data1r =  Clazz.newByteArray (0, 0);
var data1i =  Clazz.newByteArray (0, 0);
var data2rr =  Clazz.newByteArray (0, 0);
var root = null;
var title = null;
out : while ((ze = zis.getNextEntry ()) != null) {
var zeName = ze.getName ();
System.out.println (zeName);
var pt = zeName.lastIndexOf ('/');
var zeShortName = zeName.substring (pt + 1);
if (root == null) {
root = zeName.substring (0, pt + 1);
pt = root.indexOf ("/pdata/");
if (pt >= 0) root = root.substring (0, pt + 1);
}if (!zeName.startsWith (root)) break out;
var isacq = false;
if (zeShortName.equals ("title")) {
title =  String.instantialize (this.getBytes (zis, ze.getSize (), false));
map.put ("##title", title);
} else if (zeShortName.equals ("1r")) {
data1r = this.getBytes (zis, ze.getSize (), false);
} else if (zeShortName.equals ("1i")) {
if (this.allowPhasing) data1i = this.getBytes (zis, ze.getSize (), false);
} else if (zeShortName.equals ("2rr")) {
data2rr = this.getBytes (zis, ze.getSize (), false);
} else if (zeShortName.equals ("proc2s") || zeShortName.equals ("acqu2s")) {
JSV.source.JDXReader.getHeaderMapS ( new java.io.ByteArrayInputStream (this.getBytes (zis, ze.getSize (), false)), map, "_2");
} else if (zeShortName.equals ("procs") || (isacq = zeShortName.equals ("acqus"))) {
if (isacq) {
root = zeName.substring (0, pt + 1);
}JSV.source.JDXReader.getHeaderMap ( new java.io.ByteArrayInputStream (this.getBytes (zis, ze.getSize (), false)), map);
}}
zis.close ();
map.put ("##TITLE", (title == null ? "" : title));
return this.getSource (fullPath, map, data1r, data1i, data2rr);
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
return null;
} else {
throw e;
}
}
}, "~A,~S");
Clazz.defineMethod (c$, "readBrukerDir", 
function (fullPath) {
var dir =  new java.io.File (fullPath);
if (!dir.isDirectory ()) {
dir = dir.getParentFile ();
}var procs =  new java.io.File (dir, "procs");
if (!procs.exists ()) procs =  new java.io.File (dir, "pdata/1/procs");
var pdata = procs.getParentFile ();
var brukerDir = pdata.getParentFile ().getParentFile ();
var map =  new java.util.Hashtable ();
this.mapParameters (brukerDir, "acqus", map, null);
this.mapParameters (brukerDir, "acqu2s", map, "_2");
this.mapParameters (pdata, "procs", map, null);
this.mapParameters (pdata, "proc2s", map, "_2");
map.put ("##TITLE",  String.instantialize (this.getFileContentsAsBytes ( new java.io.File (pdata, "title"))));
var data1r = this.getFileContentsAsBytes ( new java.io.File (procs.getParent (), "1r"));
var data1i = (this.allowPhasing ? this.getFileContentsAsBytes ( new java.io.File (procs.getParent (), "1i")) :  Clazz.newByteArray (0, 0));
var data2rr = this.getFileContentsAsBytes ( new java.io.File (procs.getParent (), "2rr"));
return this.getSource (brukerDir.toString (), map, data1r, data1i, data2rr);
}, "~S");
Clazz.defineMethod (c$, "mapParameters", 
 function (dir, fname, map, suffix) {
var f =  new java.io.File (dir, fname);
if (!f.exists ()) return;
var is =  new java.io.FileInputStream (f);
JSV.source.JDXReader.getHeaderMapS (is, map, suffix);
is.close ();
}, "java.io.File,~S,java.util.Map,~S");
Clazz.defineMethod (c$, "getSource", 
 function (brukerDir, map, data1r, data1i, data2rr) {
var dtypp = Integer.parseInt (map.get ("##$DTYPP"));
var byteorp = (dtypp == 0 ? Integer.parseInt (map.get ("##$BYTORDP")) : 2147483647);
if (dtypp == -2147483648 || byteorp == -2147483648) return null;
var source = null;
if (data1r.length > 0) {
source =  new JSV.source.JDXSource ((data1i.length == 0 ? 0 : 2), brukerDir);
this.setSource (this.getData (data1r, dtypp, byteorp), this.getData (data1i, dtypp, byteorp), map, source, false);
} else if (data2rr.length > 0) {
source =  new JSV.source.JDXSource (2, brukerDir);
this.setSource (this.getData (data2rr, dtypp, byteorp), null, map, source, true);
}return source;
}, "~S,java.util.Map,~A,~A,~A");
Clazz.defineMethod (c$, "setSource", 
 function (datar, datai, map, source, is2D) {
var LDRTable =  new JU.Lst ();
var spectrum0 =  new JSV.common.Spectrum ();
spectrum0.setTitle (map.get ("##TITLE"));
spectrum0.setJcampdx (is2D ? "6.0" : "5.1");
spectrum0.setDataClass ("XYDATA");
spectrum0.setDataType (is2D ? "nD NMR SPECTRUM" : "NMR SPECTRUM");
spectrum0.setContinuous (true);
spectrum0.setIncreasing (false);
spectrum0.setLongDate (map.get ("##$DATE"));
spectrum0.setOrigin ("Bruker BioSpin GmbH/JSpecView");
spectrum0.setOwner (map.get ("##OWNER"));
var freq = JSV.source.BrukerReader.parseDouble (map.get ("##$SFO1"));
var ref = JSV.source.BrukerReader.parseDouble (map.get ("##$ABSF1"));
if (ref == 0) {
ref = JSV.source.BrukerReader.parseDouble (map.get ("##$OFFSET"));
}var nuc1 = this.cleanJDXValue (map.get ("##$NUC1"));
var nuc2 = this.cleanJDXValue (map.get ("##$NUC2"));
if (nuc2.length == 0) nuc2 = nuc1;
var sw_hz = JSV.source.BrukerReader.parseDouble (map.get ("##$SWP"));
var sw = sw_hz / freq;
var shift = ref - sw;
var solvent = this.cleanJDXValue (map.get ("##$SOLVENT"));
var shiftType = "INTERNAL";
JSV.source.JDXReader.addHeader (LDRTable, "##.SHIFTREFERENCE", shiftType + ", " + solvent + ", 1, " + ref);
JSV.source.JDXReader.addHeader (LDRTable, "##.OBSERVEFREQUENCY", "" + freq);
JSV.source.JDXReader.addHeader (LDRTable, "##.OBSERVENUCLEUS", nuc1);
JSV.source.JDXReader.addHeader (LDRTable, "##SPECTROMETER/DATA SYSTEM", this.cleanJDXValue (map.get ("##$INSTRUM")));
spectrum0.setHeaderTable (LDRTable);
spectrum0.setObservedNucleus (nuc1);
spectrum0.setObservedFreq (freq);
spectrum0.setHZtoPPM (true);
if (is2D) {
source.isCompoundSource = true;
spectrum0.setNumDim (2);
spectrum0.setNucleusAndFreq (nuc2, false);
var si0 = Integer.parseInt (map.get ("##$SI"));
var si1 = Integer.parseInt (map.get ("##$SI_2"));
var ref1 = JSV.source.BrukerReader.parseDouble (map.get ("##$ABSF1_2"));
if (ref1 == 0) {
ref1 = JSV.source.BrukerReader.parseDouble (map.get ("##$OFFSET"));
}var freq1 = JSV.source.BrukerReader.parseDouble (map.get ("##$SFO1_2"));
var sw_hz1 = JSV.source.BrukerReader.parseDouble (map.get ("##$SWP_2"));
var npoints = si0;
var xfactor = sw_hz / npoints;
var xfactor1 = sw_hz1 / si1;
var freq2 = freq1;
freq1 = ref1 * freq1 - xfactor1;
spectrum0.fileNPoints = npoints;
spectrum0.fileFirstX = sw_hz - xfactor;
spectrum0.fileLastX = 0;
var f = 1;
for (var j = 0, pt = 0; j < si1; j++) {
var spectrum =  new JSV.common.Spectrum ();
spectrum0.copyTo (spectrum);
spectrum.setTitle (spectrum0.getTitle ());
spectrum.setY2D (freq1);
spectrum.blockID = Math.random ();
spectrum0.fileNPoints = npoints;
spectrum0.fileFirstX = sw_hz - xfactor;
spectrum0.fileLastX = 0;
spectrum.setY2DUnits ("HZ");
spectrum.setXFactor (1);
spectrum.setYFactor (1);
spectrum.setObservedNucleus (nuc2);
spectrum.setObservedFreq (freq2);
var xyCoords =  new Array (npoints);
for (var i = 0; i < npoints; i++) {
xyCoords[npoints - i - 1] =  new JSV.common.Coordinate ().set ((npoints - i) * xfactor / freq + shift, datar[pt++] * f);
}
spectrum.setXYCoords (xyCoords);
source.addJDXSpectrum (null, spectrum, j > 0);
freq1 -= xfactor1;
}
} else {
var npoints = datar.length;
var xfactor = sw_hz / npoints;
spectrum0.fileFirstX = sw_hz - xfactor;
spectrum0.fileLastX = 0;
spectrum0.fileNPoints = npoints;
var xyCoords =  new Array (npoints);
for (var i = 0; i < npoints; i++) {
xyCoords[npoints - i - 1] =  new JSV.common.Coordinate ().set ((npoints - i - 1) * xfactor / freq + shift, datar[i]);
}
spectrum0.setXYCoords (xyCoords);
spectrum0.fileNPoints = npoints;
spectrum0.setXFactor (xfactor);
spectrum0.setYFactor (1);
spectrum0.setXUnits ("ppm");
spectrum0.setYUnits ("ARBITRARY UNITS");
spectrum0.setNumDim (1);
if (spectrum0.getMaxY () >= 10000) spectrum0.normalizeSimulation (1000);
source.addJDXSpectrum (null, spectrum0, false);
}}, "~A,~A,java.util.Map,JSV.source.JDXSource,~B");
c$.parseDouble = Clazz.defineMethod (c$, "parseDouble", 
 function (val) {
return (val == null || val.length == 0 ? NaN : Double.parseDouble (val));
}, "~S");
Clazz.defineMethod (c$, "getData", 
 function (bytes, dtypp, byteorp) {
var len = Clazz.doubleToInt (bytes.length / (dtypp == 0 ? 4 : 8));
var doc =  new JU.BinaryDocument ();
doc.setStream ( new java.io.BufferedInputStream ( new java.io.ByteArrayInputStream (bytes)), byteorp != 0);
var ad =  Clazz.newDoubleArray (len, 0);
var d = 0;
var dmin = 1.7976931348623157E308;
var dmax = -1.7976931348623157E308;
if (dtypp == 0) {
for (var i = 0; i < len; i++) {
var f = 1;
ad[i] = d = doc.readInt () * f;
if (d < dmin) dmin = d;
if (d > dmax) dmax = d;
}
} else {
for (var i = 0; i < len; i++) {
ad[i] = d = doc.readDouble ();
if (d < dmin) dmin = d;
if (d > dmax) dmax = d;
}
}doc.close ();
return ad;
}, "~A,~N,~N");
Clazz.defineMethod (c$, "cleanJDXValue", 
 function (val) {
var s = (val == null ? "" : val.startsWith ("<") ? val.substring (1, val.length - 1) : val);
return (s.equals ("off") ? "" : s);
}, "~S");
Clazz.defineMethod (c$, "getFileContentsAsBytes", 
 function (file) {
if (!file.exists ()) return  Clazz.newByteArray (0, 0);
var len = file.length ();
return this.getBytes ( new java.io.FileInputStream (file), len, true);
}, "java.io.File");
Clazz.defineMethod (c$, "getBytes", 
 function ($in, len, andClose) {
try {
return JU.Rdr.getLimitedStreamBytes ($in, len);
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
} else {
throw e;
}
}
return  Clazz.newByteArray (0, 0);
}, "java.io.InputStream,~N,~B");
Clazz.defineStatics (c$,
"TYPE_INT", 0);
});
