biojs-vis-pdbviewer/external/jmol-14.2.4/jsmol/j2s/JU/Rdr.js

A BioJS 2.0 component to view protein structures

Clazz.declarePackage ("JU");
Clazz.load (["javajs.api.GenericLineReader"], "JU.Rdr", ["java.io.BufferedInputStream", "$.BufferedReader", "$.ByteArrayInputStream", "$.InputStreamReader", "$.StringReader", "javajs.api.Interface", "JU.AU", "$.Base64", "$.Encoding", "$.SB"], function () {
c$ = Clazz.decorateAsClass (function () {
this.reader = null;
Clazz.instantialize (this, arguments);
}, JU, "Rdr", null, javajs.api.GenericLineReader);
Clazz.makeConstructor (c$, 
function (reader) {
this.reader = reader;
}, "java.io.BufferedReader");
Clazz.overrideMethod (c$, "readNextLine", 
function () {
return this.reader.readLine ();
});
c$.getCifParser = Clazz.defineMethod (c$, "getCifParser", 
function () {
return javajs.api.Interface.getInterface ("JU.CifDataParser");
});
c$.readCifData = Clazz.defineMethod (c$, "readCifData", 
function (br) {
return JU.Rdr.getCifParser ().set (null, br).getAllCifData ();
}, "java.io.BufferedReader");
c$.fixUTF = Clazz.defineMethod (c$, "fixUTF", 
function (bytes) {
var encoding = JU.Rdr.getUTFEncoding (bytes);
if (encoding !== JU.Encoding.NONE) try {
var s =  String.instantialize (bytes, encoding.name ().$replace ('_', '-'));
switch (encoding) {
case JU.Encoding.UTF8:
case JU.Encoding.UTF_16BE:
case JU.Encoding.UTF_16LE:
s = s.substring (1);
break;
default:
break;
}
return s;
} catch (e) {
if (Clazz.exceptionOf (e, java.io.UnsupportedEncodingException)) {
System.out.println (e);
} else {
throw e;
}
}
return  String.instantialize (bytes);
}, "~A");
c$.getUTFEncoding = Clazz.defineMethod (c$, "getUTFEncoding", 
 function (bytes) {
if (bytes.length >= 3 && bytes[0] == 0xEF && bytes[1] == 0xBB && bytes[2] == 0xBF) return JU.Encoding.UTF8;
if (bytes.length >= 4 && bytes[0] == 0 && bytes[1] == 0 && bytes[2] == 0xFE && bytes[3] == 0xFF) return JU.Encoding.UTF_32BE;
if (bytes.length >= 4 && bytes[0] == 0xFF && bytes[1] == 0xFE && bytes[2] == 0 && bytes[3] == 0) return JU.Encoding.UTF_32LE;
if (bytes.length >= 2 && bytes[0] == 0xFF && bytes[1] == 0xFE) return JU.Encoding.UTF_16LE;
if (bytes.length >= 2 && bytes[0] == 0xFE && bytes[1] == 0xFF) return JU.Encoding.UTF_16BE;
return JU.Encoding.NONE;
}, "~A");
c$.getUTFEncodingForStream = Clazz.defineMethod (c$, "getUTFEncodingForStream", 
 function (is) {
{
is.resetStream();
}var abMagic =  Clazz.newByteArray (4, 0);
abMagic[3] = 1;
try {
is.mark (5);
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
return JU.Encoding.NONE;
} else {
throw e;
}
}
is.read (abMagic, 0, 4);
is.reset ();
return JU.Rdr.getUTFEncoding (abMagic);
}, "java.io.BufferedInputStream");
c$.isBase64 = Clazz.defineMethod (c$, "isBase64", 
function (sb) {
return (sb.indexOf (";base64,") == 0);
}, "JU.SB");
c$.isCompoundDocumentS = Clazz.defineMethod (c$, "isCompoundDocumentS", 
function (is) {
return JU.Rdr.isCompoundDocumentB (JU.Rdr.getMagic (is, 8));
}, "java.io.InputStream");
c$.isCompoundDocumentB = Clazz.defineMethod (c$, "isCompoundDocumentB", 
function (bytes) {
return (bytes.length >= 8 && bytes[0] == 0xD0 && bytes[1] == 0xCF && bytes[2] == 0x11 && bytes[3] == 0xE0 && bytes[4] == 0xA1 && bytes[5] == 0xB1 && bytes[6] == 0x1A && bytes[7] == 0xE1);
}, "~A");
c$.isGzipS = Clazz.defineMethod (c$, "isGzipS", 
function (is) {
return JU.Rdr.isGzipB (JU.Rdr.getMagic (is, 2));
}, "java.io.InputStream");
c$.isGzipB = Clazz.defineMethod (c$, "isGzipB", 
function (bytes) {
return (bytes != null && bytes.length >= 2 && bytes[0] == 0x1F && bytes[1] == 0x8B);
}, "~A");
c$.isPickleS = Clazz.defineMethod (c$, "isPickleS", 
function (is) {
return JU.Rdr.isPickleB (JU.Rdr.getMagic (is, 2));
}, "java.io.InputStream");
c$.isPickleB = Clazz.defineMethod (c$, "isPickleB", 
function (bytes) {
return (bytes != null && bytes.length >= 2 && bytes[0] == 0x7D && bytes[1] == 0x71);
}, "~A");
c$.isPngZipStream = Clazz.defineMethod (c$, "isPngZipStream", 
function (is) {
return JU.Rdr.isPngZipB (JU.Rdr.getMagic (is, 55));
}, "java.io.InputStream");
c$.isPngZipB = Clazz.defineMethod (c$, "isPngZipB", 
function (bytes) {
return (bytes[50] == 0 && bytes[51] == 0x50 && bytes[52] == 0x4E && bytes[53] == 0x47 && bytes[54] == 0x4A);
}, "~A");
c$.isZipS = Clazz.defineMethod (c$, "isZipS", 
function (is) {
return JU.Rdr.isZipB (JU.Rdr.getMagic (is, 4));
}, "java.io.InputStream");
c$.isZipB = Clazz.defineMethod (c$, "isZipB", 
function (bytes) {
return (bytes.length >= 4 && bytes[0] == 0x50 && bytes[1] == 0x4B && bytes[2] == 0x03 && bytes[3] == 0x04);
}, "~A");
c$.getMagic = Clazz.defineMethod (c$, "getMagic", 
 function (is, n) {
var abMagic =  Clazz.newByteArray (n, 0);
{
is.resetStream();
}try {
is.mark (n + 1);
is.read (abMagic, 0, n);
} catch (e) {
if (Clazz.exceptionOf (e, java.io.IOException)) {
} else {
throw e;
}
}
try {
is.reset ();
} catch (e) {
if (Clazz.exceptionOf (e, java.io.IOException)) {
} else {
throw e;
}
}
return abMagic;
}, "java.io.InputStream,~N");
c$.getBIS = Clazz.defineMethod (c$, "getBIS", 
function (bytes) {
return  new java.io.BufferedInputStream ( new java.io.ByteArrayInputStream (bytes));
}, "~A");
c$.getBR = Clazz.defineMethod (c$, "getBR", 
function (string) {
return  new java.io.BufferedReader ( new java.io.StringReader (string));
}, "~S");
c$.getUnzippedInputStream = Clazz.defineMethod (c$, "getUnzippedInputStream", 
function (bis) {
while (JU.Rdr.isGzipS (bis)) bis =  new java.io.BufferedInputStream (JU.Rdr.newGZIPInputStream (bis));

return bis;
}, "java.io.BufferedInputStream");
c$.getBytesFromSB = Clazz.defineMethod (c$, "getBytesFromSB", 
function (sb) {
return (JU.Rdr.isBase64 (sb) ? JU.Base64.decodeBase64 (sb.substring (8)) : sb.toBytes (0, -1));
}, "JU.SB");
c$.getStreamAsBytes = Clazz.defineMethod (c$, "getStreamAsBytes", 
function (bis, out) {
var buf =  Clazz.newByteArray (1024, 0);
var bytes = (out == null ?  Clazz.newByteArray (4096, 0) : null);
var len = 0;
var totalLen = 0;
while ((len = bis.read (buf, 0, 1024)) > 0) {
totalLen += len;
if (out == null) {
if (totalLen >= bytes.length) bytes = JU.AU.ensureLengthByte (bytes, totalLen * 2);
System.arraycopy (buf, 0, bytes, totalLen - len, len);
} else {
out.write (buf, 0, len);
}}
bis.close ();
if (out == null) {
return JU.AU.arrayCopyByte (bytes, totalLen);
}return totalLen + " bytes";
}, "java.io.BufferedInputStream,JU.OC");
c$.getBufferedReader = Clazz.defineMethod (c$, "getBufferedReader", 
function (bis, charSet) {
if (JU.Rdr.getUTFEncodingForStream (bis) === JU.Encoding.NONE) return  new java.io.BufferedReader ( new java.io.InputStreamReader (bis, (charSet == null ? "UTF-8" : charSet)));
var bytes = JU.Rdr.getLimitedStreamBytes (bis, -1);
bis.close ();
return JU.Rdr.getBR (charSet == null ? JU.Rdr.fixUTF (bytes) :  String.instantialize (bytes, charSet));
}, "java.io.BufferedInputStream,~S");
c$.getLimitedStreamBytes = Clazz.defineMethod (c$, "getLimitedStreamBytes", 
function (is, n) {
var buflen = (n > 0 && n < 1024 ? n : 1024);
var buf =  Clazz.newByteArray (buflen, 0);
var bytes =  Clazz.newByteArray (n < 0 ? 4096 : n, 0);
var len = 0;
var totalLen = 0;
if (n < 0) n = 2147483647;
while (totalLen < n && (len = is.read (buf, 0, buflen)) > 0) {
totalLen += len;
if (totalLen > bytes.length) bytes = JU.AU.ensureLengthByte (bytes, totalLen * 2);
System.arraycopy (buf, 0, bytes, totalLen - len, len);
if (n != 2147483647 && totalLen + buflen > bytes.length) buflen = bytes.length - totalLen;
}
if (totalLen == bytes.length) return bytes;
buf =  Clazz.newByteArray (totalLen, 0);
System.arraycopy (bytes, 0, buf, 0, totalLen);
return buf;
}, "java.io.InputStream,~N");
c$.StreamToUTF8String = Clazz.defineMethod (c$, "StreamToUTF8String", 
function (bis) {
var data =  new Array (1);
try {
JU.Rdr.readAllAsString (JU.Rdr.getBufferedReader (bis, "UTF-8"), -1, true, data, 0);
} catch (e) {
if (Clazz.exceptionOf (e, java.io.IOException)) {
} else {
throw e;
}
}
return data[0];
}, "java.io.BufferedInputStream");
c$.readAllAsString = Clazz.defineMethod (c$, "readAllAsString", 
function (br, nBytesMax, allowBinary, data, i) {
try {
var sb = JU.SB.newN (8192);
var line;
if (nBytesMax < 0) {
line = br.readLine ();
if (allowBinary || line != null && line.indexOf ('\0') < 0 && (line.length != 4 || line.charCodeAt (0) != 65533 || line.indexOf ("PNG") != 1)) {
sb.append (line).appendC ('\n');
while ((line = br.readLine ()) != null) sb.append (line).appendC ('\n');

}} else {
var n = 0;
var len;
while (n < nBytesMax && (line = br.readLine ()) != null) {
if (nBytesMax - n < (len = line.length) + 1) line = line.substring (0, nBytesMax - n - 1);
sb.append (line).appendC ('\n');
n += len + 1;
}
}br.close ();
data[i] = sb.toString ();
return true;
} catch (ioe) {
if (Clazz.exceptionOf (ioe, Exception)) {
data[i] = ioe.toString ();
return false;
} else {
throw ioe;
}
}
}, "java.io.BufferedReader,~N,~B,~A,~N");
c$.getPngZipPointAndCount = Clazz.defineMethod (c$, "getPngZipPointAndCount", 
function (bis, pt_count) {
bis.mark (75);
try {
var data = JU.Rdr.getLimitedStreamBytes (bis, 74);
bis.reset ();
var pt = 0;
for (var i = 64, f = 1; --i > 54; f *= 10) pt += (data[i] - 48) * f;

var n = 0;
for (var i = 74, f = 1; --i > 64; f *= 10) n += (data[i] - 48) * f;

pt_count[0] = pt;
pt_count[1] = n;
} catch (e) {
pt_count[1] = 0;
}
}, "java.io.BufferedInputStream,~A");
c$.getPngZipStream = Clazz.defineMethod (c$, "getPngZipStream", 
function (bis, asNewStream) {
if (!JU.Rdr.isPngZipStream (bis)) return bis;
var data =  Clazz.newByteArray (0, 0);
bis.mark (75);
try {
var pt_count =  Clazz.newIntArray (2, 0);
JU.Rdr.getPngZipPointAndCount (bis, pt_count);
if (pt_count[1] != 0) {
var pt = pt_count[0];
while (pt > 0) pt -= bis.skip (pt);

if (!asNewStream) return bis;
data = JU.Rdr.getLimitedStreamBytes (bis, pt_count[1]);
}} catch (e) {
} finally {
try {
if (asNewStream) bis.close ();
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
} else {
throw e;
}
}
}
return JU.Rdr.getBIS (data);
}, "java.io.BufferedInputStream,~B");
c$.getJzt = Clazz.defineMethod (c$, "getJzt", 
function () {
return (JU.Rdr.jzt == null ? JU.Rdr.jzt = javajs.api.Interface.getInterface ("JU.ZipTools") : JU.Rdr.jzt);
});
c$.readFileAsMap = Clazz.defineMethod (c$, "readFileAsMap", 
function (is, bdata, name) {
JU.Rdr.getJzt ().readFileAsMap (is, bdata, name);
}, "java.io.BufferedInputStream,java.util.Map,~S");
c$.getZipDirectoryAsStringAndClose = Clazz.defineMethod (c$, "getZipDirectoryAsStringAndClose", 
function (t) {
return JU.Rdr.getJzt ().getZipDirectoryAsStringAndClose (t);
}, "java.io.BufferedInputStream");
c$.newGZIPInputStream = Clazz.defineMethod (c$, "newGZIPInputStream", 
function (bis) {
return JU.Rdr.getJzt ().newGZIPInputStream (bis);
}, "java.io.BufferedInputStream");
c$.newZipInputStream = Clazz.defineMethod (c$, "newZipInputStream", 
function ($in) {
return JU.Rdr.getJzt ().newZipInputStream ($in);
}, "java.io.InputStream");
c$.getZipFileDirectory = Clazz.defineMethod (c$, "getZipFileDirectory", 
function (bis, subFileList, listPtr, asBufferedInputStream) {
return JU.Rdr.getJzt ().getZipFileDirectory (bis, subFileList, listPtr, asBufferedInputStream);
}, "java.io.BufferedInputStream,~A,~N,~B");
c$.getZipDirectoryAndClose = Clazz.defineMethod (c$, "getZipDirectoryAndClose", 
function (t, manifestID) {
return JU.Rdr.getJzt ().getZipDirectoryAndClose (t, manifestID);
}, "java.io.BufferedInputStream,~S");
c$.getAllZipData = Clazz.defineMethod (c$, "getAllZipData", 
function (bis, subFileList, replace, string, fileData) {
JU.Rdr.getJzt ().getAllZipData (bis, subFileList, replace, string, fileData);
}, "java.io.BufferedInputStream,~A,~S,~S,java.util.Map");
c$.getZipFileContentsAsBytes = Clazz.defineMethod (c$, "getZipFileContentsAsBytes", 
function (bis, subFileList, i) {
return JU.Rdr.getJzt ().getZipFileContentsAsBytes (bis, subFileList, i);
}, "java.io.BufferedInputStream,~A,~N");
c$.addZipEntry = Clazz.defineMethod (c$, "addZipEntry", 
function (zos, fileName) {
JU.Rdr.getJzt ().addZipEntry (zos, fileName);
}, "~O,~S");
c$.closeZipEntry = Clazz.defineMethod (c$, "closeZipEntry", 
function (zos) {
JU.Rdr.getJzt ().closeZipEntry (zos);
}, "~O");
c$.getZipOutputStream = Clazz.defineMethod (c$, "getZipOutputStream", 
function (bos) {
return JU.Rdr.getJzt ().getZipOutputStream (bos);
}, "~O");
c$.getCrcValue = Clazz.defineMethod (c$, "getCrcValue", 
function (bytes) {
return JU.Rdr.getJzt ().getCrcValue (bytes);
}, "~A");
c$.getZipRoot = Clazz.defineMethod (c$, "getZipRoot", 
function (fileName) {
var pt = fileName.indexOf ("|");
return (pt < 0 ? fileName : fileName.substring (0, pt));
}, "~S");
Clazz.defineStatics (c$,
"jzt", null);
});