X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fio%2FIdentifyFile.js;h=cf352415eb256ec0bf0b0b70e45b4d10ca312991;hp=4d88cdd5b89f236787c01f986857a2db3eef8e72;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/io/IdentifyFile.js b/site/j2s/jalview/io/IdentifyFile.js
index 4d88cdd..cf35241 100644
--- a/site/j2s/jalview/io/IdentifyFile.js
+++ b/site/j2s/jalview/io/IdentifyFile.js
@@ -1,157 +1,157 @@
-Clazz.declarePackage ("jalview.io");
-Clazz.load (null, "jalview.io.IdentifyFile", ["jalview.io.FileParse"], function () {
-c$ = Clazz.declareType (jalview.io, "IdentifyFile");
-Clazz.defineMethod (c$, "Identify", 
-function (file, protocol) {
-var emessage = "UNIDENTIFIED FILE PARSING ERROR";
-var parser = null;
-try {
-parser =  new jalview.io.FileParse (file, protocol);
-if (parser.isValid ()) {
-return this.Identify (parser);
-}} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-System.err.println ("Error whilst identifying");
-e.printStackTrace (System.err);
-emessage = e.getMessage ();
-} else {
-throw e;
-}
-}
-if (parser != null) {
-return parser.errormessage;
-}return emessage;
-}, "~S,~S");
-Clazz.defineMethod (c$, "Identify", 
-function (source) {
-return this.Identify (source, true);
-}, "jalview.io.FileParse");
-Clazz.defineMethod (c$, "Identify", 
-function (source, closeSource) {
-var reply = "PFAM";
-var data;
-var length = 0;
-var lineswereskipped = false;
-var isBinary = false;
-try {
-if (!closeSource) {
-source.mark ();
-}while ((data = source.nextLine ()) != null) {
-length += data.trim ().length;
-if (!lineswereskipped) {
-for (var i = 0; !isBinary && i < data.length; i++) {
-var c = data.charAt (i);
-isBinary = (c.charCodeAt (0) < 32 && c != '\t' && c != '\n' && c != '\r' && c.charCodeAt (0) != 5 && c.charCodeAt (0) != 27);
-}
-}if (isBinary) {
-if (source.inFile != null) {
-var fileStr = source.inFile.getName ();
-if (fileStr.lastIndexOf (".jar") > -1 || fileStr.lastIndexOf (".zip") > -1) {
-reply = "Jalview";
-}}if (!lineswereskipped && data.startsWith ("PK")) {
-reply = "Jalview";
-break;
-}}data = data.toUpperCase ();
-if (data.startsWith ("##GFF-VERSION")) {
-reply = "GFF v2 or v3";
-break;
-}if (data.indexOf ("# STOCKHOLM") > -1) {
-reply = "STH";
-break;
-}if (data.matches ("<HTML(\"[^\"]*\"|'[^']*'|[^'\">])*>")) {
-reply = "HTML";
-break;
-}if (data.matches ("<RNAML (\"[^\"]*\"|'[^']*'|[^'\">])*>")) {
-reply = "RNAML";
-break;
-}if (data.indexOf ("{\"") > -1) {
-reply = "JSON";
-break;
-}if ((data.length < 1) || (data.indexOf ("#") == 0)) {
-lineswereskipped = true;
-continue;
-}if (data.indexOf ("PILEUP") > -1) {
-reply = "PileUp";
-break;
-}if ((data.indexOf ("//") == 0) || ((data.indexOf ("!!") > -1) && (data.indexOf ("!!") < data.indexOf ("_MULTIPLE_ALIGNMENT ")))) {
-reply = "MSF";
-break;
-} else if (data.indexOf ("CLUSTAL") > -1) {
-reply = "CLUSTAL";
-break;
-} else if (data.indexOf (">") > -1) {
-var checkPIR = false;
-var starterm = false;
-if ((data.indexOf (">P1;") > -1) || (data.indexOf (">DL;") > -1)) {
-checkPIR = true;
-reply = "PIR";
-}data = source.nextLine ();
-if (data.indexOf (">") > -1) {
-reply = "BLC";
-} else {
-var data1 = source.nextLine ();
-var data2 = source.nextLine ();
-var c1;
-if (checkPIR) {
-starterm = (data1 != null && data1.indexOf ("*") > -1) || (data2 != null && data2.indexOf ("*") > -1);
-}if (data2 != null && (c1 = data.indexOf ("*")) > -1) {
-if (c1 == 0 && c1 == data2.indexOf ("*")) {
-reply = "BLC";
-} else {
-reply = "FASTA";
-}} else {
-reply = "FASTA";
-if (!checkPIR) {
-break;
-}}}if (checkPIR) {
-var dta = null;
-if (!starterm) {
-do {
-try {
-dta = source.nextLine ();
-} catch (ex) {
-if (Clazz.exceptionOf (ex, java.io.IOException)) {
-} else {
-throw ex;
-}
-}
-;if (dta != null && dta.indexOf ("*") > -1) {
-starterm = true;
-}} while (dta != null && !starterm);
-}if (starterm) {
-reply = "PIR";
-break;
-} else {
-reply = "FASTA";
-}}break;
-} else if (data.indexOf ("HEADER") == 0 || data.indexOf ("ATOM") == 0) {
-reply = "PDB";
-break;
-} else if (data.matches ("\\s*\\d+\\s+\\d+\\s*")) {
-reply = "PHYLIP";
-break;
-} else if (!lineswereskipped && data.charAt (0) != '*' && data.charAt (0) != ' ' && data.indexOf (":") < data.indexOf (",")) {
-reply = "JnetFile";
-break;
-}lineswereskipped = true;
-}
-if (closeSource) {
-source.close ();
-} else {
-source.reset ();
-}} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-System.err.println ("File Identification failed!\n" + ex);
-return source.errormessage;
-} else {
-throw ex;
-}
-}
-if (length == 0) {
-System.err.println ("File Identification failed! - Empty file was read.");
-return "EMPTY DATA FILE";
-}return reply;
-}, "jalview.io.FileParse,~B");
-Clazz.defineStatics (c$,
-"GFF3File", "GFF v2 or v3");
-});
+Clazz.declarePackage ("jalview.io");
+Clazz.load (null, "jalview.io.IdentifyFile", ["jalview.io.FileParse"], function () {
+c$ = Clazz.declareType (jalview.io, "IdentifyFile");
+Clazz.defineMethod (c$, "Identify", 
+function (file, protocol) {
+var emessage = "UNIDENTIFIED FILE PARSING ERROR";
+var parser = null;
+try {
+parser =  new jalview.io.FileParse (file, protocol);
+if (parser.isValid ()) {
+return this.Identify (parser);
+}} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+System.err.println ("Error whilst identifying");
+e.printStackTrace (System.err);
+emessage = e.getMessage ();
+} else {
+throw e;
+}
+}
+if (parser != null) {
+return parser.errormessage;
+}return emessage;
+}, "~S,~S");
+Clazz.defineMethod (c$, "Identify", 
+function (source) {
+return this.Identify (source, true);
+}, "jalview.io.FileParse");
+Clazz.defineMethod (c$, "Identify", 
+function (source, closeSource) {
+var reply = "PFAM";
+var data;
+var length = 0;
+var lineswereskipped = false;
+var isBinary = false;
+try {
+if (!closeSource) {
+source.mark ();
+}while ((data = source.nextLine ()) != null) {
+length += data.trim ().length;
+if (!lineswereskipped) {
+for (var i = 0; !isBinary && i < data.length; i++) {
+var c = data.charAt (i);
+isBinary = (c.charCodeAt (0) < 32 && c != '\t' && c != '\n' && c != '\r' && c.charCodeAt (0) != 5 && c.charCodeAt (0) != 27);
+}
+}if (isBinary) {
+if (source.inFile != null) {
+var fileStr = source.inFile.getName ();
+if (fileStr.lastIndexOf (".jar") > -1 || fileStr.lastIndexOf (".zip") > -1) {
+reply = "Jalview";
+}}if (!lineswereskipped && data.startsWith ("PK")) {
+reply = "Jalview";
+break;
+}}data = data.toUpperCase ();
+if (data.startsWith ("##GFF-VERSION")) {
+reply = "GFF v2 or v3";
+break;
+}if (data.indexOf ("# STOCKHOLM") > -1) {
+reply = "STH";
+break;
+}if (data.matches ("<HTML(\"[^\"]*\"|'[^']*'|[^'\">])*>")) {
+reply = "HTML";
+break;
+}if (data.matches ("<RNAML (\"[^\"]*\"|'[^']*'|[^'\">])*>")) {
+reply = "RNAML";
+break;
+}if (data.indexOf ("{\"") > -1) {
+reply = "JSON";
+break;
+}if ((data.length < 1) || (data.indexOf ("#") == 0)) {
+lineswereskipped = true;
+continue;
+}if (data.indexOf ("PILEUP") > -1) {
+reply = "PileUp";
+break;
+}if ((data.indexOf ("//") == 0) || ((data.indexOf ("!!") > -1) && (data.indexOf ("!!") < data.indexOf ("_MULTIPLE_ALIGNMENT ")))) {
+reply = "MSF";
+break;
+} else if (data.indexOf ("CLUSTAL") > -1) {
+reply = "CLUSTAL";
+break;
+} else if (data.indexOf (">") > -1) {
+var checkPIR = false;
+var starterm = false;
+if ((data.indexOf (">P1;") > -1) || (data.indexOf (">DL;") > -1)) {
+checkPIR = true;
+reply = "PIR";
+}data = source.nextLine ();
+if (data.indexOf (">") > -1) {
+reply = "BLC";
+} else {
+var data1 = source.nextLine ();
+var data2 = source.nextLine ();
+var c1;
+if (checkPIR) {
+starterm = (data1 != null && data1.indexOf ("*") > -1) || (data2 != null && data2.indexOf ("*") > -1);
+}if (data2 != null && (c1 = data.indexOf ("*")) > -1) {
+if (c1 == 0 && c1 == data2.indexOf ("*")) {
+reply = "BLC";
+} else {
+reply = "FASTA";
+}} else {
+reply = "FASTA";
+if (!checkPIR) {
+break;
+}}}if (checkPIR) {
+var dta = null;
+if (!starterm) {
+do {
+try {
+dta = source.nextLine ();
+} catch (ex) {
+if (Clazz.exceptionOf (ex, java.io.IOException)) {
+} else {
+throw ex;
+}
+}
+;if (dta != null && dta.indexOf ("*") > -1) {
+starterm = true;
+}} while (dta != null && !starterm);
+}if (starterm) {
+reply = "PIR";
+break;
+} else {
+reply = "FASTA";
+}}break;
+} else if (data.indexOf ("HEADER") == 0 || data.indexOf ("ATOM") == 0) {
+reply = "PDB";
+break;
+} else if (data.matches ("\\s*\\d+\\s+\\d+\\s*")) {
+reply = "PHYLIP";
+break;
+} else if (!lineswereskipped && data.charAt (0) != '*' && data.charAt (0) != ' ' && data.indexOf (":") < data.indexOf (",")) {
+reply = "JnetFile";
+break;
+}lineswereskipped = true;
+}
+if (closeSource) {
+source.close ();
+} else {
+source.reset ();
+}} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+System.err.println ("File Identification failed!\n" + ex);
+return source.errormessage;
+} else {
+throw ex;
+}
+}
+if (length == 0) {
+System.err.println ("File Identification failed! - Empty file was read.");
+return "EMPTY DATA FILE";
+}return reply;
+}, "jalview.io.FileParse,~B");
+Clazz.defineStatics (c$,
+"GFF3File", "GFF v2 or v3");
+});