X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fio%2FFileParse.js;h=a16b90a035b6b4479994a669321eb79c1478d7ba;hp=51d1e87ddff75ab5caf4cdae5b11c5ab71f21263;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/io/FileParse.js b/bin/jalview/io/FileParse.js
index 51d1e87..a16b90a 100644
--- a/bin/jalview/io/FileParse.js
+++ b/bin/jalview/io/FileParse.js
@@ -1,250 +1,250 @@
-Clazz.declarePackage ("jalview.io");
-Clazz.load (null, "jalview.io.FileParse", ["jalview.io.AppletFormatAdapter", "jalview.util.MessageManager", "java.io.BufferedReader", "$.IOException", "$.InputStreamReader", "$.StringReader", "java.lang.Error", "java.net.URL", "java.util.zip.GZIPInputStream"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.dataName = "unknown source";
-this.inFile = null;
-this.viewport = null;
-this.exportSettings = null;
-this.index = 1;
-this.suffixSeparator = '#';
-this.newline = null;
-this.suffix = null;
-this.type = null;
-this.dataIn = null;
-this.errormessage = "UNITIALISED SOURCE";
-this.error = true;
-this.warningMessage = null;
-this.READAHEAD_LIMIT = 2048;
-Clazz.instantialize (this, arguments);
-}, jalview.io, "FileParse");
-Clazz.prepareFields (c$, function () {
-this.newline = System.getProperty ("line.separator");
-});
-Clazz.defineMethod (c$, "setNewlineString", 
-function (nl) {
-this.newline = nl;
-}, "~S");
-Clazz.defineMethod (c$, "getNewlineString", 
-function () {
-return this.newline;
-});
-Clazz.makeConstructor (c$, 
-function () {
-});
-Clazz.makeConstructor (c$, 
-function (from) {
-if (from == null) {
-throw  new Error (jalview.util.MessageManager.getString ("error.implementation_error_null_fileparse"));
-}if (from === this) {
-return;
-}this.index = ++from.index;
-this.inFile = from.inFile;
-this.suffixSeparator = from.suffixSeparator;
-this.suffix = from.suffix;
-this.errormessage = from.errormessage;
-this.error = false;
-this.type = from.type;
-this.dataIn = from.dataIn;
-if (this.dataIn != null) {
-this.mark ();
-}this.dataName = from.dataName;
-}, "jalview.io.FileParse");
-Clazz.defineMethod (c$, "tryAsGzipSource", 
-($fz = function (inputStream) {
-var inData =  new java.io.BufferedReader ( new java.io.InputStreamReader ( new java.util.zip.GZIPInputStream (inputStream)));
-inData.mark (2048);
-inData.read ();
-inData.reset ();
-return inData;
-}, $fz.isPrivate = true, $fz), "java.io.InputStream");
-Clazz.defineMethod (c$, "checkURLSource", 
-($fz = function (fileStr) {
-this.errormessage = "URL NOT FOUND";
-var url =  new java.net.URL (fileStr);
-var e = null;
-if (fileStr.toLowerCase ().endsWith (".gz")) {
-try {
-var inputStream = url.openStream ();
-this.dataIn = this.tryAsGzipSource (inputStream);
-this.dataName = fileStr;
-return false;
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-e = ex;
-} else {
-throw ex;
-}
-}
-}try {
-this.dataIn =  new java.io.BufferedReader ( new java.io.InputStreamReader (url.openStream ()));
-} catch (q) {
-if (Clazz.exceptionOf (q, java.io.IOException)) {
-if (e != null) {
-throw  new java.io.IOException (jalview.util.MessageManager.getString ("exception.failed_to_resolve_gzip_stream"), e);
-}throw q;
-} else {
-throw q;
-}
-}
-this.dataName = fileStr;
-return false;
-}, $fz.isPrivate = true, $fz), "~S");
-Clazz.defineMethod (c$, "extractSuffix", 
-($fz = function (fileStr) {
-var sfpos = fileStr.lastIndexOf (this.suffixSeparator);
-if (sfpos > -1 && sfpos < fileStr.length - 1) {
-this.suffix = fileStr.substring (sfpos + 1);
-return fileStr.substring (0, sfpos);
-}return null;
-}, $fz.isPrivate = true, $fz), "~S");
-Clazz.makeConstructor (c$, 
-function (fileStr, type) {
-this.type = type;
-this.error = false;
-if (type.equals (jalview.io.AppletFormatAdapter.FILE)) {
-{
-}} else if (type.equals (jalview.io.AppletFormatAdapter.URL)) {
-try {
-try {
-this.checkURLSource (fileStr);
-if (this.suffixSeparator == '#') {
-this.extractSuffix (fileStr);
-}} catch (e) {
-if (Clazz.exceptionOf (e, java.io.IOException)) {
-var suffixLess = this.extractSuffix (fileStr);
-if (suffixLess == null) {
-throw (e);
-} else {
-try {
-this.checkURLSource (suffixLess);
-} catch (e2) {
-if (Clazz.exceptionOf (e2, java.io.IOException)) {
-this.errormessage = "BAD URL WITH OR WITHOUT SUFFIX";
-throw (e);
-} else {
-throw e2;
-}
-}
-}} else {
-throw e;
-}
-}
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-this.errormessage = "CANNOT ACCESS DATA AT URL '" + fileStr + "' (" + e.getMessage () + ")";
-this.error = true;
-} else {
-throw e;
-}
-}
-} else if (type.equals (jalview.io.AppletFormatAdapter.PASTE)) {
-this.errormessage = "PASTE INACCESSIBLE!";
-this.dataIn =  new java.io.BufferedReader ( new java.io.StringReader (fileStr));
-this.dataName = "Paste";
-} else if (type.equals (jalview.io.AppletFormatAdapter.CLASSLOADER)) {
-this.errormessage = "RESOURCE CANNOT BE LOCATED";
-var is = this.getClass ().getResourceAsStream ("/" + fileStr);
-if (is == null) {
-var suffixLess = this.extractSuffix (fileStr);
-if (suffixLess != null) {
-is = this.getClass ().getResourceAsStream ("/" + suffixLess);
-}}if (is != null) {
-this.dataIn =  new java.io.BufferedReader ( new java.io.InputStreamReader (is));
-this.dataName = fileStr;
-} else {
-this.error = true;
-}} else {
-this.errormessage = "PROBABLE IMPLEMENTATION ERROR : Datasource Type given as '" + (type != null ? type : "null") + "'";
-this.error = true;
-}if (this.dataIn == null || this.error) {
-throw  new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.failed_to_read_data_from_source",  Clazz.newArray (-1, [this.errormessage])));
-}this.error = false;
-this.dataIn.mark (2048);
-}, "~S,~S");
-Clazz.defineMethod (c$, "mark", 
-function () {
-if (this.dataIn != null) {
-this.dataIn.mark (2048);
-} else {
-throw  new java.io.IOException (jalview.util.MessageManager.getString ("exception.no_init_source_stream"));
-}});
-Clazz.defineMethod (c$, "nextLine", 
-function () {
-if (!this.error) {
-return this.dataIn.readLine ();
-}throw  new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.invalid_source_stream",  Clazz.newArray (-1, [this.errormessage])));
-});
-Clazz.defineMethod (c$, "isExporting", 
-function () {
-return !this.error && this.dataIn == null;
-});
-Clazz.defineMethod (c$, "isValid", 
-function () {
-return !this.error;
-});
-Clazz.defineMethod (c$, "close", 
-function () {
-this.errormessage = "EXCEPTION ON CLOSE";
-this.error = true;
-this.dataIn.close ();
-this.dataIn = null;
-this.errormessage = "SOURCE IS CLOSED";
-});
-Clazz.defineMethod (c$, "reset", 
-function () {
-if (this.dataIn != null && !this.error) {
-this.dataIn.reset ();
-} else {
-throw  new java.io.IOException (jalview.util.MessageManager.getString ("error.implementation_error_reset_called_for_invalid_source"));
-}});
-Clazz.defineMethod (c$, "hasWarningMessage", 
-function () {
-return (this.warningMessage != null && this.warningMessage.length > 0);
-});
-Clazz.defineMethod (c$, "getWarningMessage", 
-function () {
-return this.warningMessage;
-});
-Clazz.defineMethod (c$, "getInFile", 
-function () {
-if (this.inFile != null) {
-return this.inFile.getAbsolutePath () + " (" + this.index + ")";
-} else {
-return "From Paste + (" + this.index + ")";
-}});
-Clazz.defineMethod (c$, "getDataName", 
-function () {
-return this.dataName;
-});
-Clazz.defineMethod (c$, "setDataName", 
-function (dataname) {
-this.dataName = dataname;
-}, "~S");
-Clazz.defineMethod (c$, "getReader", 
-function () {
-if (this.dataIn != null) {
-return this.dataIn;
-}return null;
-});
-Clazz.defineMethod (c$, "getViewport", 
-function () {
-return this.viewport;
-});
-Clazz.defineMethod (c$, "setViewport", 
-function (viewport) {
-this.viewport = viewport;
-}, "jalview.api.AlignViewportI");
-Clazz.defineMethod (c$, "getExportSettings", 
-function () {
-return this.exportSettings;
-});
-Clazz.defineMethod (c$, "setExportSettings", 
-function (exportSettings) {
-this.exportSettings = exportSettings;
-}, "jalview.api.AlignExportSettingI");
-Clazz.defineMethod (c$, "configureForView", 
-function (avpanel) {
-if (avpanel != null) {
-this.setViewport (avpanel.getAlignViewport ());
-}}, "jalview.api.AlignmentViewPanel");
-});
+Clazz.declarePackage ("jalview.io");
+Clazz.load (null, "jalview.io.FileParse", ["jalview.io.AppletFormatAdapter", "jalview.util.MessageManager", "java.io.BufferedReader", "$.IOException", "$.InputStreamReader", "$.StringReader", "java.lang.Error", "java.net.URL", "java.util.zip.GZIPInputStream"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.dataName = "unknown source";
+this.inFile = null;
+this.viewport = null;
+this.exportSettings = null;
+this.index = 1;
+this.suffixSeparator = '#';
+this.newline = null;
+this.suffix = null;
+this.type = null;
+this.dataIn = null;
+this.errormessage = "UNITIALISED SOURCE";
+this.error = true;
+this.warningMessage = null;
+this.READAHEAD_LIMIT = 2048;
+Clazz.instantialize (this, arguments);
+}, jalview.io, "FileParse");
+Clazz.prepareFields (c$, function () {
+this.newline = System.getProperty ("line.separator");
+});
+Clazz.defineMethod (c$, "setNewlineString", 
+function (nl) {
+this.newline = nl;
+}, "~S");
+Clazz.defineMethod (c$, "getNewlineString", 
+function () {
+return this.newline;
+});
+Clazz.makeConstructor (c$, 
+function () {
+});
+Clazz.makeConstructor (c$, 
+function (from) {
+if (from == null) {
+throw  new Error (jalview.util.MessageManager.getString ("error.implementation_error_null_fileparse"));
+}if (from === this) {
+return;
+}this.index = ++from.index;
+this.inFile = from.inFile;
+this.suffixSeparator = from.suffixSeparator;
+this.suffix = from.suffix;
+this.errormessage = from.errormessage;
+this.error = false;
+this.type = from.type;
+this.dataIn = from.dataIn;
+if (this.dataIn != null) {
+this.mark ();
+}this.dataName = from.dataName;
+}, "jalview.io.FileParse");
+Clazz.defineMethod (c$, "tryAsGzipSource", 
+($fz = function (inputStream) {
+var inData =  new java.io.BufferedReader ( new java.io.InputStreamReader ( new java.util.zip.GZIPInputStream (inputStream)));
+inData.mark (2048);
+inData.read ();
+inData.reset ();
+return inData;
+}, $fz.isPrivate = true, $fz), "java.io.InputStream");
+Clazz.defineMethod (c$, "checkURLSource", 
+($fz = function (fileStr) {
+this.errormessage = "URL NOT FOUND";
+var url =  new java.net.URL (fileStr);
+var e = null;
+if (fileStr.toLowerCase ().endsWith (".gz")) {
+try {
+var inputStream = url.openStream ();
+this.dataIn = this.tryAsGzipSource (inputStream);
+this.dataName = fileStr;
+return false;
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+e = ex;
+} else {
+throw ex;
+}
+}
+}try {
+this.dataIn =  new java.io.BufferedReader ( new java.io.InputStreamReader (url.openStream ()));
+} catch (q) {
+if (Clazz.exceptionOf (q, java.io.IOException)) {
+if (e != null) {
+throw  new java.io.IOException (jalview.util.MessageManager.getString ("exception.failed_to_resolve_gzip_stream"), e);
+}throw q;
+} else {
+throw q;
+}
+}
+this.dataName = fileStr;
+return false;
+}, $fz.isPrivate = true, $fz), "~S");
+Clazz.defineMethod (c$, "extractSuffix", 
+($fz = function (fileStr) {
+var sfpos = fileStr.lastIndexOf (this.suffixSeparator);
+if (sfpos > -1 && sfpos < fileStr.length - 1) {
+this.suffix = fileStr.substring (sfpos + 1);
+return fileStr.substring (0, sfpos);
+}return null;
+}, $fz.isPrivate = true, $fz), "~S");
+Clazz.makeConstructor (c$, 
+function (fileStr, type) {
+this.type = type;
+this.error = false;
+if (type.equals (jalview.io.AppletFormatAdapter.FILE)) {
+{
+}} else if (type.equals (jalview.io.AppletFormatAdapter.URL)) {
+try {
+try {
+this.checkURLSource (fileStr);
+if (this.suffixSeparator == '#') {
+this.extractSuffix (fileStr);
+}} catch (e) {
+if (Clazz.exceptionOf (e, java.io.IOException)) {
+var suffixLess = this.extractSuffix (fileStr);
+if (suffixLess == null) {
+throw (e);
+} else {
+try {
+this.checkURLSource (suffixLess);
+} catch (e2) {
+if (Clazz.exceptionOf (e2, java.io.IOException)) {
+this.errormessage = "BAD URL WITH OR WITHOUT SUFFIX";
+throw (e);
+} else {
+throw e2;
+}
+}
+}} else {
+throw e;
+}
+}
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+this.errormessage = "CANNOT ACCESS DATA AT URL '" + fileStr + "' (" + e.getMessage () + ")";
+this.error = true;
+} else {
+throw e;
+}
+}
+} else if (type.equals (jalview.io.AppletFormatAdapter.PASTE)) {
+this.errormessage = "PASTE INACCESSIBLE!";
+this.dataIn =  new java.io.BufferedReader ( new java.io.StringReader (fileStr));
+this.dataName = "Paste";
+} else if (type.equals (jalview.io.AppletFormatAdapter.CLASSLOADER)) {
+this.errormessage = "RESOURCE CANNOT BE LOCATED";
+var is = this.getClass ().getResourceAsStream ("/" + fileStr);
+if (is == null) {
+var suffixLess = this.extractSuffix (fileStr);
+if (suffixLess != null) {
+is = this.getClass ().getResourceAsStream ("/" + suffixLess);
+}}if (is != null) {
+this.dataIn =  new java.io.BufferedReader ( new java.io.InputStreamReader (is));
+this.dataName = fileStr;
+} else {
+this.error = true;
+}} else {
+this.errormessage = "PROBABLE IMPLEMENTATION ERROR : Datasource Type given as '" + (type != null ? type : "null") + "'";
+this.error = true;
+}if (this.dataIn == null || this.error) {
+throw  new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.failed_to_read_data_from_source",  Clazz.newArray (-1, [this.errormessage])));
+}this.error = false;
+this.dataIn.mark (2048);
+}, "~S,~S");
+Clazz.defineMethod (c$, "mark", 
+function () {
+if (this.dataIn != null) {
+this.dataIn.mark (2048);
+} else {
+throw  new java.io.IOException (jalview.util.MessageManager.getString ("exception.no_init_source_stream"));
+}});
+Clazz.defineMethod (c$, "nextLine", 
+function () {
+if (!this.error) {
+return this.dataIn.readLine ();
+}throw  new java.io.IOException (jalview.util.MessageManager.formatMessage ("exception.invalid_source_stream",  Clazz.newArray (-1, [this.errormessage])));
+});
+Clazz.defineMethod (c$, "isExporting", 
+function () {
+return !this.error && this.dataIn == null;
+});
+Clazz.defineMethod (c$, "isValid", 
+function () {
+return !this.error;
+});
+Clazz.defineMethod (c$, "close", 
+function () {
+this.errormessage = "EXCEPTION ON CLOSE";
+this.error = true;
+this.dataIn.close ();
+this.dataIn = null;
+this.errormessage = "SOURCE IS CLOSED";
+});
+Clazz.defineMethod (c$, "reset", 
+function () {
+if (this.dataIn != null && !this.error) {
+this.dataIn.reset ();
+} else {
+throw  new java.io.IOException (jalview.util.MessageManager.getString ("error.implementation_error_reset_called_for_invalid_source"));
+}});
+Clazz.defineMethod (c$, "hasWarningMessage", 
+function () {
+return (this.warningMessage != null && this.warningMessage.length > 0);
+});
+Clazz.defineMethod (c$, "getWarningMessage", 
+function () {
+return this.warningMessage;
+});
+Clazz.defineMethod (c$, "getInFile", 
+function () {
+if (this.inFile != null) {
+return this.inFile.getAbsolutePath () + " (" + this.index + ")";
+} else {
+return "From Paste + (" + this.index + ")";
+}});
+Clazz.defineMethod (c$, "getDataName", 
+function () {
+return this.dataName;
+});
+Clazz.defineMethod (c$, "setDataName", 
+function (dataname) {
+this.dataName = dataname;
+}, "~S");
+Clazz.defineMethod (c$, "getReader", 
+function () {
+if (this.dataIn != null) {
+return this.dataIn;
+}return null;
+});
+Clazz.defineMethod (c$, "getViewport", 
+function () {
+return this.viewport;
+});
+Clazz.defineMethod (c$, "setViewport", 
+function (viewport) {
+this.viewport = viewport;
+}, "jalview.api.AlignViewportI");
+Clazz.defineMethod (c$, "getExportSettings", 
+function () {
+return this.exportSettings;
+});
+Clazz.defineMethod (c$, "setExportSettings", 
+function (exportSettings) {
+this.exportSettings = exportSettings;
+}, "jalview.api.AlignExportSettingI");
+Clazz.defineMethod (c$, "configureForView", 
+function (avpanel) {
+if (avpanel != null) {
+this.setViewport (avpanel.getAlignViewport ());
+}}, "jalview.api.AlignmentViewPanel");
+});