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