X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fio%2FAppletFormatAdapter.js;h=f4dab9f79dd364538ebf30a59cb7094deb5593fa;hp=681a44d1e03f12823a2e328bd58a8ba02cf14094;hb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/io/AppletFormatAdapter.js b/bin/jalview/io/AppletFormatAdapter.js
index 681a44d..f4dab9f 100644
--- a/bin/jalview/io/AppletFormatAdapter.js
+++ b/bin/jalview/io/AppletFormatAdapter.js
@@ -1,389 +1,389 @@
-Clazz.declarePackage ("jalview.io");
-Clazz.load (null, "jalview.io.AppletFormatAdapter", ["MCview.PDBfile", "jalview.datamodel.Alignment", "jalview.io.FileParse", "$.IdentifyFile", "jalview.jsdev.GenericFileAdapter", "jalview.util.MessageManager", "java.io.IOException", "java.lang.Exception", "$.StringBuffer"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.viewpanel = null;
-this.annotFromStructure = false;
-this.localSecondaryStruct = false;
-this.serviceSecondaryStruct = false;
-this.alignFile = null;
-this.inFile = null;
-this.newline = null;
-this.exportSettings = null;
-Clazz.instantialize (this, arguments);
-}, jalview.io, "AppletFormatAdapter");
-Clazz.prepareFields (c$, function () {
-this.newline = System.getProperty ("line.separator");
-});
-Clazz.makeConstructor (c$, 
-function () {
-});
-Clazz.makeConstructor (c$, 
-function (viewpanel) {
-this.viewpanel = viewpanel;
-}, "jalview.api.AlignmentViewPanel");
-Clazz.makeConstructor (c$, 
-function (alignPanel, settings) {
-this.viewpanel = alignPanel;
-this.exportSettings = settings;
-}, "jalview.api.AlignmentViewPanel,jalview.api.AlignExportSettingI");
-c$.prettyPrint = Clazz.defineMethod (c$, "prettyPrint", 
-function (els) {
-var list =  new StringBuffer ();
-for (var i = 0, iSize = els.length - 1; i < iSize; i++) {
-list.append (els[i]);
-list.append (", ");
-}
-list.append (" and " + els[els.length - 1] + ".");
-return list.toString ();
-}, "~A");
-Clazz.defineMethod (c$, "setNewlineString", 
-function (nl) {
-this.newline = nl;
-}, "~S");
-Clazz.defineMethod (c$, "getNewlineString", 
-function () {
-return this.newline;
-});
-c$.isValidFormat = Clazz.defineMethod (c$, "isValidFormat", 
-function (format) {
-return jalview.io.AppletFormatAdapter.isValidFormat (format, false);
-}, "~S");
-c$.isValidFormat = Clazz.defineMethod (c$, "isValidFormat", 
-function (format, forwriting) {
-var valid = false;
-var format_list = (forwriting) ? jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS : jalview.io.AppletFormatAdapter.READABLE_FORMATS;
-for (var element, $element = 0, $$element = format_list; $element < $$element.length && ((element = $$element[$element]) || true); $element++) {
-if (element.equalsIgnoreCase (format)) {
-return true;
-}}
-return valid;
-}, "~S,~B");
-Clazz.defineMethod (c$, "readFile", 
-function (inFile, type, format) {
-this.inFile = inFile;
-try {
-if (format.equals ("FASTA")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", [inFile, type]);
-} else if (format.equals ("MSF")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("MSFfile", [inFile, type]);
-} else if (format.equals ("PileUp")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PileUpfile", [inFile, type]);
-} else if (format.equals ("CLUSTAL")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("ClustalFile", [inFile, type]);
-} else if (format.equals ("BLC")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("BLCFile", [inFile, type]);
-} else if (format.equals ("PIR")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PIRFile", [inFile, type]);
-} else if (format.equals ("PFAM")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PfamFile", [inFile, type]);
-} else if (format.equals ("JnetFile")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("JPredFile", [inFile, type]);
-(this.alignFile).removeNonSequences ();
-} else if (format.equals ("PDB")) {
-this.alignFile =  new MCview.PDBfile (this.annotFromStructure, this.localSecondaryStruct, this.serviceSecondaryStruct, inFile, type);
-} else if (format.equals ("STH")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("StockholmFile", [inFile, type]);
-} else if (format.equals ("SimpleBLAST")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("SimpleBlastFile", [inFile, type]);
-} else if (format.equals ("PHYLIP")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PhylipFile", [inFile, type]);
-} else if (format.equals ("JSON")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("JSONFile", [inFile, type]);
-} else if (format.equals ("HTML")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("HtmlFile", [inFile, type]);
-} else if (format.equals ("RNAML")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("RnamlFile", [inFile, type]);
-} else if (format.equals ("GFF v2 or v3")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("Gff3File", [inFile, type]);
-}return this.buildAlignmentFrom (this.alignFile);
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-e.printStackTrace ();
-System.err.println ("Failed to read alignment using the '" + format + "' reader.\n" + e);
-if (e.getMessage () != null && e.getMessage ().startsWith (jalview.io.AppletFormatAdapter.INVALID_CHARACTERS)) {
-throw  new java.io.IOException (e.getMessage ());
-}if (type.equalsIgnoreCase ("Paste")) {
-try {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", [">UNKNOWN\n" + inFile, "Paste"]);
-return this.buildAlignmentFrom (this.alignFile);
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-if (ex.toString ().startsWith (jalview.io.AppletFormatAdapter.INVALID_CHARACTERS)) {
-throw  new java.io.IOException (e.getMessage ());
-}ex.printStackTrace ();
-} else {
-throw ex;
-}
-}
-}throw  new java.io.IOException (jalview.io.AppletFormatAdapter.SUPPORTED_FORMATS);
-} else {
-throw e;
-}
-}
-}, "~S,~S,~S");
-Clazz.defineMethod (c$, "readFromFile", 
-function (source, format) {
-this.inFile = source.getInFile ();
-var type = source.type;
-try {
-if (format.equals ("FASTA")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", [source]);
-} else if (format.equals ("MSF")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("MSFfile", [source]);
-} else if (format.equals ("PileUp")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PileUpfile", [source]);
-} else if (format.equals ("CLUSTAL")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("ClustalFile", [source]);
-} else if (format.equals ("BLC")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("BLCFile", [source]);
-} else if (format.equals ("PIR")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PIRFile", [source]);
-} else if (format.equals ("PFAM")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PfamFile", [source]);
-} else if (format.equals ("JnetFile")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("JPredFile", [source]);
-(this.alignFile).removeNonSequences ();
-} else if (format.equals ("PDB")) {
-this.alignFile =  new MCview.PDBfile (this.annotFromStructure, this.localSecondaryStruct, this.serviceSecondaryStruct, source);
-} else if (format.equals ("STH")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("StockholmFile", [source]);
-} else if (format.equals ("RNAML")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("RnamlFile", [source]);
-} else if (format.equals ("SimpleBLAST")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("SimpleBlastFile", [source]);
-} else if (format.equals ("PHYLIP")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PhylipFile", [source]);
-} else if (format.equals ("GFF v2 or v3")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("Gff3File", [this.inFile, type]);
-} else if (format.equals ("JSON")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("JSONFile", [source]);
-} else if (format.equals ("HTML")) {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("HtmlFile", [source]);
-}return this.buildAlignmentFrom (this.alignFile);
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-e.printStackTrace ();
-System.err.println ("Failed to read alignment using the '" + format + "' reader.\n" + e);
-if (e.getMessage () != null && e.getMessage ().startsWith (jalview.io.AppletFormatAdapter.INVALID_CHARACTERS)) {
-throw  new java.io.IOException (e.getMessage ());
-}if (type.equalsIgnoreCase ("Paste")) {
-try {
-this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", [">UNKNOWN\n" + this.inFile, "Paste"]);
-return this.buildAlignmentFrom (this.alignFile);
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-if (ex.toString ().startsWith (jalview.io.AppletFormatAdapter.INVALID_CHARACTERS)) {
-throw  new java.io.IOException (e.getMessage ());
-}ex.printStackTrace ();
-} else {
-throw ex;
-}
-}
-}throw  new java.io.IOException (jalview.io.AppletFormatAdapter.SUPPORTED_FORMATS);
-} else {
-throw e;
-}
-}
-}, "jalview.io.FileParse,~S");
-Clazz.defineMethod (c$, "buildAlignmentFrom", 
-($fz = function (alignFile2) {
-var al =  new jalview.datamodel.Alignment (this.alignFile.getSeqsAsArray ());
-this.alignFile.addAnnotations (al);
-this.alignFile.addGroups (al);
-return al;
-}, $fz.isPrivate = true, $fz), "jalview.io.AlignFile");
-Clazz.defineMethod (c$, "formatSequences", 
-function (format, jvsuffix, ap, selectedOnly) {
-var selvew = ap.getAlignViewport ().getAlignmentView (selectedOnly, false);
-var aselview = selvew.getVisibleAlignment (ap.getAlignViewport ().getGapCharacter ());
-var ala = (ap.getAlignViewport ().getVisibleAlignmentAnnotation (selectedOnly));
-if (ala != null) {
-for (var aa, $aa = ala.iterator (); $aa.hasNext () && ((aa = $aa.next ()) || true);) {
-aselview.addAnnotation (aa);
-}
-}this.viewpanel = ap;
-return this.formatSequences (format, aselview, jvsuffix);
-}, "~S,~B,jalview.api.AlignmentViewPanel,~B");
-Clazz.defineMethod (c$, "formatSequences", 
-function (format, alignment, jvsuffix) {
-try {
-var afile = null;
-if (format.equalsIgnoreCase ("FASTA")) {
-afile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", []);
-} else if (format.equalsIgnoreCase ("MSF")) {
-afile = jalview.jsdev.GenericFileAdapter.getFile ("MSFfile", []);
-} else if (format.equalsIgnoreCase ("PileUp")) {
-afile = jalview.jsdev.GenericFileAdapter.getFile ("PileUpfile", []);
-} else if (format.equalsIgnoreCase ("CLUSTAL")) {
-afile = jalview.jsdev.GenericFileAdapter.getFile ("ClustalFile", []);
-} else if (format.equalsIgnoreCase ("BLC")) {
-afile = jalview.jsdev.GenericFileAdapter.getFile ("BLCFile", []);
-} else if (format.equalsIgnoreCase ("PIR")) {
-afile = jalview.jsdev.GenericFileAdapter.getFile ("PIRFile", []);
-} else if (format.equalsIgnoreCase ("PFAM")) {
-afile = jalview.jsdev.GenericFileAdapter.getFile ("PfamFile", []);
-} else if (format.equalsIgnoreCase ("STH")) {
-afile = jalview.jsdev.GenericFileAdapter.getFile ("StockholmFile", [alignment]);
-} else if (format.equalsIgnoreCase ("AMSA")) {
-afile = jalview.jsdev.GenericFileAdapter.getFile ("AMSAFile", [alignment]);
-} else if (format.equalsIgnoreCase ("PHYLIP")) {
-afile = jalview.jsdev.GenericFileAdapter.getFile ("PhylipFile", []);
-} else if (format.equalsIgnoreCase ("JSON")) {
-afile = jalview.jsdev.GenericFileAdapter.getFile ("JSONFile", []);
-} else if (format.equalsIgnoreCase ("RNAML")) {
-afile = jalview.jsdev.GenericFileAdapter.getFile ("RnamlFile", []);
-} else {
-throw  new Exception (jalview.util.MessageManager.getString ("error.implementation_error_unknown_file_format_string"));
-}afile.setNewlineString (this.newline);
-afile.addJVSuffix (jvsuffix);
-afile.setExportSettings (this.exportSettings);
-afile.configureForView (this.viewpanel);
-if (this.viewpanel == null || this.viewpanel.getAlignment () == null || this.viewpanel.getAlignment () !== alignment) {
-afile.setSeqs (alignment.getSequencesArray ());
-} else {
-afile.setSeqs (this.viewpanel.getAlignment ().getSequencesArray ());
-}var afileresp = afile.print ();
-if (afile.hasWarningMessage ()) {
-System.err.println ("Warning raised when writing as " + format + " : " + afile.getWarningMessage ());
-}return afileresp;
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-System.err.println ("Failed to write alignment as a '" + format + "' file\n");
-e.printStackTrace ();
-} else {
-throw e;
-}
-}
-return null;
-}, "~S,jalview.datamodel.AlignmentI,~B");
-c$.checkProtocol = Clazz.defineMethod (c$, "checkProtocol", 
-function (file) {
-var protocol = jalview.io.AppletFormatAdapter.FILE;
-var ft = file.toLowerCase ().trim ();
-if (ft.indexOf ("http:") == 0 || ft.indexOf ("https:") == 0 || ft.indexOf ("file:") == 0) {
-protocol = jalview.io.AppletFormatAdapter.URL;
-}return protocol;
-}, "~S");
-c$.resolveProtocol = Clazz.defineMethod (c$, "resolveProtocol", 
-function (file, format) {
-return jalview.io.AppletFormatAdapter.resolveProtocol (file, format, false);
-}, "~S,~S");
-c$.resolveProtocol = Clazz.defineMethod (c$, "resolveProtocol", 
-function (file, format, debug) {
-var protocol = null;
-if (debug) {
-System.out.println ("resolving datasource started with:\n>>file\n" + file + ">>endfile");
-}try {
-var rtn = false;
-var is = System.getSecurityManager ().getClass ().getResourceAsStream ("/" + file);
-if (is != null) {
-rtn = true;
-is.close ();
-}if (debug) {
-System.err.println ("Resource '" + file + "' was " + (rtn ? "" : "not") + " located by classloader.");
-};if (rtn) {
-protocol = jalview.io.AppletFormatAdapter.CLASSLOADER;
-}} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-System.err.println ("Exception checking resources: " + file + " " + ex);
-} else {
-throw ex;
-}
-}
-if (file.indexOf ("://") > -1) {
-protocol = jalview.io.AppletFormatAdapter.URL;
-} else {
-protocol = jalview.io.AppletFormatAdapter.FILE;
-}var fp = null;
-try {
-if (debug) {
-System.out.println ("Trying to get contents of resource as " + protocol + ":");
-}fp =  new jalview.io.FileParse (file, protocol);
-if (!fp.isValid ()) {
-fp = null;
-} else {
-if (debug) {
-System.out.println ("Successful.");
-}}} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-if (debug) {
-System.err.println ("Exception when accessing content: " + e);
-}fp = null;
-} else {
-throw e;
-}
-}
-if (fp == null) {
-if (debug) {
-System.out.println ("Accessing as paste.");
-}protocol = jalview.io.AppletFormatAdapter.PASTE;
-fp = null;
-try {
-fp =  new jalview.io.FileParse (file, protocol);
-if (!fp.isValid ()) {
-fp = null;
-}} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-System.err.println ("Failed to access content as paste!");
-e.printStackTrace ();
-fp = null;
-} else {
-throw e;
-}
-}
-}if (fp == null) {
-return null;
-}if (format == null || format.length == 0) {
-return protocol;
-} else {
-try {
-var idformat =  new jalview.io.IdentifyFile ().Identify (file, protocol);
-if (idformat == null) {
-if (debug) {
-System.out.println ("Format not identified. Inaccessible file.");
-}return null;
-}if (debug) {
-System.out.println ("Format identified as " + idformat + "and expected as " + format);
-}if (idformat.equals (format)) {
-if (debug) {
-System.out.println ("Protocol identified as " + protocol);
-}return protocol;
-} else {
-if (debug) {
-System.out.println ("File deemed not accessible via " + protocol);
-}fp.close ();
-return null;
-}} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-if (debug) {
-System.err.println ("File deemed not accessible via " + protocol);
-e.printStackTrace ();
-};} else {
-throw e;
-}
-}
-}return null;
-}, "~S,~S,~B");
-Clazz.defineMethod (c$, "getAlignFile", 
-function () {
-return this.alignFile;
-});
-Clazz.defineMethod (c$, "setAlignFile", 
-function (alignFile) {
-this.alignFile = alignFile;
-}, "jalview.io.AlignFile");
-Clazz.defineStatics (c$,
-"FILE", "File",
-"URL", "URL",
-"PASTE", "Paste",
-"CLASSLOADER", "ClassLoader");
-c$.READABLE_FORMATS = c$.prototype.READABLE_FORMATS =  Clazz.newArray (-1, ["BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB", "JnetFile", "RNAML", "PHYLIP", "JSON", "GFF v2 or v3", "HTML"]);
-c$.READABLE_EXTENSIONS = c$.prototype.READABLE_EXTENSIONS =  Clazz.newArray (-1, ["fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "sto,stk", "xml,rnaml", "phy", "json", ".gff2,gff3", "jar,jvp", "html"]);
-c$.READABLE_FNAMES = c$.prototype.READABLE_FNAMES =  Clazz.newArray (-1, ["Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML", "PHYLIP", "JSON", "GFF v2 or v3", "Jalview", "HTML"]);
-c$.WRITEABLE_FORMATS = c$.prototype.WRITEABLE_FORMATS =  Clazz.newArray (-1, ["BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH", "PHYLIP", "JSON"]);
-c$.WRITABLE_EXTENSIONS = c$.prototype.WRITABLE_EXTENSIONS =  Clazz.newArray (-1, ["fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "sto,stk", "phy", "json", "jvp"]);
-c$.WRITABLE_FNAMES = c$.prototype.WRITABLE_FNAMES =  Clazz.newArray (-1, ["Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH", "PHYLIP", "JSON", "Jalview"]);
-Clazz.defineStatics (c$,
-"INVALID_CHARACTERS", "Contains invalid characters");
-c$.SUPPORTED_FORMATS = c$.prototype.SUPPORTED_FORMATS = "Formats currently supported are\n" + jalview.io.AppletFormatAdapter.prettyPrint (jalview.io.AppletFormatAdapter.READABLE_FORMATS);
-});
+Clazz.declarePackage ("jalview.io");
+Clazz.load (null, "jalview.io.AppletFormatAdapter", ["MCview.PDBfile", "jalview.datamodel.Alignment", "jalview.io.FileParse", "$.IdentifyFile", "jalview.jsdev.GenericFileAdapter", "jalview.util.MessageManager", "java.io.IOException", "java.lang.Exception", "$.StringBuffer"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.viewpanel = null;
+this.annotFromStructure = false;
+this.localSecondaryStruct = false;
+this.serviceSecondaryStruct = false;
+this.alignFile = null;
+this.inFile = null;
+this.newline = null;
+this.exportSettings = null;
+Clazz.instantialize (this, arguments);
+}, jalview.io, "AppletFormatAdapter");
+Clazz.prepareFields (c$, function () {
+this.newline = System.getProperty ("line.separator");
+});
+Clazz.makeConstructor (c$, 
+function () {
+});
+Clazz.makeConstructor (c$, 
+function (viewpanel) {
+this.viewpanel = viewpanel;
+}, "jalview.api.AlignmentViewPanel");
+Clazz.makeConstructor (c$, 
+function (alignPanel, settings) {
+this.viewpanel = alignPanel;
+this.exportSettings = settings;
+}, "jalview.api.AlignmentViewPanel,jalview.api.AlignExportSettingI");
+c$.prettyPrint = Clazz.defineMethod (c$, "prettyPrint", 
+function (els) {
+var list =  new StringBuffer ();
+for (var i = 0, iSize = els.length - 1; i < iSize; i++) {
+list.append (els[i]);
+list.append (", ");
+}
+list.append (" and " + els[els.length - 1] + ".");
+return list.toString ();
+}, "~A");
+Clazz.defineMethod (c$, "setNewlineString", 
+function (nl) {
+this.newline = nl;
+}, "~S");
+Clazz.defineMethod (c$, "getNewlineString", 
+function () {
+return this.newline;
+});
+c$.isValidFormat = Clazz.defineMethod (c$, "isValidFormat", 
+function (format) {
+return jalview.io.AppletFormatAdapter.isValidFormat (format, false);
+}, "~S");
+c$.isValidFormat = Clazz.defineMethod (c$, "isValidFormat", 
+function (format, forwriting) {
+var valid = false;
+var format_list = (forwriting) ? jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS : jalview.io.AppletFormatAdapter.READABLE_FORMATS;
+for (var element, $element = 0, $$element = format_list; $element < $$element.length && ((element = $$element[$element]) || true); $element++) {
+if (element.equalsIgnoreCase (format)) {
+return true;
+}}
+return valid;
+}, "~S,~B");
+Clazz.defineMethod (c$, "readFile", 
+function (inFile, type, format) {
+this.inFile = inFile;
+try {
+if (format.equals ("FASTA")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", [inFile, type]);
+} else if (format.equals ("MSF")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("MSFfile", [inFile, type]);
+} else if (format.equals ("PileUp")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PileUpfile", [inFile, type]);
+} else if (format.equals ("CLUSTAL")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("ClustalFile", [inFile, type]);
+} else if (format.equals ("BLC")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("BLCFile", [inFile, type]);
+} else if (format.equals ("PIR")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PIRFile", [inFile, type]);
+} else if (format.equals ("PFAM")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PfamFile", [inFile, type]);
+} else if (format.equals ("JnetFile")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("JPredFile", [inFile, type]);
+(this.alignFile).removeNonSequences ();
+} else if (format.equals ("PDB")) {
+this.alignFile =  new MCview.PDBfile (this.annotFromStructure, this.localSecondaryStruct, this.serviceSecondaryStruct, inFile, type);
+} else if (format.equals ("STH")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("StockholmFile", [inFile, type]);
+} else if (format.equals ("SimpleBLAST")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("SimpleBlastFile", [inFile, type]);
+} else if (format.equals ("PHYLIP")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PhylipFile", [inFile, type]);
+} else if (format.equals ("JSON")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("JSONFile", [inFile, type]);
+} else if (format.equals ("HTML")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("HtmlFile", [inFile, type]);
+} else if (format.equals ("RNAML")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("RnamlFile", [inFile, type]);
+} else if (format.equals ("GFF v2 or v3")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("Gff3File", [inFile, type]);
+}return this.buildAlignmentFrom (this.alignFile);
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+e.printStackTrace ();
+System.err.println ("Failed to read alignment using the '" + format + "' reader.\n" + e);
+if (e.getMessage () != null && e.getMessage ().startsWith (jalview.io.AppletFormatAdapter.INVALID_CHARACTERS)) {
+throw  new java.io.IOException (e.getMessage ());
+}if (type.equalsIgnoreCase ("Paste")) {
+try {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", [">UNKNOWN\n" + inFile, "Paste"]);
+return this.buildAlignmentFrom (this.alignFile);
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+if (ex.toString ().startsWith (jalview.io.AppletFormatAdapter.INVALID_CHARACTERS)) {
+throw  new java.io.IOException (e.getMessage ());
+}ex.printStackTrace ();
+} else {
+throw ex;
+}
+}
+}throw  new java.io.IOException (jalview.io.AppletFormatAdapter.SUPPORTED_FORMATS);
+} else {
+throw e;
+}
+}
+}, "~S,~S,~S");
+Clazz.defineMethod (c$, "readFromFile", 
+function (source, format) {
+this.inFile = source.getInFile ();
+var type = source.type;
+try {
+if (format.equals ("FASTA")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", [source]);
+} else if (format.equals ("MSF")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("MSFfile", [source]);
+} else if (format.equals ("PileUp")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PileUpfile", [source]);
+} else if (format.equals ("CLUSTAL")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("ClustalFile", [source]);
+} else if (format.equals ("BLC")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("BLCFile", [source]);
+} else if (format.equals ("PIR")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PIRFile", [source]);
+} else if (format.equals ("PFAM")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PfamFile", [source]);
+} else if (format.equals ("JnetFile")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("JPredFile", [source]);
+(this.alignFile).removeNonSequences ();
+} else if (format.equals ("PDB")) {
+this.alignFile =  new MCview.PDBfile (this.annotFromStructure, this.localSecondaryStruct, this.serviceSecondaryStruct, source);
+} else if (format.equals ("STH")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("StockholmFile", [source]);
+} else if (format.equals ("RNAML")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("RnamlFile", [source]);
+} else if (format.equals ("SimpleBLAST")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("SimpleBlastFile", [source]);
+} else if (format.equals ("PHYLIP")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("PhylipFile", [source]);
+} else if (format.equals ("GFF v2 or v3")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("Gff3File", [this.inFile, type]);
+} else if (format.equals ("JSON")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("JSONFile", [source]);
+} else if (format.equals ("HTML")) {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("HtmlFile", [source]);
+}return this.buildAlignmentFrom (this.alignFile);
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+e.printStackTrace ();
+System.err.println ("Failed to read alignment using the '" + format + "' reader.\n" + e);
+if (e.getMessage () != null && e.getMessage ().startsWith (jalview.io.AppletFormatAdapter.INVALID_CHARACTERS)) {
+throw  new java.io.IOException (e.getMessage ());
+}if (type.equalsIgnoreCase ("Paste")) {
+try {
+this.alignFile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", [">UNKNOWN\n" + this.inFile, "Paste"]);
+return this.buildAlignmentFrom (this.alignFile);
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+if (ex.toString ().startsWith (jalview.io.AppletFormatAdapter.INVALID_CHARACTERS)) {
+throw  new java.io.IOException (e.getMessage ());
+}ex.printStackTrace ();
+} else {
+throw ex;
+}
+}
+}throw  new java.io.IOException (jalview.io.AppletFormatAdapter.SUPPORTED_FORMATS);
+} else {
+throw e;
+}
+}
+}, "jalview.io.FileParse,~S");
+Clazz.defineMethod (c$, "buildAlignmentFrom", 
+($fz = function (alignFile2) {
+var al =  new jalview.datamodel.Alignment (this.alignFile.getSeqsAsArray ());
+this.alignFile.addAnnotations (al);
+this.alignFile.addGroups (al);
+return al;
+}, $fz.isPrivate = true, $fz), "jalview.io.AlignFile");
+Clazz.defineMethod (c$, "formatSequences", 
+function (format, jvsuffix, ap, selectedOnly) {
+var selvew = ap.getAlignViewport ().getAlignmentView (selectedOnly, false);
+var aselview = selvew.getVisibleAlignment (ap.getAlignViewport ().getGapCharacter ());
+var ala = (ap.getAlignViewport ().getVisibleAlignmentAnnotation (selectedOnly));
+if (ala != null) {
+for (var aa, $aa = ala.iterator (); $aa.hasNext () && ((aa = $aa.next ()) || true);) {
+aselview.addAnnotation (aa);
+}
+}this.viewpanel = ap;
+return this.formatSequences (format, aselview, jvsuffix);
+}, "~S,~B,jalview.api.AlignmentViewPanel,~B");
+Clazz.defineMethod (c$, "formatSequences", 
+function (format, alignment, jvsuffix) {
+try {
+var afile = null;
+if (format.equalsIgnoreCase ("FASTA")) {
+afile = jalview.jsdev.GenericFileAdapter.getFile ("FastaFile", []);
+} else if (format.equalsIgnoreCase ("MSF")) {
+afile = jalview.jsdev.GenericFileAdapter.getFile ("MSFfile", []);
+} else if (format.equalsIgnoreCase ("PileUp")) {
+afile = jalview.jsdev.GenericFileAdapter.getFile ("PileUpfile", []);
+} else if (format.equalsIgnoreCase ("CLUSTAL")) {
+afile = jalview.jsdev.GenericFileAdapter.getFile ("ClustalFile", []);
+} else if (format.equalsIgnoreCase ("BLC")) {
+afile = jalview.jsdev.GenericFileAdapter.getFile ("BLCFile", []);
+} else if (format.equalsIgnoreCase ("PIR")) {
+afile = jalview.jsdev.GenericFileAdapter.getFile ("PIRFile", []);
+} else if (format.equalsIgnoreCase ("PFAM")) {
+afile = jalview.jsdev.GenericFileAdapter.getFile ("PfamFile", []);
+} else if (format.equalsIgnoreCase ("STH")) {
+afile = jalview.jsdev.GenericFileAdapter.getFile ("StockholmFile", [alignment]);
+} else if (format.equalsIgnoreCase ("AMSA")) {
+afile = jalview.jsdev.GenericFileAdapter.getFile ("AMSAFile", [alignment]);
+} else if (format.equalsIgnoreCase ("PHYLIP")) {
+afile = jalview.jsdev.GenericFileAdapter.getFile ("PhylipFile", []);
+} else if (format.equalsIgnoreCase ("JSON")) {
+afile = jalview.jsdev.GenericFileAdapter.getFile ("JSONFile", []);
+} else if (format.equalsIgnoreCase ("RNAML")) {
+afile = jalview.jsdev.GenericFileAdapter.getFile ("RnamlFile", []);
+} else {
+throw  new Exception (jalview.util.MessageManager.getString ("error.implementation_error_unknown_file_format_string"));
+}afile.setNewlineString (this.newline);
+afile.addJVSuffix (jvsuffix);
+afile.setExportSettings (this.exportSettings);
+afile.configureForView (this.viewpanel);
+if (this.viewpanel == null || this.viewpanel.getAlignment () == null || this.viewpanel.getAlignment () !== alignment) {
+afile.setSeqs (alignment.getSequencesArray ());
+} else {
+afile.setSeqs (this.viewpanel.getAlignment ().getSequencesArray ());
+}var afileresp = afile.print ();
+if (afile.hasWarningMessage ()) {
+System.err.println ("Warning raised when writing as " + format + " : " + afile.getWarningMessage ());
+}return afileresp;
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+System.err.println ("Failed to write alignment as a '" + format + "' file\n");
+e.printStackTrace ();
+} else {
+throw e;
+}
+}
+return null;
+}, "~S,jalview.datamodel.AlignmentI,~B");
+c$.checkProtocol = Clazz.defineMethod (c$, "checkProtocol", 
+function (file) {
+var protocol = jalview.io.AppletFormatAdapter.FILE;
+var ft = file.toLowerCase ().trim ();
+if (ft.indexOf ("http:") == 0 || ft.indexOf ("https:") == 0 || ft.indexOf ("file:") == 0) {
+protocol = jalview.io.AppletFormatAdapter.URL;
+}return protocol;
+}, "~S");
+c$.resolveProtocol = Clazz.defineMethod (c$, "resolveProtocol", 
+function (file, format) {
+return jalview.io.AppletFormatAdapter.resolveProtocol (file, format, false);
+}, "~S,~S");
+c$.resolveProtocol = Clazz.defineMethod (c$, "resolveProtocol", 
+function (file, format, debug) {
+var protocol = null;
+if (debug) {
+System.out.println ("resolving datasource started with:\n>>file\n" + file + ">>endfile");
+}try {
+var rtn = false;
+var is = System.getSecurityManager ().getClass ().getResourceAsStream ("/" + file);
+if (is != null) {
+rtn = true;
+is.close ();
+}if (debug) {
+System.err.println ("Resource '" + file + "' was " + (rtn ? "" : "not") + " located by classloader.");
+};if (rtn) {
+protocol = jalview.io.AppletFormatAdapter.CLASSLOADER;
+}} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+System.err.println ("Exception checking resources: " + file + " " + ex);
+} else {
+throw ex;
+}
+}
+if (file.indexOf ("://") > -1) {
+protocol = jalview.io.AppletFormatAdapter.URL;
+} else {
+protocol = jalview.io.AppletFormatAdapter.FILE;
+}var fp = null;
+try {
+if (debug) {
+System.out.println ("Trying to get contents of resource as " + protocol + ":");
+}fp =  new jalview.io.FileParse (file, protocol);
+if (!fp.isValid ()) {
+fp = null;
+} else {
+if (debug) {
+System.out.println ("Successful.");
+}}} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+if (debug) {
+System.err.println ("Exception when accessing content: " + e);
+}fp = null;
+} else {
+throw e;
+}
+}
+if (fp == null) {
+if (debug) {
+System.out.println ("Accessing as paste.");
+}protocol = jalview.io.AppletFormatAdapter.PASTE;
+fp = null;
+try {
+fp =  new jalview.io.FileParse (file, protocol);
+if (!fp.isValid ()) {
+fp = null;
+}} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+System.err.println ("Failed to access content as paste!");
+e.printStackTrace ();
+fp = null;
+} else {
+throw e;
+}
+}
+}if (fp == null) {
+return null;
+}if (format == null || format.length == 0) {
+return protocol;
+} else {
+try {
+var idformat =  new jalview.io.IdentifyFile ().Identify (file, protocol);
+if (idformat == null) {
+if (debug) {
+System.out.println ("Format not identified. Inaccessible file.");
+}return null;
+}if (debug) {
+System.out.println ("Format identified as " + idformat + "and expected as " + format);
+}if (idformat.equals (format)) {
+if (debug) {
+System.out.println ("Protocol identified as " + protocol);
+}return protocol;
+} else {
+if (debug) {
+System.out.println ("File deemed not accessible via " + protocol);
+}fp.close ();
+return null;
+}} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+if (debug) {
+System.err.println ("File deemed not accessible via " + protocol);
+e.printStackTrace ();
+};} else {
+throw e;
+}
+}
+}return null;
+}, "~S,~S,~B");
+Clazz.defineMethod (c$, "getAlignFile", 
+function () {
+return this.alignFile;
+});
+Clazz.defineMethod (c$, "setAlignFile", 
+function (alignFile) {
+this.alignFile = alignFile;
+}, "jalview.io.AlignFile");
+Clazz.defineStatics (c$,
+"FILE", "File",
+"URL", "URL",
+"PASTE", "Paste",
+"CLASSLOADER", "ClassLoader");
+c$.READABLE_FORMATS = c$.prototype.READABLE_FORMATS =  Clazz.newArray (-1, ["BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB", "JnetFile", "RNAML", "PHYLIP", "JSON", "GFF v2 or v3", "HTML"]);
+c$.READABLE_EXTENSIONS = c$.prototype.READABLE_EXTENSIONS =  Clazz.newArray (-1, ["fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "sto,stk", "xml,rnaml", "phy", "json", ".gff2,gff3", "jar,jvp", "html"]);
+c$.READABLE_FNAMES = c$.prototype.READABLE_FNAMES =  Clazz.newArray (-1, ["Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML", "PHYLIP", "JSON", "GFF v2 or v3", "Jalview", "HTML"]);
+c$.WRITEABLE_FORMATS = c$.prototype.WRITEABLE_FORMATS =  Clazz.newArray (-1, ["BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH", "PHYLIP", "JSON"]);
+c$.WRITABLE_EXTENSIONS = c$.prototype.WRITABLE_EXTENSIONS =  Clazz.newArray (-1, ["fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "sto,stk", "phy", "json", "jvp"]);
+c$.WRITABLE_FNAMES = c$.prototype.WRITABLE_FNAMES =  Clazz.newArray (-1, ["Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH", "PHYLIP", "JSON", "Jalview"]);
+Clazz.defineStatics (c$,
+"INVALID_CHARACTERS", "Contains invalid characters");
+c$.SUPPORTED_FORMATS = c$.prototype.SUPPORTED_FORMATS = "Formats currently supported are\n" + jalview.io.AppletFormatAdapter.prettyPrint (jalview.io.AppletFormatAdapter.READABLE_FORMATS);
+});