- /*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
- package jalview.io;\r
-\r
- import jalview.datamodel.*;\r
-\r
- import java.util.Vector;\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
- public class AppletFormatAdapter\r
- {\r
- /** DOCUMENT ME!! */\r
- public static final Vector formats = new Vector();\r
-\r
- public static String INVALID_CHARACTERS = "Contains invalid characters";\r
-\r
- public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +\r
- "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM";\r
-\r
- static\r
- {\r
- formats.addElement("BLC");\r
- formats.addElement("CLUSTAL");\r
- formats.addElement("FASTA");\r
- formats.addElement("MSF");\r
- formats.addElement("PileUp");\r
- formats.addElement("PIR");\r
- formats.addElement("PFAM");\r
- }\r
-\r
- AlignFile afile = null;\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param inFile DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- * @param format DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceI[] readFile(String inFile, String type, String format)\r
- throws java.io.IOException\r
- {\r
- try\r
- {\r
- if (format.equals("FASTA"))\r
- {\r
- afile = new FastaFile(inFile, type);\r
- }\r
- else if (format.equals("MSF"))\r
- {\r
- afile = new MSFfile(inFile, type);\r
- }\r
- else if (format.equals("PileUp"))\r
- {\r
- afile = new PileUpfile(inFile, type);\r
- }\r
- else if (format.equals("CLUSTAL"))\r
- {\r
- afile = new ClustalFile(inFile, type);\r
- }\r
- else if (format.equals("BLC"))\r
- {\r
- afile = new BLCFile(inFile, type);\r
- }\r
- else if (format.equals("PIR"))\r
- {\r
- afile = new PIRFile(inFile, type);\r
- }\r
- else if (format.equals("PFAM"))\r
- {\r
- afile = new PfamFile(inFile, type);\r
- }\r
-\r
- return afile.getSeqsAsArray();\r
- }\r
- catch (Exception e)\r
- {\r
- System.err.println("Failed to read alignment using the '" + format +\r
- "' reader.\n"+e);\r
-\r
- if(e.getMessage()!=null && e.getMessage().startsWith(INVALID_CHARACTERS))\r
- throw new java.io.IOException(e.getMessage());\r
-\r
- // Finally test if the user has pasted just the sequence, no id\r
- if(type.equalsIgnoreCase("Paste"))\r
- {\r
- try{\r
- // Possible sequence is just residues with no label\r
- afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");\r
- return afile.getSeqsAsArray();\r
- }\r
- catch(Exception ex)\r
- {\r
- if(ex.toString().startsWith(INVALID_CHARACTERS))\r
- throw new java.io.IOException(e.getMessage());\r
-\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- // If we get to this stage, the format was not supported\r
- throw new java.io.IOException(SUPPORTED_FORMATS);\r
- }\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param format DOCUMENT ME!\r
- * @param seqs DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String formatSequences(String format,\r
- Vector seqs,\r
- boolean jvsuffix)\r
- {\r
- SequenceI[] s = new SequenceI[seqs.size()];\r
-\r
- for (int i = 0; i < seqs.size(); i++)\r
- s[i] = (SequenceI) seqs.elementAt(i);\r
-\r
- try\r
- {\r
- AlignFile afile = null;\r
-\r
- if (format.equalsIgnoreCase("FASTA"))\r
- {\r
- afile = new FastaFile();\r
- }\r
- else if (format.equalsIgnoreCase("MSF"))\r
- {\r
- afile = new MSFfile();\r
- }\r
- else if (format.equalsIgnoreCase("PileUp"))\r
- {\r
- afile = new PileUpfile();\r
- }\r
- else if (format.equalsIgnoreCase("CLUSTAL"))\r
- {\r
- afile = new ClustalFile();\r
- }\r
- else if (format.equalsIgnoreCase("BLC"))\r
- {\r
- afile = new BLCFile();\r
- }\r
- else if (format.equalsIgnoreCase("PIR"))\r
- {\r
- afile = new PIRFile();\r
- }\r
- else if (format.equalsIgnoreCase("PFAM"))\r
- {\r
- afile = new PfamFile();\r
- }\r
-\r
- afile.addJVSuffix(jvsuffix);\r
-\r
- afile.setSeqs(s);\r
-\r
- return afile.print();\r
- }\r
- catch (Exception e)\r
- {\r
- System.err.println("Failed to write alignment as a '" + format +\r
- "' file\n");\r
- e.printStackTrace();\r
- }\r
-\r
- return null;\r
- }\r
- }\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import java.util.Locale;
+
+import jalview.api.AlignExportSettingsI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SeqDistanceContactMatrix;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
+import jalview.structure.StructureImportSettings;
+import jalview.util.Platform;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.List;
+
+/**
+ * A low level class for alignment and feature IO with alignment formatting
+ * methods used by both applet and application for generating flat alignment
+ * files. It also holds the lists of magic format names that the applet and
+ * application will allow the user to read or write files with.
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AppletFormatAdapter
+{
+ private AlignmentViewPanel viewpanel;
+
+ /**
+ * add jalview-derived non-secondary structure annotation from PDB structure
+ */
+ boolean annotFromStructure = false;
+
+ /**
+ * add secondary structure from PDB data with built-in algorithms
+ */
+ boolean localSecondaryStruct = false;
+
+ /**
+ * process PDB data with web services
+ */
+ boolean serviceSecondaryStruct = false;
+
+ private AlignmentFileReaderI alignFile = null;
+
+ String inFile;
+
+ /**
+ * character used to write newlines
+ */
+ protected String newline = System.getProperty("line.separator");
+
+ private AlignExportSettingsI exportSettings;
+
+ private File selectedFile;
+
+ public static String INVALID_CHARACTERS = "Contains invalid characters";
+
+ /**
+ * Returns an error message with a list of supported readable file formats
+ *
+ * @return
+ */
+ public static String getSupportedFormats()
+ {
+ return "Formats currently supported are\n"
+ + prettyPrint(FileFormats.getInstance().getReadableFormats());
+ }
+
+ public AppletFormatAdapter()
+ {
+ }
+
+ public AppletFormatAdapter(AlignmentViewPanel viewpanel)
+ {
+ this.viewpanel = viewpanel;
+ }
+
+ public AppletFormatAdapter(AlignmentViewPanel alignPanel,
+ AlignExportSettingsI settings)
+ {
+ viewpanel = alignPanel;
+ exportSettings = settings;
+ }
+
+ /**
+ * Formats a grammatically correct(ish) list consisting of the given objects
+ *
+ * @param things
+ * @return
+ */
+ public static String prettyPrint(List<? extends Object> things)
+ {
+ StringBuffer list = new StringBuffer();
+ for (int i = 0, iSize = things.size() - 1; i < iSize; i++)
+ {
+ list.append(things.get(i).toString());
+ list.append(", ");
+ }
+ // could i18n 'and' here
+ list.append(" and " + things.get(things.size() - 1).toString() + ".");
+ return list.toString();
+ }
+
+ public void setNewlineString(String nl)
+ {
+ newline = nl;
+ }
+
+ public String getNewlineString()
+ {
+ return newline;
+ }
+
+ /**
+ * Constructs the correct filetype parser for a characterised datasource
+ *
+ * @param inFile
+ * data/data location
+ * @param sourceType
+ * type of datasource
+ * @param fileFormat
+ *
+ * @return
+ */
+ public AlignmentI readFile(String file, DataSourceType sourceType,
+ FileFormatI fileFormat) throws IOException
+ {
+ return readFile(null, file, sourceType, fileFormat);
+ }
+
+ public AlignmentI readFile(File selectedFile, String file,
+ DataSourceType sourceType, FileFormatI fileFormat)
+ throws IOException
+ {
+
+ this.selectedFile = selectedFile;
+ if (selectedFile != null)
+ {
+ this.inFile = selectedFile.getPath();
+ }
+ this.inFile = file;
+ try
+ {
+ if (fileFormat.isStructureFile())
+ {
+ String structureParser = StructureImportSettings
+ .getDefaultPDBFileParser();
+ boolean isParseWithJMOL = structureParser.equalsIgnoreCase(
+ StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString());
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ if (isParseWithJMOL)
+ {
+ // needs a File option
+ alignFile = new JmolParser(
+ selectedFile == null ? inFile : selectedFile, sourceType);
+ }
+ else
+ {
+ // todo is mc_view parsing obsolete yet? JAL-2120
+ StructureImportSettings.setShowSeqFeatures(true);
+ alignFile = new mc_view.PDBfile(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, inFile,
+ sourceType);
+ }
+ ((StructureFile) alignFile).setDbRefType(
+ FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF);
+ }
+ else if (selectedFile != null)
+ {
+ alignFile = fileFormat
+ .getReader(new FileParse(selectedFile, sourceType));
+ }
+ else
+ {
+ // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+ alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
+ }
+ return buildAlignmentFromFile();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ System.err.println("Failed to read alignment using the '" + fileFormat
+ + "' reader.\n" + e);
+
+ if (e.getMessage() != null
+ && e.getMessage().startsWith(INVALID_CHARACTERS))
+ {
+ throw new IOException(e.getMessage());
+ }
+
+ // Finally test if the user has pasted just the sequence, no id
+ if (sourceType == DataSourceType.PASTE)
+ {
+ try
+ {
+ // Possible sequence is just residues with no label
+ alignFile = new FastaFile(">UNKNOWN\n" + inFile,
+ DataSourceType.PASTE);
+ return buildAlignmentFromFile();
+
+ } catch (Exception ex)
+ {
+ if (ex.toString().startsWith(INVALID_CHARACTERS))
+ {
+ throw new IOException(e.getMessage());
+ }
+
+ ex.printStackTrace();
+ }
+ }
+ if (FileFormat.Html.equals(fileFormat))
+ {
+ throw new IOException(e.getMessage());
+ }
+ }
+ throw new FileFormatException(getSupportedFormats());
+ }
+
+ /**
+ * Constructs the correct filetype parser for an already open datasource
+ *
+ * @param source
+ * an existing datasource
+ * @param format
+ * File format of data that will be provided by datasource
+ *
+ * @return
+ */
+ public AlignmentI readFromFile(FileParse source, FileFormatI format)
+ throws IOException
+ {
+ this.inFile = source.getInFile();
+ DataSourceType type = source.dataSourceType;
+ try
+ {
+ if (FileFormat.PDB.equals(format) || FileFormat.MMCif.equals(format))
+ {
+ // TODO obtain config value from preference settings
+ boolean isParseWithJMOL = false;
+ if (isParseWithJMOL)
+ {
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ alignFile = new JmolParser(source);
+ }
+ else
+ {
+ StructureImportSettings.setShowSeqFeatures(true);
+ alignFile = new mc_view.PDBfile(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, source);
+ }
+ ((StructureFile) alignFile).setDbRefType(Type.PDB);
+ }
+ else
+ {
+ alignFile = format.getReader(source);
+ }
+
+ return buildAlignmentFromFile();
+
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ System.err.println("Failed to read alignment using the '" + format
+ + "' reader.\n" + e);
+
+ if (e.getMessage() != null
+ && e.getMessage().startsWith(INVALID_CHARACTERS))
+ {
+ throw new FileFormatException(e.getMessage());
+ }
+
+ // Finally test if the user has pasted just the sequence, no id
+ if (type == DataSourceType.PASTE)
+ {
+ try
+ {
+ // Possible sequence is just residues with no label
+ alignFile = new FastaFile(">UNKNOWN\n" + inFile,
+ DataSourceType.PASTE);
+ return buildAlignmentFromFile();
+
+ } catch (Exception ex)
+ {
+ if (ex.toString().startsWith(INVALID_CHARACTERS))
+ {
+ throw new IOException(e.getMessage());
+ }
+
+ ex.printStackTrace();
+ }
+ }
+
+ // If we get to this stage, the format was not supported
+ throw new FileFormatException(getSupportedFormats());
+ }
+ }
+
+ /**
+ * boilerplate method to handle data from an AlignFile and construct a new
+ * alignment or import to an existing alignment
+ *
+ * @return AlignmentI instance ready to pass to a UI constructor
+ */
+ private AlignmentI buildAlignmentFromFile()
+ {
+ // Standard boilerplate for creating alignment from parser
+ // alignFile.configureForView(viewpanel);
+
+ AlignmentI al = new Alignment(alignFile.getSeqsAsArray());
+
+ alignFile.addAnnotations(al);
+
+ alignFile.addGroups(al);
+
+ return al;
+ }
+
+ /**
+ * create an alignment flatfile from a Jalview alignment view
+ *
+ * @param format
+ * @param jvsuffix
+ * @param av
+ * @param selectedOnly
+ * @return flatfile in a string
+ */
+ public String formatSequences(FileFormatI format, boolean jvsuffix,
+ AlignmentViewPanel ap, boolean selectedOnly)
+ {
+
+ AlignmentView selvew = ap.getAlignViewport()
+ .getAlignmentView(selectedOnly, false);
+ AlignmentI aselview = selvew
+ .getVisibleAlignment(ap.getAlignViewport().getGapCharacter());
+ List<AlignmentAnnotation> ala = (ap.getAlignViewport()
+ .getVisibleAlignmentAnnotation(selectedOnly));
+ if (ala != null)
+ {
+ for (AlignmentAnnotation aa : ala)
+ {
+ aselview.addAnnotation(aa);
+ }
+ }
+ viewpanel = ap;
+ return formatSequences(format, aselview, jvsuffix);
+ }
+
+ /**
+ * Construct an output class for an alignment in a particular filetype TODO:
+ * allow caller to detect errors and warnings encountered when generating
+ * output
+ *
+ * @param format
+ * string name of alignment format
+ * @param alignment
+ * the alignment to be written out
+ * @param jvsuffix
+ * passed to AlnFile class controls whether /START-END is added to
+ * sequence names
+ *
+ * @return alignment flat file contents
+ */
+ public String formatSequences(FileFormatI format, AlignmentI alignment,
+ boolean jvsuffix)
+ {
+ try
+ {
+ AlignmentFileWriterI afile = format.getWriter(alignment);
+
+ afile.setNewlineString(newline);
+ afile.setExportSettings(exportSettings);
+ afile.configureForView(viewpanel);
+
+ // check whether we were given a specific alignment to export, rather than
+ // the one in the viewpanel
+ SequenceI[] seqs = null;
+ if (viewpanel == null || viewpanel.getAlignment() == null
+ || viewpanel.getAlignment() != alignment)
+ {
+ seqs = alignment.getSequencesArray();
+ }
+ else
+ {
+ seqs = viewpanel.getAlignment().getSequencesArray();
+ }
+
+ String afileresp = afile.print(seqs, jvsuffix);
+ if (afile.hasWarningMessage())
+ {
+ System.err.println("Warning raised when writing as " + format
+ + " : " + afile.getWarningMessage());
+ }
+ return afileresp;
+ } catch (Exception e)
+ {
+ System.err.println("Failed to write alignment as a '"
+ + format.getName() + "' file\n");
+ e.printStackTrace();
+ }
+
+ return null;
+ }
+
+ /**
+ * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input
+ * data
+ *
+ * BH 2018 allows File or String, and can return RELATIVE_URL
+ *
+ * @param dataObject
+ * File or String
+ * @return the protocol for the input data
+ */
+ public static DataSourceType checkProtocol(Object dataObject)
+ {
+ if (dataObject instanceof File)
+ {
+ return DataSourceType.FILE;
+ }
+
+ String data = dataObject.toString();
+ DataSourceType protocol = DataSourceType.PASTE;
+ String ft = data.toLowerCase(Locale.ROOT).trim();
+ if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
+ || ft.indexOf("file:") == 0)
+ {
+ protocol = DataSourceType.URL;
+ }
+ else if (Platform.isJS())
+ {
+ protocol = DataSourceType.RELATIVE_URL;
+ }
+ else if (new File(data).exists())
+ {
+ protocol = DataSourceType.FILE;
+ }
+ return protocol;
+ }
+
+ /**
+ * @param args
+ * @j2sIgnore
+ */
+ public static void main(String[] args)
+ {
+ int i = 0;
+ while (i < args.length)
+ {
+ File f = new File(args[i]);
+ if (f.exists())
+ {
+ try
+ {
+ System.out.println("Reading file: " + f);
+ AppletFormatAdapter afa = new AppletFormatAdapter();
+ Runtime r = Runtime.getRuntime();
+ System.gc();
+ long memf = -r.totalMemory() + r.freeMemory();
+ long t1 = -System.currentTimeMillis();
+ AlignmentI al = afa.readFile(args[i], DataSourceType.FILE,
+ new IdentifyFile().identify(args[i],
+ DataSourceType.FILE));
+ t1 += System.currentTimeMillis();
+ System.gc();
+ memf += r.totalMemory() - r.freeMemory();
+ if (al != null)
+ {
+ System.out.println("Alignment contains " + al.getHeight()
+ + " sequences and " + al.getWidth() + " columns.");
+ try
+ {
+ System.out.println(new AppletFormatAdapter()
+ .formatSequences(FileFormat.Fasta, al, true));
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Couln't format the alignment for output as a FASTA file.");
+ e.printStackTrace(System.err);
+ }
+ }
+ else
+ {
+ System.out.println("Couldn't read alignment");
+ }
+ System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
+ System.out.println(
+ "Difference between free memory now and before is "
+ + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
+ } catch (Exception e)
+ {
+ System.err.println("Exception when dealing with " + i
+ + "'th argument: " + args[i] + "\n" + e);
+ }
+ }
+ else
+ {
+ System.err.println("Ignoring argument '" + args[i] + "' (" + i
+ + "'th)- not a readable file.");
+ }
+ i++;
+ }
+ }
+
+ /**
+ * try to discover how to access the given file as a valid datasource that
+ * will be identified as the given type.
+ *
+ * @param file
+ * @param format
+ * @return protocol that yields the data parsable as the given type
+ */
+ public static DataSourceType resolveProtocol(String file,
+ FileFormatI format)
+ {
+ return resolveProtocol(file, format, false);
+ }
+
+ public static DataSourceType resolveProtocol(String file,
+ FileFormatI format, boolean debug)
+ {
+ // TODO: test thoroughly!
+ DataSourceType protocol = null;
+ if (debug)
+ {
+ System.out.println("resolving datasource started with:\n>>file\n"
+ + file + ">>endfile");
+ }
+
+ // This might throw a security exception in certain browsers
+ // Netscape Communicator for instance.
+ try
+ {
+ boolean rtn = false;
+ InputStream 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 = DataSourceType.CLASSLOADER;
+ }
+
+ } catch (Exception ex)
+ {
+ System.err
+ .println("Exception checking resources: " + file + " " + ex);
+ }
+
+ if (file.indexOf("://") > -1)
+ {
+ protocol = DataSourceType.URL;
+ }
+ else
+ {
+ // skipping codebase prepend check.
+ protocol = DataSourceType.FILE;
+ }
+ FileParse fp = null;
+ try
+ {
+ if (debug)
+ {
+ System.out.println(
+ "Trying to get contents of resource as " + protocol + ":");
+ }
+ fp = new FileParse(file, protocol);
+ if (!fp.isValid())
+ {
+ fp = null;
+ }
+ else
+ {
+ if (debug)
+ {
+ System.out.println("Successful.");
+ }
+ }
+ } catch (Exception e)
+ {
+ if (debug)
+ {
+ System.err.println("Exception when accessing content: " + e);
+ }
+ fp = null;
+ }
+ if (fp == null)
+ {
+ if (debug)
+ {
+ System.out.println("Accessing as paste.");
+ }
+ protocol = DataSourceType.PASTE;
+ fp = null;
+ try
+ {
+ fp = new FileParse(file, protocol);
+ if (!fp.isValid())
+ {
+ fp = null;
+ }
+ } catch (Exception e)
+ {
+ System.err.println("Failed to access content as paste!");
+ e.printStackTrace();
+ fp = null;
+ }
+ }
+ if (fp == null)
+ {
+ return null;
+ }
+ if (format == null)
+ {
+ return protocol;
+ }
+ else
+ {
+ try
+ {
+ FileFormatI idformat = new 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 (Exception e)
+ {
+ if (debug)
+ {
+ System.err.println("File deemed not accessible via " + protocol);
+ e.printStackTrace();
+ }
+ }
+ }
+ return null;
+ }
+
+ public AlignmentFileReaderI getAlignFile()
+ {
+ return alignFile;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff