import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
-import jalview.util.MessageManager;
import java.io.File;
import java.io.IOException;
{
private AlignmentViewPanel viewpanel;
- public static String FILE = "File";
-
- public static String URL = "URL";
-
- public static String PASTE = "Paste";
-
- public static String CLASSLOADER = "ClassLoader";
-
/**
* add jalview-derived non-secondary structure annotation from PDB structure
*/
*/
boolean serviceSecondaryStruct = false;
- private AlignFile alignFile = null;
+ private AlignmentFileI alignFile = null;
String inFile;
/**
* List of valid format strings used in the isValidFormat method
*/
- public static final String[] READABLE_FORMATS = new String[] { "BLC",
- "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB",
- "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
- IdentifyFile.FeaturesFile, "HTML", "mmCIF" };
+ // public static final String[] READABLE_FORMATS = new String[] { "BLC",
+ // "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB",
+ // "JnetFile", "RNAML", "PHYLIP", "JSON",
+ // IdentifyFile.FeaturesFile, "HTML", "mmCIF" };
/**
* List of readable format file extensions by application in order
* corresponding to READABLE_FNAMES
*/
- public static final String[] READABLE_EXTENSIONS = new String[] {
- "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
- "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
- ".gff2,gff3", "jar,jvp", HtmlFile.FILE_EXT, "cif" };
-
- /**
- * List of readable formats by application in order corresponding to
- * READABLE_EXTENSIONS
- */
- public static final String[] READABLE_FNAMES = new String[] { "Fasta",
- "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML",
- PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.FeaturesFile,
- "Jalview", HtmlFile.FILE_DESC, "mmCIF" };
+ // public static final String[] READABLE_EXTENSIONS = new String[] {
+ // "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ // "sto,stk", "xml,rnaml", "phy", "json", ".gff2,gff3", "jar,jvp",
+ // "html", "cif" };
+
+ //
+ // /**
+ // * List of readable formats by application in order corresponding to
+ // * READABLE_EXTENSIONS
+ // */
+ // public static final String[] READABLE_FNAMES = new String[] { "Fasta",
+ // "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML",
+ // "PHYLIP", "JSON", IdentifyFile.FeaturesFile,
+ // "Jalview", HtmlFile.FILE_DESC, "mmCIF" };
/**
* List of valid format strings for use by callers of the formatSequences
* method
*/
- public static final String[] WRITEABLE_FORMATS = new String[] { "BLC",
- "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH",
- PhylipFile.FILE_DESC, JSONFile.FILE_DESC };
+ // public static final String[] WRITEABLE_FORMATS = new String[] { "BLC",
+ // "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH",
+ // "PHYLIP", "JSON" };
/**
* List of extensions corresponding to file format types in WRITABLE_FNAMES
* that are writable by the application.
*/
- public static final String[] WRITABLE_EXTENSIONS = new String[] {
- "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
- "sto,stk", PhylipFile.FILE_EXT, JSONFile.FILE_EXT, "jvp" };
+ // public static final String[] WRITABLE_EXTENSIONS = new String[] {
+ // "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ // "sto,stk", "phy", "json", "jvp" };
/**
* List of writable formats by the application. Order must correspond with the
* WRITABLE_EXTENSIONS list of formats.
*/
- public static final String[] WRITABLE_FNAMES = new String[] { "Fasta",
- "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
- PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" };
+ // public static final String[] WRITABLE_FNAMES = new String[] { "Fasta",
+ // "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH", "PHYLIP",
+ // "JSON", "Jalview" };
public static String INVALID_CHARACTERS = "Contains invalid characters";
// TODO: make these messages dynamic
public static String SUPPORTED_FORMATS = "Formats currently supported are\n"
- + prettyPrint(READABLE_FORMATS);
+ + prettyPrint(FileFormat.getReadableFormats());
public AppletFormatAdapter()
{
}
/**
- *
- * @param els
- * @return grammatically correct(ish) list consisting of els elements.
+ * Formats a grammatically correct(ish) list consisting of the given objects
+ *
+ * @param things
+ * @return
*/
- public static String prettyPrint(String[] els)
+ public static String prettyPrint(List<? extends Object> things)
{
StringBuffer list = new StringBuffer();
- for (int i = 0, iSize = els.length - 1; i < iSize; i++)
+ for (int i = 0, iSize = things.size() - 1; i < iSize; i++)
{
- list.append(els[i]);
+ list.append(things.get(i).toString());
list.append(", ");
}
- list.append(" and " + els[els.length - 1] + ".");
+ // could i18n 'and' here
+ list.append(" and " + things.get(things.size() - 1).toString() + ".");
return list.toString();
}
}
/**
- * check that this format is valid for reading
- *
- * @param format
- * a format string to be compared with READABLE_FORMATS
- * @return true if format is readable
- */
- public static final boolean isValidFormat(String format)
- {
- return isValidFormat(format, false);
- }
-
- /**
- * validate format is valid for IO
- *
- * @param format
- * a format string to be compared with either READABLE_FORMATS or
- * WRITEABLE_FORMATS
- * @param forwriting
- * when true, format is checked for containment in WRITEABLE_FORMATS
- * @return true if format is valid
- */
- public static final boolean isValidFormat(String format,
- boolean forwriting)
- {
- if (format == null)
- {
- return false;
- }
- boolean valid = false;
- String[] format_list = (forwriting) ? WRITEABLE_FORMATS
- : READABLE_FORMATS;
- for (String element : format_list)
- {
- if (element.equalsIgnoreCase(format))
- {
- return true;
- }
- }
-
- return valid;
- }
-
- /**
* Constructs the correct filetype parser for a characterised datasource
*
* @param inFile
* data/data location
- * @param type
+ * @param sourceType
* type of datasource
- * @param format
- * File format of data provided by datasource
+ * @param fileFormat
*
- * @return DOCUMENT ME!
+ * @return
*/
- public AlignmentI readFile(String inFile, String type, String format)
- throws java.io.IOException
+ public AlignmentI readFile(String file, DataSourceType sourceType,
+ FileFormatI fileFormat) throws IOException
{
- // TODO: generalise mapping between format string and io. class instances
- // using Constructor.invoke reflection
- this.inFile = inFile;
+ this.inFile = file;
try
{
- if (format.equals("FASTA"))
- {
- alignFile = new FastaFile(inFile, type);
- }
- else if (format.equals("MSF"))
- {
- alignFile = new MSFfile(inFile, type);
- }
- else if (format.equals("PileUp"))
- {
- alignFile = new PileUpfile(inFile, type);
- }
- else if (format.equals("CLUSTAL"))
- {
- alignFile = new ClustalFile(inFile, type);
- }
- else if (format.equals("BLC"))
- {
- alignFile = new BLCFile(inFile, type);
- }
- else if (format.equals("PIR"))
- {
- alignFile = new PIRFile(inFile, type);
- }
- else if (format.equals("PFAM"))
- {
- alignFile = new PfamFile(inFile, type);
- }
- else if (format.equals("JnetFile"))
- {
- alignFile = new JPredFile(inFile, type);
- ((JPredFile) alignFile).removeNonSequences();
- }
- else if (format.equals("PDB"))
+ if (fileFormat == FileFormat.PDB || fileFormat == FileFormat.MMCif)
{
// TODO obtain config value from preference settings.
// Set value to 'true' to test PDB processing with Jmol: JAL-1213
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
+ alignFile = new JmolParser(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, inFile,
- type);
+ sourceType);
}
else
{
StructureImportSettings.setShowSeqFeatures(true);
alignFile = new MCview.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, inFile,
- type);
+ sourceType);
}
- ((StructureFile) alignFile).setDbRefType(format);
- }
- else if (format.equalsIgnoreCase("mmCIF"))
- {
- StructureImportSettings.addSettings(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, inFile, type);
- ((StructureFile) alignFile).setDbRefType(format);
+ ((StructureFile) alignFile)
+ .setDbRefType(fileFormat == FileFormat.PDB ? Type.PDB
+ : Type.MMCIF);
}
- else if (format.equals("STH"))
- {
- alignFile = new StockholmFile(inFile, type);
- }
- else if (format.equals("SimpleBLAST"))
- {
- alignFile = new SimpleBlastFile(inFile, type);
- }
- else if (format.equals(PhylipFile.FILE_DESC))
- {
- alignFile = new PhylipFile(inFile, type);
- }
- else if (format.equals(JSONFile.FILE_DESC))
- {
- alignFile = new JSONFile(inFile, type);
- }
- else if (format.equals(HtmlFile.FILE_DESC))
- {
- alignFile = new HtmlFile(inFile, type);
- }
- else if (format.equals("RNAML"))
- {
- alignFile = new RnamlFile(inFile, type);
- }
- else if (format.equals(IdentifyFile.FeaturesFile))
+ else
{
- alignFile = new FeaturesFile(true, inFile, type);
- }
- return buildAlignmentFrom(alignFile);
+ alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+ }
+ // new FastaFile(inFile, sourceType);
+ // new MSFfile(inFile, sourceType);
+ // new PileUpfile(inFile, sourceType);
+ // new ClustalFile(inFile, sourceType);
+ // new BLCFile(inFile, sourceType);
+ // new PIRFile(inFile, sourceType);
+ // new PfamFile(inFile, sourceType);
+ // alignFile = new JPredFile(inFile, sourceType);
+ // ((JPredFile) alignFile).removeNonSequences();
+ // new StockholmFile(inFile, sourceType);
+ // new SimpleBlastFile(inFile, sourceType);
+ // new PhylipFile(inFile, sourceType);
+ // new JSONFile(inFile, sourceType);
+ // new HtmlFile(inFile, sourceType);
+ // new RnamlFile(inFile, sourceType);
+ // alignFile = new FeaturesFile(true, inFile, sourceType);
+ return buildAlignmentFromFile();
} catch (Exception e)
{
e.printStackTrace();
- System.err.println("Failed to read alignment using the '" + format
- + "' reader.\n" + e);
+ System.err.println("Failed to read alignment using the '"
+ + fileFormat + "' reader.\n" + e);
if (e.getMessage() != null
&& e.getMessage().startsWith(INVALID_CHARACTERS))
{
- throw new java.io.IOException(e.getMessage());
+ throw new IOException(e.getMessage());
}
// Finally test if the user has pasted just the sequence, no id
- if (type.equalsIgnoreCase("Paste"))
+ if (sourceType == DataSourceType.PASTE)
{
try
{
// Possible sequence is just residues with no label
- alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
- return buildAlignmentFrom(alignFile);
+ alignFile = new FastaFile(">UNKNOWN\n" + inFile,
+ DataSourceType.PASTE);
+ return buildAlignmentFromFile();
} catch (Exception ex)
{
if (ex.toString().startsWith(INVALID_CHARACTERS))
{
- throw new java.io.IOException(e.getMessage());
+ throw new IOException(e.getMessage());
}
ex.printStackTrace();
}
}
- if (format.equalsIgnoreCase("HTML"))
+ if (fileFormat == FileFormat.Html)
{
throw new IOException(e.getMessage());
}
- // If we get to this stage, the format was not supported
- throw new java.io.IOException(SUPPORTED_FORMATS);
}
+ throw new FileFormatException(SUPPORTED_FORMATS);
}
/**
* @param format
* File format of data that will be provided by datasource
*
- * @return DOCUMENT ME!
+ * @return
*/
- public AlignmentI readFromFile(FileParse source, String format)
- throws java.io.IOException
+ public AlignmentI readFromFile(FileParse source, FileFormatI format)
+ throws IOException
{
- // TODO: generalise mapping between format string and io. class instances
- // using Constructor.invoke reflection
- // This is exactly the same as the readFile method except we substitute
- // 'inFile, type' with 'source'
this.inFile = source.getInFile();
- String type = source.type;
+ DataSourceType type = source.dataSourceType;
try
{
- if (format.equals("FASTA"))
- {
- alignFile = new FastaFile(source);
- }
- else if (format.equals("MSF"))
- {
- alignFile = new MSFfile(source);
- }
- else if (format.equals("PileUp"))
- {
- alignFile = new PileUpfile(source);
- }
- else if (format.equals("CLUSTAL"))
- {
- alignFile = new ClustalFile(source);
- }
- else if (format.equals("BLC"))
- {
- alignFile = new BLCFile(source);
- }
- else if (format.equals("PIR"))
- {
- alignFile = new PIRFile(source);
- }
- else if (format.equals("PFAM"))
- {
- alignFile = new PfamFile(source);
- }
- else if (format.equals("JnetFile"))
- {
- alignFile = new JPredFile(source);
- ((JPredFile) alignFile).removeNonSequences();
- }
- else if (format.equals("PDB"))
+ if (format == FileFormat.PDB || format == FileFormat.MMCif)
{
// TODO obtain config value from preference settings
boolean isParseWithJMOL = false;
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
+ alignFile = new JmolParser(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, source);
}
else
}
((StructureFile) alignFile).setDbRefType(Type.PDB);
}
- else if (format.equalsIgnoreCase("mmCIF"))
- {
- StructureImportSettings.addSettings(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, source);
- ((StructureFile) alignFile).setDbRefType(Type.MMCIF);
- }
- else if (format.equals("STH"))
- {
- alignFile = new StockholmFile(source);
- }
- else if (format.equals("RNAML"))
- {
- alignFile = new RnamlFile(source);
- }
- else if (format.equals("SimpleBLAST"))
- {
- alignFile = new SimpleBlastFile(source);
- }
- else if (format.equals(PhylipFile.FILE_DESC))
- {
- alignFile = new PhylipFile(source);
- }
- else if (format.equals(IdentifyFile.FeaturesFile))
- {
- alignFile = new FeaturesFile(inFile, type);
- }
- else if (format.equals(JSONFile.FILE_DESC))
- {
- alignFile = new JSONFile(source);
- }
- else if (format.equals(HtmlFile.FILE_DESC))
+ else
{
- alignFile = new HtmlFile(source);
+ alignFile = format.getAlignmentFile(source);
}
- return buildAlignmentFrom(alignFile);
+ return buildAlignmentFromFile();
} catch (Exception e)
{
if (e.getMessage() != null
&& e.getMessage().startsWith(INVALID_CHARACTERS))
{
- throw new java.io.IOException(e.getMessage());
+ throw new FileFormatException(e.getMessage());
}
// Finally test if the user has pasted just the sequence, no id
- if (type.equalsIgnoreCase("Paste"))
+ if (type == DataSourceType.PASTE)
{
try
{
// Possible sequence is just residues with no label
- alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
- return buildAlignmentFrom(alignFile);
+ alignFile = new FastaFile(">UNKNOWN\n" + inFile,
+ DataSourceType.PASTE);
+ return buildAlignmentFromFile();
} catch (Exception ex)
{
if (ex.toString().startsWith(INVALID_CHARACTERS))
{
- throw new java.io.IOException(e.getMessage());
+ throw new IOException(e.getMessage());
}
ex.printStackTrace();
}
// If we get to this stage, the format was not supported
- throw new java.io.IOException(SUPPORTED_FORMATS);
+ throw new FileFormatException(SUPPORTED_FORMATS);
}
}
* boilerplate method to handle data from an AlignFile and construct a new
* alignment or import to an existing alignment
*
- * @param alignFile2
* @return AlignmentI instance ready to pass to a UI constructor
*/
- private AlignmentI buildAlignmentFrom(AlignFile alignFile2)
+ private AlignmentI buildAlignmentFromFile()
{
// Standard boilerplate for creating alignment from parser
// alignFile.configureForView(viewpanel);
* @param selectedOnly
* @return flatfile in a string
*/
- public String formatSequences(String format, boolean jvsuffix,
+ public String formatSequences(FileFormatI format, boolean jvsuffix,
AlignmentViewPanel ap, boolean selectedOnly)
{
*
* @return alignment flat file contents
*/
- public String formatSequences(String format, AlignmentI alignment,
+ public String formatSequences(FileFormatI format, AlignmentI alignment,
boolean jvsuffix)
{
try
{
- AlignFile afile = null;
- if (format.equalsIgnoreCase("FASTA"))
- {
- afile = new FastaFile();
- }
- else if (format.equalsIgnoreCase("MSF"))
- {
- afile = new MSFfile();
- }
- else if (format.equalsIgnoreCase("PileUp"))
- {
- afile = new PileUpfile();
- }
- else if (format.equalsIgnoreCase("CLUSTAL"))
- {
- afile = new ClustalFile();
- }
- else if (format.equalsIgnoreCase("BLC"))
- {
- afile = new BLCFile();
- }
- else if (format.equalsIgnoreCase("PIR"))
- {
- afile = new PIRFile();
- }
- else if (format.equalsIgnoreCase("PFAM"))
- {
- afile = new PfamFile();
- }
- else if (format.equalsIgnoreCase("STH"))
- {
- afile = new StockholmFile(alignment);
- }
- else if (format.equalsIgnoreCase("AMSA"))
- {
- afile = new AMSAFile(alignment);
- }
- else if (format.equalsIgnoreCase(PhylipFile.FILE_DESC))
- {
- afile = new PhylipFile();
- }
- else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
- {
- afile = new JSONFile();
- }
- else if (format.equalsIgnoreCase("RNAML"))
- {
- afile = new RnamlFile();
- }
-
- else
- {
- throw new Exception(
- MessageManager
- .getString("error.implementation_error_unknown_file_format_string"));
- }
+ AlignmentFileI afile = format.getAlignmentFile();
afile.setNewlineString(newline);
- afile.addJVSuffix(jvsuffix);
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)
{
- afile.setSeqs(alignment.getSequencesArray());
+ seqs = alignment.getSequencesArray();
}
else
{
- afile.setSeqs(viewpanel.getAlignment().getSequencesArray());
+ seqs = viewpanel.getAlignment().getSequencesArray();
}
- String afileresp = afile.print();
+ String afileresp = afile.print(seqs, jvsuffix);
if (afile.hasWarningMessage())
{
System.err.println("Warning raised when writing as " + format
return null;
}
- public static String checkProtocol(String file)
+ public static DataSourceType checkProtocol(String file)
{
- String protocol = FILE;
+ DataSourceType protocol = DataSourceType.FILE;
String ft = file.toLowerCase().trim();
if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
|| ft.indexOf("file:") == 0)
{
- protocol = URL;
+ protocol = DataSourceType.URL;
}
return protocol;
}
System.gc();
long memf = -r.totalMemory() + r.freeMemory();
long t1 = -System.currentTimeMillis();
- AlignmentI al = afa.readFile(args[i], FILE,
- new IdentifyFile().identify(args[i], FILE));
+ 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();
try
{
System.out.println(new AppletFormatAdapter().formatSequences(
- "FASTA", al, true));
+ FileFormat.Fasta, al, true));
} catch (Exception e)
{
System.err
* @param format
* @return protocol that yields the data parsable as the given type
*/
- public static String resolveProtocol(String file, String format)
+ public static DataSourceType resolveProtocol(String file,
+ FileFormatI format)
{
return resolveProtocol(file, format, false);
}
- public static String resolveProtocol(String file, String format,
- boolean debug)
+ public static DataSourceType resolveProtocol(String file,
+ FileFormatI format, boolean debug)
{
// TODO: test thoroughly!
- String protocol = null;
+ DataSourceType protocol = null;
if (debug)
{
System.out.println("resolving datasource started with:\n>>file\n"
System.err.println("Resource '" + file + "' was "
+ (rtn ? "" : "not") + " located by classloader.");
}
- ;
if (rtn)
{
- protocol = AppletFormatAdapter.CLASSLOADER;
+ protocol = DataSourceType.CLASSLOADER;
}
} catch (Exception ex)
if (file.indexOf("://") > -1)
{
- protocol = AppletFormatAdapter.URL;
+ protocol = DataSourceType.URL;
}
else
{
// skipping codebase prepend check.
- protocol = AppletFormatAdapter.FILE;
+ protocol = DataSourceType.FILE;
}
FileParse fp = null;
try
{
System.out.println("Accessing as paste.");
}
- protocol = AppletFormatAdapter.PASTE;
+ protocol = DataSourceType.PASTE;
fp = null;
try
{
{
return null;
}
- if (format == null || format.length() == 0)
+ if (format == null)
{
return protocol;
}
{
try
{
- String idformat = new jalview.io.IdentifyFile().identify(file,
- protocol);
+ FileFormatI idformat = new IdentifyFile().identify(file, protocol);
if (idformat == null)
{
if (debug)
System.err.println("File deemed not accessible via " + protocol);
e.printStackTrace();
}
- ;
-
}
}
return null;
}
- public AlignFile getAlignFile()
+ public AlignmentFileI getAlignFile()
{
return alignFile;
}
-
- public void setAlignFile(AlignFile alignFile)
- {
- this.alignFile = alignFile;
- }
}
git://source.jalview.org / jalview.git / blobdiff