/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
- *
+ * 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
+ * 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
+ *
+ * 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 jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+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 java.io.File;
+import java.io.IOException;
import java.io.InputStream;
import java.util.List;
-import jalview.api.AlignViewportI;
-import jalview.datamodel.*;
-import jalview.util.MessageManager;
-
/**
* 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
{
- /**
- * 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" }; // , "SimpleBLAST" };
+ private AlignmentViewPanel viewpanel;
/**
- * List of valid format strings for use by callers of the formatSequences
- * method
+ * add jalview-derived non-secondary structure annotation from PDB structure
*/
- public static final String[] WRITEABLE_FORMATS = new String[]
- { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH" };
+ boolean annotFromStructure = false;
/**
- * List of extensions corresponding to file format types in WRITABLE_FNAMES
- * that are writable by the application.
+ * add secondary structure from PDB data with built-in algorithms
*/
- public static final String[] WRITABLE_EXTENSIONS = new String[]
- { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
- "jvp", "sto,stk", "jar" };
+ boolean localSecondaryStruct = false;
/**
- * List of writable formats by the application. Order must correspond with the
- * WRITABLE_EXTENSIONS list of formats.
+ * process PDB data with web services
*/
- public static final String[] WRITABLE_FNAMES = new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
- "STH", "Jalview" };
+ boolean serviceSecondaryStruct = false;
- /**
- * 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",
- "jar,jvp", "sto,stk", "xml,rnaml" }; // ".blast"
+ private AlignmentFileReaderI alignFile = null;
+
+ String inFile;
/**
- * List of readable formats by application in order corresponding to
- * READABLE_EXTENSIONS
+ * character used to write newlines
*/
- public static final String[] READABLE_FNAMES = new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
- "Stockholm", "RNAML" };// ,
+ protected String newline = System.getProperty("line.separator");
- // "SimpleBLAST"
- // };
+ private AlignExportSettingI exportSettings;
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);
-
/**
+ * Returns an error message with a list of supported readable file formats
*
- * @param els
- * @return grammatically correct(ish) list consisting of els elements.
+ * @return
*/
- public static String prettyPrint(String[] els)
+ public static String getSupportedFormats()
{
- StringBuffer list = new StringBuffer();
- for (int 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();
+ return "Formats currently supported are\n"
+ + prettyPrint(FileFormats.getInstance().getReadableFormats());
}
-
- public static String FILE = "File";
-
- public static String URL = "URL";
-
- public static String PASTE = "Paste";
-
- public static String CLASSLOADER = "ClassLoader";
-
- AlignFile afile = null;
-
- String inFile;
-
- /**
- * character used to write newlines
- */
- protected String newline = System.getProperty("line.separator");
-
- public void setNewlineString(String nl)
+ public AppletFormatAdapter()
{
- newline = nl;
}
- public String getNewlineString()
+ public AppletFormatAdapter(AlignmentViewPanel viewpanel)
{
- return newline;
+ this.viewpanel = viewpanel;
}
- /**
- * 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)
+ public AppletFormatAdapter(AlignmentViewPanel alignPanel,
+ AlignExportSettingI settings)
{
- return isValidFormat(format, false);
+ viewpanel = alignPanel;
+ exportSettings = settings;
}
/**
- * validate format is valid for IO
+ * Formats a grammatically correct(ish) list consisting of the given objects
*
- * @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
+ * @param things
+ * @return
*/
- public static final boolean isValidFormat(String format,
- boolean forwriting)
+ public static String prettyPrint(List<? extends Object> things)
{
- boolean valid = false;
- String[] format_list = (forwriting) ? WRITEABLE_FORMATS
- : READABLE_FORMATS;
- for (int i = 0; i < format_list.length; i++)
+ StringBuffer list = new StringBuffer();
+ for (int i = 0, iSize = things.size() - 1; i < iSize; i++)
{
- if (format_list[i].equalsIgnoreCase(format))
- {
- return true;
- }
+ 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;
+ }
- return valid;
+ public String getNewlineString()
+ {
+ return newline;
}
/**
* 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
- *
- * @return DOCUMENT ME!
+ * @param fileFormat
+ *
+ * @return
*/
- public Alignment 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"))
- {
- afile = new FastaFile(inFile, type);
- }
- else if (format.equals("MSF"))
- {
- afile = new MSFfile(inFile, type);
- }
- else if (format.equals("PileUp"))
- {
- afile = new PileUpfile(inFile, type);
- }
- else if (format.equals("CLUSTAL"))
- {
- afile = new ClustalFile(inFile, type);
- }
- else if (format.equals("BLC"))
- {
- afile = new BLCFile(inFile, type);
- }
- else if (format.equals("PIR"))
- {
- afile = new PIRFile(inFile, type);
- }
- else if (format.equals("PFAM"))
- {
- afile = new PfamFile(inFile, type);
- }
- else if (format.equals("JnetFile"))
- {
- afile = new JPredFile(inFile, type);
- ((JPredFile) afile).removeNonSequences();
- }
- else if (format.equals("PDB"))
- {
- afile = new MCview.PDBfile(inFile, type);
- // Uncomment to test Jmol data based PDB processing: JAL-1213
- // afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type);
- }
- else if (format.equals("STH"))
- {
- afile = new StockholmFile(inFile, type);
- }
- else if (format.equals("SimpleBLAST"))
- {
- afile = new SimpleBlastFile(inFile, type);
+ if (fileFormat.isStructureFile())
+ {
+ String structureParser = StructureImportSettings
+ .getDefaultPDBFileParser();
+ boolean isParseWithJMOL = structureParser.equalsIgnoreCase(
+ StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString());
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ if (isParseWithJMOL)
+ {
+ alignFile = new JmolParser(inFile, sourceType);
+ }
+ else
+ {
+ // todo is MCview parsing obsolete yet? JAL-2120
+ StructureImportSettings.setShowSeqFeatures(true);
+ alignFile = new MCview.PDBfile(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, inFile,
+ sourceType);
+ }
+ ((StructureFile) alignFile).setDbRefType(FileFormat.PDB
+ .equals(fileFormat) ? Type.PDB : Type.MMCIF);
}
- else if (format.equals("RNAML"))
+ else
{
- afile = new RnamlFile(inFile, type);
+ // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+ alignFile = fileFormat.getReader(new FileParse(inFile,
+ sourceType));
}
-
- Alignment al = new Alignment(afile.getSeqsAsArray());
-
- afile.addAnnotations(al);
-
- return al;
+ 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
- afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
- Alignment al = new Alignment(afile.getSeqsAsArray());
- afile.addAnnotations(al);
- return al;
+ 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);
+ 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 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"))
- {
- afile = new FastaFile(source);
- }
- else if (format.equals("MSF"))
- {
- afile = new MSFfile(source);
- }
- else if (format.equals("PileUp"))
- {
- afile = new PileUpfile(source);
- }
- else if (format.equals("CLUSTAL"))
- {
- afile = new ClustalFile(source);
- }
- else if (format.equals("BLC"))
- {
- afile = new BLCFile(source);
- }
- else if (format.equals("PIR"))
- {
- afile = new PIRFile(source);
- }
- else if (format.equals("PFAM"))
- {
- afile = new PfamFile(source);
- }
- else if (format.equals("JnetFile"))
- {
- afile = new JPredFile(source);
- ((JPredFile) afile).removeNonSequences();
- }
- else if (format.equals("PDB"))
- {
- afile = new MCview.PDBfile(source);
- }
- else if (format.equals("STH"))
- {
- afile = new StockholmFile(source);
- }
- else if (format.equals("RNAML"))
+ if (FileFormat.PDB.equals(format) || FileFormat.MMCif.equals(format))
{
- afile = new RnamlFile(source);
+ // 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 MCview.PDBfile(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, source);
+ }
+ ((StructureFile) alignFile).setDbRefType(Type.PDB);
}
- else if (format.equals("SimpleBLAST"))
+ else
{
- afile = new SimpleBlastFile(source);
+ alignFile = format.getReader(source);
}
- Alignment al = new Alignment(afile.getSeqsAsArray());
-
- afile.addAnnotations(al);
+ return buildAlignmentFromFile();
- return al;
} catch (Exception e)
{
e.printStackTrace();
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
- afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
- Alignment al = new Alignment(afile.getSeqsAsArray());
- afile.addAnnotations(al);
- return al;
+ 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(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
+ * 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(String format, boolean jvsuffix,
- AlignViewportI av, boolean selectedOnly)
+ public String formatSequences(FileFormatI format, boolean jvsuffix,
+ AlignmentViewPanel ap, boolean selectedOnly)
{
- AlignmentView selvew = av.getAlignmentView(selectedOnly, false);
- AlignmentI aselview = selvew.getVisibleAlignment(av
+ AlignmentView selvew = ap.getAlignViewport().getAlignmentView(
+ selectedOnly, false);
+ AlignmentI aselview = selvew.getVisibleAlignment(ap.getAlignViewport()
.getGapCharacter());
- List<AlignmentAnnotation> ala = (av
+ List<AlignmentAnnotation> ala = (ap.getAlignViewport()
.getVisibleAlignmentAnnotation(selectedOnly));
if (ala != null)
{
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
* @param jvsuffix
* passed to AlnFile class controls whether /START-END is added to
* sequence names
- *
+ *
* @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;
+ AlignmentFileWriterI afile = format.getWriter(alignment);
- 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("RNAML"))
+ 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)
{
- afile = new RnamlFile();
+ seqs = alignment.getSequencesArray();
}
-
else
{
- throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
+ seqs = viewpanel.getAlignment().getSequencesArray();
}
- afile.setNewlineString(newline);
- afile.addJVSuffix(jvsuffix);
- afile.setSeqs(alignment.getSequencesArray());
-
- String afileresp = afile.print();
+ String afileresp = afile.print(seqs, jvsuffix);
if (afile.hasWarningMessage())
{
System.err.println("Warning raised when writing as " + format
return afileresp;
} catch (Exception e)
{
- System.err.println("Failed to write alignment as a '" + format
+ System.err.println("Failed to write alignment as a '"
+ + format.getName()
+ "' file\n");
e.printStackTrace();
}
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();
- Alignment 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
/**
* 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 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 AlignmentFileReaderI getAlignFile()
+ {
+ return alignFile;
+ }
}
git://source.jalview.org / jalview.git / blobdiff