/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * 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
+ * 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/>.
+ *
+ * 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.AlignViewportI;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.util.MessageManager;
+
import java.io.File;
import java.io.InputStream;
-
-import jalview.datamodel.*;
+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 AlignViewportI viewport;
+
+ public static String FILE = "File";
+
+ public static String URL = "URL";
+
+ public static String PASTE = "Paste";
+
+ public static String CLASSLOADER = "ClassLoader";
+
/**
- * List of valid format strings used in the isValidFormat method
+ * add jalview-derived non-secondary structure annotation from PDB structure
*/
- public static final String[] READABLE_FORMATS = new String[]
- { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
- "PDB", "JnetFile" , "RNAML"}; // , "SimpleBLAST" };
+ boolean annotFromStructure = false;
/**
- * List of valid format strings for use by callers of the formatSequences
- * method
+ * add secondary structure from PDB data with built-in algorithms
*/
- public static final String[] WRITEABLE_FORMATS = new String[]
- { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA" };
+ boolean localSecondaryStruct = false;
/**
- * List of extensions corresponding to file format types in WRITABLE_FNAMES
- * that are writable by the application.
+ * process PDB data with web services
*/
- public static final String[] WRITABLE_EXTENSIONS = new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
+ boolean serviceSecondaryStruct = false;
+
+ private AlignFile alignFile = null;
+
+ String inFile;
/**
- * List of writable formats by the application. Order must correspond with the
- * WRITABLE_EXTENSIONS list of formats.
+ * character used to write newlines
*/
- public static final String[] WRITABLE_FNAMES = new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" };
+ protected String newline = System.getProperty("line.separator");
+
+ /**
+ * 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.GFF3File,
+ "HTML" };
/**
* List of readable format file extensions by application in order
* corresponding to READABLE_FNAMES
*/
public static final String[] READABLE_EXTENSIONS = new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "sto,stk","xml" }; // ,
-
- // ".blast"
- // };
+ { "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 };
/**
* 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", "Jalview",
- "Stockholm","RNAML" };// ,
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm",
+ "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File, "Jalview",
+ HtmlFile.FILE_DESC };
+
+ /**
+ * 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 };
- // "SimpleBLAST"
- // };
+ /**
+ * 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" };
+
+ /**
+ * 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 String INVALID_CHARACTERS = "Contains invalid characters";
public static String SUPPORTED_FORMATS = "Formats currently supported are\n"
+ prettyPrint(READABLE_FORMATS);
+ public AppletFormatAdapter()
+ {
+ }
+
+ public AppletFormatAdapter(AlignViewportI viewport)
+ {
+ this.viewport = viewport;
+ }
+
/**
- *
+ *
* @param els
* @return grammatically correct(ish) list consisting of els elements.
*/
for (int i = 0, iSize = els.length - 1; i < iSize; i++)
{
list.append(els[i]);
- list.append(",");
+ list.append(", ");
}
list.append(" and " + els[els.length - 1] + ".");
return list.toString();
}
- 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)
{
newline = nl;
}
+
public String getNewlineString()
{
return newline;
}
+
/**
* 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
/**
* validate format is valid for IO
- *
+ *
* @param format
* a format string to be compared with either READABLE_FORMATS or
* WRITEABLE_FORMATS
boolean valid = false;
String[] format_list = (forwriting) ? WRITEABLE_FORMATS
: READABLE_FORMATS;
- for (int i = 0; i < format_list.length; i++)
+ for (String element : format_list)
{
- if (format_list[i].equalsIgnoreCase(format))
+ if (element.equalsIgnoreCase(format))
{
return true;
}
/**
* Constructs the correct filetype parser for a characterised datasource
- *
+ *
* @param inFile
* data/data location
* @param type
* type of datasource
* @param format
* File format of data provided by datasource
- *
+ *
* @return DOCUMENT ME!
*/
public Alignment readFile(String inFile, String type, String format)
this.inFile = inFile;
try
{
+ Alignment al;
if (format.equals("FASTA"))
{
- afile = new FastaFile(inFile, type);
+ alignFile = new FastaFile(inFile, type);
}
else if (format.equals("MSF"))
{
- afile = new MSFfile(inFile, type);
+ alignFile = new MSFfile(inFile, type);
}
else if (format.equals("PileUp"))
{
- afile = new PileUpfile(inFile, type);
+ alignFile = new PileUpfile(inFile, type);
}
else if (format.equals("CLUSTAL"))
{
- afile = new ClustalFile(inFile, type);
+ alignFile = new ClustalFile(inFile, type);
}
else if (format.equals("BLC"))
{
- afile = new BLCFile(inFile, type);
+ alignFile = new BLCFile(inFile, type);
}
else if (format.equals("PIR"))
{
- afile = new PIRFile(inFile, type);
+ alignFile = new PIRFile(inFile, type);
}
else if (format.equals("PFAM"))
{
- afile = new PfamFile(inFile, type);
+ alignFile = new PfamFile(inFile, type);
}
else if (format.equals("JnetFile"))
{
- afile = new JPredFile(inFile, type);
- ((JPredFile) afile).removeNonSequences();
+ alignFile = new JPredFile(inFile, type);
+ ((JPredFile) alignFile).removeNonSequences();
}
else if (format.equals("PDB"))
{
- //if (contient de l'ARN)
- // {
- System.out.println(inFile); //donne le path
-
- //new URL = http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data=inFile;
- //afile = new RnamlFile(inFile, type);
-
- //}
- afile = new MCview.PDBfile(inFile, type);
-
+ alignFile = new MCview.PDBfile(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, 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);
+ alignFile = new StockholmFile(inFile, type);
}
else if (format.equals("SimpleBLAST"))
{
- afile = new SimpleBlastFile(inFile, type);
+ 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"))
{
- afile = new RnamlFile(inFile, type);
+ alignFile = new RnamlFile(inFile, type);
+ }
+ else if (format.equals(IdentifyFile.GFF3File))
+ {
+ alignFile = new Gff3File(inFile, type);
}
+ // Standard boilerplate for creating alignment from parser
+ alignFile.setViewport(viewport);
- Alignment al = new Alignment(afile.getSeqsAsArray());
+ al = new Alignment(alignFile.getSeqsAsArray());
- afile.addAnnotations(al);
+ alignFile.addAnnotations(al);
+
+ alignFile.addGroups(al);
return al;
} catch (Exception e)
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);
+ alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
+ Alignment al = new Alignment(alignFile.getSeqsAsArray());
+
+ alignFile.addSeqGroups(al);
+ alignFile.addAnnotations(al);
return al;
} catch (Exception ex)
/**
* 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!
*/
- public Alignment readFromFile(FileParse source, String format)
+ public AlignmentI readFromFile(FileParse source, String format)
throws java.io.IOException
{
// TODO: generalise mapping between format string and io. class instances
String type = source.type;
try
{
+ Alignment al;
if (format.equals("FASTA"))
{
- afile = new FastaFile(source);
+ alignFile = new FastaFile(source);
}
else if (format.equals("MSF"))
{
- afile = new MSFfile(source);
+ alignFile = new MSFfile(source);
}
else if (format.equals("PileUp"))
{
- afile = new PileUpfile(source);
+ alignFile = new PileUpfile(source);
}
else if (format.equals("CLUSTAL"))
{
- afile = new ClustalFile(source);
+ alignFile = new ClustalFile(source);
}
else if (format.equals("BLC"))
{
- afile = new BLCFile(source);
+ alignFile = new BLCFile(source);
}
else if (format.equals("PIR"))
{
- afile = new PIRFile(source);
+ alignFile = new PIRFile(source);
}
else if (format.equals("PFAM"))
{
- afile = new PfamFile(source);
+ alignFile = new PfamFile(source);
}
else if (format.equals("JnetFile"))
{
- afile = new JPredFile(source);
- ((JPredFile) afile).removeNonSequences();
+ alignFile = new JPredFile(source);
+ ((JPredFile) alignFile).removeNonSequences();
}
else if (format.equals("PDB"))
{
- afile = new MCview.PDBfile(source);
+ alignFile = new MCview.PDBfile(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, source);
}
else if (format.equals("STH"))
{
- afile = new StockholmFile(source);
+ alignFile = new StockholmFile(source);
}
else if (format.equals("RNAML"))
{
- afile = new RnamlFile(source);
+ alignFile = new RnamlFile(source);
}
else if (format.equals("SimpleBLAST"))
{
- afile = new SimpleBlastFile(source);
+ alignFile = new SimpleBlastFile(source);
}
-
- Alignment al = new Alignment(afile.getSeqsAsArray());
-
- afile.addAnnotations(al);
+ else if (format.equals(PhylipFile.FILE_DESC))
+ {
+ alignFile = new PhylipFile(source);
+ }
+ else if (format.equals(IdentifyFile.GFF3File))
+ {
+ alignFile = new Gff3File(inFile, type);
+ }
+ else if (format.equals(JSONFile.FILE_DESC))
+ {
+ alignFile = new JSONFile(source);
+ al = new Alignment(alignFile.getSeqsAsArray());
+ alignFile.addAnnotations(al);
+ alignFile.addSeqGroups(al);
+ return al;
+ }
+ else if (format.equals(HtmlFile.FILE_DESC))
+ {
+ alignFile = new HtmlFile(source);
+ }
+ al = new Alignment(alignFile.getSeqsAsArray());
+ alignFile.addAnnotations(al);
return al;
} catch (Exception e)
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);
+ alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
+ Alignment al = new Alignment(alignFile.getSeqsAsArray());
+ alignFile.addAnnotations(al);
+ alignFile.addSeqGroups(al);
return al;
} catch (Exception ex)
}
}
+
+ /**
+ * 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)
+ {
+
+ AlignmentView selvew = av.getAlignmentView(selectedOnly, false);
+ AlignmentI aselview = selvew.getVisibleAlignment(av
+ .getGapCharacter());
+ List<AlignmentAnnotation> ala = (av
+ .getVisibleAlignmentAnnotation(selectedOnly));
+ if (ala != null)
+ {
+ for (AlignmentAnnotation aa : ala)
+ {
+ aselview.addAnnotation(aa);
+ }
+ }
+
+ 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,
try
{
AlignFile afile = null;
-
if (format.equalsIgnoreCase("FASTA"))
{
afile = new FastaFile();
}
else if (format.equalsIgnoreCase("STH"))
{
- afile = new StockholmFile();
+ 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();
+ afile.setViewport(viewport);
+ // Add groups to AlignFile
+ afile.seqGroups = alignment.getGroups();
+
+ // Add non auto calculated annotation to AlignFile
+ for (AlignmentAnnotation annot : alignment.getAlignmentAnnotation())
+ {
+ if (annot != null && !annot.autoCalculated)
+ {
+ if (annot.label.equals("PDB.CATempFactor"))
+ {
+ continue;
+ }
+ afile.annotations.add(annot);
+ }
+ }
+ }
else if (format.equalsIgnoreCase("RNAML"))
{
afile = new RnamlFile();
}
-
+
else
{
- throw new Exception(
- "Implementation error: Unknown file format string");
+ throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
}
afile.setNewlineString(newline);
afile.addJVSuffix(jvsuffix);
afile.setSeqs(alignment.getSequencesArray());
+
String afileresp = afile.print();
if (afile.hasWarningMessage())
{
{
String protocol = FILE;
String ft = file.toLowerCase().trim();
- if (ft.indexOf("http:") ==0 || ft.indexOf("https:") ==0 || ft.indexOf("file:") == 0)
+ if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
+ || ft.indexOf("file:") == 0)
{
protocol = URL;
}
} catch (Exception e)
{
System.err
- .println("Couln't format the alignment for output as a FASTA file.");
+ .println("Couln't format the alignment for output as a FASTA file.");
e.printStackTrace(System.err);
}
}
}
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");
-
+ .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
/**
* 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
} catch (Exception ex)
{
System.err
- .println("Exception checking resources: " + file + " " + ex);
+ .println("Exception checking resources: " + file + " " + ex);
}
if (file.indexOf("://") > -1)
if (debug)
{
System.out
- .println("File deemed not accessible via " + protocol);
+ .println("File deemed not accessible via " + protocol);
}
fp.close();
return null;
}
return null;
}
+
+ public AlignFile getAlignFile()
+ {
+ return alignFile;
+ }
+
+ public void setAlignFile(AlignFile alignFile)
+ {
+ this.alignFile = alignFile;
+ }
}
git://source.jalview.org / jalview.git / blobdiff