/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 $Revision$
*/
* 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" }; // , "SimpleBLAST" };
+ { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
+ "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC }; // , "SimpleBLAST" };
/**
* 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", "STH", "AMSA" };
+ { "AMSA", "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR",
+ PhylipFile.FILE_DESC, "PFAM", "STH" };
/**
* 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, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar", "sto,stk" };
+ { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ "jvp", "sto,stk", "jar", PhylipFile.FILE_EXT };
/**
* 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", "Jalview", "STH"};
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+ "STH", "Jalview", PhylipFile.FILE_DESC };
/**
* 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" }; // ,
-
- // ".blast"
- // };
+ { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ "jar,jvp", "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT }; // ".blast"
/**
* 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" };// ,
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+ "Stockholm", "RNAML", PhylipFile.FILE_DESC };// ,
// "SimpleBLAST"
// };
+ prettyPrint(READABLE_FORMATS);
/**
- *
+ *
* @param els
* @return grammatically correct(ish) list consisting of els elements.
*/
/**
* 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)
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 SimpleBlastFile(inFile, type);
}
+ else if (format.equals(PhylipFile.FILE_DESC))
+ {
+ afile = new PhylipFile(inFile, type);
+ }
+ else if (format.equals("RNAML"))
+ {
+ afile = new RnamlFile(inFile, type);
+ }
Alignment al = new Alignment(afile.getSeqsAsArray());
/**
* 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
{
afile = new StockholmFile(source);
}
+ else if (format.equals("RNAML"))
+ {
+ afile = new RnamlFile(source);
+ }
else if (format.equals("SimpleBLAST"))
{
afile = new SimpleBlastFile(source);
}
-
+ else if (format.equals(PhylipFile.FILE_DESC))
+ {
+ afile = new PhylipFile(source);
+ }
Alignment al = new Alignment(afile.getSeqsAsArray());
afile.addAnnotations(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(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,
{
afile = new AMSAFile(alignment);
}
+ else if (format.equalsIgnoreCase(PhylipFile.FILE_DESC))
+ {
+ afile = new PhylipFile();
+ }
+ 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);
{
System.out.println("Reading file: " + f);
AppletFormatAdapter afa = new AppletFormatAdapter();
- String fName = f.getName();
- String extension = fName.substring(fName.lastIndexOf(".") + 1, fName.length());
- if (extension.equals("stk") || extension.equals("sto"))
- {
- afa.test(f);
- }
- else
- {
Runtime r = Runtime.getRuntime();
System.gc();
long memf = -r.totalMemory() + r.freeMemory();
} 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
+ "'th argument: " + args[i] + "\n" + e);
}
-
}
else
{
}
}
- private void test(File f) {
- System.out.println("Reading file: " + f);
- String ff = f.getPath();
- try
- {
- Alignment al = readFile(ff, FILE, new IdentifyFile().Identify(ff, FILE));
- for (int i = 0; i < al.getSequencesArray().length; ++i) {
- al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
- }
- AlignFile stFile = new StockholmFile(al);
- stFile.setSeqs(al.getSequencesArray());
-
- String stockholmoutput = stFile.print();
- Alignment al_input = readFile(stockholmoutput, AppletFormatAdapter.PASTE, "STH");
- if (al != null && al_input!= null)
- {
- System.out.println("Alignment contains: " + al.getHeight() + " and " + al_input.getHeight()
- + " sequences; " + al.getWidth() + " and " + al_input.getWidth() + " columns.");
- AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation();
- AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation();
-
- // check Alignment annotation
- if (aa_new != null && aa_original != null)
- {
- System.out.println("Alignment contains: " + aa_new.length
- + " and " + aa_original.length + " alignment annotation(s)");
- for (int i = 0; i < aa_original.length; i++)
- {
- if (!equalss(aa_original[i], aa_new[i]))
- System.out.println("Different alignment annotation");
- }
- }
-
- // check sequences, annotation and features
- SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
- seq_original = al.getSequencesArray();
- SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length];
- seq_new = al_input.getSequencesArray();
- SequenceFeature[] sequenceFeatures_original,sequenceFeatures_new;
- AlignmentAnnotation annot_original, annot_new;
- //
- for (int i = 0; i < al.getSequencesArray().length; i++)
- {
- String name = seq_original[i].getName();
- int start = seq_original[i].getStart();
- int end = seq_original[i].getEnd();
- System.out.println("Check sequence: " + name + "/" + start + "-" + end);
-
- // search equal sequence
- for (int in = 0; in < al_input.getSequencesArray().length; in++) {
- if (name.equals(seq_new[in].getName()) &&
- start == seq_new[in].getStart() &&
- end ==seq_new[in].getEnd())
- {
- String ss_original = seq_original[i].getSequenceAsString();
- String ss_new = seq_new[in].getSequenceAsString();
- if (!ss_original.equals(ss_new))
- {
- System.out.println("The sequences " + name + "/" + start + "-" + end + " are not equal");
- }
-
- // compare sequence features
- if (seq_original[i].getSequenceFeatures() != null && seq_new[in].getSequenceFeatures() != null)
- {
- System.out.println("There are feature!!!");
- sequenceFeatures_original = new SequenceFeature[seq_original[i].getSequenceFeatures().length];
- sequenceFeatures_original = seq_original[i].getSequenceFeatures();
- sequenceFeatures_new = new SequenceFeature[seq_new[in].getSequenceFeatures().length];
- sequenceFeatures_new = seq_new[in].getSequenceFeatures();
-
- if (seq_original[i].getSequenceFeatures().length == seq_new[in].getSequenceFeatures().length)
- {
- for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++) {
- if (!sequenceFeatures_original[feat].equals(sequenceFeatures_new[feat])) {
- System.out.println("Different features");
- break;
- }
- }
- } else
- {
- System.out.println("different number of features");
- }
- } else if (seq_original[i].getSequenceFeatures() == null && seq_new[in].getSequenceFeatures() == null)
- {
- System.out.println("No sequence features");
- } else if (seq_original[i].getSequenceFeatures() != null && seq_new[in].getSequenceFeatures() == null)
- {
- System.out.println("Coudn't compare sequence features new one");
- }
- // compare alignment annotation
- if (al.getSequenceAt(i).getAnnotation() != null && al_input.getSequenceAt(in).getAnnotation() != null)
- {
- for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++)
- {
- if (al.getSequenceAt(i).getAnnotation()[j] != null &&
- al_input.getSequenceAt(in).getAnnotation()[j] != null)
- {
- annot_original = al.getSequenceAt(i).getAnnotation()[j];
- annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
- if (!equalss(annot_original, annot_new))
- System.out.println("Different annotation");
- }
- }
- } else if (al.getSequenceAt(i).getAnnotation() == null && al_input.getSequenceAt(in).getAnnotation() == null)
- {
- System.out.println("No annotations");
- } else if (al.getSequenceAt(i).getAnnotation() != null && al_input.getSequenceAt(in).getAnnotation() == null)
- {
- System.out.println("Coudn't compare annotations new one");
- }
- break;
- }
- }
- }
- } else
- {
- System.out.println("Couldn't read alignment");
- }
- } catch (Exception e)
- {
- System.err.println("Couln't format the alignment for output file.");
- e.printStackTrace(System.err);
- }
- }
-
- /*
- * compare annotations
- */
- private boolean equalss(AlignmentAnnotation annot_or, AlignmentAnnotation annot_new)
- {
- if (annot_or.annotations.length != annot_new.annotations.length)
- {
- return false;
- }
- for (int i = 0; i < annot_or.annotations.length; i++)
- {
- if (annot_or.annotations[i] != null && annot_new.annotations[i] != null)
- {
- if (!annot_or.annotations[i].displayCharacter.equals(annot_new.annotations[i].displayCharacter) &&
- annot_or.annotations[i].secondaryStructure != annot_new.annotations[i].secondaryStructure &&
- !annot_or.annotations[i].description.equals(annot_new.annotations[i].description))
- {
- return false;
- }
- } else if (annot_or.annotations[i] == null && annot_new.annotations[i] == null)
- {
- continue;
- } else
- {
- return false;
- }
- }
- return true;
- }
/**
* 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;
git://source.jalview.org / jalview.git / blobdiff