/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
*
* 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
* method
*/
public static final String[] WRITEABLE_FORMATS = new String[]
- { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA" };
+ { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
+ "AMSA" };
/**
* 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" };
+ { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+ "sto,stk" };
/**
* 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" };
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+ "STH" };
/**
* List of readable format file extensions by application in order
*/
public static final String[] READABLE_EXTENSIONS = new String[]
{ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "sto" }; // ,
+ "sto,stk" }; // ,
// ".blast"
// };
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
}
else if (format.equalsIgnoreCase("STH"))
{
- afile = new StockholmFile();
+ afile = new StockholmFile(alignment);
}
else if (format.equalsIgnoreCase("AMSA"))
{
throw new Exception(
"Implementation error: Unknown file format string");
}
-
+ afile.setNewlineString(newline);
afile.addJVSuffix(jvsuffix);
afile.setSeqs(alignment.getSequencesArray());
return null;
}
+ public static String checkProtocol(String file)
+ {
+ String protocol = FILE;
+ String ft = file.toLowerCase().trim();
+ if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
+ || ft.indexOf("file:") == 0)
+ {
+ protocol = URL;
+ }
+ return protocol;
+ }
+
public static void main(String[] args)
{
int i = 0;
{
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();
- Alignment al = afa.readFile(args[i], FILE,
- new IdentifyFile().Identify(args[i], FILE));
- t1 += System.currentTimeMillis();
- System.gc();
- memf += r.totalMemory() - r.freeMemory();
- if (al != null)
+ String fName = f.getName();
+ String extension = fName.substring(fName.lastIndexOf(".") + 1,
+ fName.length());
+ if (extension.equals("stk") || extension.equals("sto"))
{
- System.out.println("Alignment contains " + al.getHeight()
- + " sequences and " + al.getWidth() + " columns.");
- try
- {
- System.out.println(new AppletFormatAdapter().formatSequences(
- "FASTA", al, true));
- } catch (Exception e)
- {
- System.err
- .println("Couln't format the alignment for output as a FASTA file.");
- e.printStackTrace(System.err);
- }
+ afa.test(f);
}
else
{
- System.out.println("Couldn't read alignment");
+ Runtime r = Runtime.getRuntime();
+ 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));
+ 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("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");
}
- 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
{
}
}
+ 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.
git://source.jalview.org / jalview.git / blobdiff