/*
- * 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.
*
*/
package jalview.io;
-import jalview.api.AlignViewportI;
-import jalview.datamodel.*;
+import java.util.Locale;
+
+import jalview.api.AlignExportSettingsI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+import java.io.File;
+import java.io.IOException;
/**
* Additional formatting methods used by the application in a number of places.
*/
public class FormatAdapter extends AppletFormatAdapter
{
+ public FormatAdapter(AlignmentViewPanel viewpanel)
+ {
+ super(viewpanel);
+ init();
+ }
+
+ public FormatAdapter()
+ {
+ super();
+ init();
+ }
+
+ public FormatAdapter(AlignmentViewPanel alignPanel,
+ AlignExportSettingsI settings)
+ {
+ super(alignPanel, settings);
+ }
- public String formatSequences(String format, SequenceI[] seqs,
- String[] omitHiddenColumns)
+ private void init()
+ {
+ if (Cache.getDefault("STRUCT_FROM_PDB", true))
+ {
+ annotFromStructure = Cache.getDefault("ADD_TEMPFACT_ANN",
+ true);
+ localSecondaryStruct = Cache.getDefault("ADD_SS_ANN",
+ true);
+ serviceSecondaryStruct = Cache.getDefault("USE_RNAVIEW",
+ true);
+ }
+ else
+ {
+ // disable all PDB annotation options
+ annotFromStructure = false;
+ localSecondaryStruct = false;
+ serviceSecondaryStruct = false;
+ }
+ }
+
+ public String formatSequences(FileFormatI format, SequenceI[] seqs,
+ String[] omitHiddenColumns, int[] exportRange)
{
- return formatSequences(format, replaceStrings(seqs, omitHiddenColumns));
+ return formatSequences(format,
+ replaceStrings(seqs, omitHiddenColumns, exportRange));
}
/**
* @return new sequences
*/
public SequenceI[] replaceStrings(SequenceI[] seqs,
- String[] omitHiddenColumns)
+ String[] omitHiddenColumns, int[] startEnd)
{
if (omitHiddenColumns != null)
{
SequenceI[] tmp = new SequenceI[seqs.length];
+
+ int startRes;
+ int endRes;
+ int startIndex;
+ int endIndex;
for (int i = 0; i < seqs.length; i++)
{
+ startRes = seqs[i].getStart();
+ endRes = seqs[i].getEnd();
+ if (startEnd != null)
+ {
+ startIndex = startEnd[0];
+ endIndex = startEnd[1];
+ // get first non-gaped residue start position
+ while (Comparison.isGap(seqs[i].getCharAt(startIndex))
+ && startIndex < endIndex)
+ {
+ startIndex++;
+ }
+
+ // get last non-gaped residue end position
+ while (Comparison.isGap(seqs[i].getCharAt(endIndex))
+ && endIndex > startIndex)
+ {
+ endIndex--;
+ }
+
+ startRes = seqs[i].findPosition(startIndex);
+ endRes = seqs[i].findPosition(endIndex);
+ }
+
tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
- seqs[i].getStart(), seqs[i].getEnd());
+ startRes, endRes);
tmp[i].setDescription(seqs[i].getDescription());
}
seqs = tmp;
*
*
* @param format
- * Format string as givien in the AppletFormatAdaptor list (exact
- * match to name of class implementing file io for that format)
* @param seqs
* vector of sequences to write
*
* @return String containing sequences in desired format
*/
- public String formatSequences(String format, SequenceI[] seqs)
+ public String formatSequences(FileFormatI format, SequenceI[] seqs)
{
-
- try
- {
- AlignFile afile = null;
-
- if (format.equalsIgnoreCase("FASTA"))
- {
- afile = new FastaFile();
- afile.addJVSuffix(jalview.bin.Cache.getDefault("FASTA_JVSUFFIX",
- true));
- }
- else if (format.equalsIgnoreCase("MSF"))
- {
- afile = new MSFfile();
- afile.addJVSuffix(jalview.bin.Cache
- .getDefault("MSF_JVSUFFIX", true));
- }
- else if (format.equalsIgnoreCase("PileUp"))
- {
- afile = new PileUpfile();
- afile.addJVSuffix(jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX",
- true));
- }
- else if (format.equalsIgnoreCase("CLUSTAL"))
- {
- afile = new ClustalFile();
- afile.addJVSuffix(jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX",
- true));
- }
- else if (format.equalsIgnoreCase("BLC"))
- {
- afile = new BLCFile();
- afile.addJVSuffix(jalview.bin.Cache
- .getDefault("BLC_JVSUFFIX", true));
- }
- else if (format.equalsIgnoreCase("PIR"))
- {
- afile = new PIRFile();
- afile.addJVSuffix(jalview.bin.Cache
- .getDefault("PIR_JVSUFFIX", true));
- }
- else if (format.equalsIgnoreCase("PFAM"))
- {
- afile = new PfamFile();
- afile.addJVSuffix(jalview.bin.Cache.getDefault("PFAM_JVSUFFIX",
- true));
- }
- /*
- * amsa is not supported by this function - it requires an alignment
- * rather than a sequence vector else if (format.equalsIgnoreCase("AMSA"))
- * { afile = new AMSAFile(); afile.addJVSuffix(
- * jalview.bin.Cache.getDefault("AMSA_JVSUFFIX", true)); }
- */
-
- afile.setSeqs(seqs);
- String afileresp = afile.print();
- if (afile.hasWarningMessage())
- {
- System.err.println("Warning raised when writing as " + format
- + " : " + afile.getWarningMessage());
- }
- return afileresp;
- } catch (Exception e)
- {
- System.err.println("Failed to write alignment as a '" + format
- + "' file\n");
- e.printStackTrace();
- }
-
- return null;
- }
-
- public boolean getCacheSuffixDefault(String format)
- {
- if (isValidFormat(format))
- return jalview.bin.Cache.getDefault(format.toUpperCase()
- + "_JVSUFFIX", true);
- return false;
+ boolean withSuffix = getCacheSuffixDefault(format);
+ return format.getWriter(null).print(seqs, withSuffix);
}
- public String formatSequences(String format, AlignmentI alignment,
- String[] omitHidden, ColumnSelection colSel)
+ public boolean getCacheSuffixDefault(FileFormatI format)
{
- return formatSequences(format, alignment, omitHidden,
- getCacheSuffixDefault(format), colSel, null);
+ return Cache.getDefault(format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX",
+ true);
}
- public String formatSequences(String format, AlignmentI alignment,
- String[] omitHidden, ColumnSelection colSel, SequenceGroup sgp)
+ public String formatSequences(FileFormatI format, AlignmentI alignment,
+ String[] omitHidden, int[] exportRange, HiddenColumns hidden)
{
- return formatSequences(format, alignment, omitHidden,
- getCacheSuffixDefault(format), colSel, sgp);
+ return formatSequences(format, alignment, omitHidden, exportRange,
+ getCacheSuffixDefault(format), hidden, null);
}
/**
- * hack function to replace seuqences with visible sequence strings before
+ * hack function to replace sequences with visible sequence strings before
* generating a string of the alignment in the given format.
*
* @param format
* defines hidden columns that are edited out of annotation
* @return string representation of the alignment formatted as format
*/
- public String formatSequences(String format, AlignmentI alignment,
- String[] omitHidden, boolean suffix, ColumnSelection colSel)
+ public String formatSequences(FileFormatI format, AlignmentI alignment,
+ String[] omitHidden, int[] exportRange, boolean suffix,
+ HiddenColumns hidden)
{
- return formatSequences(format, alignment, omitHidden, suffix, colSel,
- null);
+ return formatSequences(format, alignment, omitHidden, exportRange,
+ suffix, hidden, null);
}
- public String formatSequences(String format, AlignmentI alignment,
- String[] omitHidden, boolean suffix, ColumnSelection colSel,
- jalview.datamodel.SequenceGroup selgp)
+ public String formatSequences(FileFormatI format, AlignmentI alignment,
+ String[] omitHidden, int[] exportRange, boolean suffix,
+ HiddenColumns hidden, SequenceGroup selgp)
{
if (omitHidden != null)
{
// TODO: JAL-1486 - set start and end for output correctly. basically,
// AlignmentView.getVisibleContigs does this.
Alignment alv = new Alignment(replaceStrings(
- alignment.getSequencesArray(), omitHidden));
+ alignment.getSequencesArray(), omitHidden, exportRange));
AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
if (ala != null)
{
AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
if (selgp != null)
{
- colSel.makeVisibleAnnotation(selgp.getStartRes(),
- selgp.getEndRes(), na);
+ na.makeVisibleAnnotation(selgp.getStartRes(), selgp.getEndRes(),
+ hidden);
}
else
{
- colSel.makeVisibleAnnotation(na);
+ na.makeVisibleAnnotation(hidden);
}
alv.addAnnotation(na);
}
return this.formatSequences(format, alignment, suffix);
}
- /**
- * validate format is valid for IO in Application. This is basically the
- * AppletFormatAdapter.isValidFormat call with additional checks for
- * Application only formats like 'Jalview'.
- *
- * @param format
- * a format string to be compared with list of readable or writable
- * formats (READABLE_FORMATS or WRITABLE_FORMATS)
- * @param forwriting
- * when true, format is checked against list of writable formats.
- * @return true if format is valid
- */
- public static final boolean isValidIOFormat(String format,
- boolean forwriting)
+ @Override
+ public AlignmentI readFile(String file, DataSourceType sourceType,
+ FileFormatI fileFormat) throws IOException
{
- if (format.equalsIgnoreCase("jalview"))
- {
- return true;
- }
- return AppletFormatAdapter.isValidFormat(format, forwriting);
+ AlignmentI al = super.readFile(file, sourceType, fileFormat);
+ return al;
+ }
+
+ public AlignmentI readFile(File file, DataSourceType sourceType,
+ FileFormatI fileFormat) throws IOException
+ {
+ AlignmentI al = super.readFile(file, null, sourceType, fileFormat);
+ return al;
+ }
+
+ @Override
+ public AlignmentI readFromFile(FileParse source, FileFormatI format)
+ throws IOException
+ {
+ AlignmentI al = super.readFromFile(source, format);
+ return al;
}
/**
- * Create a flat file representation of a given view or selected region of a view
+ * Create a flat file representation of a given view or selected region of a
+ * view
+ *
* @param format
- * @param av
+ * @param ap
+ * alignment panel originating the view
* @return String containing flat file
*/
- public String formatSequences(String format, AlignViewportI av, boolean selectedOnly)
+ public String formatSequences(FileFormatI format, AlignmentViewPanel ap,
+ boolean selectedOnly)
+ {
+ return formatSequences(format, getCacheSuffixDefault(format), ap,
+ selectedOnly);
+ }
+
+ public AlignmentI readFromFile(AlignmentFileReaderI source,
+ FileFormatI format) throws IOException
{
- return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
+ FileParse fp = new FileParse(source.getInFile(),
+ source.getDataSourceType());
+ return readFromFile(fp, format);
}
}
git://source.jalview.org / jalview.git / blobdiff