/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
* This program 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 2
* of the License, or (at your option) any later version.
- *
+ *
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
import jalview.datamodel.*;
/**
- * Additional formatting methods used by the application
- * in a number of places.
- *
+ * Additional formatting methods used by the application in a number of places.
+ *
* @author $author$
* @version $Revision$
*/
-public class FormatAdapter
- extends AppletFormatAdapter
+public class FormatAdapter extends AppletFormatAdapter
{
-
- public String formatSequences(String format,
- SequenceI[] seqs,
- String[] omitHiddenColumns)
+
+ public String formatSequences(String format, SequenceI[] seqs,
+ String[] omitHiddenColumns)
{
return formatSequences(format, replaceStrings(seqs, omitHiddenColumns));
}
/**
- * create sequences with each seuqence string replaced with the one given in omitHiddenCOlumns
+ * create sequences with each seuqence string replaced with the one given in
+ * omitHiddenCOlumns
+ *
* @param seqs
* @param omitHiddenColumns
* @return new sequences
*/
- public SequenceI[] replaceStrings(SequenceI[] seqs, String[] omitHiddenColumns)
+ public SequenceI[] replaceStrings(SequenceI[] seqs,
+ String[] omitHiddenColumns)
{
if (omitHiddenColumns != null)
{
SequenceI[] tmp = new SequenceI[seqs.length];
for (int i = 0; i < seqs.length; i++)
{
- tmp[i] = new Sequence(
- seqs[i].getName(), omitHiddenColumns[i],
- seqs[i].getStart(), seqs[i].getEnd());
+ tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
+ seqs[i].getStart(), seqs[i].getEnd());
tmp[i].setDescription(seqs[i].getDescription());
}
seqs = tmp;
/**
* Format a vector of sequences as a flat alignment file.
- *
- * @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
- *
+ *
+ * @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(String format, SequenceI[] seqs)
{
try
if (format.equalsIgnoreCase("FASTA"))
{
afile = new FastaFile();
- afile.addJVSuffix(
- jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", true));
+ 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));
+ 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));
+ 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));
+ 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));
+ 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));
+ 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));
+ 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));
- }*/
+ /*
+ * 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);
return afile.print();
- }
- catch (Exception e)
+ } catch (Exception e)
{
- System.err.println("Failed to write alignment as a '" + format +
- "' file\n");
+ 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 jalview.bin.Cache.getDefault(format.toUpperCase()
+ + "_JVSUFFIX", true);
return false;
}
- public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, ColumnSelection colSel)
+
+ public String formatSequences(String format, AlignmentI alignment,
+ String[] omitHidden, ColumnSelection colSel)
{
- return formatSequences(format, alignment, omitHidden, getCacheSuffixDefault(format), colSel, null);
+ return formatSequences(format, alignment, omitHidden,
+ getCacheSuffixDefault(format), colSel, null);
}
- public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, ColumnSelection colSel, SequenceGroup sgp)
+
+ public String formatSequences(String format, AlignmentI alignment,
+ String[] omitHidden, ColumnSelection colSel, SequenceGroup sgp)
{
- return formatSequences(format, alignment, omitHidden, getCacheSuffixDefault(format), colSel, sgp);
+ return formatSequences(format, alignment, omitHidden,
+ getCacheSuffixDefault(format), colSel, sgp);
}
- /**
- * hack function to replace seuqences with visible sequence strings before generating a
- * string of the alignment in the given format.
+
+ /**
+ * hack function to replace seuqences with visible sequence strings before
+ * generating a string of the alignment in the given format.
+ *
* @param format
- * @param alignment
- * @param omitHidden sequence strings to write out in order of sequences in alignment
- * @param colSel defines hidden columns that are edited out of annotation
+ * @param alignment
+ * @param omitHidden
+ * sequence strings to write out in order of sequences in
+ * alignment
+ * @param colSel
+ * 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(String format, AlignmentI alignment,
+ String[] omitHidden, boolean suffix, ColumnSelection colSel)
{
- return formatSequences(format, alignment, omitHidden, suffix, colSel, null);
+ return formatSequences(format, alignment, omitHidden, suffix, colSel,
+ null);
}
- public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, boolean suffix,
- ColumnSelection colSel, jalview.datamodel.SequenceGroup selgp)
+ public String formatSequences(String format, AlignmentI alignment,
+ String[] omitHidden, boolean suffix, ColumnSelection colSel,
+ jalview.datamodel.SequenceGroup selgp)
{
- if (omitHidden!=null)
+ if (omitHidden != null)
{
//
- Alignment alv = new Alignment(replaceStrings(alignment.getSequencesArray(), omitHidden));
+ Alignment alv = new Alignment(replaceStrings(alignment
+ .getSequencesArray(), omitHidden));
AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
- for (int i=0; i<ala.length; i++)
+ for (int i = 0; i < ala.length; i++)
{
AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
- if (selgp!=null)
+ if (selgp != null)
+ {
+ colSel.makeVisibleAnnotation(selgp.getStartRes(), selgp
+ .getEndRes(), na);
+ }
+ else
{
- colSel.makeVisibleAnnotation(selgp.getStartRes(),selgp.getEndRes(), na);
- } else {
colSel.makeVisibleAnnotation(na);
}
alv.addAnnotation(na);
git://source.jalview.org / jalview.git / blobdiff