/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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.datamodel.*;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
/**
- * 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 FormatAdapter(AlignmentViewPanel viewpanel)
{
+ super(viewpanel);
+ init();
+ }
+
+ public FormatAdapter()
+ {
+ super();
+ init();
+ }
- return formatSequences(format, replaceStrings(seqs, omitHiddenColumns));
+ public FormatAdapter(AlignmentViewPanel alignPanel,
+ AlignExportSettingI settings)
+ {
+ super(alignPanel, settings);
+ }
+
+ private void init()
+ {
+ if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+ {
+ annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+ true);
+ localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+ true);
+ serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+ true);
+ }
+ else
+ {
+ // disable all PDB annotation options
+ annotFromStructure = false;
+ localSecondaryStruct = false;
+ serviceSecondaryStruct = false;
+ }
+ }
+
+ public String formatSequences(String format, SequenceI[] seqs,
+ String[] omitHiddenColumns, int[] exportRange)
+ {
+
+ return formatSequences(format,
+ replaceStrings(seqs, omitHiddenColumns, exportRange));
}
/**
- * create sequences with each seuqence string replaced with the one given in omitHiddenCOlumns
+ * create sequences with each sequence 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, 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++)
{
- tmp[i] = new Sequence(
- seqs[i].getName(), omitHiddenColumns[i],
- seqs[i].getStart(), seqs[i].getEnd());
+ 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 (jalview.util.Comparison.isGap(seqs[i]
+ .getCharAt(startIndex)) && startIndex < endIndex)
+ {
+ startIndex++;
+ }
+
+ // get last non-gaped residue end position
+ while (jalview.util.Comparison.isGap(seqs[i].getCharAt(endIndex))
+ && endIndex > startIndex)
+ {
+ endIndex--;
+ }
+
+ startRes = seqs[i].findPosition(startIndex);
+ startRes = seqs[i].getStart() > 1 ? startRes - seqs[i].getStart()
+ : startRes;
+ endRes = seqs[i].findPosition(endIndex) - seqs[i].getStart();
+ }
+
+ tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
+ startRes, endRes);
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
- *
+ * Format a vector of sequences as a flat alignment file. TODO: allow caller
+ * to detect errors and warnings encountered when generating output
+ *
+ *
+ * @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)
+ 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");
+ 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, int[] exportRange, ColumnSelection colSel)
{
- return formatSequences(format, alignment, omitHidden, getCacheSuffixDefault(format), colSel, null);
+ return formatSequences(format, alignment, omitHidden, exportRange,
+ 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, int[] exportRange, ColumnSelection colSel,
+ SequenceGroup sgp)
{
- return formatSequences(format, alignment, omitHidden, getCacheSuffixDefault(format), colSel, sgp);
+ return formatSequences(format, alignment, omitHidden, exportRange,
+ 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, int[] exportRange, boolean suffix,
+ ColumnSelection colSel)
{
- return formatSequences(format, alignment, omitHidden, suffix, colSel, null);
+ return formatSequences(format, alignment, omitHidden, exportRange,
+ suffix, colSel, null);
}
- public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, boolean suffix,
+ public String formatSequences(String format, AlignmentI alignment,
+ String[] omitHidden, int[] exportRange, boolean suffix,
ColumnSelection colSel, jalview.datamodel.SequenceGroup selgp)
{
- if (omitHidden!=null)
+ if (omitHidden != null)
{
- //
- Alignment alv = new Alignment(replaceStrings(alignment.getSequencesArray(), omitHidden));
+ // TODO consider using AlignmentView to prune to visible region
+ // TODO prune sequence annotation and groups to visible region
+ // TODO: JAL-1486 - set start and end for output correctly. basically,
+ // AlignmentView.getVisibleContigs does this.
+ Alignment alv = new Alignment(replaceStrings(
+ alignment.getSequencesArray(), omitHidden, exportRange));
AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
- for (int i=0; i<ala.length; i++)
+ if (ala != null)
{
- AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
- if (selgp!=null)
+ for (int i = 0; i < ala.length; i++)
{
- colSel.makeVisibleAnnotation(selgp.getStartRes(),selgp.getEndRes(), na);
- } else {
- colSel.makeVisibleAnnotation(na);
+ AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
+ if (selgp != null)
+ {
+ colSel.makeVisibleAnnotation(selgp.getStartRes(),
+ selgp.getEndRes(), na);
+ }
+ else
+ {
+ colSel.makeVisibleAnnotation(na);
+ }
+ alv.addAnnotation(na);
}
- alv.addAnnotation(na);
}
return this.formatSequences(format, alv, suffix);
}
return this.formatSequences(format, alignment, suffix);
}
+
+ public AlignmentI readFile(String inFile, String type, String format)
+ throws java.io.IOException
+ {
+ AlignmentI al = super.readFile(inFile, type, format);
+ return al;
+ }
+
+ public AlignmentI readFromFile(FileParse source, String format)
+ throws java.io.IOException
+ {
+ AlignmentI al = super.readFromFile(source, format);
+ return al;
+ }
+
+ /**
+ * 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)
+ {
+ if (format.equalsIgnoreCase("jalview"))
+ {
+ return true;
+ }
+ return AppletFormatAdapter.isValidFormat(format, forwriting);
+ }
+
+ /**
+ * Create a flat file representation of a given view or selected region of a
+ * view
+ *
+ * @param format
+ * @param ap
+ * alignment panel originating the view
+ * @return String containing flat file
+ */
+ public String formatSequences(String format, AlignmentViewPanel ap,
+ boolean selectedOnly)
+ {
+ return formatSequences(format, getCacheSuffixDefault(format), ap,
+ selectedOnly);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff