/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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 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
+ * 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.AlignViewportI;
+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.
public class FormatAdapter extends AppletFormatAdapter
{
+ public FormatAdapter()
+ {
+ super();
+ 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)
{
}
/**
- * create sequences with each seuqence string replaced with the one given in
+ * create sequences with each sequence string replaced with the one given in
* omitHiddenCOlumns
*
* @param seqs
}
/**
- * Format a vector of sequences as a flat alignment file.
+ * 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)
+ * 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
+ * vector of sequences to write
*
* @return String containing sequences in desired format
*/
}
/*
* 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(
+ * 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();
+ 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
public boolean getCacheSuffixDefault(String format)
{
if (isValidFormat(format))
+ {
return jalview.bin.Cache.getDefault(format.toUpperCase()
+ "_JVSUFFIX", true);
+ }
return false;
}
* @param format
* @param alignment
* @param omitHidden
- * sequence strings to write out in order of sequences in
- * alignment
+ * sequence strings to write out in order of sequences in alignment
* @param colSel
- * defines hidden columns that are edited out of annotation
+ * 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,
{
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));
AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
- for (int i = 0; i < ala.length; i++)
+ if (ala != null)
{
- AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
- if (selgp != null)
- {
- colSel.makeVisibleAnnotation(selgp.getStartRes(), selgp
- .getEndRes(), na);
- }
- else
+ for (int i = 0; i < ala.length; i++)
{
- 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);
}
* 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)
+ * 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.
+ * when true, format is checked against list of writable formats.
* @return true if format is valid
*/
public static final boolean isValidIOFormat(String format,
}
return AppletFormatAdapter.isValidFormat(format, forwriting);
}
+
+ /**
+ * Create a flat file representation of a given view or selected region of a view
+ * @param format
+ * @param av
+ * @return String containing flat file
+ */
+ public String formatSequences(String format, AlignViewportI av, boolean selectedOnly)
+ {
+ return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
+ }
+
}