-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.io;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import java.util.Vector;\r
-\r
-\r
-public class FormatAdapter {\r
- public static Vector formats = new Vector();\r
-\r
- static {\r
- formats.addElement("FASTA");\r
- formats.addElement("MSF");\r
- formats.addElement("PileUp");\r
- formats.addElement("CLUSTAL");\r
- formats.addElement("BLC");\r
- formats.addElement("PIR");\r
- formats.addElement("PFAM");\r
- }\r
-\r
- public static SequenceI[] readFile(String inFile, String type, String format) {\r
- try {\r
- AlignFile afile = null;\r
-\r
- if (format.equals("FASTA")) {\r
- afile = new FastaFile(inFile, type);\r
- } else if (format.equals("MSF")) {\r
- afile = new MSFfile(inFile, type);\r
- } else if (format.equals("PileUp")) {\r
- afile = new PileUpfile(inFile, type);\r
- } else if (format.equals("CLUSTAL")) {\r
- afile = new ClustalFile(inFile, type);\r
- } else if (format.equals("BLC")) {\r
- afile = new BLCFile(inFile, type);\r
- } else if (format.equals("PIR")) {\r
- afile = new PIRFile(inFile, type);\r
- } else if (format.equals("PFAM")) {\r
- afile = new PfamFile(inFile, type);\r
- }\r
-\r
- return afile.getSeqsAsArray();\r
- } catch (Exception e) {\r
- System.err.println("Failed to read alignment using the '" + format +\r
- "' reader.");\r
- e.printStackTrace();\r
- }\r
-\r
- return null;\r
- }\r
-\r
- public static String formatSequences(String format, Vector seqs) {\r
- SequenceI[] s = new SequenceI[seqs.size()];\r
-\r
- for (int i = 0; i < seqs.size(); i++)\r
- s[i] = (SequenceI) seqs.elementAt(i);\r
-\r
- try {\r
- AlignFile afile = null;\r
-\r
- if (format.equals("FASTA")) {\r
- afile = new FastaFile();\r
- } else if (format.equals("MSF")) {\r
- afile = new MSFfile();\r
- } else if (format.equals("PileUp")) {\r
- afile = new PileUpfile();\r
- } else if (format.equals("CLUSTAL")) {\r
- afile = new ClustalFile();\r
- } else if (format.equals("BLC")) {\r
- afile = new BLCFile();\r
- } else if (format.equals("PIR")) {\r
- afile = new PIRFile();\r
- } else if (format.equals("PFAM")) {\r
- afile = new PfamFile();\r
- }\r
-\r
- afile.setSeqs(s);\r
-\r
- return afile.print();\r
- } catch (Exception e) {\r
- System.err.println("Failed to write alignment as a '" + format +\r
- "' file\n");\r
- e.printStackTrace();\r
- }\r
-\r
- return null;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+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.
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+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);
+ }
+
+ 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, exportRange));
+ }
+
+ /**
+ * 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, 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],
+ startRes, endRes);
+ tmp[i].setDescription(seqs[i].getDescription());
+ }
+ seqs = tmp;
+ }
+ return seqs;
+ }
+
+ /**
+ * Format a vector of sequences as a flat alignment file. TODO: allow caller
+ * to detect errors and warnings encountered when generating output
+ *
+ *
+ * @param format
+ * @param seqs
+ * vector of sequences to write
+ *
+ * @return String containing sequences in desired format
+ */
+ public String formatSequences(FileFormatI format, SequenceI[] seqs)
+ {
+ boolean withSuffix = getCacheSuffixDefault(format);
+ return format.getWriter(null).print(seqs, withSuffix);
+ }
+
+ public boolean getCacheSuffixDefault(FileFormatI format)
+ {
+ return Cache.getDefault(format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX",
+ true);
+ }
+
+ public String formatSequences(FileFormatI format, AlignmentI alignment,
+ String[] omitHidden, int[] exportRange, HiddenColumns hidden)
+ {
+ return formatSequences(format, alignment, omitHidden, exportRange,
+ getCacheSuffixDefault(format), hidden, null);
+ }
+
+ /**
+ * hack function to replace sequences 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
+ * @return string representation of the alignment formatted as format
+ */
+ public String formatSequences(FileFormatI format, AlignmentI alignment,
+ String[] omitHidden, int[] exportRange, boolean suffix,
+ HiddenColumns hidden)
+ {
+ return formatSequences(format, alignment, omitHidden, exportRange,
+ suffix, hidden, null);
+ }
+
+ public String formatSequences(FileFormatI format, AlignmentI alignment,
+ String[] omitHidden, int[] exportRange, boolean suffix,
+ HiddenColumns hidden, SequenceGroup selgp)
+ {
+ if (omitHidden != null)
+ {
+ // 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();
+ if (ala != null)
+ {
+ for (int i = 0; i < ala.length; i++)
+ {
+ AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
+ if (selgp != null)
+ {
+ na.makeVisibleAnnotation(selgp.getStartRes(), selgp.getEndRes(),
+ hidden);
+ }
+ else
+ {
+ na.makeVisibleAnnotation(hidden);
+ }
+ alv.addAnnotation(na);
+ }
+ }
+ return this.formatSequences(format, alv, suffix);
+ }
+ return this.formatSequences(format, alignment, suffix);
+ }
+
+ @Override
+ public AlignmentI readFile(String file, DataSourceType sourceType,
+ FileFormatI fileFormat) throws IOException
+ {
+ 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
+ *
+ * @param format
+ * @param ap
+ * alignment panel originating the view
+ * @return String containing flat file
+ */
+ 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
+ {
+ FileParse fp = new FileParse(source.getInFile(),
+ source.getDataSourceType());
+ return readFromFile(fp, format);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff