-/*\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
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class FormatAdapter\r
-{\r
- /** DOCUMENT ME!! */\r
- public static final Vector formats = new Vector();\r
-\r
- static\r
- {\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param inFile DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- * @param format DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static SequenceI[] readFile(String inFile, String type, String format)\r
- {\r
- try\r
- {\r
- AlignFile afile = null;\r
-\r
- if (format.equals("FASTA"))\r
- {\r
- afile = new FastaFile(inFile, type);\r
- }\r
- else if (format.equals("MSF"))\r
- {\r
- afile = new MSFfile(inFile, type);\r
- }\r
- else if (format.equals("PileUp"))\r
- {\r
- afile = new PileUpfile(inFile, type);\r
- }\r
- else if (format.equals("CLUSTAL"))\r
- {\r
- afile = new ClustalFile(inFile, type);\r
- }\r
- else if (format.equals("BLC"))\r
- {\r
- afile = new BLCFile(inFile, type);\r
- }\r
- else if (format.equals("PIR"))\r
- {\r
- afile = new PIRFile(inFile, type);\r
- }\r
- else if (format.equals("PFAM"))\r
- {\r
- afile = new PfamFile(inFile, type);\r
- }\r
-\r
- return afile.getSeqsAsArray();\r
- }\r
- catch (Exception e)\r
- {\r
- System.err.println("Failed to read alignment using the '" + format +\r
- "' reader.");\r
- e.printStackTrace();\r
- }\r
-\r
- return null;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param format DOCUMENT ME!\r
- * @param seqs DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static String formatSequences(String format, Vector seqs)\r
- {\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
- {\r
- AlignFile afile = null;\r
-\r
- if (format.equalsIgnoreCase("FASTA"))\r
- {\r
- afile = new FastaFile();\r
- }\r
- else if (format.equalsIgnoreCase("MSF"))\r
- {\r
- afile = new MSFfile();\r
- }\r
- else if (format.equalsIgnoreCase("PileUp"))\r
- {\r
- afile = new PileUpfile();\r
- }\r
- else if (format.equalsIgnoreCase("CLUSTAL"))\r
- {\r
- afile = new ClustalFile();\r
- }\r
- else if (format.equalsIgnoreCase("BLC"))\r
- {\r
- afile = new BLCFile();\r
- }\r
- else if (format.equalsIgnoreCase("PIR"))\r
- {\r
- afile = new PIRFile();\r
- }\r
- else if (format.equalsIgnoreCase("PFAM"))\r
- {\r
- afile = new PfamFile();\r
- }\r
-\r
- afile.setSeqs(s);\r
-\r
- return afile.print();\r
- }\r
- catch (Exception e)\r
- {\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 2.9.0b1)
+ * 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.
+ *
+ * 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 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.
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FormatAdapter extends AppletFormatAdapter
+{
+ public FormatAdapter(AlignmentViewPanel viewpanel)
+ {
+ super(viewpanel);
+ init();
+ }
+
+ public FormatAdapter()
+ {
+ super();
+ init();
+ }
+
+ 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 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 (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);
+ 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
+ * 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)
+ {
+
+ 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;
+ }
+
+ public String formatSequences(String format, AlignmentI alignment,
+ String[] omitHidden, int[] exportRange, ColumnSelection colSel)
+ {
+ return formatSequences(format, alignment, omitHidden, exportRange,
+ getCacheSuffixDefault(format), colSel, null);
+ }
+
+ public String formatSequences(String format, AlignmentI alignment,
+ String[] omitHidden, int[] exportRange, ColumnSelection colSel,
+ SequenceGroup 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.
+ *
+ * @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(String format, AlignmentI alignment,
+ String[] omitHidden, int[] exportRange, boolean suffix,
+ ColumnSelection colSel)
+ {
+ return formatSequences(format, alignment, omitHidden, exportRange,
+ suffix, colSel, null);
+ }
+
+ public String formatSequences(String format, AlignmentI alignment,
+ String[] omitHidden, int[] exportRange, boolean suffix,
+ ColumnSelection colSel, jalview.datamodel.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)
+ {
+ colSel.makeVisibleAnnotation(selgp.getStartRes(),
+ selgp.getEndRes(), na);
+ }
+ else
+ {
+ colSel.makeVisibleAnnotation(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