X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=2735fb3a2ee359b78917292575a11304e1e433c4;hb=aa5a15ade3b078f6c2cf78db5aa05e0dcb1ce792;hp=2901969d0f9a0a85d4e2263d843dcd84d87d08d5;hpb=04528015839067053e02cfc2f7a1ced70302bb1f;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 2901969..2735fb3 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,124 +1,243 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-*/
-package jalview.io;
-
-import jalview.datamodel.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class FormatAdapter extends AppletFormatAdapter
-{
-
-    public String formatSequences(String format,
-                                  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());
-
-        seqs = tmp;
-      }
-
-      return formatSequences(format, seqs);
-    }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param format DOCUMENT ME!
-     * @param seqs DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    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));
-            }
-
-            afile.setSeqs(seqs);
-
-            return afile.print();
-        }
-        catch (Exception e)
-        {
-            System.err.println("Failed to write alignment as a '" + format +
-                "' file\n");
-            e.printStackTrace();
-        }
-
-        return null;
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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
+ */
+package jalview.io;
+
+import jalview.datamodel.*;
+
+/**
+ * Additional formatting methods used by the application in a number of places.
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class FormatAdapter extends AppletFormatAdapter
+{
+
+  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
+   * 
+   * @param seqs
+   * @param omitHiddenColumns
+   * @return new sequences
+   */
+  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].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, ColumnSelection colSel)
+  {
+    return formatSequences(format, alignment, omitHidden,
+            getCacheSuffixDefault(format), colSel, null);
+  }
+
+  public String formatSequences(String format, AlignmentI alignment,
+          String[] omitHidden, ColumnSelection colSel, SequenceGroup 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.
+   * 
+   * @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, boolean suffix, ColumnSelection colSel)
+  {
+    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)
+  {
+    if (omitHidden != null)
+    {
+      // 
+      Alignment alv = new Alignment(replaceStrings(alignment
+              .getSequencesArray(), omitHidden));
+      AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
+      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);
+  }
+
+  /**
+   * 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);
+  }
+}