X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=6d94616f12ccbcbd2a2ba5d0140ee5f47e1bf730;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=d4179b6685a02ce9dc11817b2fc28b00c94776a9;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index d4179b6..6d94616 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,46 +1,346 @@
-package jalview.io;
-
-import jalview.datamodel.*;
-import java.util.*;
-
-public class FormatAdapter {
-
-  public static String get(String format,Vector seqs) {
-
-    SequenceI [] s = new SequenceI[seqs.size()];
-
-    for (int i=0;i<seqs.size(); i++)
-      s[i] = (SequenceI)seqs.elementAt(i);
-
-
-    if (FormatProperties.contains(format))
-    {
-      AlignFile afile = FormatFactory.get(format);
-      afile.setSeqs(s);
-      return afile.print();
-    }
-    else
-       return null;
-  }
-
-  public static SequenceI[] read(String format,String inStr) {
-    if (FormatProperties.contains(format)) {
-      AlignFile afile = FormatFactory.get(format,inStr);
-      return afile.getSeqsAsArray();
-    } else {
-    // Should throw exception
-      return null;
-    }
-  }
-
-
-  public static SequenceI[] read(String inFile, String type, String format) {
-      try {
-        AlignFile afile = FormatFactory.get(format,inFile,type);
-        return afile.getSeqsAsArray();
-      } catch (Exception e) {    }
-
-    return null;
-  }
-
-}
+/*
+ * 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 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);
+  }
+
+  /**
+   * 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);
+  }
+
+}