X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=92e5810c71f123183a0f68534f739cdced07ded6;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=24c9109151b16dc22e68ae2d5b6e914d341a8389;hpb=8cf069b967632cb55cc1a7e4799e677b0fa36101;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 24c9109..92e5810 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,59 +1,136 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * 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.
- *
- * 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 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.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;
 
 /**
- * DOCUMENT ME!
- *
+ * Additional formatting methods used by the application in a number of places.
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class FormatAdapter
-    extends AppletFormatAdapter
+public class FormatAdapter extends AppletFormatAdapter
 {
-  
-  public String formatSequences(String format,
-                                SequenceI[] seqs,
-                                String[] omitHiddenColumns)
+  public FormatAdapter(AlignmentViewPanel viewpanel)
   {
+    super(viewpanel);
+    init();
+  }
+
+  public FormatAdapter()
+  {
+    super();
+    init();
+  }
+
+  public FormatAdapter(AlignmentViewPanel alignPanel,
+          AlignExportSettingI settings)
+  {
+    super(alignPanel, settings);
+  }
 
-    return formatSequences(format, replaceStrings(seqs, omitHiddenColumns));
+  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 seuqence string replaced with the one given in omitHiddenCOlumns
+   * 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)
+  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++)
       {
-        tmp[i] = new Sequence(
-            seqs[i].getName(), omitHiddenColumns[i],
-            seqs[i].getStart(), seqs[i].getEnd());
+        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;
@@ -62,15 +139,19 @@ public class FormatAdapter
   }
 
   /**
-   * Format a vector of sequences as a flat alignment file.
-   *
-   * @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
-   *
+   * 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)
+  public String formatSequences(String format, SequenceI[] seqs)
   {
 
     try
@@ -80,94 +161,186 @@ public class FormatAdapter
       if (format.equalsIgnoreCase("FASTA"))
       {
         afile = new FastaFile();
-        afile.addJVSuffix(
-            jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", true));
+        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));
+        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));
+        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));
+        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));
+        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));
+        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.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);
-
-      return afile.print();
-    }
-    catch (Exception e)
+      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");
+      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 jalview.bin.Cache.getDefault(format.toUpperCase()
+              + "_JVSUFFIX", true);
+    }
     return false;
   }
-  public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, ColumnSelection colSel)
+
+  public String formatSequences(String format, AlignmentI alignment,
+          String[] omitHidden, int[] exportRange, ColumnSelection colSel)
   {
-    return formatSequences(format, alignment, omitHidden, getCacheSuffixDefault(format), colSel);
+    return formatSequences(format, alignment, omitHidden, exportRange,
+            getCacheSuffixDefault(format), colSel, null);
   }
-    /**
-   * hack function to replace seuqences with visible sequence strings before generating a
-   * string of the alignment in the given format.
+
+  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 
+   * @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)
+  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)
   {
-    AlignFile afile = null;
-    if (omitHidden!=null)
+    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, exportRange));
       AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
-      for (int i=0; i<ala.length; i++)
+      if (ala != null)
       {
-        AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
-        colSel.makeVisibleAnnotation(na);
-        alv.addAnnotation(na);
+        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);
+  }
+
 }