X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=dc93cf9fe9e4232027e4c9a92c9bc513ca2ad34c;hb=20dd6fc13a9d903dc580939e7f2722bc9b043c4f;hp=3c741f4303ff7c9a7e3ab1fd61af7c4ad7bed41f;hpb=65b3877f9041a45bfbb7cbc1dd444a8cf87c9f3d;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 3c741f4..dc93cf9 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,23 +1,36 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
- * 
+ * 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/>.
+ * 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.datamodel.*;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+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;
+import jalview.util.Comparison;
 
 /**
  * Additional formatting methods used by the application in a number of places.
@@ -27,16 +40,54 @@ import jalview.datamodel.*;
  */
 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 (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(String format, SequenceI[] seqs,
-          String[] omitHiddenColumns)
+          String[] omitHiddenColumns, int[] exportRange)
   {
 
-    return formatSequences(format, replaceStrings(seqs, omitHiddenColumns));
+    return formatSequences(format,
+            replaceStrings(seqs, omitHiddenColumns, exportRange));
   }
 
   /**
-   * create sequences with each seuqence string replaced with the one given in
+   * create sequences with each sequence string replaced with the one given in
    * omitHiddenCOlumns
    * 
    * @param seqs
@@ -44,15 +95,48 @@ public class FormatAdapter extends AppletFormatAdapter
    * @return new sequences
    */
   public SequenceI[] replaceStrings(SequenceI[] seqs,
-          String[] omitHiddenColumns)
+          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();
+
+        startIndex = startEnd[0];
+        endIndex = startEnd[1];
+
+        if (startEnd != null)
+        {
+          // 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);
+          startRes = seqs[i].getStart() > 1 ? startRes - seqs[i].getStart()
+                  : startRes;
+          endRes = seqs[i].findPosition(endIndex) - seqs[i].getStart();
+        }
+
         tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
-                seqs[i].getStart(), seqs[i].getEnd());
+                startRes, endRes);
         tmp[i].setDescription(seqs[i].getDescription());
       }
       seqs = tmp;
@@ -83,50 +167,50 @@ public class FormatAdapter extends AppletFormatAdapter
       if (format.equalsIgnoreCase("FASTA"))
       {
         afile = new FastaFile();
-        afile.addJVSuffix(jalview.bin.Cache.getDefault("FASTA_JVSUFFIX",
+        afile.addJVSuffix(Cache.getDefault("FASTA_JVSUFFIX",
                 true));
       }
       else if (format.equalsIgnoreCase("MSF"))
       {
         afile = new MSFfile();
-        afile.addJVSuffix(jalview.bin.Cache
+        afile.addJVSuffix(Cache
                 .getDefault("MSF_JVSUFFIX", true));
       }
       else if (format.equalsIgnoreCase("PileUp"))
       {
         afile = new PileUpfile();
-        afile.addJVSuffix(jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX",
+        afile.addJVSuffix(Cache.getDefault("PILEUP_JVSUFFIX",
                 true));
       }
       else if (format.equalsIgnoreCase("CLUSTAL"))
       {
         afile = new ClustalFile();
-        afile.addJVSuffix(jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX",
+        afile.addJVSuffix(Cache.getDefault("CLUSTAL_JVSUFFIX",
                 true));
       }
       else if (format.equalsIgnoreCase("BLC"))
       {
         afile = new BLCFile();
-        afile.addJVSuffix(jalview.bin.Cache
+        afile.addJVSuffix(Cache
                 .getDefault("BLC_JVSUFFIX", true));
       }
       else if (format.equalsIgnoreCase("PIR"))
       {
         afile = new PIRFile();
-        afile.addJVSuffix(jalview.bin.Cache
+        afile.addJVSuffix(Cache
                 .getDefault("PIR_JVSUFFIX", true));
       }
       else if (format.equalsIgnoreCase("PFAM"))
       {
         afile = new PfamFile();
-        afile.addJVSuffix(jalview.bin.Cache.getDefault("PFAM_JVSUFFIX",
+        afile.addJVSuffix(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)); }
+       * Cache.getDefault("AMSA_JVSUFFIX", true)); }
        */
 
       afile.setSeqs(seqs);
@@ -150,22 +234,25 @@ public class FormatAdapter extends AppletFormatAdapter
   public boolean getCacheSuffixDefault(String format)
   {
     if (isValidFormat(format))
-      return jalview.bin.Cache.getDefault(format.toUpperCase()
+    {
+      return Cache.getDefault(format.toUpperCase()
               + "_JVSUFFIX", true);
+    }
     return false;
   }
 
   public String formatSequences(String format, AlignmentI alignment,
-          String[] omitHidden, ColumnSelection colSel)
+          String[] omitHidden, int[] exportRange, ColumnSelection colSel)
   {
-    return formatSequences(format, alignment, omitHidden,
+    return formatSequences(format, alignment, omitHidden, exportRange,
             getCacheSuffixDefault(format), colSel, null);
   }
 
   public String formatSequences(String format, AlignmentI alignment,
-          String[] omitHidden, ColumnSelection colSel, SequenceGroup sgp)
+          String[] omitHidden, int[] exportRange, ColumnSelection colSel,
+          SequenceGroup sgp)
   {
-    return formatSequences(format, alignment, omitHidden,
+    return formatSequences(format, alignment, omitHidden, exportRange,
             getCacheSuffixDefault(format), colSel, sgp);
   }
 
@@ -182,21 +269,26 @@ public class FormatAdapter extends AppletFormatAdapter
    * @return string representation of the alignment formatted as format
    */
   public String formatSequences(String format, AlignmentI alignment,
-          String[] omitHidden, boolean suffix, ColumnSelection colSel)
+          String[] omitHidden, int[] exportRange, boolean suffix,
+          ColumnSelection colSel)
   {
-    return formatSequences(format, alignment, omitHidden, suffix, colSel,
+    return formatSequences(format, alignment, omitHidden, exportRange,
+            suffix, colSel,
             null);
   }
 
   public String formatSequences(String format, AlignmentI alignment,
-          String[] omitHidden, boolean suffix, ColumnSelection colSel,
-          jalview.datamodel.SequenceGroup selgp)
+          String[] omitHidden, int[] exportRange, boolean suffix,
+          ColumnSelection colSel, SequenceGroup selgp)
   {
     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();
       if (ala != null)
       {
@@ -205,8 +297,8 @@ public class FormatAdapter extends AppletFormatAdapter
           AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
           if (selgp != null)
           {
-            colSel.makeVisibleAnnotation(selgp.getStartRes(), selgp
-                    .getEndRes(), na);
+            colSel.makeVisibleAnnotation(selgp.getStartRes(),
+                    selgp.getEndRes(), na);
           }
           else
           {
@@ -220,6 +312,20 @@ public class FormatAdapter extends AppletFormatAdapter
     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
@@ -241,4 +347,22 @@ public class FormatAdapter extends AppletFormatAdapter
     }
     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);
+  }
+
+
 }