X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=d241308b7142ec69fa7bf8d3c5ba12a10c66a305;hb=2a9991ef1eb02d97e9c8ed1644f292117ae6f600;hp=9913428b0937f183f74d79eda02b6fcdcc06f4d5;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 9913428..d241308 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,7 +20,14 @@
  */
 package jalview.io;
 
-import jalview.datamodel.*;
+import jalview.api.AlignViewportI;
+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.
@@ -30,12 +37,44 @@ import jalview.datamodel.*;
  */
 public class FormatAdapter extends AppletFormatAdapter
 {
+  public FormatAdapter(AlignViewportI viewport)
+  {
+    super(viewport);
+    init();
+  }
+
+  public FormatAdapter()
+  {
+    super();
+    init();
+  }
+
+  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)
+          String[] omitHiddenColumns, int[] exportRange)
   {
 
-    return formatSequences(format, replaceStrings(seqs, omitHiddenColumns));
+    return formatSequences(format,
+            replaceStrings(seqs, omitHiddenColumns, exportRange));
   }
 
   /**
@@ -47,15 +86,48 @@ 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 (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);
+          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;
@@ -153,22 +225,25 @@ public class FormatAdapter extends AppletFormatAdapter
   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)
+          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);
   }
 
@@ -185,14 +260,17 @@ 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,
+          String[] omitHidden, int[] exportRange, boolean suffix,
+          ColumnSelection colSel,
           jalview.datamodel.SequenceGroup selgp)
   {
     if (omitHidden != null)
@@ -202,7 +280,7 @@ public class FormatAdapter extends AppletFormatAdapter
       // TODO: JAL-1486 - set start and end for output correctly. basically,
       // AlignmentView.getVisibleContigs does this.
       Alignment alv = new Alignment(replaceStrings(
-              alignment.getSequencesArray(), omitHidden));
+              alignment.getSequencesArray(), omitHidden, exportRange));
       AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
       if (ala != null)
       {
@@ -226,6 +304,20 @@ public class FormatAdapter extends AppletFormatAdapter
     return this.formatSequences(format, alignment, suffix);
   }
 
+  public Alignment readFile(String inFile, String type, String format)
+          throws java.io.IOException
+  {
+    Alignment al = super.readFile(inFile, type, format);
+    return al;
+  }
+
+  public AlignmentI readFromFile(FileParse source, String format)
+          throws java.io.IOException
+  {
+    Alignment al = (Alignment) 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
@@ -247,4 +339,17 @@ 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 av
+   * @return String containing flat file
+   */
+  public String formatSequences(String format, AlignViewportI av, boolean selectedOnly)
+  {
+    return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
+  }
+
+
 }