JAL-2089 Merge branch releases/Release_2_10_Branch to master

[jalview.git] / src / jalview / io / FormatAdapter.java

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index d241308..92e5810 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,7 +20,8 @@
  */
 package jalview.io;
 
-import jalview.api.AlignViewportI;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -37,9 +38,9 @@ import jalview.datamodel.SequenceI;
  */
 public class FormatAdapter extends AppletFormatAdapter
 {
-  public FormatAdapter(AlignViewportI viewport)
+  public FormatAdapter(AlignmentViewPanel viewpanel)
   {
-    super(viewport);
+    super(viewpanel);
     init();
   }
 
@@ -49,6 +50,12 @@ public class FormatAdapter extends AppletFormatAdapter
     init();
   }
 
+  public FormatAdapter(AlignmentViewPanel alignPanel,
+          AlignExportSettingI settings)
+  {
+    super(alignPanel, settings);
+  }
+
   private void init()
   {
     if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
@@ -56,9 +63,9 @@ public class FormatAdapter extends AppletFormatAdapter
       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);
+              true);
+      serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+              true);
     }
     else
     {
@@ -100,12 +107,10 @@ public class FormatAdapter extends AppletFormatAdapter
       {
         startRes = seqs[i].getStart();
         endRes = seqs[i].getEnd();
-
-        startIndex = startEnd[0];
-        endIndex = startEnd[1];
-
         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)
@@ -121,9 +126,7 @@ public class FormatAdapter extends AppletFormatAdapter
           }
 
           startRes = seqs[i].findPosition(startIndex);
-          startRes = seqs[i].getStart() > 1 ? startRes - seqs[i].getStart()
-                  : startRes;
-          endRes = seqs[i].findPosition(endIndex) - seqs[i].getStart();
+          endRes = seqs[i].findPosition(endIndex);
         }
 
         tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
@@ -264,14 +267,12 @@ public class FormatAdapter extends AppletFormatAdapter
           ColumnSelection colSel)
   {
     return formatSequences(format, alignment, omitHidden, exportRange,
-            suffix, colSel,
-            null);
+            suffix, colSel, null);
   }
 
   public String formatSequences(String format, AlignmentI alignment,
           String[] omitHidden, int[] exportRange, boolean suffix,
-          ColumnSelection colSel,
-          jalview.datamodel.SequenceGroup selgp)
+          ColumnSelection colSel, jalview.datamodel.SequenceGroup selgp)
   {
     if (omitHidden != null)
     {
@@ -304,20 +305,6 @@ 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
@@ -341,15 +328,19 @@ public class FormatAdapter extends AppletFormatAdapter
   }
 
   /**
-   * Create a flat file representation of a given view or selected region of a view
+   * Create a flat file representation of a given view or selected region of a
+   * view
+   * 
    * @param format
-   * @param av
+   * @param ap
+   *          alignment panel originating the view
    * @return String containing flat file
    */
-  public String formatSequences(String format, AlignViewportI av, boolean selectedOnly)
+  public String formatSequences(String format, AlignmentViewPanel ap,
+          boolean selectedOnly)
   {
-    return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
+    return formatSequences(format, getCacheSuffixDefault(format), ap,
+            selectedOnly);
   }
 
-
 }