Merge branch 'develop' into feature/JAL-2759

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

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index ce584f2..6d3c18a 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -26,7 +26,7 @@ import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -116,8 +116,8 @@ public class FormatAdapter extends AppletFormatAdapter
           startIndex = startEnd[0];
           endIndex = startEnd[1];
           // get first non-gaped residue start position
-          while (Comparison.isGap(seqs[i]
-                  .getCharAt(startIndex)) && startIndex < endIndex)
+          while (Comparison.isGap(seqs[i].getCharAt(startIndex))
+                  && startIndex < endIndex)
           {
             startIndex++;
           }
@@ -161,18 +161,19 @@ public class FormatAdapter extends AppletFormatAdapter
 
   public boolean getCacheSuffixDefault(FileFormatI format)
   {
-    return Cache.getDefault(format.getName() + "_JVSUFFIX", true);
+    return Cache.getDefault(format.getName().toUpperCase() + "_JVSUFFIX",
+            true);
   }
 
   public String formatSequences(FileFormatI format, AlignmentI alignment,
-          String[] omitHidden, int[] exportRange, ColumnSelection colSel)
+          String[] omitHidden, int[] exportRange, HiddenColumns hidden)
   {
     return formatSequences(format, alignment, omitHidden, exportRange,
-            getCacheSuffixDefault(format), colSel, null);
+            getCacheSuffixDefault(format), hidden, null);
   }
 
   /**
-   * hack function to replace seuqences with visible sequence strings before
+   * hack function to replace sequences with visible sequence strings before
    * generating a string of the alignment in the given format.
    * 
    * @param format
@@ -185,15 +186,15 @@ public class FormatAdapter extends AppletFormatAdapter
    */
   public String formatSequences(FileFormatI format, AlignmentI alignment,
           String[] omitHidden, int[] exportRange, boolean suffix,
-          ColumnSelection colSel)
+          HiddenColumns hidden)
   {
     return formatSequences(format, alignment, omitHidden, exportRange,
-            suffix, colSel, null);
+            suffix, hidden, null);
   }
 
   public String formatSequences(FileFormatI format, AlignmentI alignment,
           String[] omitHidden, int[] exportRange, boolean suffix,
-          ColumnSelection colSel, SequenceGroup selgp)
+          HiddenColumns hidden, SequenceGroup selgp)
   {
     if (omitHidden != null)
     {
@@ -211,12 +212,12 @@ public class FormatAdapter extends AppletFormatAdapter
           AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
           if (selgp != null)
           {
-            colSel.makeVisibleAnnotation(selgp.getStartRes(),
-                    selgp.getEndRes(), na);
+            na.makeVisibleAnnotation(selgp.getStartRes(), selgp.getEndRes(),
+                    hidden);
           }
           else
           {
-            colSel.makeVisibleAnnotation(na);
+            na.makeVisibleAnnotation(hidden);
           }
           alv.addAnnotation(na);
         }
@@ -258,8 +259,8 @@ public class FormatAdapter extends AppletFormatAdapter
             selectedOnly);
   }
 
-  public AlignmentI readFromFile(AlignmentFileI source, FileFormatI format)
-          throws IOException
+  public AlignmentI readFromFile(AlignmentFileReaderI source,
+          FileFormatI format) throws IOException
   {
     FileParse fp = new FileParse(source.getInFile(),
             source.getDataSourceType());