JAL-3725 restrict mapped virtual feature location to mapped region

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

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index a8a3746..71fc659 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -20,6 +20,20 @@
  */
 package jalview.io;
 
+import java.util.Locale;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.TreeMap;
+
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.SequenceIdMatcher;
 import jalview.api.AlignViewportI;
@@ -44,18 +58,6 @@ import jalview.util.MapList;
 import jalview.util.ParseHtmlBodyAndLinks;
 import jalview.util.StringUtils;
 
-import java.awt.Color;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.TreeMap;
-
 /**
  * Parses and writes features files, which may be in Jalview, GFF2 or GFF3
  * format. These are tab-delimited formats but with differences in the use of
@@ -108,11 +110,11 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
   /**
    * Constructor which does not parse the file immediately
    * 
-   * @param file
+   * @param file File or String filename
    * @param paste
    * @throws IOException
    */
-  public FeaturesFile(String file, DataSourceType paste)
+  public FeaturesFile(Object file, DataSourceType paste)
           throws IOException
   {
     super(false, file, paste);
@@ -135,7 +137,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * @param type
    * @throws IOException
    */
-  public FeaturesFile(boolean parseImmediately, String file,
+  public FeaturesFile(boolean parseImmediately, Object file,
           DataSourceType type) throws IOException
   {
     super(parseImmediately, file, type);
@@ -234,7 +236,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
         // skip comments/process pragmas
         if (line.length() == 0 || line.startsWith("#"))
         {
-          if (line.toLowerCase().startsWith("##"))
+          if (line.toLowerCase(Locale.ROOT).startsWith("##"))
           {
             processGffPragma(line, gffProps, align, newseqs);
           }
@@ -346,7 +348,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
     String line;
     while ((line = nextLine()) != null)
     {
-      if (line.toUpperCase().startsWith(ENDFILTERS))
+      if (line.toUpperCase(Locale.ROOT).startsWith(ENDFILTERS))
       {
         return;
       }
@@ -736,7 +738,6 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
 
       if (mf != null)
       {
-        MapList mapping = mf.mapping.getMap();
         for (SequenceFeature sf : mf.features)
         {
           /*
@@ -752,9 +753,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
             found.add(sf);
             int begin = sf.getBegin();
             int end = sf.getEnd();
-            int[] range = mf.mapping.getTo() == seq.getDatasetSequence()
-                    ? mapping.locateInTo(begin, end)
-                    : mapping.locateInFrom(begin, end);
+            int[] range = mf.getMappedPositions(begin, end);
             SequenceFeature sf2 = new SequenceFeature(sf, range[0],
                     range[1], group, sf.getScore());
             complementary.add(sf2);
@@ -1394,7 +1393,9 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
     } catch (IOException q)
     {
     }
-    FastaFile parser = new FastaFile(this);
+    // Opening a FastaFile object with the remainder of this object's dataIn.
+    // Tell the constructor to NOT close the dataIn when finished.
+    FastaFile parser = new FastaFile(this, false);
     List<SequenceI> includedseqs = parser.getSeqs();
 
     SequenceIdMatcher smatcher = new SequenceIdMatcher(newseqs);