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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
92473ec
..
71fc659
100755
(executable)
--- a/
src/jalview/io/FeaturesFile.java
+++ b/
src/jalview/io/FeaturesFile.java
@@
-20,6
+20,8
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.util.Locale;
+
import java.awt.Color;
import java.io.IOException;
import java.util.ArrayList;
import java.awt.Color;
import java.io.IOException;
import java.util.ArrayList;
@@
-108,11
+110,11
@@
public class FeaturesFile extends AlignFile implements FeaturesSourceI
/**
* Constructor which does not parse the file immediately
*
/**
* Constructor which does not parse the file immediately
*
- * @param file
+ * @param file File or String filename
* @param paste
* @throws IOException
*/
* @param paste
* @throws IOException
*/
- public FeaturesFile(String file, DataSourceType paste)
+ public FeaturesFile(Object file, DataSourceType paste)
throws IOException
{
super(false, file, paste);
throws IOException
{
super(false, file, paste);
@@
-135,7
+137,7
@@
public class FeaturesFile extends AlignFile implements FeaturesSourceI
* @param type
* @throws IOException
*/
* @param type
* @throws IOException
*/
- public FeaturesFile(boolean parseImmediately, String file,
+ public FeaturesFile(boolean parseImmediately, Object file,
DataSourceType type) throws IOException
{
super(parseImmediately, file, type);
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("#"))
{
// 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);
}
{
processGffPragma(line, gffProps, align, newseqs);
}
@@
-346,7
+348,7
@@
public class FeaturesFile extends AlignFile implements FeaturesSourceI
String line;
while ((line = nextLine()) != null)
{
String line;
while ((line = nextLine()) != null)
{
- if (line.toUpperCase().startsWith(ENDFILTERS))
+ if (line.toUpperCase(Locale.ROOT).startsWith(ENDFILTERS))
{
return;
}
{
return;
}
@@
-1391,7
+1393,9
@@
public class FeaturesFile extends AlignFile implements FeaturesSourceI
} catch (IOException q)
{
}
} 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);
List<SequenceI> includedseqs = parser.getSeqs();
SequenceIdMatcher smatcher = new SequenceIdMatcher(newseqs);