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JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix delegate of
[jalview.git]
/
src
/
jalview
/
io
/
IdentifyFile.java
diff --git
a/src/jalview/io/IdentifyFile.java
b/src/jalview/io/IdentifyFile.java
index
bc91e09
..
4b6f8e4
100755
(executable)
--- a/
src/jalview/io/IdentifyFile.java
+++ b/
src/jalview/io/IdentifyFile.java
@@
-30,8
+30,6
@@
import java.io.IOException;
*/
public class IdentifyFile
{
*/
public class IdentifyFile
{
- public static final String FeaturesFile = "GFF or Jalview features";
-
/**
* Identify a datasource's file content.
*
/**
* Identify a datasource's file content.
*
@@
-74,7
+72,7
@@
public class IdentifyFile
// preserves original behaviour prior to version 2.3
}
// preserves original behaviour prior to version 2.3
}
- public FileFormatI identify(AlignmentFileI file, boolean closeSource)
+ public FileFormatI identify(AlignmentFileReaderI file, boolean closeSource)
throws IOException
{
FileParse fp = new FileParse(file.getInFile(), file.getDataSourceType());
throws IOException
{
FileParse fp = new FileParse(file.getInFile(), file.getDataSourceType());
@@
-143,6
+141,11
@@
public class IdentifyFile
}
data = data.toUpperCase();
}
data = data.toUpperCase();
+ if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
+ {
+ reply = FileFormat.ScoreMatrix;
+ break;
+ }
if (data.startsWith("##GFF-VERSION"))
{
// GFF - possibly embedded in a Jalview features file!
if (data.startsWith("##GFF-VERSION"))
{
// GFF - possibly embedded in a Jalview features file!
@@
-261,7
+264,7
@@
public class IdentifyFile
}
int lessThan = data.indexOf("<");
if ((lessThan > -1)) // possible Markup Language data i.e HTML,
}
int lessThan = data.indexOf("<");
if ((lessThan > -1)) // possible Markup Language data i.e HTML,
- // RNAML, XML
+ // RNAML, XML
{
String upper = data.toUpperCase();
if (upper.substring(lessThan).startsWith("<HTML"))
{
String upper = data.toUpperCase();
if (upper.substring(lessThan).startsWith("<HTML"))
@@
-372,8
+375,9
@@
public class IdentifyFile
}
/**
}
/**
- * Returns true if the data has at least 6 tab-delimited fields _and_
- * fields 4 and 5 are integer (start/end)
+ * Returns true if the data has at least 6 tab-delimited fields _and_ fields 4
+ * and 5 are integer (start/end)
+ *
* @param data
* @return
*/
* @param data
* @return
*/
@@
-384,14
+388,17
@@
public class IdentifyFile
return false;
}
String[] columns = data.split("\t");
return false;
}
String[] columns = data.split("\t");
- if (columns.length < 6) {
+ if (columns.length < 6)
+ {
return false;
}
for (int col = 3; col < 5; col++)
{
return false;
}
for (int col = 3; col < 5; col++)
{
- try {
+ try
+ {
Integer.parseInt(columns[col]);
Integer.parseInt(columns[col]);
- } catch (NumberFormatException e) {
+ } catch (NumberFormatException e)
+ {
return false;
}
}
return false;
}
}