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JAL-2446 merged to spike branch
[jalview.git]
/
src
/
jalview
/
ws
/
rest
/
params
/
Alignment.java
diff --git
a/src/jalview/ws/rest/params/Alignment.java
b/src/jalview/ws/rest/params/Alignment.java
index
c78bced
..
b85073f
100644
(file)
--- a/
src/jalview/ws/rest/params/Alignment.java
+++ b/
src/jalview/ws/rest/params/Alignment.java
@@
-23,6
+23,7
@@
package jalview.ws.rest.params;
import jalview.datamodel.AlignmentI;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import jalview.datamodel.AlignmentI;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FormatAdapter;
import jalview.ws.params.OptionI;
import jalview.ws.params.simple.BooleanOption;
import jalview.io.FormatAdapter;
import jalview.ws.params.OptionI;
import jalview.ws.params.simple.BooleanOption;
@@
-38,7
+39,6
@@
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
import java.io.PrintWriter;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.List;
import org.apache.http.entity.mime.content.ContentBody;
import java.util.List;
import org.apache.http.entity.mime.content.ContentBody;
@@
-108,8
+108,8
@@
public class Alignment extends InputType
@Override
public List<String> getURLEncodedParameter()
{
@Override
public List<String> getURLEncodedParameter()
{
- ArrayList<String> prms = new ArrayList<String>();
- prms.add("format='" + format + "'");
+ List<String> prms = new ArrayList<String>();
+ prms.add("format='" + format.getName() + "'");
if (type != null)
{
prms.add("type='" + type.toString() + "'");
if (type != null)
{
prms.add("type='" + type.toString() + "'");
@@
-148,9
+148,9
@@
public class Alignment extends InputType
if (tok.startsWith("format"))
{
if (tok.startsWith("format"))
{
- for (FileFormatI fmt : FileFormat.values())
+ for (FileFormatI fmt : FileFormats.getInstance().getFormats())
{
{
- if (fmt.isWritable() && val.equalsIgnoreCase(fmt.toString()))
+ if (fmt.isWritable() && val.equalsIgnoreCase(fmt.getName()))
{
format = fmt;
return true;
{
format = fmt;
return true;
@@
-158,12
+158,9
@@
public class Alignment extends InputType
}
warnings.append("Invalid alignment format '" + val
+ "'. Must be one of (");
}
warnings.append("Invalid alignment format '" + val
+ "'. Must be one of (");
- for (FileFormatI fmt : FileFormat.values())
+ for (String fmt : FileFormats.getInstance().getWritableFormats(true))
{
{
- if (fmt.isWritable())
- {
- warnings.append(" " + fmt).toString();
- }
+ warnings.append(" ").append(fmt);
}
warnings.append(")\n");
}
}
warnings.append(")\n");
}
@@
-198,10
+195,10
@@
public class Alignment extends InputType
"Append jalview style /start-end suffix to ID", false, false,
writeAsFile, null));
"Append jalview style /start-end suffix to ID", false, false,
writeAsFile, null));
+ List<String> writable = FileFormats
+ .getInstance().getWritableFormats(true);
lst.add(new Option("format", "Alignment upload format", true,
lst.add(new Option("format", "Alignment upload format", true,
- FileFormat.Fasta.toString(),
- format.toString(), Arrays
- .asList(jalview.io.FormatAdapter.WRITEABLE_FORMATS),
+ FileFormat.Fasta.toString(), format.getName(), writable,
null));
lst.add(createMolTypeOption("type", "Sequence type", false, type, null));
null));
lst.add(createMolTypeOption("type", "Sequence type", false, type, null));