X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FAlignment.java;h=b85073f825fa9abf0ce756043d1dae714361cd3e;hb=1cd51de3fa6a6949947a5faf9f579e57f165ecf1;hp=770b564d14dd1c192b59325f5eab5ab74caf474c;hpb=231cba7c0cb9097957cd61ef96aab8e32e2d0337;p=jalview.git
diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index 770b564..b85073f 100644
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -1,22 +1,43 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.rest.params;
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.ws.params.simple.Option;
import jalview.ws.rest.InputType;
import jalview.ws.rest.NoValidInputDataException;
import jalview.ws.rest.RestJob;
-import jalview.ws.rest.InputType.molType;
-import jalview.ws.rest.RestServiceDescription;
import java.io.BufferedOutputStream;
-import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
-import java.io.StringWriter;
import java.io.UnsupportedEncodingException;
-import java.net.URLEncoder;
-import java.nio.charset.Charset;
import java.util.ArrayList;
import java.util.List;
@@ -34,11 +55,10 @@ public class Alignment extends InputType
{
public Alignment()
{
- super(new Class[]
- { AlignmentI.class });
+ super(new Class[] { AlignmentI.class });
}
- String format = "FASTA";
+ FileFormatI format = FileFormat.Fasta;
molType type;
@@ -47,7 +67,7 @@ public class Alignment extends InputType
/**
* input data as a file upload rather than inline content
*/
- public boolean writeAsFile;
+ public boolean writeAsFile = false;
@Override
public ContentBody formatForInput(RestJob rj)
@@ -62,7 +82,7 @@ public class Alignment extends InputType
PrintWriter pw = new PrintWriter(
new OutputStreamWriter(new BufferedOutputStream(
new FileOutputStream(fa)), "UTF-8"));
- pw.append(new jalview.io.FormatAdapter().formatSequences(format,
+ pw.append(new FormatAdapter().formatSequences(format,
alignment, jvsuffix));
pw.close();
return new FileBody(fa, "text/plain");
@@ -74,7 +94,7 @@ public class Alignment extends InputType
}
else
{
- jalview.io.FormatAdapter fa = new jalview.io.FormatAdapter();
+ FormatAdapter fa = new FormatAdapter();
fa.setNewlineString("\r\n");
return new StringBody(
(fa.formatSequences(format, alignment, jvsuffix)));
@@ -88,8 +108,8 @@ public class Alignment extends InputType
@Override
public List getURLEncodedParameter()
{
- ArrayList prms = new ArrayList();
- prms.add("format='" + format + "'");
+ List prms = new ArrayList();
+ prms.add("format='" + format.getName() + "'");
if (type != null)
{
prms.add("type='" + type.toString() + "'");
@@ -98,12 +118,10 @@ public class Alignment extends InputType
{
prms.add("jvsuffix");
}
- ;
if (writeAsFile)
{
prms.add("writeasfile");
}
- ;
return prms;
}
@@ -130,9 +148,9 @@ public class Alignment extends InputType
if (tok.startsWith("format"))
{
- for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+ for (FileFormatI fmt : FileFormats.getInstance().getFormats())
{
- if (val.equalsIgnoreCase(fmt))
+ if (fmt.isWritable() && val.equalsIgnoreCase(fmt.getName()))
{
format = fmt;
return true;
@@ -140,9 +158,9 @@ public class Alignment extends InputType
}
warnings.append("Invalid alignment format '" + val
+ "'. Must be one of (");
- for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+ for (String fmt : FileFormats.getInstance().getWritableFormats(true))
{
- warnings.append(" " + fmt);
+ warnings.append(" ").append(fmt);
}
warnings.append(")\n");
}
@@ -165,4 +183,26 @@ public class Alignment extends InputType
}
return false;
}
-}
\ No newline at end of file
+
+ @Override
+ public List getOptions()
+ {
+ List lst = getBaseOptions();
+ lst.add(new BooleanOption("jvsuffix",
+ "Append jalview style /start-end suffix to ID", false, false,
+ jvsuffix, null));
+ lst.add(new BooleanOption("writeasfile",
+ "Append jalview style /start-end suffix to ID", false, false,
+ writeAsFile, null));
+
+ List writable = FileFormats
+ .getInstance().getWritableFormats(true);
+ lst.add(new Option("format", "Alignment upload format", true,
+ FileFormat.Fasta.toString(), format.getName(), writable,
+ null));
+ lst.add(createMolTypeOption("type", "Sequence type", false, type, null));
+
+ return lst;
+ }
+
+}