X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FAlignment.java;h=4426c5f7e79d041e6e0589bdce37b77d21fe5f30;hb=7f09e6ac5717bc78373c5d77f309831403e6ebf8;hp=dc6e6e8e1be0e015cde914855a2b1d02a2b173b5;hpb=a789f790fbb3ab13f1967b42781b837b58bf9bbc;p=jalview.git
diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index dc6e6e8..4426c5f 100644
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -1,27 +1,44 @@
+/*
+ * 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.Arrays;
import java.util.List;
import org.apache.http.entity.mime.content.ContentBody;
@@ -38,11 +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;
@@ -51,7 +67,7 @@ public class Alignment extends InputType
/**
* input data as a file upload rather than inline content
*/
- public boolean writeAsFile=false;
+ public boolean writeAsFile = false;
@Override
public ContentBody formatForInput(RestJob rj)
@@ -63,11 +79,11 @@ public class Alignment extends InputType
try
{
File fa = File.createTempFile("jvmime", ".fa");
- PrintWriter pw = new PrintWriter(
- new OutputStreamWriter(new BufferedOutputStream(
- new FileOutputStream(fa)), "UTF-8"));
- pw.append(new jalview.io.FormatAdapter().formatSequences(format,
- alignment, jvsuffix));
+ PrintWriter pw = new PrintWriter(new OutputStreamWriter(
+ new BufferedOutputStream(new FileOutputStream(fa)),
+ "UTF-8"));
+ pw.append(new FormatAdapter().formatSequences(format, alignment,
+ jvsuffix));
pw.close();
return new FileBody(fa, "text/plain");
} catch (Exception ex)
@@ -78,7 +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)));
@@ -92,8 +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() + "'");
@@ -102,12 +118,10 @@ public class Alignment extends InputType
{
prms.add("jvsuffix");
}
- ;
if (writeAsFile)
{
prms.add("writeasfile");
}
- ;
return prms;
}
@@ -134,19 +148,19 @@ 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;
}
}
- warnings.append("Invalid alignment format '" + val
- + "'. Must be one of (");
- for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+ warnings.append(
+ "Invalid alignment format '" + val + "'. Must be one of (");
+ for (String fmt : FileFormats.getInstance().getWritableFormats(true))
{
- warnings.append(" " + fmt);
+ warnings.append(" ").append(fmt);
}
warnings.append(")\n");
}
@@ -158,8 +172,8 @@ public class Alignment extends InputType
return true;
} catch (Exception x)
{
- warnings.append("Invalid molecule type '" + val
- + "'. Must be one of (");
+ warnings.append(
+ "Invalid molecule type '" + val + "'. Must be one of (");
for (molType v : molType.values())
{
warnings.append(" " + v);
@@ -169,20 +183,26 @@ public class Alignment extends InputType
}
return false;
}
+
@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));
-
- lst.add(new Option("format",
- "Alignment upload format", true, "FASTA",
- format, Arrays.asList(jalview.io.FormatAdapter.WRITEABLE_FORMATS), null));
+ 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;
}
-}
\ No newline at end of file
+}