X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FAlignment.java;h=4426c5f7e79d041e6e0589bdce37b77d21fe5f30;hb=2b6a74893883a246d40a99a2e981ef6cad4fed5a;hp=0027057390c4fde89434f92b8afbb2340eefb4f9;hpb=9f37d5a58dad274e24d847f1042b60b5ae754fef;p=jalview.git
diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index 0027057..4426c5f 100644
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -1,21 +1,45 @@
+/*
+ * 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 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;
import org.apache.http.entity.mime.content.ContentBody;
import org.apache.http.entity.mime.content.FileBody;
@@ -23,46 +47,162 @@ import org.apache.http.entity.mime.content.StringBody;
/**
* format an alignment for input to rest service.
+ *
* @author JimP
- *
+ *
*/
-public class Alignment extends InputType {
+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;
- boolean jvsuffix=false;
+
+ boolean jvsuffix = false;
+
/**
* input data as a file upload rather than inline content
*/
- public boolean writeAsFile;
+ public boolean writeAsFile = false;
+
@Override
- public ContentBody formatForInput(RestJob rj) throws UnsupportedEncodingException, NoValidInputDataException
+ public ContentBody formatForInput(RestJob rj)
+ throws UnsupportedEncodingException, NoValidInputDataException
{
- AlignmentI alignment = rj.getAlignmentForInput(token,type);
+ AlignmentI alignment = rj.getAlignmentForInput(token, type);
if (writeAsFile)
{
- 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));
- pw.close();
- return new FileBody(fa, "text/plain");
- } catch (Exception ex)
- {
- throw new NoValidInputDataException("Couldn't write out alignment to file.",ex);
+ try
+ {
+ File fa = File.createTempFile("jvmime", ".fa");
+ 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)
+ {
+ throw new NoValidInputDataException(
+ "Couldn't write out alignment to file.", ex);
+ }
}
- } else {
- jalview.io.FormatAdapter fa = new jalview.io.FormatAdapter();
+ else
+ {
+ FormatAdapter fa = new FormatAdapter();
fa.setNewlineString("\r\n");
- return new StringBody((fa.formatSequences(format, alignment, jvsuffix)));
- //,
- //"text/plain",Charset.forName("UTF-8"));
+ return new StringBody(
+ (fa.formatSequences(format, alignment, jvsuffix)));
+ // ,
+ // "text/plain",Charset.forName("UTF-8"));
// , "text/plain", Charset.forName("UTF-8"));
- // sb.getContentTypeParameters().put("filename", "alignment.fa");
+ // sb.getContentTypeParameters().put("filename", "alignment.fa");
+ }
+ }
+
+ @Override
+ public List getURLEncodedParameter()
+ {
+ List prms = new ArrayList();
+ prms.add("format='" + format.getName() + "'");
+ if (type != null)
+ {
+ prms.add("type='" + type.toString() + "'");
+ }
+ if (jvsuffix)
+ {
+ prms.add("jvsuffix");
+ }
+ if (writeAsFile)
+ {
+ prms.add("writeasfile");
+ }
+ return prms;
+ }
+
+ @Override
+ public String getURLtokenPrefix()
+ {
+ return "ALIGNMENT";
+ }
+
+ @Override
+ public boolean configureProperty(String tok, String val,
+ StringBuffer warnings)
+ {
+ if (tok.startsWith("jvsuffix"))
+ {
+ jvsuffix = true;
+ return true;
+ }
+ if (tok.startsWith("writeasfile"))
+ {
+ writeAsFile = true;
+ return true;
}
+
+ if (tok.startsWith("format"))
+ {
+ for (FileFormatI fmt : FileFormats.getInstance().getFormats())
+ {
+ if (fmt.isWritable() && val.equalsIgnoreCase(fmt.getName()))
+ {
+ format = fmt;
+ return true;
+ }
+ }
+ warnings.append(
+ "Invalid alignment format '" + val + "'. Must be one of (");
+ for (String fmt : FileFormats.getInstance().getWritableFormats(true))
+ {
+ warnings.append(" ").append(fmt);
+ }
+ warnings.append(")\n");
+ }
+ if (tok.startsWith("type"))
+ {
+ try
+ {
+ type = molType.valueOf(val);
+ return true;
+ } catch (Exception x)
+ {
+ warnings.append(
+ "Invalid molecule type '" + val + "'. Must be one of (");
+ for (molType v : molType.values())
+ {
+ warnings.append(" " + v);
+ }
+ warnings.append(")\n");
+ }
+ }
+ 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));
+
+ 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
+
+}