X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FAlignment.java;h=d7b1fc711d08353610064dfbd793bd4d9a6b5a4d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;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..d7b1fc7 100644
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -1,21 +1,42 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.rest.params;
 
 import jalview.datamodel.AlignmentI;
+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.Arrays;
+import java.util.List;
 
 import org.apache.http.entity.mime.content.ContentBody;
 import org.apache.http.entity.mime.content.FileBody;
@@ -23,46 +44,163 @@ 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";
+  String format = "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 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);
+      }
     }
-    } else {
+    else
+    {
       jalview.io.FormatAdapter fa = new jalview.io.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<String> getURLEncodedParameter()
+  {
+    ArrayList<String> prms = new ArrayList<String>();
+    prms.add("format='" + format + "'");
+    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 (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+      {
+        if (val.equalsIgnoreCase(fmt))
+        {
+          format = fmt;
+          return true;
+        }
+      }
+      warnings.append("Invalid alignment format '" + val
+              + "'. Must be one of (");
+      for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+      {
+        warnings.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<OptionI> getOptions()
+  {
+    List<OptionI> 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(createMolTypeOption("type", "Sequence type", false, type, null));
+
+    return lst;
   }
-}
\ No newline at end of file
+
+}