Merge branch 'develop' into features/filetypeEnum

[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 770b564..c78bced 100644 (file)
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -1,23 +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 <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.io.FileFormat;
+import jalview.io.FileFormatI;
+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;
@@ -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)));
@@ -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 : FileFormat.values())
       {
-        if (val.equalsIgnoreCase(fmt))
+        if (fmt.isWritable() && val.equalsIgnoreCase(fmt.toString()))
         {
           format = fmt;
           return true;
@@ -140,9 +158,12 @@ public class Alignment extends InputType
       }
       warnings.append("Invalid alignment format '" + val
               + "'. Must be one of (");
-      for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+      for (FileFormatI fmt : FileFormat.values())
       {
-        warnings.append(" " + fmt);
+        if (fmt.isWritable())
+        {
+          warnings.append(" " + fmt).toString();
+        }
       }
       warnings.append(")\n");
     }
@@ -165,4 +186,26 @@ public class Alignment extends InputType
     }
     return false;
   }
-}
\ No newline at end of file
+
+  @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,
+            FileFormat.Fasta.toString(),
+ format.toString(), Arrays
+                    .asList(jalview.io.FormatAdapter.WRITEABLE_FORMATS),
+            null));
+    lst.add(createMolTypeOption("type", "Sequence type", false, type, null));
+
+    return lst;
+  }
+
+}