X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws2%2Foperations%2FOperation.java;h=bd120418f4ed3c56a67861fa1f02d9a23016eeb0;hb=2bbba7f7426314bfd6a1f206861542244b5f511a;hp=f02bb59296120cb6d95fa720cd1f43584abf4962;hpb=158e0595615ae4bfb13554f41f03b570642f6bb2;p=jalview.git

diff --git a/src/jalview/ws2/operations/Operation.java b/src/jalview/ws2/operations/Operation.java
index f02bb59..bd12041 100644
--- a/src/jalview/ws2/operations/Operation.java
+++ b/src/jalview/ws2/operations/Operation.java
@@ -3,38 +3,117 @@ package jalview.ws2.operations;
 import jalview.ws.params.ParamDatastoreI;
 import jalview.ws2.MenuEntryProviderI;
 
+/**
+ * Operation represents an action which can be performed with a (web)service or
+ * calculator. Examples of operations are multiple sequence alignment or
+ * sequence annotation. There should be one Operation implementation for each
+ * operation that Jalview can perform on sequences or alignments. The concrete
+ * implementations may be further parameterized to alter the functionality (e.g.
+ * making the operation interactive) or restrict input data (e.g. limit to
+ * proteins only).
+ * 
+ * @author mmwarowny
+ *
+ */
 public interface Operation
 {
+  /**
+   * Get the name of the operation. Typically fetched from the server.
+   * 
+   * @return operation name
+   */
   public String getName();
-  
+
+  /**
+   * Get the description of the operation. Typically fetched from the server.
+   * 
+   * @return operation description
+   */
   public String getDescription();
 
+  /**
+   * Get the name of the category that the operation falls into. Used to group
+   * the operations under the web services menu.
+   * 
+   * @return category name
+   */
   public String getTypeName();
 
+  /**
+   * Get the hostname/url of the server which this operation is delegated to.
+   * Typically fetched from the accompanying web service instance.
+   * 
+   * @return server url
+   */
   public String getHostName();
-  
+
+  /**
+   * Check if the operation has user-customizable input parameters.
+   * 
+   * @return if has parameters
+   */
   public boolean hasParameters();
-  
+
+  /**
+   * Returns parameter datastore for this operations containing input parameters
+   * and available presets.
+   * 
+   * @return parameter datastore of the operation
+   */
   public ParamDatastoreI getParamStore();
 
+  /**
+   * @return minimum accepted number of sequences
+   */
   public int getMinSequences();
 
+  /**
+   * @return maximum accepted number of sequences
+   */
   public int getMaxSequences();
 
+  /**
+   * @return whether gaps should be included
+   */
   public boolean canSubmitGaps();
 
+  /**
+   * @return whether works with protein sequences
+   */
   public boolean isProteinOperation();
 
+  /**
+   * @return whether works with nucleotide sequences
+   */
   public boolean isNucleotideOperation();
 
+  /**
+   * @return whether should be run interactively
+   */
   public boolean isInteractive();
 
+  /**
+   * Get the menu builder for this operation which will be used to construct the
+   * web services menu. The builder will be given the parent menu entry which it
+   * should attach menu items to and the current align frame.
+   * 
+   * @return menu entry builder instance
+   */
   public MenuEntryProviderI getMenuBuilder();
 
+  /**
+   * @return whether this operation is alignment analysis
+   */
   public boolean isAlignmentAnalysis();
-  
+
+  /**
+   * @return whether non-standatds symbols should be filtered out
+   */
   public boolean getFilterNonStandardSymbols();
-  
+
+  /**
+   * @return whether it needs aligned sequences
+   */
   public boolean getNeedsAlignedSequences();
 
 }