Merge branch 'patch/JAL-2976_vaqua4_fallback' into releases/Release_2_10_4_Branch

[jalview.git] / src / jalview / fts / core / FTSRestClient.java

diff --git a/src/jalview/fts/core/FTSRestClient.java b/src/jalview/fts/core/FTSRestClient.java
index 2f24a01..f94d455 100644 (file)
--- a/src/jalview/fts/core/FTSRestClient.java
+++ b/src/jalview/fts/core/FTSRestClient.java
@@ -1,3 +1,23 @@
+/*
+ * 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.fts.core;
 
 import jalview.fts.api.FTSDataColumnI;
@@ -45,9 +65,9 @@ public abstract class FTSRestClient implements FTSRestClientI
   public void parseDataColumnsConfigFile()
   {
     String fileName = getColumnDataConfigFileName();
-    
-    InputStream in = getClass().getResourceAsStream(fileName); 
-    
+
+    InputStream in = getClass().getResourceAsStream(fileName);
+
     try (BufferedReader br = new BufferedReader(new InputStreamReader(in)))
     {
       String line;
@@ -62,8 +82,8 @@ public abstract class FTSRestClient implements FTSRestClientI
             {
               primaryKeyColumnCode = lineData[1];
             }
-            if (lineData[0]
-                    .equalsIgnoreCase("_data_column.default_response_page_size"))
+            if (lineData[0].equalsIgnoreCase(
+                    "_data_column.default_response_page_size"))
             {
               defaultResponsePageSize = Integer.valueOf(lineData[1]);
             }
@@ -138,26 +158,68 @@ public abstract class FTSRestClient implements FTSRestClientI
               @Override
               public String getAltCode()
               {
-                return lineData[1].split("\\|").length > 1 ? lineData[1]
-                        .split("\\|")[1] : getCode();
+                return lineData[1].split("\\|").length > 1
+                        ? lineData[1].split("\\|")[1]
+                        : getCode();
               }
 
               @Override
-              public Class<?> getDataColumnClass()
+              public DataTypeI getDataType()
               {
-                String classString = lineData[2];
-                classString = classString.toUpperCase();
-                switch (classString)
+                final String[] dataTypeString = lineData[2].split("\\|");
+                final String classString = dataTypeString[0].toUpperCase();
+
+                return new DataTypeI()
                 {
-                case "INT":
-                case "INTEGER":
-                  return Integer.class;
-                case "DOUBLE":
-                  return Double.class;
-                case "STRING":
-                default:
-                  return String.class;
-                }
+
+                  @Override
+                  public boolean isFormtted()
+                  {
+                    if (dataTypeString.length > 1
+                            && dataTypeString[1] != null)
+                    {
+                      switch (dataTypeString[1].toUpperCase())
+                      {
+                      case "T":
+                      case "TRUE":
+                        return true;
+                      case "F":
+                      case "False":
+                      default:
+                        return false;
+                      }
+                    }
+                    return false;
+                  }
+
+                  @Override
+                  public int getSignificantFigures()
+                  {
+                    if (dataTypeString.length > 2
+                            && dataTypeString[2] != null)
+                    {
+                      return Integer.valueOf(dataTypeString[2]);
+                    }
+                    return 0;
+                  }
+
+                  @Override
+                  public Class getDataTypeClass()
+                  {
+                    switch (classString)
+                    {
+                    case "INT":
+                    case "INTEGER":
+                      return Integer.class;
+                    case "DOUBLE":
+                      return Double.class;
+                    case "STRING":
+                    default:
+                      return String.class;
+                    }
+                  }
+                };
+
               }
 
               @Override
@@ -218,12 +280,12 @@ public abstract class FTSRestClient implements FTSRestClientI
                         this.getGroup());
               }
 
-
               @Override
               public boolean equals(Object otherObject)
               {
                 FTSDataColumnI that = (FTSDataColumnI) otherObject;
-                return this.getCode().equals(that.getCode())
+                return otherObject == null ? false
+                        : this.getCode().equals(that.getCode())
                         && this.getName().equals(that.getName())
                         && this.getGroup().equals(that.getGroup());
               }
@@ -253,7 +315,8 @@ public abstract class FTSRestClient implements FTSRestClientI
       }
       try
       {
-        this.primaryKeyColumn = getDataColumnByNameOrCode(primaryKeyColumnCode);
+        this.primaryKeyColumn = getDataColumnByNameOrCode(
+                primaryKeyColumnCode);
       } catch (Exception e)
       {
         e.printStackTrace();
@@ -303,7 +366,6 @@ public abstract class FTSRestClient implements FTSRestClientI
     return result;
   }
 
-
   @Override
   public Collection<FTSDataColumnI> getAllFTSDataColumns()
   {
@@ -325,7 +387,7 @@ public abstract class FTSRestClient implements FTSRestClientI
   }
 
   @Override
-  public Collection<FTSDataColumnI> getAllDefaulDisplayedDataColumns()
+  public Collection<FTSDataColumnI> getAllDefaultDisplayedFTSDataColumns()
   {
     if (defaulDisplayedDataColumns == null
             || defaulDisplayedDataColumns.isEmpty())
@@ -362,8 +424,8 @@ public abstract class FTSRestClient implements FTSRestClientI
         return column;
       }
     }
-    throw new Exception("Couldn't find data column with name : "
-            + nameOrCode);
+    throw new Exception(
+            "Couldn't find data column with name : " + nameOrCode);
   }
 
   @Override
@@ -390,10 +452,9 @@ public abstract class FTSRestClient implements FTSRestClientI
     switch (code)
     {
     case 400:
-      message = MessageManager
-              .getString("exception.bad_request");
+      message = MessageManager.getString("exception.bad_request");
       break;
-      
+
     case 410:
       message = MessageManager.formatMessage(
               "exception.fts_rest_service_no_longer_available", service);
@@ -409,7 +470,8 @@ public abstract class FTSRestClient implements FTSRestClientI
     case 502:
     case 504:
     case 505:
-      message = MessageManager.getString("exception.fts_server_error");
+      message = MessageManager.formatMessage("exception.fts_server_error",
+              service);
       break;
     case 503:
       message = MessageManager.getString("exception.service_not_available");