JAL-2101 JAL-2071 JAL-1563 Added fix to enable searching for old entry names in Unipr...

diff --git a/resources/fts/uniprot_data_columns.txt b/resources/fts/uniprot_data_columns.txt
index 6c78c16..c6b037c 100644 (file)
--- a/resources/fts/uniprot_data_columns.txt
+++ b/resources/fts/uniprot_data_columns.txt
@@ -1,3 +1,24 @@
+/*
+ * 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.
+ */
+
 uniprot_data_columns
 #
 _group.id
@@ -35,16 +56,16 @@ _data_column.preferred_col_width
 _data_column.is_shown_by_default
 _data_column.is_searchable
 Uniprot Id;id;String;g3;80;150;85;true;true
-Entry Name;entry name|name;String;g3;100;150;105;true;true
-Protein names;protein names|protein name;String;g3;300;1500;500;true;true
+Entry Name;entry name|mnemonic;String;g3;100;150;105;true;true
+Protein names;protein names|name;String;g3;300;1500;500;true;true
 Gene Names;genes|gene;String;g3;100;1000;145;true;true
 Organism;organism;String;g3;100;1000;200;true;true
-Organism ID;organism-id;int;g3;60;100;80;false;true
-Proteomes;proteome;String;g3;50;1000;95;false;true
-Taxonomic lineage (ALL);lineage(ALL);String;g3;50;400;95;false;false
-Virus hosts;virus hosts;String;g3;50;1000;95;false;true
-Fragment;fragment;String;g7;50;1000;95;false;true
-Gene encoded by;encodedon;String;g7;50;1000;95;false;true
+Organism ID;organism-id;int;g3;60;100;80;false;false
+Proteomes;proteome;String;g3;50;1000;95;false;false
+Taxonomic lineage (ALL);lineage(ALL)|taxonomy;String;g3;50;400;95;false;false
+Virus hosts;virus hosts|host;String;g3;50;1000;95;false;true
+Fragment;fragment;String;g7;50;1000;95;false;false
+Gene encoded by;encodedon;String;g7;50;1000;95;false;false
 Alternative products (isoforms);comment(ALTERNATIVE PRODUCTS);String;g7;50;1000;95;false;false
 Erroneous gene model prediction;comment(ERRONEOUS GENE MODEL PREDICTION);String;g7;50;1000;95;false;false
 Erroneous initiation;comment(ERRONEOUS INITIATION);String;g7;50;1000;95;false;false
@@ -55,9 +76,9 @@ Polymorphism;comment(POLYMORPHISM);String;g7;50;1000;95;false;false
 RNA editing;comment(RNA EDITING);String;g7;50;1000;95;false;false
 Sequence caution;comment(SEQUENCE CAUTION);String;g7;50;1000;95;false;false
 Status;reviewed;String;g6;50;100;95;true;true
-Length;length;int;g7;50;100;65;true;true
+Length;length;int|T|0;g7;50;100;65;true;true
 Mass;mass;String;g7;50;100;80;false;true
-Sequence;sequence;String;g7;50;1000;95;false;true
+Sequence;sequence;String;g7;50;1000;95;false;false
 Alternative sequence;feature(ALTERNATIVE SEQUENCE);String;g7;50;1000;95;false;false
 Natural variant;feature(NATURAL VARIANT);String;g7;50;1000;95;false;false
 Non-adjacent residues;feature(NON ADJACENT RESIDUES);String;g7;50;1000;95;false;false
@@ -83,15 +104,15 @@ DNA binding;feature(DNA BINDING);String;g8;50;1000;95;false;false
 Metal binding;feature(METAL BINDING);String;g8;50;1000;95;false;false
 Nucleotide binding;feature(NP BIND);String;g8;50;1000;95;false;false
 Site;feature(SITE);String;g8;50;1000;95;false;false
-Annotation;annotation score;String;g6;50;1000;95;false;true
-Features;features;String;g6;50;1000;95;false;true
+Annotation;annotation score;String;g6;50;1000;95;false;false
+Features;features;String;g6;50;1000;95;false;false
 Caution;comment(CAUTION);String;g6;50;1000;95;false;false
 Miscellaneous [CC];comment(GENERAL);String;g6;50;1000;95;false;false
-Keywords;keywords;String;g6;50;1000;95;false;true
+Keywords;keywords|keyword;String;g6;50;1000;95;false;true
 Protein existence;existence;String;g6;50;1000;95;false;true
 ALL;Search All;String;g7;50;1000;95;false;true;
 Subunit structure [CC];comment(SUBUNIT);String;g9;50;1000;95;false;false
-Interacts with;interactor;String;g9;50;1000;95;false;true
+Interacts with;interactor;String;g9;50;1000;95;false;false
 Developmental stage;comment(DEVELOPMENTAL STAGE);String;g10;50;1000;95;false;false
 Induction;comment(INDUCTION);String;g10;50;1000;95;false;false
 Tissue specificity;comment(TISSUE SPECIFICITY);String;g10;50;1000;95;false;false

diff --git a/src/jalview/fts/core/GFTSPanel.java b/src/jalview/fts/core/GFTSPanel.java
index 3e4a1cd..4dc61f0 100644 (file)
--- a/src/jalview/fts/core/GFTSPanel.java
+++ b/src/jalview/fts/core/GFTSPanel.java
@@ -41,6 +41,7 @@ import java.awt.event.KeyAdapter;
 import java.awt.event.KeyEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.text.DecimalFormat;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -143,6 +144,9 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
 
   protected HashSet<String> paginatorCart = new HashSet<String>();
 
+  protected static final DecimalFormat totalNumberformatter = new DecimalFormat(
+          "###,###");
+
   private JTable tbl_summary = new JTable()
   {
     private boolean inLayout;

diff --git a/src/jalview/fts/service/pdb/PDBFTSPanel.java b/src/jalview/fts/service/pdb/PDBFTSPanel.java
index 74b7853..0dd1369 100644 (file)
--- a/src/jalview/fts/service/pdb/PDBFTSPanel.java
+++ b/src/jalview/fts/service/pdb/PDBFTSPanel.java
@@ -116,9 +116,14 @@ public class PDBFTSPanel extends GFTSPanel
           if (isPaginationEnabled() && resultSetCount > 0)
           {
             updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
-                    + " " + (offSet + 1) + " to "
-                    + (offSet + resultSetCount) + " of "
-                    + totalResultSetCount
+                    + " "
+                    + totalNumberformatter.format((Number) (offSet + 1))
+                    + " to "
+                    + totalNumberformatter
+                            .format((Number) (offSet + resultSetCount))
+                    + " of "
+                    + totalNumberformatter
+                            .format((Number) totalResultSetCount)
                     + " " + " (" + (endTime - startTime) + " milli secs)");
           }
           else

diff --git a/src/jalview/fts/service/pdb/PDBFTSRestClient.java b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
index 29450e8..93a7df3 100644 (file)
--- a/src/jalview/fts/service/pdb/PDBFTSRestClient.java
+++ b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
@@ -326,11 +326,13 @@ public class PDBFTSRestClient extends FTSRestClient
       {
         try
         {
-          summaryRowData[colCounter++] = (field.getDataColumnClass() == Integer.class) ? Integer
+          summaryRowData[colCounter++] = (field.getDataType()
+                  .getDataTypeClass() == Integer.class) ? Integer
                   .valueOf(fieldData)
-                  : (field.getDataColumnClass() == Double.class) ? Double
+ : (field.getDataType()
+                  .getDataTypeClass() == Double.class) ? Double
                           .valueOf(fieldData)
-                          : fieldData;
+ : sanitiseData(fieldData);
         } catch (Exception e)
         {
           e.printStackTrace();
@@ -389,6 +391,14 @@ public class PDBFTSRestClient extends FTSRestClient
     };
   }
 
+  private static String sanitiseData(String data)
+  {
+    String cleanData = data.replaceAll("\\[\"", "").replaceAll("\\]\"", "")
+            .replaceAll("\\[", "").replaceAll("\\]", "")
+            .replaceAll("\",\"", ", ").replaceAll("\"", "");
+    return cleanData;
+  }
+
   @Override
   public String getColumnDataConfigFileName()
   {

diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index 0447715..a4f82cf 100644 (file)
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -66,6 +66,9 @@ public class UniProtFTSRestClient extends FTSRestClient
 
       String query = uniportRestRequest.getFieldToSearchBy()
               .equalsIgnoreCase("Search All") ? uniportRestRequest
+              .getSearchTerm()
+              + " or mnemonic:"
+              + uniportRestRequest
               .getSearchTerm() : uniportRestRequest.getFieldToSearchBy()
               + ":" + uniportRestRequest.getSearchTerm();
 
@@ -226,9 +229,11 @@ public class UniProtFTSRestClient extends FTSRestClient
         {
           try
           {
-            summaryRowData[colCounter++] = (field.getDataColumnClass() == Integer.class) ? Integer
+            summaryRowData[colCounter++] = (field.getDataType()
+                    .getDataTypeClass() == Integer.class) ? Integer
                     .valueOf(fieldData)
-                    : (field.getDataColumnClass() == Double.class) ? Double
+ : (field.getDataType()
+                    .getDataTypeClass() == Double.class) ? Double
                             .valueOf(fieldData) : fieldData;
           } catch (Exception e)
           {

diff --git a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
index 6c28ee5..f2fcb76 100644 (file)
--- a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
+++ b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
@@ -118,9 +118,14 @@ public class UniprotFTSPanel extends GFTSPanel
           if (isPaginationEnabled() && resultSetCount > 0)
           {
             updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
-                    + " " + (offSet + 1) + " to "
-                    + (offSet + resultSetCount) + " of "
-                    + totalResultSetCount
+                    + " "
+                    + totalNumberformatter.format((Number) (offSet + 1))
+                    + " to "
+                    + totalNumberformatter
+                            .format((Number) (offSet + resultSetCount))
+                    + " of "
+                    + totalNumberformatter
+                            .format((Number) totalResultSetCount)
                     + " " + " (" + (endTime - startTime) + " milli secs)");
           }
           else

diff --git a/test/jalview/fts/core/FTSRestClientTest.java b/test/jalview/fts/core/FTSRestClientTest.java
index 0dac04b..ddf60bc 100644 (file)
--- a/test/jalview/fts/core/FTSRestClientTest.java
+++ b/test/jalview/fts/core/FTSRestClientTest.java
@@ -76,7 +76,7 @@ public class FTSRestClientTest
     String actual = ftsRestClient
             .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
     Assert.assertEquals(actual,
-            "id,entry name,protein names,genes,organism,length,reviewed");
+            "id,entry name,protein names,genes,organism,reviewed,length");
   }
 
 
@@ -151,7 +151,7 @@ public class FTSRestClientTest
   public void getDefaultResponsePageSize()
   {
     int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
-    Assert.assertEquals(defaultResSize, 100);
+    Assert.assertEquals(defaultResSize, 500);
   }
 
   @Test(groups = { "Functional" })
@@ -213,10 +213,12 @@ public class FTSRestClientTest
       FTSDataColumnI foundDataCol = ftsRestClient
               .getDataColumnByNameOrCode("Protein names");
       Assert.assertNotNull(foundDataCol);
-      Assert.assertEquals(foundDataCol.getDataColumnClass(), String.class);
+      Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
+              String.class);
       foundDataCol = ftsRestClient.getDataColumnByNameOrCode("length");
       Assert.assertNotNull(foundDataCol);
-      Assert.assertEquals(foundDataCol.getDataColumnClass(), Integer.class);
+      Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
+              Integer.class);
       // foundDataCol = ftsRestClient.getDataColumnByNameOrCode("length");
       // Assert.assertNotNull(foundDataCol);
       // Assert.assertEquals(foundDataCol.getDataColumnClass(), Double.class);