JAL-1563 Modified Uniprot data column configurations and improved implementation...

diff --git a/resources/fts/uniprot_data_columns.txt b/resources/fts/uniprot_data_columns.txt
index 40e28e4..a7365c5 100644 (file)
--- a/resources/fts/uniprot_data_columns.txt
+++ b/resources/fts/uniprot_data_columns.txt
@@ -23,10 +23,10 @@ g17;Date of;17
 g18;Family & Domain;18
 #
 _data_column.primary_key;entry name
-_data_column.default_response_page_size;100
+_data_column.default_response_page_size;150
 #
 _data_column.name
-_data_column.code
+_data_column.code|_data_column.alt_code (optional: used for specifying search code when different from original code)
 _data_column.group_id
 _data_column.data_type
 _data_column.min_col_width
@@ -35,7 +35,7 @@ _data_column.preferred_col_width
 _data_column.is_shown_by_default
 _data_column.is_searchable
 Entry Name;entry name;String;g3;90;150;95;true;true
-Protein names;protein names;String;g3;300;1500;500;true;true
+Protein names;protein names|protein name;String;g3;300;1500;500;true;true
 Gene Names;genes;String;g3;50;1000;95;true;true
 Organism;organism;String;g3;50;1000;95;true;true
 Organism ID;organism-id;int;g3;60;100;80;false;true
@@ -53,7 +53,7 @@ Mass spectrometry;comment(MASS SPECTROMETRY);String;g7;50;1000;95;false;false
 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
-Length;length;int;g7;50;100;95;false;true
+Length;length;int;g7;50;100;65;true;true
 Mass;mass;String;g7;50;100;80;false;true
 Sequence;sequence;String;g7;50;1000;95;false;true
 Alternative sequence;feature(ALTERNATIVE SEQUENCE);String;g7;50;1000;95;false;false
@@ -87,8 +87,8 @@ 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
 Protein existence;existence;String;g6;50;1000;95;false;true
-Status;reviewed;String;g6;50;1000;95;false;true
-ALL;name;String;g7;50;1000;95;false;true;
+Status;reviewed;String;g6;50;100;95;true;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
 Developmental stage;comment(DEVELOPMENTAL STAGE);String;g10;50;1000;95;false;false
@@ -126,8 +126,8 @@ Beta strand;feature(BETA STRAND);String;g15;50;1000;95;false;false
 Helix;feature(HELIX);String;g15;50;1000;95;false;false
 Turn;feature(TURN);String;g15;50;1000;95;false;false
 PubMed ID;citation;String;g16;50;1000;95;false;true
-Date of creation;created;String;g17;80;150;100;true;true
-Date of last modification;last-modified;String;g17;80;150;100;true;true
+Date of creation;created;String;g17;80;150;100;false;true
+Date of last modification;last-modified;String;g17;80;150;100;false;true
 Date of last sequence modification;sequence-modified;String;g17;80;150;100;false;true
 Version (entry);version(entry);int;g17;80;100;80;false;false
 Domain [CC];comment(DOMAIN);String;g18;80;1000;95;false;false

diff --git a/src/jalview/fts/api/FTSDataColumnI.java b/src/jalview/fts/api/FTSDataColumnI.java
index ea30d01..7741d73 100644 (file)
--- a/src/jalview/fts/api/FTSDataColumnI.java
+++ b/src/jalview/fts/api/FTSDataColumnI.java
@@ -44,6 +44,13 @@ public interface FTSDataColumnI
   public String getCode();
 
   /**
+   * Returns the alternative code value for the data column
+   * 
+   * @return the data column's code
+   */
+  public String getAltCode();
+
+  /**
    * Returns the minimum width of the data column
    * 
    * @return the data column's minimum width

diff --git a/src/jalview/fts/core/FTSRestClient.java b/src/jalview/fts/core/FTSRestClient.java
index 0605fef..e3e2354 100644 (file)
--- a/src/jalview/fts/core/FTSRestClient.java
+++ b/src/jalview/fts/core/FTSRestClient.java
@@ -131,7 +131,14 @@ public abstract class FTSRestClient implements FTSRestClientI
               @Override
               public String getCode()
               {
-                return lineData[1];
+                return lineData[1].split("\\|")[0];
+              }
+
+              @Override
+              public String getAltCode()
+              {
+                return lineData[1].split("\\|").length > 1 ? lineData[1]
+                        .split("\\|")[1] : getCode();
               }
 
               @Override

diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index c8e21e0..7eda9f8 100644 (file)
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -58,8 +58,12 @@ public class UniProtFTSRestClient extends FTSRestClient
     int responseSize = (uniportRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
             : uniportRestRequest.getResponseSize();
 
-    String query = uniportRestRequest.getFieldToSearchBy() + ":"
-            + uniportRestRequest.getSearchTerm();
+    String query = uniportRestRequest.getFieldToSearchBy()
+            .equalsIgnoreCase("Search All") ? uniportRestRequest
+            .getSearchTerm()
+            : uniportRestRequest.getFieldToSearchBy() + ":"
+                    + uniportRestRequest.getSearchTerm();
+
     // + (uniportRestRequest.isAllowUnpublishedEntries() ? ""
     // : " AND status:REL");
     // System.out.println(">>>>> Query : " + query);

diff --git a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
index dcef358..21343d3 100644 (file)
--- a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
+++ b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
@@ -63,7 +63,7 @@ public class UniprotFTSPanel extends GFTSPanel
           long startTime = System.currentTimeMillis();
 
           String searchTarget = ((FTSDataColumnI) cmb_searchTarget
-                  .getSelectedItem()).getCode();
+                  .getSelectedItem()).getAltCode();
 
           wantedFields = UniProtFTSRestClient.getInstance()
                   .getAllDefaulDisplayedDataColumns();