JAL-1563 Further increased swing timer for search textfield to 2500ms, removed 1200ms...

diff --git a/resources/fts/uniprot_data_columns.txt b/resources/fts/uniprot_data_columns.txt
index 883f2f3..6c78c16 100644 (file)
--- a/resources/fts/uniprot_data_columns.txt
+++ b/resources/fts/uniprot_data_columns.txt
@@ -54,6 +54,7 @@ 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
+Status;reviewed;String;g6;50;100;95;true;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
@@ -88,7 +89,6 @@ 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;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

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 3c79b58..b68a358 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -790,7 +790,7 @@ label.select_backgroud_colour = Select Background Colour
 label.invalid_font = Invalid Font
 label.separate_multiple_accession_ids = Enter one or more accession IDs separated by a semi-colon ";"
 label.separate_multiple_query_values = Enter one or more {0}s separated by a semi-colon ";"
-label.search_all = Enter one or more search values separated by a semi-colon ";" (Note: This Searches the entire PDB database)
+label.search_all = Enter one or more search values separated by a semi-colon ";" (Note: This Searches the entire database)
 label.replace_commas_semicolons = Replace commas with semi-colons
 label.parsing_failed_syntax_errors_shown_below_param = Parsing failed. Syntax errors shown below {0}
 label.parsing_failed_unrecoverable_exception_thrown_param = \nParsing failed. An unrecoverable exception was thrown\:\n {0}
@@ -1295,4 +1295,6 @@ info.error_creating_file = Error creating {0} file.
 label.run_groovy = Run Groovy console script
 label.run_groovy_tip = Run the script in the Groovy console over this alignment
 label.couldnt_run_groovy_script = Failed to run Groovy script
-label.uniprot_sequence_fetcher = UniProt Sequence Fetcher
\ No newline at end of file
+label.uniprot_sequence_fetcher = UniProt Sequence Fetcher
+action.next_page= >> 
+action.prev_page= << 
\ No newline at end of file

diff --git a/src/jalview/fts/api/GFTSPanelI.java b/src/jalview/fts/api/GFTSPanelI.java
index 46121fc..07ae5a1 100644 (file)
--- a/src/jalview/fts/api/GFTSPanelI.java
+++ b/src/jalview/fts/api/GFTSPanelI.java
@@ -92,4 +92,10 @@ public interface GFTSPanelI
    * @param isSearchInProgress
    */
   public void setSearchInProgress(Boolean isSearchInProgress);
+
+  public void prevPageAction();
+
+  public void nextPageAction();
+
+  public boolean isPaginationEnabled();
 }

diff --git a/src/jalview/fts/core/FTSRestClient.java b/src/jalview/fts/core/FTSRestClient.java
index 7a4f72e..8bf1dc2 100644 (file)
--- a/src/jalview/fts/core/FTSRestClient.java
+++ b/src/jalview/fts/core/FTSRestClient.java
@@ -400,6 +400,10 @@ public abstract class FTSRestClient implements FTSRestClientI
   @Override
   public int getDefaultResponsePageSize()
   {
+    if (dataColumns == null || dataColumns.isEmpty())
+    {
+      parseDataColumnsConfigFile();
+    }
     return defaultResponsePageSize;
   }
 

diff --git a/src/jalview/fts/core/FTSRestRequest.java b/src/jalview/fts/core/FTSRestRequest.java
index 68068d7..164b102 100644 (file)
--- a/src/jalview/fts/core/FTSRestRequest.java
+++ b/src/jalview/fts/core/FTSRestRequest.java
@@ -56,6 +56,8 @@ public class FTSRestRequest
 
   private int responseSize;
 
+  private int offSet;
+
   private boolean isSortAscending;
 
   private Collection<FTSDataColumnI> wantedFields;
@@ -176,4 +178,14 @@ public class FTSRestRequest
   {
     this.facetPivotMinCount = facetPivotMinCount;
   }
+
+  public int getOffSet()
+  {
+    return offSet;
+  }
+
+  public void setOffSet(int offSet)
+  {
+    this.offSet = offSet;
+  }
 }

diff --git a/src/jalview/fts/core/FTSRestResponse.java b/src/jalview/fts/core/FTSRestResponse.java
index c56b8c8..6cce2c4 100644 (file)
--- a/src/jalview/fts/core/FTSRestResponse.java
+++ b/src/jalview/fts/core/FTSRestResponse.java
@@ -135,14 +135,6 @@ public class FTSRestResponse
   public static void configureTableColumn(JTable tbl_summary,
           Collection<FTSDataColumnI> wantedFields)
   {
-    try
-    {
-      // wait for table model initialisation to complete
-      Thread.sleep(1200);
-    } catch (InterruptedException e1)
-    {
-      e1.printStackTrace();
-    }
     for (FTSDataColumnI wantedField : wantedFields)
     {
       try

diff --git a/src/jalview/fts/core/GFTSPanel.java b/src/jalview/fts/core/GFTSPanel.java
index 139dcb4..c9ee297 100644 (file)
--- a/src/jalview/fts/core/GFTSPanel.java
+++ b/src/jalview/fts/core/GFTSPanel.java
@@ -99,6 +99,10 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
 
   private String lastSearchTerm = "";
 
+  protected JButton btn_next_page = new JButton();
+
+  protected JButton btn_prev_page = new JButton();
+
   private JTable tbl_summary = new JTable()
   {
     private boolean inLayout;
@@ -322,6 +326,63 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
       }
     });
 
+    btn_next_page.setEnabled(false);
+    btn_next_page.setFont(new java.awt.Font("Verdana", 0, 12));
+    btn_next_page.setText(MessageManager.getString("action.next_page"));
+    btn_next_page.addActionListener(new java.awt.event.ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        nextPageAction();
+      }
+    });
+    btn_next_page.addKeyListener(new KeyAdapter()
+    {
+      @Override
+      public void keyPressed(KeyEvent evt)
+      {
+        if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+        {
+          nextPageAction();
+        }
+      }
+    });
+
+    btn_prev_page.setEnabled(false);
+    btn_prev_page.setFont(new java.awt.Font("Verdana", 0, 12));
+    btn_prev_page.setText(MessageManager.getString("action.prev_page"));
+    btn_prev_page.addActionListener(new java.awt.event.ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        prevPageAction();
+      }
+    });
+    btn_prev_page.addKeyListener(new KeyAdapter()
+    {
+      @Override
+      public void keyPressed(KeyEvent evt)
+      {
+        if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+        {
+          prevPageAction();
+        }
+      }
+    });
+
+    if (isPaginationEnabled())
+    {
+      btn_prev_page.setVisible(true);
+      btn_next_page.setVisible(true);
+    }
+    else
+    {
+      btn_prev_page.setVisible(false);
+      btn_next_page.setVisible(false);
+    }
+
     btn_cancel.setFont(new java.awt.Font("Verdana", 0, 12));
     btn_cancel.setText(MessageManager.getString("action.cancel"));
     btn_cancel.addActionListener(new java.awt.event.ActionListener()
@@ -404,7 +465,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
     });
 
     final DeferredTextInputListener listener = new DeferredTextInputListener(
-            1500,
+            2500,
             new ActionListener()
             {
               @Override
@@ -491,6 +552,8 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
     pnl_inputs.add(txt_search);
     pnl_inputs.add(lbl_loading);
     pnl_inputs.add(lbl_warning);
+    pnl_inputs.add(btn_prev_page);
+    pnl_inputs.add(btn_next_page);
 
     this.setLayout(mainLayout);
     this.add(pnl_inputs, java.awt.BorderLayout.NORTH);

diff --git a/src/jalview/fts/service/pdb/PDBFTSPanel.java b/src/jalview/fts/service/pdb/PDBFTSPanel.java
index 826a505..ca1a902 100644 (file)
--- a/src/jalview/fts/service/pdb/PDBFTSPanel.java
+++ b/src/jalview/fts/service/pdb/PDBFTSPanel.java
@@ -232,4 +232,24 @@ public class PDBFTSPanel extends GFTSPanel
   }
 
 
+  @Override
+  public void prevPageAction()
+  {
+    // TODO pagination not yet implemented for PDB FTS
+
+  }
+
+  @Override
+  public void nextPageAction()
+  {
+    // TODO pagination not yet implemented for PDB FTS
+
+  }
+
+  @Override
+  public boolean isPaginationEnabled()
+  {
+    return false;
+  }
+
 }

diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index 2af1d56..57689f9 100644 (file)
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -58,6 +58,9 @@ public class UniProtFTSRestClient extends FTSRestClient
     int responseSize = (uniportRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
             : uniportRestRequest.getResponseSize();
 
+    int offSet = (uniportRestRequest.getOffSet() == 0) ? getDefaultResponsePageSize()
+            : uniportRestRequest.getOffSet();
+
     String query = uniportRestRequest.getFieldToSearchBy()
             .equalsIgnoreCase("Search All") ? uniportRestRequest
             .getSearchTerm()
@@ -73,6 +76,7 @@ public class UniProtFTSRestClient extends FTSRestClient
             .queryParam("format", "tab")
             .queryParam("columns", wantedFields)
             .queryParam("limit", String.valueOf(responseSize))
+            .queryParam("offset", String.valueOf(offSet))
             .queryParam("sort", "score")
             .queryParam("query", query);
     // Execute the REST request

diff --git a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
index 21343d3..c40e1e8 100644 (file)
--- a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
+++ b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
@@ -40,6 +40,13 @@ public class UniprotFTSPanel extends GFTSPanel
 
   private String ftsFrameTitle = defaultFTSFrameTitle;
 
+  private int resultSetCount;
+
+  private int offSet;
+
+  private static int pageLimit = UniProtFTSRestClient.getInstance()
+          .getDefaultResponsePageSize();
+
   public UniprotFTSPanel(SequenceFetcher seqFetcher)
   {
     this.seqFetcher = seqFetcher;
@@ -50,6 +57,12 @@ public class UniprotFTSPanel extends GFTSPanel
   @Override
   public void searchAction()
   {
+    offSet = 0;
+    executeSearch();
+  }
+
+  public void executeSearch()
+  {
     new Thread()
   {
       @Override
@@ -72,6 +85,7 @@ public class UniprotFTSPanel extends GFTSPanel
           FTSRestRequest request = new FTSRestRequest();
           request.setFieldToSearchBy(searchTarget);
           request.setSearchTerm(searchTerm);
+          request.setOffSet(offSet);
           request.setWantedFields(wantedFields);
           FTSRestClientI uniProtRestCleint = UniProtFTSRestClient
                   .getInstance();
@@ -92,27 +106,82 @@ public class UniprotFTSPanel extends GFTSPanel
           {
             getResultTable().setModel(
                     FTSRestResponse.getTableModel(request,
-                    resultList.getSearchSummary()));
+                            resultList.getSearchSummary()));
             FTSRestResponse.configureTableColumn(getResultTable(),
                     wantedFields);
             getResultTable().setVisible(true);
           }
 
           long endTime = System.currentTimeMillis();
-          int resultSetCount = resultList.getNumberOfItemsFound();
+          resultSetCount = resultList.getNumberOfItemsFound();
           String result = (resultSetCount > 1) ? MessageManager
                   .getString("label.results") : MessageManager
                   .getString("label.result");
-          updateSearchFrameTitle(defaultFTSFrameTitle + " - "
-                  + resultSetCount + " " + result + " ("
-                  + (endTime - startTime) + " milli secs)");
+          if (isPaginationEnabled() && resultSetCount > 1)
+          {
+            updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
+                    + " " + offSet + " to " + (offSet + resultSetCount)
+                    + " " + " (" + (endTime - startTime) + " milli secs)");
+          }
+          else
+          {
+            updateSearchFrameTitle(defaultFTSFrameTitle + " - "
+                    + resultSetCount + " " + result + " ("
+                    + (endTime - startTime) + " milli secs)");
+          }
           setSearchInProgress(false);
+          refreshPaginatorState();
         }
       }
     }.start();
 
   }
 
+
+
+  public void refreshPaginatorState()
+  {
+    // System.out.println("resultSet count : " + resultSetCount);
+    // System.out.println("offSet : " + offSet);
+    // System.out.println("page limit : " + pageLimit);
+    btn_prev_page.setEnabled(false);
+    btn_next_page.setEnabled(false);
+    if (resultSetCount >= pageLimit)
+    {
+      btn_next_page.setEnabled(true);
+    }
+    if (offSet >= pageLimit)
+    {
+      btn_prev_page.setEnabled(true);
+    }
+  }
+
+  @Override
+  public void prevPageAction()
+  {
+    if (offSet >= pageLimit)
+    {
+      offSet = offSet - pageLimit;
+      executeSearch();
+    }else{
+      refreshPaginatorState();
+    }
+  }
+
+  @Override
+  public void nextPageAction()
+  {
+    offSet = offSet + pageLimit;
+    executeSearch();
+
+  }
+
+  @Override
+  public boolean isPaginationEnabled()
+  {
+    return true;
+  }
+
   @Override
   public void okAction()
   {