house keeping

diff --git a/src/jalview/gui/EBIFetchPanel.java b/src/jalview/gui/EBIFetchPanel.java
index 8c2ef29..7fe9f2e 100644 (file)
--- a/src/jalview/gui/EBIFetchPanel.java
+++ b/src/jalview/gui/EBIFetchPanel.java
@@ -12,6 +12,18 @@ import javax.swing.SwingUtilities;
 @SuppressWarnings("serial")
 public class EBIFetchPanel extends GEBIFetchPanel
 {
+  private SequenceFetcher seqFetcher;
+
+  public EBIFetchPanel()
+  {
+  }
+
+  public EBIFetchPanel(SequenceFetcher seqFetcher)
+  {
+    this();
+    this.seqFetcher = seqFetcher;
+  }
+
   public static void main(String[] args)
   {
     SwingUtilities.invokeLater(new Runnable()
@@ -51,9 +63,10 @@ public class EBIFetchPanel extends GEBIFetchPanel
   @Override
   public void okActionPerformed()
   {
-    System.out.println("ok! pressed!");
+    processPDBResponseData();
   }
 
+
   @Override
   public void backActionPerformed()
   {
@@ -66,4 +79,43 @@ public class EBIFetchPanel extends GEBIFetchPanel
     mainFrame.dispose();
   }
 
+  private void processPDBResponseData()
+  {
+    mainFrame.dispose();
+    StringBuilder selectedIds = new StringBuilder();
+    for (PDBSummaryListModel dataSelected : jListSearchResult
+            .getSelectedValuesList())
+    {
+      selectedIds.append(";").append(dataSelected.getPdbId());
+    }
+    String ids = selectedIds.deleteCharAt(0).toString();
+    seqFetcher.textArea.setText(ids);
+    Thread worker = new Thread(seqFetcher);
+
+    // Thread worker = new Thread(this);
+    worker.start();
+  }
+
+  // @Override
+  // public void run()
+  // {
+  // for (PDBSummaryListModel sum : jListSearchResult
+  // .getSelectedValuesList())
+  // {
+  // System.out.println("you selected ------------> " + sum.getPdbId());
+  // }
+  // seqFetcher.guiWindow.setProgressBar(MessageManager
+  // .getString("status.processing"), Thread.currentThread()
+  // .hashCode());
+  // try
+  // {
+  // Thread.sleep(1000 * 2);
+  // } catch (InterruptedException e)
+  // {
+  // e.printStackTrace();
+  // }
+  // seqFetcher.guiWindow.setProgressBar(null, Thread.currentThread()
+  // .hashCode());
+  // }
+
 }

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index fb94c05..2f4ace3 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -115,7 +115,7 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   private static Thread initingThread = null;
 
-  int x = 0;
+  int debounceTrap = 0;
   /**
    * Blocking method that initialises and returns the shared instance of the
    * SequenceFetcher client
@@ -357,17 +357,16 @@ public class SequenceFetcher extends JPanel implements Runnable
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        x++;
+        debounceTrap++;
         String currentSelection = database.getSelectedItem();
 
         if (!currentSelection.equalsIgnoreCase("pdb"))
         {
             otherSourceAction();
         }
-        if (currentSelection.equalsIgnoreCase("pdb") && ((x % 2) == 0))
+        if (currentSelection.equalsIgnoreCase("pdb") && ((debounceTrap % 2) == 0))
         {
-          frame.dispose();
-          new EBIFetchPanel();
+          pdbSourceAction();
         }
 
       }
@@ -388,10 +387,13 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   }
 
-  private void hideX()
+  private void pdbSourceAction()
   {
-    this.setVisible(false);
+    databaseButt.setText(database.getSelectedItem());
+    new EBIFetchPanel(this);
+    frame.dispose();
   }
+
   private void otherSourceAction()
   {
     try

diff --git a/src/jalview/jbgui/GEBIFetchPanel.java b/src/jalview/jbgui/GEBIFetchPanel.java
index 74091af..e00830b 100644 (file)
--- a/src/jalview/jbgui/GEBIFetchPanel.java
+++ b/src/jalview/jbgui/GEBIFetchPanel.java
@@ -53,6 +53,7 @@ public abstract class GEBIFetchPanel extends JPanel
   private BorderLayout mainLayout = new BorderLayout();
 
 
+
   public GEBIFetchPanel()
   {
     try

diff --git a/src/jalview/util/Format.java b/src/jalview/util/Format.java
index a7b311b..d490df8 100755 (executable)
--- a/src/jalview/util/Format.java
+++ b/src/jalview/util/Format.java
@@ -622,7 +622,7 @@ public class Format
   /**
    * Formats a character into a string (like sprintf in C)
    * 
-   * @param x
+   * @param debounceTrap
    *          the value to format
    * @return the formatted string
    */
@@ -641,7 +641,7 @@ public class Format
   /**
    * Formats a string into a larger string (like sprintf in C)
    * 
-   * @param x
+   * @param debounceTrap
    *          the value to format
    * @return the formatted string
    */

diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java
index c26c88f..0c41d61 100644 (file)
--- a/src/jalview/ws/dbsources/PDBRestClient.java
+++ b/src/jalview/ws/dbsources/PDBRestClient.java
@@ -39,6 +39,7 @@ public class PDBRestClient
     Client client = Client.create(clientConfig);
     WebResource webResource = client.resource(pdbSearchEndpoint)
             .queryParam("wt", "json")
+.queryParam("rows", "100")
             .queryParam("q", qParam + ":" + searchTerm);
     ClientResponse clientResponse = webResource.accept(
             MediaType.APPLICATION_JSON).get(ClientResponse.class);

diff --git a/src/jalview/ws/uimodel/PDBSummaryListModel.java b/src/jalview/ws/uimodel/PDBSummaryListModel.java
index ef93aed..37c0855 100644 (file)
--- a/src/jalview/ws/uimodel/PDBSummaryListModel.java
+++ b/src/jalview/ws/uimodel/PDBSummaryListModel.java
@@ -13,16 +13,14 @@ public class PDBSummaryListModel extends DefaultListModel
 
   private String summary;
 
+  private JSONObject rawJson;
+
   private int width = 480;
 
-  public PDBSummaryListModel(String pdbId, String summary)
-  {
-    this.pdbId = pdbId;
-    this.summary = summary;
-  }
 
   public PDBSummaryListModel(JSONObject doc)
   {
+    this.rawJson = doc;
     StringBuilder summary = new StringBuilder();
     if (doc.get("molecule_type") != null)
     {
@@ -95,6 +93,16 @@ public class PDBSummaryListModel extends DefaultListModel
     this.summary = summary;
   }
 
+  public JSONObject getRawJson()
+  {
+    return rawJson;
+  }
+
+  public void setRawJson(JSONObject rawJson)
+  {
+    this.rawJson = rawJson;
+  }
+
   public String toString()
   {
     StringBuilder html = new StringBuilder();
@@ -104,5 +112,4 @@ public class PDBSummaryListModel extends DefaultListModel
     html.append("</div></html>");
     return html.toString();
   }
-
 }