JAL-845 linked protein/dna 'slave' further PoC functionality

[jalview.git] / src / jalview / gui / SequenceFetcher.java

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index b2bf35f..e159d41 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -20,24 +20,42 @@
  */
 package jalview.gui;
 
-import java.util.*;
-import java.util.List;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.tree.DefaultMutableTreeNode;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.*;
-import jalview.io.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
 import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
 import jalview.ws.seqfetcher.DbSourceProxy;
+
 import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.SwingConstants;
+import javax.swing.tree.DefaultMutableTreeNode;
+
+import com.stevesoft.pat.Regex;
 
 public class SequenceFetcher extends JPanel implements Runnable
 {
@@ -78,7 +96,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       if (guiWindow != null)
       {
         guiWindow.setProgressBar(
-                "Waiting for Sequence Database Fetchers to initialise",
+                MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
                 Thread.currentThread().hashCode());
       }
       // initting happening on another thread - so wait around to see if it
@@ -97,7 +115,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       if (guiWindow != null)
       {
         guiWindow.setProgressBar(
-                "Waiting for Sequence Database Fetchers to initialise",
+                       MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
                 Thread.currentThread().hashCode());
       }
     }
@@ -115,7 +133,7 @@ public class SequenceFetcher extends JPanel implements Runnable
        */
       if (guiWindow != null)
       {
-        guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+        guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
                 Thread.currentThread().hashCode());
       }
       dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
@@ -124,7 +142,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
       if (guiWindow != null)
       {
-        guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+        guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
                 Thread.currentThread().hashCode());
       }
       lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
@@ -161,8 +179,8 @@ public class SequenceFetcher extends JPanel implements Runnable
               JOptionPane
                       .showInternalMessageDialog(
                               Desktop.desktop,
-                              "Could not create the sequence fetcher client. Check error logs for details.",
-                              "Couldn't create SequenceFetcher",
+                              MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"),
+                              MessageManager.getString("label.couldnt_create_sequence_fetcher"),
                               JOptionPane.ERROR_MESSAGE);
             }
           });
@@ -219,8 +237,7 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   private String getFrameTitle()
   {
-    return ((alignFrame == null) ? "New " : "Additional ")
-            + "Sequence Fetcher";
+    return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher"));
   }
 
   private void jbInit() throws Exception
@@ -284,7 +301,9 @@ public class SequenceFetcher extends JPanel implements Runnable
       public void keyPressed(KeyEvent e)
       {
         if (e.getKeyCode() == KeyEvent.VK_ENTER)
+        {
           ok_actionPerformed();
+        }
       }
     });
     jPanel3.setLayout(borderLayout1);
@@ -494,8 +513,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       try
       {
         // update status
-        guiWindow.setProgressBar("Fetching " + nqueries
-                + " sequence queries from " + proxy.getDbName(), Thread
+        guiWindow.setProgressBar(MessageManager.formatMessage("status.fetching_sequence_queries_from", new String[]{Integer.valueOf(nqueries).toString(),proxy.getDbName()}), Thread
                 .currentThread().hashCode());
         isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
         if (proxy.getAccessionSeparator() == null)
@@ -693,11 +711,11 @@ public class SequenceFetcher extends JPanel implements Runnable
           presultTitle.add(titl);
         }
       }
-      guiWindow.setProgressBar("Finished querying", Thread.currentThread()
+      guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread()
               .hashCode());
     }
-    guiWindow.setProgressBar((presult.size() > 0) ? "Parsing results."
-            : "Processing ..", Thread.currentThread().hashCode());
+    guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results")
+            : MessageManager.getString("status.processing"), Thread.currentThread().hashCode());
     // process results
     while (presult.size() > 0)
     {
@@ -823,21 +841,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       }
       else
       {
-        for (int i = 0; i < al.getHeight(); i++)
-        {
-          alignFrame.viewport.getAlignment().addSequence(
-                  al.getSequenceAt(i)); // this
-          // also
-          // creates
-          // dataset
-          // sequence
-          // entries
-        }
-        alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
-                .getHeight());
-        alignFrame.viewport.getAlignment().getWidth();
-        alignFrame.viewport.firePropertyChange("alignment", null,
-                alignFrame.viewport.getAlignment().getSequences());
+        alignFrame.viewport.addAlignment(al, title);
       }
     }
     return al;