Check endRes

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

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 501f03c..6d49d12 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -44,6 +44,7 @@ public class SequenceFetcher
     database.addItem("EMBL");\r
     database.addItem("EMBLCDS");\r
     database.addItem("PDB");\r
+    database.addItem("PFAM");\r
 \r
     try\r
     {\r
@@ -64,8 +65,7 @@ public class SequenceFetcher
 \r
   private String getFrameTitle()\r
   {\r
-    return ( (alignFrame == null) ? "New " : "Additional ") +\r
-        "Sequence Fetcher (WSDBfetch@EBI)";\r
+    return ( (alignFrame == null) ? "New " : "Additional ") + "Sequence Fetcher";\r
   }\r
 \r
   private void jbInit()\r
@@ -87,12 +87,12 @@ public class SequenceFetcher
         ok_actionPerformed(e);\r
       }\r
     });\r
-    cancel.setText("Cancel");\r
-    cancel.addActionListener(new ActionListener()\r
+    close.setText("Close");\r
+    close.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        cancel_actionPerformed(e);\r
+        close_actionPerformed(e);\r
       }\r
     });\r
     textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
@@ -104,7 +104,7 @@ public class SequenceFetcher
       }\r
     });\r
     jPanel1.add(ok);\r
-    jPanel1.add(cancel);\r
+    jPanel1.add(close);\r
     this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
                                              , GridBagConstraints.WEST,\r
                                              GridBagConstraints.NONE,\r
@@ -126,11 +126,11 @@ public class SequenceFetcher
   JComboBox database = new JComboBox();\r
   JLabel jLabel1 = new JLabel();\r
   JButton ok = new JButton();\r
-  JButton cancel = new JButton();\r
+  JButton close = new JButton();\r
   JPanel jPanel1 = new JPanel();\r
   JTextField textfield = new JTextField();\r
   GridBagLayout gridBagLayout1 = new GridBagLayout();\r
-  public void cancel_actionPerformed(ActionEvent e)\r
+  public void close_actionPerformed(ActionEvent e)\r
   {\r
     try\r
     {\r
@@ -142,11 +142,10 @@ public class SequenceFetcher
 \r
   public void ok_actionPerformed(ActionEvent e)\r
   {\r
-    frame.setTitle("Sequence Fetcher (WSDBfetch@EBI) - Fetching Sequence...");\r
     database.setEnabled(false);\r
     textfield.setEnabled(false);\r
     ok.setEnabled(false);\r
-    cancel.setEnabled(false);\r
+    close.setEnabled(false);\r
 \r
     Thread worker = new Thread(this);\r
     worker.start();\r
@@ -157,8 +156,7 @@ public class SequenceFetcher
     database.setEnabled(true);\r
     textfield.setEnabled(true);\r
     ok.setEnabled(true);\r
-    cancel.setEnabled(true);\r
-    frame.setTitle(getFrameTitle());\r
+    close.setEnabled(true);\r
   }\r
 \r
   public void run()\r
@@ -214,13 +212,27 @@ public class SequenceFetcher
       if (result.length()>0)\r
         parseResult(result.toString());\r
     }\r
+    else if( database.getSelectedItem().equals("PFAM"))\r
+    {\r
+      try{\r
+        result.append(new FastaFile(\r
+           "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="\r
+           +  textfield.getText().toUpperCase(), "URL").print()\r
+           );\r
+\r
+         if(result.length()>0)\r
+           parseResult( result.toString() );\r
+\r
+      }catch(java.io.IOException ex)\r
+      {   result = null;    }\r
+    }\r
 \r
     if (result == null || result.length() == 0)\r
       showErrorMessage("Error retrieving " + textfield.getText()\r
                        + " from " + database.getSelectedItem());\r
-    else\r
-      textfield.setText("");\r
+\r
     resetDialog();\r
+    return;\r
   }\r
 \r
   void getUniprotFile(String id)\r
@@ -399,8 +411,9 @@ public class SequenceFetcher
                                       + "=" + sequences[i].getStart()\r
                                       + "-" + sequences[i].getEnd());\r
               sequences[i].getDatasetSequence().addPDBId(entry);\r
-              // JBPNote - should add a PDB DBRefEntry too since we\r
-              // have obtained the PDB file from a verifiable source\r
+\r
+              // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source\r
+              // JBPNote - PDB DBRefEntry should also carry the chain and mapping information\r
               DBRefEntry dbentry = new DBRefEntry("PDB","0",pdbid);\r
               sequences[i].getDatasetSequence().addDBRef(dbentry);\r
             }\r
@@ -432,9 +445,11 @@ public class SequenceFetcher
 \r
   void showErrorMessage(String error)\r
   {\r
+    resetDialog();\r
     JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
                                           error, "Error Retrieving Data",\r
                                           JOptionPane.WARNING_MESSAGE);\r
+    return;\r
   }\r
 }\r
 \r