2.08, not 2.07

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

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 0884d44..fc8f042 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
@@ -142,7 +142,6 @@ 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
@@ -158,7 +157,6 @@ public class SequenceFetcher
     textfield.setEnabled(true);\r
     ok.setEnabled(true);\r
     close.setEnabled(true);\r
-    frame.setTitle(getFrameTitle());\r
   }\r
 \r
   public void run()\r
@@ -196,7 +194,7 @@ public class SequenceFetcher
         for (int i = 0; i < reply.length; i++)\r
           result.append(reply[i] + "\n");\r
 \r
-        parseResult(result.toString());\r
+        parseResult(result.toString(), null);\r
       }\r
     }\r
     else if (database.getSelectedItem().equals("PDB"))\r
@@ -212,21 +210,36 @@ public class SequenceFetcher
 \r
 \r
       if (result.length()>0)\r
-        parseResult(result.toString());\r
+        parseResult(result.toString(), null);\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(), textfield.getText().toUpperCase() );\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
   {\r
     EBIFetchClient ebi = new EBIFetchClient();\r
     File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);\r
+   // File file = new File("H:/jalview/classes/fer1.xml");\r
     SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
     Vector entries = sff.getUniprotEntries(file);\r
 \r
@@ -237,7 +250,8 @@ public class SequenceFetcher
       while (en.hasMoreElements())\r
       {\r
         UniprotEntry entry = (UniprotEntry) en.nextElement();\r
-        StringBuffer name = new StringBuffer(">Uniprot/Swiss-Prot");\r
+\r
+        StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");\r
         Enumeration en2 = entry.getAccession().elements();\r
         while (en2.hasMoreElements())\r
         {\r
@@ -251,8 +265,10 @@ public class SequenceFetcher
           name.append(en2.nextElement());\r
         }\r
 \r
-        if (entry.getProteinName() != null)\r
-          name.append(" " + entry.getProteinName().elementAt(0));\r
+        if (entry.getProtein() != null)\r
+        {\r
+           name.append(" " + entry.getProtein().getName().elementAt(0));\r
+        }\r
 \r
         result.append(name + "\n" + entry.getUniprotSequence().getContent() +\r
                       "\n");\r
@@ -260,7 +276,7 @@ public class SequenceFetcher
       }\r
 \r
       //Then read in the features and apply them to the dataset\r
-      SequenceI[] sequence = parseResult(result.toString());\r
+      SequenceI[] sequence = parseResult(result.toString(), null);\r
       for (int i = 0; i < entries.size(); i++)\r
       {\r
         UniprotEntry entry = (UniprotEntry) entries.elementAt(i);\r
@@ -276,8 +292,16 @@ public class SequenceFetcher
         }\r
 \r
         sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
-        sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());\r
-\r
+        if (entry.getFeature() != null)\r
+        {\r
+          e = entry.getFeature().elements();\r
+          while (e.hasMoreElements())\r
+          {\r
+            SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+            sf.setFeatureGroup("Uniprot");\r
+            sequence[i].getDatasetSequence().addSequenceFeature( sf );\r
+          }\r
+        }\r
       }\r
     }\r
   }\r
@@ -324,23 +348,28 @@ public class SequenceFetcher
     return result;\r
   }\r
 \r
-  SequenceI[] parseResult(String result)\r
+  SequenceI[] parseResult(String result, String title)\r
   {\r
-    String format = IdentifyFile.Identify(result, "Paste");\r
+    String format = new IdentifyFile().Identify(result, "Paste");\r
     SequenceI[] sequences = null;\r
 \r
     if (FormatAdapter.formats.contains(format))\r
     {\r
-      sequences = new FormatAdapter().readFile(result.toString(), "Paste",\r
-                                               format);\r
+      sequences = null;\r
+      try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",\r
+                                               format);}\r
+      catch(Exception ex){}\r
+\r
       if (sequences != null && sequences.length > 0)\r
       {\r
         if (alignFrame == null)\r
         {\r
           AlignFrame af = new AlignFrame(new Alignment(sequences));\r
           af.currentFileFormat = format;\r
+          if(title==null)\r
+            title = "Retrieved from " + database.getSelectedItem();\r
           Desktop.addInternalFrame(af,\r
-                                   "Retrieved from " + database.getSelectedItem(),\r
+                                   title,\r
                                    AlignFrame.NEW_WINDOW_WIDTH,\r
                                    AlignFrame.NEW_WINDOW_HEIGHT);\r
           af.statusBar.setText("Successfully pasted alignment file");\r
@@ -358,7 +387,7 @@ public class SequenceFetcher
             alignFrame.viewport.alignment.addSequence(sequences[i]);\r
 \r
             ////////////////////////////\r
-            //Datset needs extension;\r
+            //Dataset needs extension;\r
             /////////////////////////////\r
             Sequence ds = new Sequence(sequences[i].getName(),\r
                                        AlignSeq.extractGaps("-. ",\r
@@ -433,9 +462,11 @@ 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