Uniprot retrieves features from XML

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index b0476ce..36f9a40 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -2,23 +2,22 @@ package jalview.gui;
 \r
 import javax.swing.*;\r
 import java.awt.*;\r
-import java.awt.event.ActionListener;\r
-import java.awt.event.ActionEvent;\r
-import MCview.PDBfile;\r
+import java.awt.event.*;\r
 import jalview.io.EBIFetchClient;\r
-import MCview.PDBChain;\r
-import jalview.datamodel.Alignment;\r
-import jalview.io.FormatAdapter;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.io.IdentifyFile;\r
-import jalview.analysis.AlignSeq;\r
+import MCview.*;\r
 import jalview.datamodel.*;\r
+import jalview.analysis.AlignSeq;\r
+import java.io.File;\r
+import jalview.io.*;\r
+import java.util.*;\r
+\r
 \r
 public class SequenceFetcher\r
     extends JPanel implements Runnable\r
 {\r
   JInternalFrame frame;\r
   AlignFrame alignFrame;\r
+  StringBuffer result;\r
   public SequenceFetcher(AlignFrame af)\r
   {\r
     alignFrame = af;\r
@@ -40,9 +39,9 @@ public class SequenceFetcher
     frame = new JInternalFrame();\r
     frame.setContentPane(this);\r
     if(System.getProperty("os.name").startsWith("Mac"))\r
-      Desktop.addInternalFrame(frame, "Sequence Fetcher", 390, 135);\r
+      Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 390, 135);\r
     else\r
-      Desktop.addInternalFrame(frame, "Sequence Fetcher", 390, 120);\r
+      Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 390, 120);\r
   }\r
 \r
   private void jbInit()\r
@@ -116,7 +115,7 @@ public class SequenceFetcher
 \r
   public void ok_actionPerformed(ActionEvent e)\r
   {\r
-    frame.setTitle("WSDBfetch@EBI Sequence Fetcher - Fetching Sequence...");\r
+    frame.setTitle("Sequence Fetcher (WSDBfetch@EBI) - Fetching Sequence...");\r
     database.setEnabled(false);\r
     textfield.setEnabled(false);\r
     ok.setEnabled(false);\r
@@ -128,57 +127,144 @@ public class SequenceFetcher
 \r
   public void run()\r
   {\r
-    String error = null;\r
-    StringBuffer result = new StringBuffer();\r
-      if (database.getSelectedItem().equals("Uniprot")\r
-          || database.getSelectedItem().equals("EMBL")\r
-          || database.getSelectedItem().equals("EMBLCDS"))\r
+   result = new StringBuffer();\r
+    if (database.getSelectedItem().equals("Uniprot"))\r
+    {\r
+      getUniprotFile(textfield.getText());\r
+    }\r
+    else if (database.getSelectedItem().equals("EMBL")\r
+        || database.getSelectedItem().equals("EMBLCDS"))\r
+    {\r
+      EBIFetchClient dbFetch = new EBIFetchClient();\r
+      String[] reply = dbFetch.fetchData(\r
+          database.getSelectedItem().toString().toLowerCase(\r
+          ) + ":" + textfield.getText(),\r
+          "fasta", "raw");\r
+\r
+      for (int i = 0; i < reply.length; i++)\r
+        result.append(reply[i] + "\n");\r
+\r
+      parseResult(result.toString());\r
+    }\r
+    else if (database.getSelectedItem().equals("PDB"))\r
+    {\r
+      result = getPDBFile(textfield.getText().toUpperCase());\r
+      parseResult(result.toString());\r
+    }\r
+\r
+\r
+    if (result == null || result.length() == 0)\r
+      showErrorMessage("Error retrieving " + textfield.getText()\r
+                       + " from " + database.getSelectedItem());\r
+\r
+\r
+      database.setEnabled(true);\r
+      textfield.setEnabled(true);\r
+      ok.setEnabled(true);\r
+      cancel.setEnabled(true);\r
+      frame.setTitle("Sequence Fetcher (WSDBfetch@EBI)");\r
+  }\r
+\r
+  void getUniprotFile(String id)\r
+  {\r
+    EBIFetchClient ebi = new EBIFetchClient();\r
+    File file = ebi.fetchDataAsFile("uniprot:"+id,"xml", null);\r
+    SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
+    Vector entries = sff.getUniprotEntries(file);\r
+\r
+    if(entries!=null)\r
+    {\r
+      //First, make the new sequences\r
+      Enumeration en = entries.elements();\r
+      while (en.hasMoreElements())\r
       {\r
-        EBIFetchClient dbFetch = new EBIFetchClient();\r
-        String[] reply = dbFetch.fetchData(\r
-            database.getSelectedItem().toString().toLowerCase(\r
-            ) + ":" + textfield.getText(),\r
-            "fasta", "raw");\r
-\r
-        for (int i = 0; i < reply.length; i++)\r
-          result.append(reply[i] + "\n");\r
+        UniprotEntry entry = (UniprotEntry) en.nextElement();\r
+        StringBuffer name = new StringBuffer( ">Uniprot/Swiss-Prot" );\r
+        Enumeration en2 = entry.getAccession().elements();\r
+        while(en2.hasMoreElements())\r
+        {\r
+          name.append("|");\r
+          name.append(en2.nextElement());\r
+        }\r
+        en2 = entry.getName().elements();\r
+        while(en2.hasMoreElements())\r
+        {\r
+          name.append("|");\r
+          name.append(en2.nextElement());\r
+        }\r
+\r
+        if(entry.getProteinName()!=null)\r
+          name.append(" "+entry.getProteinName().elementAt(0));\r
+\r
+        result.append(name +"\n"+entry.getUniprotSequence().getContent());\r
+\r
       }\r
-      else if (database.getSelectedItem().equals("PDB"))\r
+\r
+      //Then read in the features and apply them to the dataset\r
+      SequenceI [] sequence = parseResult(result.toString());\r
+      for(int i=0; i<entries.size(); i++)\r
       {\r
-        String id = textfield.getText().toUpperCase();\r
-        String chain=null;\r
-        if(id.indexOf(":")>-1)\r
+        UniprotEntry entry = (UniprotEntry) entries.elementAt(i);\r
+        Enumeration e = entry.getDbReference().elements();\r
+        Vector onlyPdbEntries = new Vector();\r
+        while (e.hasMoreElements())\r
         {\r
-          chain = id.substring(id.indexOf(":")+1);\r
-          id = id.substring(0,id.indexOf(":"));\r
-          System.out.println(id+" "+chain);\r
+          PDBEntry pdb = (PDBEntry) e.nextElement();\r
+          if (!pdb.getType().equals("PDB"))\r
+            continue;\r
+\r
+          onlyPdbEntries.addElement(pdb);\r
         }\r
 \r
-        EBIFetchClient ebi = new EBIFetchClient();\r
-        String[] reply = ebi.fetchData("pdb:" + id, "pdb",\r
-                                       "raw");\r
-        try{\r
-          PDBfile pdbfile = new PDBfile(reply);\r
-          for (int i = 0; i < pdbfile.chains.size(); i++)\r
-          {\r
-            if( chain == null || ((PDBChain)pdbfile.chains.elementAt(i)).id.toUpperCase().equals(chain))\r
-            result.append("\n>PDB|" + id+"|"+\r
+        sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
+        sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());\r
+\r
+      }\r
+    }\r
+  }\r
+\r
+    StringBuffer getPDBFile(String id)\r
+    {\r
+      StringBuffer result = new StringBuffer();\r
+      String chain = null;\r
+      if (id.indexOf(":") > -1)\r
+      {\r
+        chain = id.substring(id.indexOf(":") + 1);\r
+        id = id.substring(0, id.indexOf(":"));\r
+      }\r
+\r
+      EBIFetchClient ebi = new EBIFetchClient();\r
+      String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");\r
+      try\r
+      {\r
+        PDBfile pdbfile = new PDBfile(reply);\r
+        for (int i = 0; i < pdbfile.chains.size(); i++)\r
+        {\r
+          if (chain == null ||\r
+              ( (PDBChain) pdbfile.chains.elementAt(i)).id.\r
+              toUpperCase().equals(chain))\r
+            result.append("\n>PDB|" + id + "|" +\r
                           ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
                           getName() +\r
                           "\n"\r
                           +\r
                           ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
                           getSequence());\r
-          }\r
-        }catch(Exception ex)// Problem parsing PDB file\r
-        {\r
-          error = "Error retrieving "+textfield.getText()+" from "+database.getSelectedItem();\r
         }\r
       }\r
+      catch (Exception ex) // Problem parsing PDB file\r
+      {\r
+        showErrorMessage("Error retrieving " + textfield.getText() + " from " +\r
+            database.getSelectedItem());\r
+        return null;\r
+      }\r
 \r
-    if (result.length() > 0 && error==null)\r
+      return result;\r
+    }\r
+\r
+    SequenceI[] parseResult(String result)\r
     {\r
-      String format = IdentifyFile.Identify(result.toString(), "Paste");\r
+      String format = IdentifyFile.Identify(result, "Paste");\r
       SequenceI[] sequences = null;\r
 \r
       if (FormatAdapter.formats.contains(format))\r
@@ -190,7 +276,7 @@ public class SequenceFetcher
           {\r
             AlignFrame af = new AlignFrame(new Alignment(sequences));\r
             af.currentFileFormat = format;\r
-            Desktop.addInternalFrame(af, "Cut & Paste input - " + format,\r
+            Desktop.addInternalFrame(af, "Retrieved from "+database.getSelectedItem(),\r
                                      AlignFrame.NEW_WINDOW_WIDTH,\r
                                      AlignFrame.NEW_WINDOW_HEIGHT);\r
             af.statusBar.setText("Successfully pasted alignment file");\r
@@ -222,7 +308,7 @@ public class SequenceFetcher
                                           getHeight());\r
             alignFrame.viewport.alignment.getWidth();\r
             alignFrame.viewport.firePropertyChange("alignment", null,\r
-                alignFrame.viewport.getAlignment().getSequences());\r
+            alignFrame.viewport.getAlignment().getSequences());\r
 \r
           }\r
 \r
@@ -238,21 +324,12 @@ public class SequenceFetcher
 \r
         }\r
         else\r
-          error = "Error retrieving "+textfield.getText()+" from "+database.getSelectedItem();\r
-\r
-\r
-\r
+          showErrorMessage( "Error retrieving "+textfield.getText()\r
+                            +" from "+database.getSelectedItem());\r
       }\r
-    }\r
 \r
-    if(error!=null)\r
-          showErrorMessage(error);\r
+      return sequences;\r
 \r
-    database.setEnabled(true);\r
-    textfield.setEnabled(true);\r
-    ok.setEnabled(true);\r
-    cancel.setEnabled(true);\r
-    frame.setTitle("WSDBfetch@EBI Sequence Fetcher");\r
   }\r
 \r
   void showErrorMessage(String error)\r