X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=2beb3d95dfa5d58b14bbbdf62c299c413bf68b24;hb=7f7fc2e5533f7b00c86465f964e37c55bcf12fd7;hp=7b255315a03ed129f9e914938ad1163e8ce4a232;hpb=e02486484d33e20dedb020a34f31f6024d5720a2;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 7b25531..2beb3d9 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -119,8 +119,8 @@ public class SequenceFetcher
                                               new Insets(0, 4, 0, 0), 1, 0));
     this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
                                                , GridBagConstraints.CENTER,
-                                               GridBagConstraints.HORIZONTAL,
-                                               new Insets(0, 0, 0, 6), 200, 1));
+                                               GridBagConstraints.NONE,
+                                               new Insets(0, 0, 0, 6), 211, 1));
   }
 
   JComboBox database = new JComboBox();
@@ -183,16 +183,26 @@ public class SequenceFetcher
     else if (database.getSelectedItem().equals("EMBL")
              || database.getSelectedItem().equals("EMBLCDS"))
     {
-      EBIFetchClient dbFetch = new EBIFetchClient();
-      String[] reply = dbFetch.fetchData(
-          database.getSelectedItem().toString().toLowerCase(
-          ) + ":" + textfield.getText(),
-          "fasta", "raw");
+      StringTokenizer st = new StringTokenizer(textfield.getText(), ";");
+      while(st.hasMoreTokens())
+      {
+        EBIFetchClient dbFetch = new EBIFetchClient();
+
+        String[] reply = dbFetch.fetchData(
+            database.getSelectedItem().toString().toLowerCase(
+            ) + ":" + st.nextToken(),
+            "fasta", "raw");
+//
+        if (reply != null)
+        {
+          for (int i = 0; i < reply.length; i++)
+            result.append(reply[i] + "\n");
+        }
+      }
 
-      if(reply!=null)
+      if(result!=null)
       {
-        for (int i = 0; i < reply.length; i++)
-          result.append(reply[i] + "\n");
+        System.out.println(result.toString());
 
         parseResult(result.toString(), null);
       }
@@ -239,9 +249,9 @@ public class SequenceFetcher
   {
     EBIFetchClient ebi = new EBIFetchClient();
     File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
-   // File file = new File("H:/jalview/classes/fer1.xml");
-    SequenceFeatureFetcher sff = new SequenceFeatureFetcher();
-    Vector entries = sff.getUniprotEntries(file);
+
+    DBRefFetcher dbref = new DBRefFetcher();
+    Vector entries = dbref.getUniprotEntries(file);
 
     if (entries != null)
     {
@@ -291,6 +301,17 @@ public class SequenceFetcher
           onlyPdbEntries.addElement(pdb);
         }
 
+        Enumeration en2 = entry.getAccession().elements();
+        while (en2.hasMoreElements())
+        {
+          sequence[i].getDatasetSequence().addDBRef(new DBRefEntry(DBRefSource.UNIPROT,
+                    "0",
+                    en2.nextElement().toString()));
+        }
+
+
+
+
         sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
         if (entry.getFeature() != null)
         {
@@ -317,17 +338,18 @@ public class SequenceFetcher
     }
 
     EBIFetchClient ebi = new EBIFetchClient();
-    String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");
-    if (reply == null)
+    String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
+    if (file == null)
       return null;
     try
     {
-      PDBfile pdbfile = new PDBfile(reply);
+      PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
       for (int i = 0; i < pdbfile.chains.size(); i++)
       {
         if (chain == null ||
             ( (PDBChain) pdbfile.chains.elementAt(i)).id.
             toUpperCase().equals(chain))
+
           result.append("\n>PDB|" + id + "|" +
                         ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
                         getName() +
@@ -353,7 +375,7 @@ public class SequenceFetcher
     String format = new IdentifyFile().Identify(result, "Paste");
     SequenceI[] sequences = null;
 
-    if (FormatAdapter.formats.contains(format))
+    if (FormatAdapter.isValidFormat(format))
     {
       sequences = null;
       try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
@@ -364,15 +386,19 @@ public class SequenceFetcher
       {
         if (alignFrame == null)
         {
-          AlignFrame af = new AlignFrame(new Alignment(sequences));
+          AlignFrame af = new AlignFrame(new Alignment(sequences),
+                                           AlignFrame.DEFAULT_WIDTH,
+                                           AlignFrame.DEFAULT_HEIGHT
+);
           af.currentFileFormat = format;
           if(title==null)
             title = "Retrieved from " + database.getSelectedItem();
           Desktop.addInternalFrame(af,
                                    title,
-                                   AlignFrame.NEW_WINDOW_WIDTH,
-                                   AlignFrame.NEW_WINDOW_HEIGHT);
+                                   AlignFrame.DEFAULT_WIDTH,
+                                   AlignFrame.DEFAULT_HEIGHT);
           af.statusBar.setText("Successfully pasted alignment file");
+
           try
           {
             af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
@@ -431,7 +457,7 @@ public class SequenceFetcher
 
               // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source
               // JBPNote - PDB DBRefEntry should also carry the chain and mapping information
-              DBRefEntry dbentry = new DBRefEntry("PDB","0",pdbid);
+              DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,"0",pdbid);
               sequences[i].getDatasetSequence().addDBRef(dbentry);
             }
             else