Introduced DbRefEntry to DasSourceCoordinateSystem check to only call sources for...

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

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 67a3eff..e2b5730 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -239,6 +239,7 @@ public class SequenceFetcher
   {\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
@@ -249,6 +250,7 @@ public class SequenceFetcher
       while (en.hasMoreElements())\r
       {\r
         UniprotEntry entry = (UniprotEntry) en.nextElement();\r
+\r
         StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");\r
         Enumeration en2 = entry.getAccession().elements();\r
         while (en2.hasMoreElements())\r
@@ -263,8 +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
@@ -293,8 +297,9 @@ public class SequenceFetcher
           e = entry.getFeature().elements();\r
           while (e.hasMoreElements())\r
           {\r
-            sequence[i].getDatasetSequence().addSequenceFeature( (\r
-                SequenceFeature) e.nextElement());\r
+            SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+            sf.setFeatureGroup("Uniprot");\r
+            sequence[i].getDatasetSequence().addSequenceFeature( sf );\r
           }\r
         }\r
       }\r
@@ -368,6 +373,12 @@ public class SequenceFetcher
                                    AlignFrame.NEW_WINDOW_WIDTH,\r
                                    AlignFrame.NEW_WINDOW_HEIGHT);\r
           af.statusBar.setText("Successfully pasted alignment file");\r
+          if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))\r
+          {\r
+            af.wrapMenuItem.setSelected(true);\r
+            af.wrapMenuItem_actionPerformed(null);\r
+          }\r
+\r
           try\r
           {\r
             af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
@@ -426,7 +437,7 @@ public class SequenceFetcher
 \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
+              DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,"0",pdbid);\r
               sequences[i].getDatasetSequence().addDBRef(dbentry);\r
             }\r
             else\r
@@ -455,13 +466,18 @@ public class SequenceFetcher
 \r
   }\r
 \r
-  void showErrorMessage(String error)\r
+  void showErrorMessage(final String error)\r
   {\r
     resetDialog();\r
-    JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
-                                          error, "Error Retrieving Data",\r
+    javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+    {\r
+      public void run()\r
+      {\r
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+                                              error, "Error Retrieving Data",\r
                                           JOptionPane.WARNING_MESSAGE);\r
-    return;\r
+      }\r
+    });\r
   }\r
 }\r
 \r