Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

[jalview.git] / src / jalview / io / CountReader.java

diff --git a/src/jalview/io/CountReader.java b/src/jalview/io/CountReader.java
new file mode 100644 (file)
index 0000000..eea3dae
--- /dev/null
+++ b/src/jalview/io/CountReader.java
@@ -0,0 +1,63 @@
+package jalview.io;
+
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ResidueCount;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+
+import javax.swing.JFileChooser;
+
+public class CountReader
+{
+  public static ResidueCount getBackgroundFrequencies(AlignmentPanel ap, SequenceI seq) throws MalformedURLException, IOException
+  {
+    JFileChooser bkgdFreqChooser = new JFileChooser();
+    
+    bkgdFreqChooser.showOpenDialog(ap);
+    
+    File file = bkgdFreqChooser.getSelectedFile();
+    if (file == null)
+    {
+      return null;
+    }
+    
+    IdentifyFile identifier = new IdentifyFile();
+    FileFormatI format = null;
+    try
+    {
+      format = identifier.identify(file.getPath(), DataSourceType.FILE);
+    } catch (Exception e)
+    {
+
+    }
+    
+    if (format == null)
+    {
+      if (!Jalview.isHeadlessMode())
+      {
+        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                MessageManager.getString("label.couldnt_read_data") + " in "
+                        + file + "\n"
+                        + AppletFormatAdapter.getSupportedFormats(),
+                MessageManager.getString("label.couldnt_read_data"),
+                JvOptionPane.WARNING_MESSAGE);
+      }
+    }
+
+    FileParse parser = new FileParse(file.getPath(), DataSourceType.FILE);
+    AlignmentI al = new FormatAdapter().readFromFile(parser, format);
+    parser.close();
+    
+    ResidueCount counts = new ResidueCount(al.getSequences());
+    
+    return counts;
+  }
+}