View Properties

[jalview.git] / src / jalview / gui / AlignFrame.java
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java

index c60355c..bcb5771 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -911,7 +911,8 @@ public class AlignFrame
      new AnnotationExporter().exportAnnotations(
        alignPanel,
          viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
-      viewport.alignment.getGroups()
+      viewport.alignment.getGroups(),
+      ((Alignment)viewport.alignment).alignmentProperties
          );
    }
  
@@ -2266,6 +2267,51 @@ public class AlignFrame
      alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
    }
  
+  public void alignmentProperties()
+  {
+    JEditorPane editPane = new JEditorPane("text/html","");
+    editPane.setEditable(false);
+    StringBuffer contents = new StringBuffer("<html>");
+
+    float avg  = 0;
+    int min=Integer.MAX_VALUE, max=0;
+    for(int i=0; i<viewport.alignment.getHeight(); i++)
+    {
+      int size = viewport.alignment.getSequenceAt(i).getEnd()
+          -viewport.alignment.getSequenceAt(i).getStart();
+      avg += size;
+      if(size>max)
+        max = size;
+      if(size<min)
+        min = size;
+    }
+    avg = avg/(float)viewport.alignment.getHeight();
+
+    contents.append("<br>Sequences: "+ viewport.alignment.getHeight());
+    contents.append("<br>Minimum Sequence Length: "+min);
+    contents.append("<br>Maximum Sequence Length: "+max);
+    contents.append("<br>Average Length: "+(int)avg);
+
+    if (((Alignment)viewport.alignment).alignmentProperties != null)
+    {
+      Hashtable props = ((Alignment)viewport.alignment).alignmentProperties;
+      Enumeration en = props.keys();
+      contents.append("<br><br><table border=\"1\">");
+      while(en.hasMoreElements())
+      {
+        String key = en.nextElement().toString();
+        contents.append("<tr><td>"+key+"</td><td>"+props.get(key)+"</td></tr>");
+      }
+      contents.append("</table>");
+    }
+    editPane.setText(contents.toString()+"</html>");
+    JInternalFrame frame = new JInternalFrame();
+    frame.add(editPane);
+
+    Desktop.instance.addInternalFrame(frame,"Alignment Properties: "+getTitle(),500,400);
+  }
+
+
    /**
     * DOCUMENT ME!
     *