From cd340d96daf7a9f885cc1ec9061156f44ecc9fd4 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 17 Feb 2014 16:29:17 +0000
Subject: [PATCH] JAL-1445 groovy script demonstrating how to select columns
 according to a particular feature type

---
 .../groovy/selectColumnsByFeatureAndGroup.groovy   |   79 ++++++++++++++++++++
 1 file changed, 79 insertions(+)
 create mode 100644 examples/groovy/selectColumnsByFeatureAndGroup.groovy

diff --git a/examples/groovy/selectColumnsByFeatureAndGroup.groovy b/examples/groovy/selectColumnsByFeatureAndGroup.groovy
new file mode 100644
index 0000000..0a16391
--- /dev/null
+++ b/examples/groovy/selectColumnsByFeatureAndGroup.groovy
@@ -0,0 +1,79 @@
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import java.util.BitSet;
+import javax.swing.JOptionPane;
+import groovy.swing.SwingBuilder;
+def toselect = getFeatureInput(); // change this to select the desired feature type
+
+def nal=0;
+def nfeat=0;
+def nseq=0;
+
+for (ala in Jalview.getAlignframes()) {
+  def al = ala.viewport.alignment;
+    if (al!=null)
+    {
+      BitSet bs = new BitSet();
+      SequenceI[] seqs = al.getSequencesArray();
+      for (sq in seqs)
+      {
+          def tfeat=0;
+        if (sq!=null) {
+          SequenceFeature[] sf = sq.getDatasetSequence().getSequenceFeatures();
+          for (sfpos in sf)
+          {
+            if (sfpos!=null && sfpos.getType().equals(toselect))
+            {
+              tfeat++;
+              int i=sq.findIndex(sfpos.getBegin());
+              int ist=sq.findIndex(sq.getStart());
+              if (i<ist)
+              {
+                i=ist;
+              }
+              int j=sq.findIndex(sfpos.getEnd());
+              if (j>al.getWidth())
+              {
+                j = al.getWidth();
+              }
+              for (; i<=j; i++)
+              {
+                bs.set(i-1);
+              }
+            }
+          }
+        }
+        if (tfeat>0) {
+            nseq++;
+            nfeat+=tfeat;
+        }
+      }
+      if (bs.cardinality()>0)
+      {
+        nal ++;
+        ColumnSelection cs = ala.viewport.getColumnSelection();
+        if (cs == null) {
+          cs = new ColumnSelection();
+        }
+    for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i+1)) {
+        cs.addElement(i);
+        }
+      ala.viewport.setColumnSelection(cs);
+      ala.alignPanel.paintAlignment(true);
+      ala.statusBar.setText("Marked "+bs.cardinality()+" columns containing features of type "+toselect)
+      } else {
+        ala.statusBar.setText("No features of type "+toselect+" found.");
+      }
+    }
+}
+return "Found a total of ${nfeat} features across ${nseq} sequences in ${nal} alignments.";
+    
+String getFeatureInput(){
+        def swingBuilder = new SwingBuilder();
+        def response = JOptionPane.showInputDialog(
+                   null, 'Select columns by feature by type','Enter type of feature', JOptionPane.OK_OPTION)
+
+        return response
+    }
\ No newline at end of file
-- 
1.7.10.2