From 1a6d20b15b2ba810bc807f76eb44ab1b9cc4482a Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Sun, 3 Jul 2011 13:05:24 +0100
Subject: [PATCH] groovy scripting examples (JAL-???)

---
 examples/groovy/annotationsascsv.groovy      |    9 ++++++++
 examples/groovy/closures.groovy              |    5 +++++
 examples/groovy/iterateOverAlignments.groovy |   20 +++++++++++++++++
 examples/groovy/parseproperties.groovy       |   13 +++++++++++
 examples/groovy/printtitle.groovy            |   12 ++++++++++
 examples/groovy/removeFeaturesByGroup.groovy |   31 ++++++++++++++++++++++++++
 examples/groovy/stripUniprotPrefixes.groovy  |   31 ++++++++++++++++++++++++++
 7 files changed, 121 insertions(+)
 create mode 100644 examples/groovy/annotationsascsv.groovy
 create mode 100644 examples/groovy/closures.groovy
 create mode 100644 examples/groovy/iterateOverAlignments.groovy
 create mode 100644 examples/groovy/parseproperties.groovy
 create mode 100644 examples/groovy/printtitle.groovy
 create mode 100644 examples/groovy/removeFeaturesByGroup.groovy
 create mode 100644 examples/groovy/stripUniprotPrefixes.groovy

diff --git a/examples/groovy/annotationsascsv.groovy b/examples/groovy/annotationsascsv.groovy
new file mode 100644
index 0000000..5f0a66a
--- /dev/null
+++ b/examples/groovy/annotationsascsv.groovy
@@ -0,0 +1,9 @@
+// do something groovy in jalview
+print "Hello World.\n";
+def alf = Jalview.getAlignframes();
+for (ala in alf)
+{
+	def alignment = ala.viewport.alignment;
+	// ala is an jalview.gui.AlignFrame object 
+	print new jalview.io.AnnotationFile().printCSVAnnotations(alignment.getAlignmentAnnotation())+"\n";
+}
\ No newline at end of file
diff --git a/examples/groovy/closures.groovy b/examples/groovy/closures.groovy
new file mode 100644
index 0000000..9e4dd52
--- /dev/null
+++ b/examples/groovy/closures.groovy
@@ -0,0 +1,5 @@
+writeAnnot = { 
+  new File(it).append(new jalview.io.AnnotationFile().printAnnotations(Jalview.getAlignframes()[0].getViewport().getAlignment().getAlignmentAnnotation(),null,null)) 
+}
+
+
diff --git a/examples/groovy/iterateOverAlignments.groovy b/examples/groovy/iterateOverAlignments.groovy
new file mode 100644
index 0000000..83c4169
--- /dev/null
+++ b/examples/groovy/iterateOverAlignments.groovy
@@ -0,0 +1,20 @@
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+
+def af = Jalview.getAlignframes();
+
+for (ala in af)
+{
+	def al = ala.viewport.alignment;
+	if (al!=null && al.getCodonFrames()!=null)
+	{
+		al.getCodonFrames().each { 
+			it.getdnaToProt().each {
+				it2 -> println it2.fromShifts+"\n"
+			}
+		}
+	}
+}
+	
diff --git a/examples/groovy/parseproperties.groovy b/examples/groovy/parseproperties.groovy
new file mode 100644
index 0000000..646ebf8
--- /dev/null
+++ b/examples/groovy/parseproperties.groovy
@@ -0,0 +1,13 @@
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+
+def af = Jalview.getAlignframes();
+def al = af[0].viewport.alignment;
+ParseProperties pp = new ParseProperties(al);
+pp.getScoresFromDescription("Score", "ScanPS Raw Score", "([-0-9.+]+)");
+def sqs = al.getSequenceAt(0);
+def annots = sqs.getAnnotation();
+
+
diff --git a/examples/groovy/printtitle.groovy b/examples/groovy/printtitle.groovy
new file mode 100644
index 0000000..8fe91db
--- /dev/null
+++ b/examples/groovy/printtitle.groovy
@@ -0,0 +1,12 @@
+// do something groovy in jalview
+print "Hello World.\n";
+def alf = Jalview.getAlignframes();
+for (ala in alf)
+{
+	// ala is an jalview.gui.AlignFrame object 
+	print ala.getTitle()+"\n";
+	// get the parent jalview.datamodel.Alignment from the alignment viewport
+	def alignment = ala.viewport.alignment;
+	// get the first sequence from the jalview.datamodel.Alignment object
+	def seq = alignment.getSequenceAt(0); 
+}
diff --git a/examples/groovy/removeFeaturesByGroup.groovy b/examples/groovy/removeFeaturesByGroup.groovy
new file mode 100644
index 0000000..bf7f74d
--- /dev/null
+++ b/examples/groovy/removeFeaturesByGroup.groovy
@@ -0,0 +1,31 @@
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+
+def af = Jalview.getAlignframes();
+
+def todie = "PDBFile"; // about to delete this type of group
+for (ala in af)
+{
+	def al = ala.viewport.alignment.getDataset();
+	if (al!=null)
+	{
+		SequenceI[] seqs = al.getSequencesArray();
+		for (sq in seqs)
+		{
+			if (sq!=null) {
+				SequenceFeature[] sf = sq.getSequenceFeatures();
+				for (sfpos in sf)
+				{
+				    if (sfpos!=null && sfpos.getFeatureGroup().equals(todie))
+					{
+						sq.deleteFeature(sfpos);
+					}
+				}
+			}
+		}
+	}
+}
+	
+
diff --git a/examples/groovy/stripUniprotPrefixes.groovy b/examples/groovy/stripUniprotPrefixes.groovy
new file mode 100644
index 0000000..e2bb129
--- /dev/null
+++ b/examples/groovy/stripUniprotPrefixes.groovy
@@ -0,0 +1,31 @@
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+
+def af = Jalview.getAlignframes();
+
+// walk through  all alignments, stripping off all text prior to and including last '|' symbol in sequence IDs
+
+for (ala in af)
+{
+	def al = ala.viewport.alignment;
+	if (al!=null)
+	{
+		SequenceI[] seqs = al.getSequencesArray();
+		for (sq in seqs)
+		{
+			if (sq!=null) {
+				if (sq.getName().indexOf("|")>-1)
+				{
+					sq.setName(sq.getName().substring(sq.getName().lastIndexOf("|")+1));
+					if (sq.getDatasetSequence()!=null)
+					{
+						sq.getDatasetSequence().setName(sq.getName());
+					}
+				}
+			}
+		}
+	}
+}
+	
\ No newline at end of file
-- 
1.7.10.2