JAL-1542 script to show aligned positions of selected column(s)

diff --git a/examples/groovy/sitesForSelectedColumns.groovy b/examples/groovy/sitesForSelectedColumns.groovy
new file mode 100644 (file)
index 0000000..f84bc93
--- /dev/null
+++ b/examples/groovy/sitesForSelectedColumns.groovy
@@ -0,0 +1,70 @@
+// Requested by Hari Jayaram 
+// script to output residue positions and values for selected region
+
+// thanks to this thread for cut'n'paste code
+// http://comments.gmane.org/gmane.comp.lang.groovy.user/53010
+
+// Jalview issue at http://issues.jalview.org/browse/JAL-1542
+
+import java.awt.datatransfer.StringSelection
+import static java.awt.Toolkit.*
+
+def curviewport = Jalview.getAlignframes()[Jalview.getAlignframes().length-1].getViewport()
+
+def debug = false
+
+// TSV output by default.
+// change "\t" to "," to output CSV file
+def sep = "\t"
+def gapChar = "-"
+
+if (curviewport.getSelectionGroup()) {
+  // gets selection for topmost alignment
+  def selreg = curviewport.getSelectionGroup()
+  def groupStartCol = selreg.getStartRes()
+  def groupEndCol = selreg.getEndRes()
+
+    if (debug) {println "groupStartCol: " + groupStartCol + ", groupEndCol: " + groupEndCol}
+      
+  def csv=new StringBuilder(512)
+
+  // for each sequence in the current selection
+  selreg.getSequences().eachWithIndex{ seq, seqNo ->
+    csv.append(seq.getDisplayId(false).padRight(20,' '))
+    // get map of sequence sites to alignment positions 
+    def gaps = seq.gapMap()
+    if (debug) {println "gaps: " + gaps}
+
+    // initialise loop variable to 'not quite shown first column'    
+    def lastColShown = groupStartCol-1
+    
+    for (mapPos=0 ; ; mapPos++) {
+        def nextResiduePos = gaps[mapPos]
+        // skip over sites that precede selected columns
+        if (nextResiduePos < groupStartCol) {
+            continue;
+        }
+
+        if (debug) {println "mapPos: " + mapPos + ", lastColShown: " + lastColShown + ", nextResiduePos: " + nextResiduePos + ", csv: " + csv}
+
+        // fill in any gaps
+        while (lastColShown < groupEndCol && lastColShown+1 < nextResiduePos) {
+            csv.append(sep+gapChar)
+            lastColShown++
+        }
+        if (lastColShown >= groupEndCol) {
+            break
+        }
+        lastColShown = nextResiduePos
+        def residue = seq.getDatasetSequence().getCharAt(mapPos)
+        csv.append(sep+(mapPos+1) + " (" + residue + ")")    // user output is base 1
+    }
+    csv.append("\n")      
+  }
+  def result = csv.toString()
+  defaultToolkit.systemClipboard.setContents(new StringSelection(result), null)
+  print result
+  println "Sites for selected region copied to the clipboard"
+} else {
+    "Select a region in the alignment window."
+}