From 7a968a25437adc55c83ef3beba16684a8af90cc4 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 20 Oct 2017 15:09:29 +0100
Subject: [PATCH] JAL-547 updated the PID script for 2.10.x series score model
 architecture

---
 examples/groovy/PIDmatrix.groovy |   98 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 98 insertions(+)
 create mode 100644 examples/groovy/PIDmatrix.groovy

diff --git a/examples/groovy/PIDmatrix.groovy b/examples/groovy/PIDmatrix.groovy
new file mode 100644
index 0000000..4e2ad8d
--- /dev/null
+++ b/examples/groovy/PIDmatrix.groovy
@@ -0,0 +1,98 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE.  See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+import jalview.analysis.scoremodels.ScoreModels
+import jalview.analysis.scoremodels.SimilarityParams
+
+// call the method below
+printSimilarityMatrix(false,true,SimilarityParams.Jalview)
+
+/** 
+ * prints a sequence similarity matrix in PHYLIP format. 
+ * printSimilarityMatrix(selected-only, include-ids, pidMethod)
+ * 
+ * Allowed values for pidMethod:
+ * 
+ * Jalview's Comparison.PID method includes matching gaps 
+ * and counts over the length of the shorter gapped sequence
+ * SimilarityParams.Jalview;
+ *
+ * 'SeqSpace' mode PCA calculation does not count matching 
+ * gaps but uses longest gapped sequence length
+ *  SimilarityParams.SeqSpace;
+ *
+ * PID calcs from the Raghava-Barton paper
+ * SimilarityParams.PID1: ignores gap-gap, does not score gap-residue,
+ * includes gap-residue in lengths, matches on longer of two sequences.
+ * 
+ * SimilarityParams.PID2: ignores gap-gap,ignores gap-residue, 
+ * matches on longer of two sequences
+ * 
+ * SimilarityParams.PID3: ignores gap-gap,ignores gap-residue, 
+ * matches on shorter of sequences only
+ * 
+ * SimilarityParams.PID4: ignores gap-gap,does not score gap-residue,
+ * includes gap-residue in lengths,matches on shorter of sequences only.
+ */
+
+void printSimilarityMatrix(boolean selview=false, boolean includeids=true, SimilarityParams pidMethod) {
+
+  def currentAlignFrame = jalview.bin.Jalview.getCurrentAlignFrame()
+
+  jalview.gui.AlignViewport av = currentAlignFrame.getCurrentView()
+
+  jalview.datamodel.AlignmentView seqStrings = av.getAlignmentView(selview)
+
+  if (!selview) {
+    start = 0
+    end = av.getAlignment().getWidth()
+    seqs = av.getAlignment().getSequencesArray()
+  } else {
+    start = av.getSelectionGroup().getStartRes()
+    end = av.getSelectionGroup().getEndRes() + 1
+    seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment())
+  }
+
+  distanceCalc = ScoreModels.getInstance().getScoreModel("PID",
+      (jalview.api.AlignmentViewPanel) currentAlignFrame.alignPanel)
+
+  def distance=distanceCalc.findSimilarities(
+      seqStrings.getSequenceStrings(jalview.util.Comparison.GAP_DASH),pidMethod)
+
+  // output the PHYLIP Matrix
+
+  print distance.width()+" "+distance.height()+"\n"
+
+  p = 0
+
+  for (v in 1..distance.height()) {
+
+    if (includeids) {
+      print seqs[p++].getDisplayId(false)+" "
+    }
+
+    for (r in 1..distance.width()) {
+      print distance.getValue(v-1,r-1)+" "
+    }
+
+    print "\n"
+  }
+}
-- 
1.7.10.2