From c4dd9fbd848d3ffaa88134fb06bed794d69bc6f3 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 25 Sep 2006 14:05:41 +0000
Subject: [PATCH] linear interpolation between sparse annotation element
 values.

---
 src/jalview/io/VamsasDatastore.java |   16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/jalview/io/VamsasDatastore.java b/src/jalview/io/VamsasDatastore.java
index c9d5994..4b7445a 100755
--- a/src/jalview/io/VamsasDatastore.java
+++ b/src/jalview/io/VamsasDatastore.java
@@ -1285,8 +1285,22 @@ public class VamsasDatastore {
         // make bounds and automatic description strings for jalview user's benefit (these shouldn't be written back to vamsas document)
         boolean first=true;
         float min=0,max=1;
+        int lastval=0;
         for (int i=0;i<arow.length; i++) {
           if (arow[i]!=null) {
+            if (i-lastval>1) {
+              // do some interpolation *between* points
+              if (arow[lastval]!=null) {
+                float interval = arow[i].value-arow[lastval].value;
+                interval/=i-lastval;
+                float base = arow[lastval].value;
+                for (int ip=lastval+1,np=0; ip<i; np++,ip++) {
+                  arow[ip] = new jalview.datamodel.Annotation("","",' ', interval*np+base);
+                  // NB - Interpolated points don't get a tooltip and description.
+                }
+              }
+            }
+            lastval=i;
             // check range - shouldn't we have a min and max property in the annotation object ?
             if (first) { min=max=arow[i].value; first=false;}
             else { if (arow[i].value<min) { min=arow[i].value; }
@@ -1295,7 +1309,7 @@ public class VamsasDatastore {
             // make tooltip and display char value
             if (!has[HASDESCSTR]) arow[i].description = arow[i].value + "";
             if (!has[HASDC]) arow[i].displayCharacter=arow[i].value+"";
-          }
+          } 
         }
         int type=jalview.datamodel.AlignmentAnnotation.LINE_GRAPH;
         if (has[HASHPHOB]) {
-- 
1.7.10.2