From b0ed85aabdf8cdd5e8185405fbb611f14755e0c6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Marius=20W=C3=B6ste?= <mar.w@wwu.de>
Date: Fri, 2 Feb 2018 14:52:01 +0100
Subject: [PATCH] Generalize igv image directive

Now only dependent on sample, chr and pos instead of variant instance.
---
 public/viper/igv-image/IgvImageDirective.js   | 28 ++++++++++---------
 public/viper/igv-image/igv-image.tpl.html     |  6 ++--
 public/viper/pages/inspector/inspector.html   | 12 ++++----
 .../viper/visualization/IGVVisualizer.java    |  6 ++--
 4 files changed, 27 insertions(+), 25 deletions(-)

diff --git a/public/viper/igv-image/IgvImageDirective.js b/public/viper/igv-image/IgvImageDirective.js
index d1ce27f..c738dfd 100644
--- a/public/viper/igv-image/IgvImageDirective.js
+++ b/public/viper/igv-image/IgvImageDirective.js
@@ -24,9 +24,9 @@ var module = angular.module('de.imi.marw.viper.igv.image', [
 
   Ctrl.sleepMillis = 1000;
 
-  Ctrl.variant      = null;
-  Ctrl.chrColumn    = null;
-  Ctrl.bpColumn     = null;
+  Ctrl.sample       = null;
+  Ctrl.chr          = null;
+  Ctrl.pos          = null;
   Ctrl.breakpointImageLink = null;
   Ctrl.igvConfigurationHash = null;
 
@@ -40,25 +40,27 @@ var module = angular.module('de.imi.marw.viper.igv.image', [
 
   function init () {
 
-    $scope.$watch(function () { return { variant: Ctrl.variant, hash: Ctrl.igvConfigurationHash }; }, Ctrl.onUpdate, true);
+    $scope.$watch(function () { return { sample: Ctrl.sample, chr: Ctrl.chr, pos: Ctrl.pos, hash: Ctrl.igvConfigurationHash }; }, Ctrl.onUpdate, true);
 
   }
 
   function onUpdate (newVal, oldVal) {
 
-    var variant = newVal.variant;
+    var sample = newVal.sample;
+    var chr = newVal.chr;
+    var pos = newVal.pos;
     var hash = newVal.hash;
 
-    if (variant == null || hash == null) return;
+    if (sample == null || chr == null || pos == null || hash == null) return;
 
-    var key = Ctrl.getSnapshotKey(variant, hash);
+    var key = Ctrl.getSnapshotKey(sample, chr, pos, hash);
 
     Ctrl.isSnapshotAvailable(key)
     .then(function (res) {
 
       var isAvailable = res.data;
 
-      var currentKey = Ctrl.getSnapshotKey(Ctrl.variant, Ctrl.igvConfigurationHash);
+      var currentKey = Ctrl.getSnapshotKey(Ctrl.sample, Ctrl.chr, Ctrl.pos, Ctrl.igvConfigurationHash);
 
       if (currentKey === key && res.data === 'true') {
 
@@ -88,17 +90,17 @@ var module = angular.module('de.imi.marw.viper.igv.image', [
     return promise;
   }
 
-  function getSnapshotKey(variant, hash) {
-    return variant['sample'] + '-' + variant[Ctrl.chrColumn] + '-' + variant[Ctrl.bpColumn] + "-" + hash;
+  function getSnapshotKey(sample, chr, pos, hash) {
+    return sample + '-' + chr + '-' + pos + "-" + hash;
   }
 
 }])
 .directive('igvImage', [ function () {
   return {
     scope: {
-      variant: '=variant',
-      chrColumn: '=chrColumn',
-      bpColumn: '=bpColumn',
+      sample: '=sample',
+      chr: '=chr',
+      pos: '=pos',
       igvConfigurationHash: '=igvConfigurationHash'
     },
     restrict: 'E',
diff --git a/public/viper/igv-image/igv-image.tpl.html b/public/viper/igv-image/igv-image.tpl.html
index 29cbd28..d647aa7 100644
--- a/public/viper/igv-image/igv-image.tpl.html
+++ b/public/viper/igv-image/igv-image.tpl.html
@@ -20,10 +20,10 @@
 -->
 <h3>Breakpoint:
   <small>
-    {{ igvImageController.variant['sample'] }},
-    {{ igvImageController.variant[igvImageController.chrColumn] }}
+    {{ igvImageController.sample }},
+    {{ igvImageController.chr }}
     :
-    {{ igvImageController.variant[igvImageController.bpColumn] }}
+    {{ igvImageController.pos }}
   </small>
 </h3>
 
diff --git a/public/viper/pages/inspector/inspector.html b/public/viper/pages/inspector/inspector.html
index cda6a0d..b91fec4 100644
--- a/public/viper/pages/inspector/inspector.html
+++ b/public/viper/pages/inspector/inspector.html
@@ -196,18 +196,18 @@ <h4>Visualization settings</h4>
 
           <div class="col-md-6">
             <igv-image
-              variant="inspectorCtrl.relatedVariants[inspectorCtrl.relatedCallIndex]"
-              chr-column="'chr1'"
-              bp-column="'bp1'"
+              sample="inspectorCtrl.relatedVariants[inspectorCtrl.relatedCallIndex]['sample']"
+              chr="inspectorCtrl.relatedVariants[inspectorCtrl.relatedCallIndex]['chr1']"
+              pos="inspectorCtrl.relatedVariants[inspectorCtrl.relatedCallIndex]['bp1']"
               igv-configuration-hash="inspectorCtrl.configurationHash">
             </igv-image>
           </div>
 
           <div class="col-md-6">
             <igv-image
-              variant="inspectorCtrl.relatedVariants[inspectorCtrl.relatedCallIndex]"
-              chr-column="'chr2'"
-              bp-column="'bp2'"
+              sample="inspectorCtrl.relatedVariants[inspectorCtrl.relatedCallIndex]['sample']"
+              chr="inspectorCtrl.relatedVariants[inspectorCtrl.relatedCallIndex]['chr2']"
+              pos="inspectorCtrl.relatedVariants[inspectorCtrl.relatedCallIndex]['bp2']"
               igv-configuration-hash="inspectorCtrl.configurationHash">
             </igv-image>
           </div>
diff --git a/src/main/java/de/imi/marw/viper/visualization/IGVVisualizer.java b/src/main/java/de/imi/marw/viper/visualization/IGVVisualizer.java
index 7da5ea9..ce251ed 100644
--- a/src/main/java/de/imi/marw/viper/visualization/IGVVisualizer.java
+++ b/src/main/java/de/imi/marw/viper/visualization/IGVVisualizer.java
@@ -206,9 +206,9 @@ public boolean isSnapshotDone(String key) {
         return this.visualizationProgressMap.getOrDefault(key, false);
     }
 
-    public synchronized void scheduleSnapshot(String sample, String chr, int bp, boolean isUrgent) {
+    public synchronized void scheduleSnapshot(String sample, String chr, int pos, boolean isUrgent) {
 
-        String key = sample + "-" + chr + "-" + bp + "-" + this.getConfigurationHash();
+        String key = sample + "-" + chr + "-" + pos + "-" + this.getConfigurationHash();
         boolean snapshotAlreadyScheduled = this.visualizationProgressMap.containsKey(key);
 
         if (snapshotAlreadyScheduled && (!isUrgent || this.visualizationProgressMap.get(key))) {
@@ -227,7 +227,7 @@ public synchronized void scheduleSnapshot(String sample, String chr, int bp, boo
             "new",
             "load " + bamName,
             "collapse",
-            "goto " + chr + ":" + (bp - configViewRange) + "-" + (bp + configViewRange),
+            "goto " + chr + ":" + (pos - configViewRange) + "-" + (pos + configViewRange),
             "snapshot " + imageFileName
         };