From afe05002539312942412090e68dd83c03df84f15 Mon Sep 17 00:00:00 2001
From: Jim Robinson <jrobinso@broadinstitute.org>
Date: Sat, 20 Oct 2018 21:58:23 -0700
Subject: [PATCH] Support queries for "all" in straw.   See #236

---
 js/hicStraw.js     | 24 +++++++++++++++---------
 test/runTests.html | 13 +++++++++----
 test/testStraw.js  | 27 ++++++++++++++++++++++++++-
 3 files changed, 50 insertions(+), 14 deletions(-)

diff --git a/js/hicStraw.js b/js/hicStraw.js
index ab26925e..025e3e05 100644
--- a/js/hicStraw.js
+++ b/js/hicStraw.js
@@ -39,16 +39,20 @@ var hic = (function (hic) {
         var self = this,
             chr1 = region1.chr,
             chr2 = region2.chr,
-            x1 = region1.start / binsize, 
-            x2 = region1.end / binsize,
-            y1 = region2.start / binsize,
-            y2 = region2.end / binsize;
+            x1 = (region1.start === undefined) ? undefined :  region1.start / binsize,
+            x2 = (region1.end === undefined) ? undefined : region1.end / binsize,
+            y1 = (region2.start === undefined) ? undefined : region2.start / binsize,
+            y2 = (region2.end === undefined) ? undefined : region2.end / binsize;
 
         return getDataset.call(self)
+
             .then(function (dataset) {
 
                 self.dataset = dataset;
 
+                if("ALL" === chr1.toUpperCase()) chr1 = chr1.toUpperCase();
+                if("ALL" === chr2.toUpperCase()) chr2 = chr2.toUpperCase();
+
                 var chr1idx = dataset.getChrIndexFromName(chr1),
                     chr2idx = dataset.getChrIndexFromName(chr2);
 
@@ -59,8 +63,9 @@ var hic = (function (hic) {
                 return dataset.getMatrix(chr1idx, chr2idx)
             })
             .then(function (matrix) {
+
                 // Find the requested resolution
-                var z = self.dataset.getZoomIndexForBinSize(binsize, units);
+                var z = undefined === binsize ? 0 : self.dataset.getZoomIndexForBinSize(binsize, units);
                 if (z === -1) {
                     throw new Error("Invalid bin size");
                 }
@@ -69,8 +74,8 @@ var hic = (function (hic) {
                     blockBinCount = zd.blockBinCount,   // Dimension in bins of a block (width = height = blockBinCount)
                     col1 = x1 === undefined ? 0 : Math.floor(x1 / blockBinCount),
                     col2 = x1 === undefined ? zd.blockColumnCount : Math.floor(x2 / blockBinCount),
-                    row1 = Math.floor(y1 / blockBinCount),
-                    row2 = Math.floor(y2 / blockBinCount),
+                    row1 = y1 === undefined ? 0 : Math.floor(y1 / blockBinCount),
+                    row2 = y2 === undefined ? zd.blockColumnCount :  Math.floor(y2 / blockBinCount),
                     row, column, sameChr, blockNumber,
                     promises = [];
 
@@ -91,15 +96,16 @@ var hic = (function (hic) {
                 return Promise.all(promises);
             })
             .then(function (blocks) {
+
                 var contactRecords = [];
 
                 blocks.forEach(function (block) {
-                    if (block === null) { // This is most likely caused by a base pair range outside the chromosome
+                    if (!block) { // This is most likely caused by a base pair range outside the chromosome
                         return;
                     }
                     block.records.forEach(function(rec) {
                         // TODO -- transpose?
-                        if(rec.bin1 >= x1 && rec.bin1 <= x2 && rec.bin2 >= y1 && rec.bin2 <= y2) {
+                        if(x1 === undefined || (rec.bin1 >= x1 && rec.bin1 <= x2 && rec.bin2 >= y1 && rec.bin2 <= y2)) {
                             contactRecords.push(rec);
                         }
                     });
diff --git a/test/runTests.html b/test/runTests.html
index 74285be6..b75f14df 100644
--- a/test/runTests.html
+++ b/test/runTests.html
@@ -41,6 +41,11 @@
     <script src="../js/hicTrack2D.js"></script>
     <script src="../js/hicStraw.js"></script>
 
+    <script src="../vendor/colors.js"></script>
+    <script src="../vendor/jquery-ui.js"></script>
+    <script src="../vendor/throbber.js"></script>
+    <script src="../vendor/zlib_and_gzip.js"></script>
+
     <script src="testReader.js"></script>
     <script src="testColorScale.js"></script>
     <script src="testTrack2D.js"></script>
@@ -53,11 +58,11 @@
 <div id="qunit-fixture"></div>
 <script type="text/javascript">
     document.addEventListener('DOMContentLoaded', function () {
-      //  runTrack2DTests();
-      //  runColorTests();
+        runTrack2DTests();
+        runColorTests();
         runHicReaderTests();
-      //  runMathTests();
-      //  runStrawTests();
+        runMathTests();
+        runStrawTests();
     });
 </script>
 </body>
diff --git a/test/testStraw.js b/test/testStraw.js
index de8ab4d7..dbdb6851 100644
--- a/test/testStraw.js
+++ b/test/testStraw.js
@@ -29,7 +29,6 @@ function runStrawTests() {
 
     }
 
-
     asyncTest("Version 7 file", function () {
 
         var url = "https://data.broadinstitute.org/igvdata/test/data/hic/inter.hic",
@@ -51,6 +50,32 @@ function runStrawTests() {
                 start();
             })
             .catch(function (error) {
+                ok(false);
+                console.error(error);
+                start();
+            })
+    });
+
+    asyncTest("All chromosome", function () {
+
+        var url = "https://data.broadinstitute.org/igvdata/test/data/hic/inter.hic",
+            normalization = "NONE",
+            units = "BP",
+            region1 = {
+                chr: "all"
+            },
+            binSize = undefined,
+            straw;
+
+        straw = new hic.Straw({url: url});
+
+        straw.getContactRecords(normalization,region1, region1, units, binSize)
+            .then( function(records) {
+                ok(records.length > 0);
+                start();
+            })
+            .catch(function (error) {
+                ok(false);
                 console.error(error);
                 start();
             })