From 27f996ebaffb27488a846ac36d6a40efc64f84f9 Mon Sep 17 00:00:00 2001
From: Don Kirkby <donkirkby@gmail.com>
Date: Tue, 18 Jul 2023 16:43:35 -0700
Subject: [PATCH] Fix Alignment and Plasmid to make examples work.

Also bump version number.
---
 examples/Genetracks.ipynb | 373 ++++++++------------------------------
 genetracks/elements.py    |   2 +-
 genetracks/plasmid.py     |   2 +-
 setup.py                  |   2 +-
 4 files changed, 78 insertions(+), 301 deletions(-)

diff --git a/examples/Genetracks.ipynb b/examples/Genetracks.ipynb
index 2eb307d..8a4b2ca 100644
--- a/examples/Genetracks.ipynb
+++ b/examples/Genetracks.ipynb
@@ -9,8 +9,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
+   "execution_count": 22,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-07-18T23:42:53.883255337Z",
+     "start_time": "2023-07-18T23:42:53.866093429Z"
+    }
+   },
    "outputs": [],
    "source": [
     "from genetracks import Figure, Track, Alignment, Multitrack, Label"
@@ -18,42 +23,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 23,
    "metadata": {
-    "scrolled": false
+    "scrolled": false,
+    "ExecuteTime": {
+     "end_time": "2023-07-18T23:42:53.884400604Z",
+     "start_time": "2023-07-18T23:42:53.872393883Z"
+    }
    },
    "outputs": [
     {
      "data": {
-      "image/svg+xml": [
-       "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n",
-       "<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\n",
-       "     width=\"410.0\" height=\"55.0\" viewBox=\"0 -55.0 410.0 55.0\">\n",
-       "<defs>\n",
-       "</defs>\n",
-       "<g transform=\"translate(0.0 -45.0)\">\n",
-       "<rect x=\"50.0\" y=\"-10\" width=\"250.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<path d=\"M300.0,0 L305.0,-5.0 L300.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<rect x=\"50.0\" y=\"-10\" width=\"50.0\" height=\"10\" fill=\"lightblue\" stroke=\"lightblue\" />\n",
-       "<g transform=\"translate(175.0 0)\">\n",
-       "<text x=\"0\" y=\"-5.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">Another sequence</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0.0 -20.0)\">\n",
-       "<rect x=\"110.0\" y=\"-10\" width=\"300.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<path d=\"M110.0,0 L105.0,-5.0 L110.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<rect x=\"150.0\" y=\"-10\" width=\"50.0\" height=\"10\" fill=\"salmon\" stroke=\"salmon\" />\n",
-       "<g transform=\"translate(260.0 0)\">\n",
-       "<text x=\"0\" y=\"-5.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">Sequence 1</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "</svg>"
-      ],
-      "text/plain": [
-       "<drawSvg.drawing.Drawing at 0x7fa7d1585e80>"
-      ]
+      "text/plain": "<drawsvg.drawing.Drawing at 0x7fdc8c683160>",
+      "image/svg+xml": "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\n     width=\"410.0\" height=\"45.0\" viewBox=\"0.0 -45.0 410.0 45.0\">\n<defs>\n</defs>\n<g transform=\"translate(0.0 -30.0)\">\n<rect x=\"50.0\" y=\"-10\" width=\"250.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<path d=\"M300.0,0 L305.0,-5.0 L300.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<rect x=\"50.0\" y=\"-10\" width=\"50.0\" height=\"10\" fill=\"lightblue\" stroke=\"lightblue\" />\n<g transform=\"translate(175.0 0)\">\n<text x=\"0\" y=\"0\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">Another sequence</text>\n</g>\n</g>\n<g transform=\"translate(0.0 -10.0)\">\n<rect x=\"110.0\" y=\"-10\" width=\"300.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<path d=\"M110.0,0 L105.0,-5.0 L110.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<rect x=\"150.0\" y=\"-10\" width=\"50.0\" height=\"10\" fill=\"salmon\" stroke=\"salmon\" />\n<g transform=\"translate(260.0 0)\">\n<text x=\"0\" y=\"0\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">Sequence 1</text>\n</g>\n</g>\n</svg>"
      },
-     "execution_count": 4,
+     "execution_count": 23,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -79,75 +63,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
-   "metadata": {},
+   "execution_count": 24,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-07-18T23:42:53.918296167Z",
+     "start_time": "2023-07-18T23:42:53.879691288Z"
+    }
+   },
    "outputs": [
     {
      "data": {
-      "image/svg+xml": [
-       "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n",
-       "<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\n",
-       "     width=\"500.0\" height=\"80.0\" viewBox=\"0 -80.0 500.0 80.0\">\n",
-       "<defs>\n",
-       "</defs>\n",
-       "<g transform=\"translate(0 -70.0)\">\n",
-       "<path d=\"M0.0,-5.0 L450.0,-5.0\" stroke=\"lightgrey\" />\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"0.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<path d=\"M150.0,0 L155.0,-5.0 L150.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<g transform=\"translate(75.0 0)\">\n",
-       "<text x=\"0\" y=\"-5.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">Read 1, forward</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"300.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<path d=\"M300.0,0 L295.0,-5.0 L300.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<g transform=\"translate(375.0 0)\">\n",
-       "<text x=\"0\" y=\"-5.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">Read 1, reverse</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0 -45.0)\">\n",
-       "<path d=\"M30.0,-5.0 L475.0,-5.0\" stroke=\"lightgrey\" />\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"30.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<path d=\"M180.0,0 L185.0,-5.0 L180.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<g transform=\"translate(105.0 0)\">\n",
-       "<text x=\"0\" y=\"-5.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">Read 2, forward</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"325.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<path d=\"M325.0,0 L320.0,-5.0 L325.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<g transform=\"translate(400.0 0)\">\n",
-       "<text x=\"0\" y=\"-5.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">Read 2, reverse</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0 -20.0)\">\n",
-       "<path d=\"M60.0,-5.0 L500.0,-5.0\" stroke=\"lightgrey\" />\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"60.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<path d=\"M210.0,0 L215.0,-5.0 L210.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<g transform=\"translate(135.0 0)\">\n",
-       "<text x=\"0\" y=\"-5.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">Read 3, forward</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"350.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<path d=\"M350.0,0 L345.0,-5.0 L350.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<g transform=\"translate(425.0 0)\">\n",
-       "<text x=\"0\" y=\"-5.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">Read 3, reverse</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "</g>\n",
-       "</svg>"
-      ],
-      "text/plain": [
-       "<drawSvg.drawing.Drawing at 0x7fa7d1585e10>"
-      ]
+      "text/plain": "<drawsvg.drawing.Drawing at 0x7fdc8c683490>",
+      "image/svg+xml": "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\n     width=\"500.0\" height=\"65.0\" viewBox=\"0.0 -65.0 500.0 65.0\">\n<defs>\n</defs>\n<g transform=\"translate(0 -50.0)\">\n<path d=\"M0.0,-5.0 L450.0,-5.0\" stroke=\"lightgrey\" />\n<g transform=\"translate(0.0 0)\">\n<rect x=\"0.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<path d=\"M150.0,0 L155.0,-5.0 L150.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<g transform=\"translate(75.0 0)\">\n<text x=\"0\" y=\"0\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">Read 1, forward</text>\n</g>\n</g>\n<g transform=\"translate(0.0 0)\">\n<rect x=\"300.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<path d=\"M300.0,0 L295.0,-5.0 L300.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<g transform=\"translate(375.0 0)\">\n<text x=\"0\" y=\"0\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">Read 1, reverse</text>\n</g>\n</g>\n</g>\n<g transform=\"translate(0 -30.0)\">\n<path d=\"M30.0,-5.0 L475.0,-5.0\" stroke=\"lightgrey\" />\n<g transform=\"translate(0.0 0)\">\n<rect x=\"30.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<path d=\"M180.0,0 L185.0,-5.0 L180.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<g transform=\"translate(105.0 0)\">\n<text x=\"0\" y=\"0\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">Read 2, forward</text>\n</g>\n</g>\n<g transform=\"translate(0.0 0)\">\n<rect x=\"325.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<path d=\"M325.0,0 L320.0,-5.0 L325.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<g transform=\"translate(400.0 0)\">\n<text x=\"0\" y=\"0\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">Read 2, reverse</text>\n</g>\n</g>\n</g>\n<g transform=\"translate(0 -10.0)\">\n<path d=\"M60.0,-5.0 L500.0,-5.0\" stroke=\"lightgrey\" />\n<g transform=\"translate(0.0 0)\">\n<rect x=\"60.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<path d=\"M210.0,0 L215.0,-5.0 L210.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<g transform=\"translate(135.0 0)\">\n<text x=\"0\" y=\"0\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">Read 3, forward</text>\n</g>\n</g>\n<g transform=\"translate(0.0 0)\">\n<rect x=\"350.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<path d=\"M350.0,0 L345.0,-5.0 L350.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<g transform=\"translate(425.0 0)\">\n<text x=\"0\" y=\"0\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">Read 3, reverse</text>\n</g>\n</g>\n</g>\n</svg>"
      },
-     "execution_count": 5,
+     "execution_count": 24,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -173,56 +102,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
-   "metadata": {},
+   "execution_count": 25,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-07-18T23:42:53.918891057Z",
+     "start_time": "2023-07-18T23:42:53.911621618Z"
+    }
+   },
    "outputs": [
     {
      "data": {
-      "image/svg+xml": [
-       "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n",
-       "<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\n",
-       "     width=\"350.0\" height=\"80.0\" viewBox=\"0 -80.0 350.0 80.0\">\n",
-       "<defs>\n",
-       "</defs>\n",
-       "<g transform=\"translate(0 -70.0)\">\n",
-       "<path d=\"M0.0,-5.0 L350.0,-5.0\" stroke=\"lightgrey\" />\n",
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-       "<g transform=\"translate(75.0 0)\">\n",
-       "<text x=\"0\" y=\"-5.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">Forward read</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"200.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<path d=\"M200.0,0 L195.0,-5.0 L200.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<g transform=\"translate(275.0 0)\">\n",
-       "<text x=\"0\" y=\"-5.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">Reverse read</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0.0 -45.0)\">\n",
-       "<rect x=\"50.0\" y=\"-10\" width=\"200.0\" height=\"10\" fill=\"salmon\" stroke=\"salmon\" />\n",
-       "<path d=\"M250.0,0 L255.0,-5.0 L250.0,-10\" fill=\"salmon\" stroke=\"salmon\" />\n",
-       "<path d=\"M50.0,0 L45.0,-5.0 L50.0,-10\" fill=\"salmon\" stroke=\"salmon\" />\n",
-       "<rect x=\"75.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
-       "<g transform=\"translate(150.0 0)\">\n",
-       "<text x=\"0\" y=\"-5.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">Read-through</text>\n",
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-       "</g>\n",
-       "<g transform=\"translate(0.0 -20.0)\">\n",
-       "<rect x=\"50.0\" y=\"-10\" width=\"250.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n",
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-       "<text x=\"0\" y=\"-5.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">Reads overlap</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "</svg>"
-      ],
-      "text/plain": [
-       "<drawSvg.drawing.Drawing at 0x7fa7d15a2588>"
-      ]
+      "text/plain": "<drawsvg.drawing.Drawing at 0x7fdc8c6a7490>",
+      "image/svg+xml": "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\n     width=\"350.0\" height=\"65.0\" viewBox=\"0.0 -65.0 350.0 65.0\">\n<defs>\n</defs>\n<g transform=\"translate(0 -50.0)\">\n<path d=\"M0.0,-5.0 L350.0,-5.0\" stroke=\"lightgrey\" />\n<g transform=\"translate(0.0 0)\">\n<rect x=\"0.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<path d=\"M150.0,0 L155.0,-5.0 L150.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<g transform=\"translate(75.0 0)\">\n<text x=\"0\" y=\"0\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">Forward read</text>\n</g>\n</g>\n<g transform=\"translate(0.0 0)\">\n<rect x=\"200.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<path d=\"M200.0,0 L195.0,-5.0 L200.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<g transform=\"translate(275.0 0)\">\n<text x=\"0\" y=\"0\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">Reverse read</text>\n</g>\n</g>\n</g>\n<g transform=\"translate(0.0 -30.0)\">\n<rect x=\"50.0\" y=\"-10\" width=\"200.0\" height=\"10\" fill=\"salmon\" stroke=\"salmon\" />\n<path d=\"M250.0,0 L255.0,-5.0 L250.0,-10\" fill=\"salmon\" stroke=\"salmon\" />\n<path d=\"M50.0,0 L45.0,-5.0 L50.0,-10\" fill=\"salmon\" stroke=\"salmon\" />\n<rect x=\"75.0\" y=\"-10\" width=\"150.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<g transform=\"translate(150.0 0)\">\n<text x=\"0\" y=\"0\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">Read-through</text>\n</g>\n</g>\n<g transform=\"translate(0.0 -10.0)\">\n<rect x=\"50.0\" y=\"-10\" width=\"250.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<g transform=\"translate(175.0 0)\">\n<text x=\"0\" y=\"0\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">Reads overlap</text>\n</g>\n</g>\n</svg>"
      },
-     "execution_count": 8,
+     "execution_count": 25,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -249,47 +142,25 @@
    "metadata": {},
    "source": [
     "### Alignment\n",
-    "Regions beetween two tracts can be illustrated with an `Alignment`."
+    "Regions between two tracts can be illustrated with an `Alignment`."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
-   "metadata": {},
+   "execution_count": 26,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-07-18T23:42:53.919044924Z",
+     "start_time": "2023-07-18T23:42:53.911750803Z"
+    }
+   },
    "outputs": [
     {
      "data": {
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-       "<path d=\"M110.0,0 L300.0,30\" stroke=\"black\" />\n",
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-       "<path d=\"M300.0,0 L110.0,30\" stroke=\"black\" />\n",
-       "<path d=\"M300.0,-10 L300.0,0\" stroke=\"black\" />\n",
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-       "</g>\n",
-       "</svg>"
-      ],
-      "text/plain": [
-       "<drawSvg.drawing.Drawing at 0x7fa7d158f828>"
-      ]
+      "text/plain": "<drawsvg.drawing.Drawing at 0x7fdc8c6a73d0>",
+      "image/svg+xml": "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\n     width=\"365.0\" height=\"65.0\" viewBox=\"0.0 -65.0 365.0 65.0\">\n<defs>\n</defs>\n<g transform=\"translate(0 -40.0)\">\n<g transform=\"translate(0.0 0)\">\n<rect x=\"50.0\" y=\"-10\" width=\"260.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<path d=\"M50.0,0 L45.0,-5.0 L50.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<rect x=\"110.0\" y=\"-10\" width=\"190.0\" height=\"10\" fill=\"lightblue\" stroke=\"lightblue\" />\n</g>\n<g transform=\"translate(0.0 40)\">\n<rect x=\"100.0\" y=\"-10\" width=\"260.0\" height=\"10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<path d=\"M360.0,0 L365.0,-5.0 L360.0,-10\" fill=\"lightgrey\" stroke=\"lightgrey\" />\n<rect x=\"110.0\" y=\"-10\" width=\"190.0\" height=\"10\" fill=\"salmon\" stroke=\"salmon\" />\n</g>\n<path d=\"M110.0,0 L300.0,30\" stroke=\"black\" />\n<path d=\"M110.0,-10 L110.0,0\" stroke=\"black\" />\n<path d=\"M300.0,30 L300.0,40\" stroke=\"black\" />\n<path d=\"M300.0,0 L110.0,30\" stroke=\"black\" />\n<path d=\"M300.0,-10 L300.0,0\" stroke=\"black\" />\n<path d=\"M110.0,30 L110.0,40\" stroke=\"black\" />\n</g>\n</svg>"
      },
-     "execution_count": 9,
+     "execution_count": 26,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -312,108 +183,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
-   "metadata": {},
+   "execution_count": 27,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-07-18T23:42:53.919182746Z",
+     "start_time": "2023-07-18T23:42:53.911809826Z"
+    }
+   },
    "outputs": [
     {
      "data": {
-      "image/svg+xml": [
-       "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n",
-       "<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\n",
-       "     width=\"900.0\" height=\"50.0\" viewBox=\"0 -50.0 900.0 50.0\">\n",
-       "<defs>\n",
-       "</defs>\n",
-       "<g transform=\"translate(0 -40.0)\">\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"0.0\" y=\"-10\" width=\"58.709743800802556\" height=\"10\" fill=\"darkgrey\" stroke=\"darkgrey\" />\n",
-       "<g transform=\"translate(29.354871900401278 0)\">\n",
-       "<text x=\"0\" y=\"-6.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">5' LTR</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"73.15567445210414\" y=\"-10\" width=\"139.08838357855745\" height=\"10\" fill=\"lightblue\" stroke=\"lightblue\" />\n",
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-       "<text x=\"0\" y=\"-6.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">gag</text>\n",
-       "</g>\n",
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-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"466.80728470007205\" y=\"-10\" width=\"53.52402510546358\" height=\"10\" fill=\"steelblue\" stroke=\"steelblue\" />\n",
-       "<g transform=\"translate(493.56929725280384 0)\">\n",
-       "<text x=\"0\" y=\"-6.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">vif</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"775.9131597901019\" y=\"-10\" width=\"8.334190760366369\" height=\"10\" fill=\"plum\" stroke=\"plum\" />\n",
-       "<g transform=\"translate(780.080255170285 0)\">\n",
-       "<text x=\"0\" y=\"-6.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">tat</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"814.6208457660254\" y=\"-10\" width=\"57.41331412696775\" height=\"10\" fill=\"mediumaquamarine\" stroke=\"mediumaquamarine\" />\n",
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-       "<text x=\"0\" y=\"-6.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">nef</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0 -25.0)\">\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"539.9629591521762\" y=\"-10\" width=\"19.816853585759873\" height=\"10\" fill=\"plum\" stroke=\"plum\" />\n",
-       "<g transform=\"translate(549.8713859450561 0)\">\n",
-       "<text x=\"0\" y=\"-6.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">tat</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"561.3540487704497\" y=\"-10\" width=\"22.965325650787122\" height=\"10\" fill=\"red\" stroke=\"red\" />\n",
-       "<g transform=\"translate(572.8367115958433 0)\">\n",
-       "<text x=\"0\" y=\"-6.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">vpu</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"775.9131597901019\" y=\"-10\" width=\"25.37298075933745\" height=\"10\" fill=\"yellowgreen\" stroke=\"yellowgreen\" />\n",
-       "<g transform=\"translate(788.5996501697706 0)\">\n",
-       "<text x=\"0\" y=\"-6.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">rev</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"841.3828583187571\" y=\"-10\" width=\"58.617141681242856\" height=\"10\" fill=\"darkgrey\" stroke=\"darkgrey\" />\n",
-       "<g transform=\"translate(870.6914291593786 0)\">\n",
-       "<text x=\"0\" y=\"-6.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">3' LTR</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0 -10.0)\">\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"193.07541928181914\" y=\"-10\" width=\"278.8249819940323\" height=\"10\" fill=\"orange\" stroke=\"orange\" />\n",
-       "<g transform=\"translate(332.4879102788353 0)\">\n",
-       "<text x=\"0\" y=\"-6.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">pol</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"514.775182631958\" y=\"-10\" width=\"26.94721679185102\" height=\"10\" fill=\"turquoise\" stroke=\"turquoise\" />\n",
-       "<g transform=\"translate(528.2487910278835 0)\">\n",
-       "<text x=\"0\" y=\"-6.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">vpr</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"552.8346537709641\" y=\"-10\" width=\"6.945158966971917\" height=\"10\" fill=\"yellowgreen\" stroke=\"yellowgreen\" />\n",
-       "<g transform=\"translate(556.30723325445 0)\">\n",
-       "<text x=\"0\" y=\"-6.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">rev</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "<g transform=\"translate(0.0 0)\">\n",
-       "<rect x=\"576.4481942586687\" y=\"-10\" width=\"237.98744726823747\" height=\"10\" fill=\"salmon\" stroke=\"salmon\" />\n",
-       "<g transform=\"translate(695.4419178927874 0)\">\n",
-       "<text x=\"0\" y=\"-6.0\" font-size=\"10.0\" font-family=\"monospace\" text-anchor=\"middle\" transform=\"translate(0,5.0)\">env</text>\n",
-       "</g>\n",
-       "</g>\n",
-       "</g>\n",
-       "</svg>"
-      ],
-      "text/plain": [
-       "<drawSvg.drawing.Drawing at 0x7fa7d158f898>"
-      ]
+      "text/plain": "<drawsvg.drawing.Drawing at 0x7fdc8ef5e950>",
+      "image/svg+xml": "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\n     width=\"900.0\" height=\"35.0\" viewBox=\"0.0 -35.0 900.0 35.0\">\n<defs>\n</defs>\n<g transform=\"translate(0 -20.0)\">\n<g transform=\"translate(0.0 0)\">\n<rect x=\"0.0\" y=\"-10\" width=\"58.709743800802556\" height=\"10\" fill=\"darkgrey\" stroke=\"darkgrey\" />\n<g transform=\"translate(29.354871900401278 0)\">\n<text x=\"0\" y=\"-1\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">5' LTR</text>\n</g>\n</g>\n<g transform=\"translate(0.0 0)\">\n<rect x=\"73.15567445210414\" y=\"-10\" width=\"139.08838357855745\" height=\"10\" fill=\"lightblue\" stroke=\"lightblue\" />\n<g transform=\"translate(142.69986624138286 0)\">\n<text x=\"0\" y=\"-1\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">gag</text>\n</g>\n</g>\n<g transform=\"translate(0.0 0)\">\n<rect x=\"466.80728470007205\" y=\"-10\" width=\"53.52402510546358\" height=\"10\" fill=\"steelblue\" stroke=\"steelblue\" />\n<g transform=\"translate(493.56929725280384 0)\">\n<text x=\"0\" y=\"-1\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">vif</text>\n</g>\n</g>\n<g transform=\"translate(0.0 0)\">\n<rect x=\"775.9131597901019\" y=\"-10\" width=\"8.334190760366369\" height=\"10\" fill=\"plum\" stroke=\"plum\" />\n<g transform=\"translate(780.080255170285 0)\">\n<text x=\"0\" y=\"-1\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">tat</text>\n</g>\n</g>\n<g transform=\"translate(0.0 0)\">\n<rect x=\"814.6208457660254\" y=\"-10\" width=\"57.41331412696775\" height=\"10\" fill=\"mediumaquamarine\" stroke=\"mediumaquamarine\" />\n<g transform=\"translate(843.3275028295093 0)\">\n<text x=\"0\" y=\"-1\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">nef</text>\n</g>\n</g>\n</g>\n<g transform=\"translate(0 -10.0)\">\n<g transform=\"translate(0.0 0)\">\n<rect x=\"539.9629591521762\" y=\"-10\" width=\"19.816853585759873\" height=\"10\" fill=\"plum\" stroke=\"plum\" />\n<g transform=\"translate(549.8713859450561 0)\">\n<text x=\"0\" y=\"-1\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">tat</text>\n</g>\n</g>\n<g transform=\"translate(0.0 0)\">\n<rect x=\"561.3540487704497\" y=\"-10\" width=\"22.965325650787122\" height=\"10\" fill=\"red\" stroke=\"red\" />\n<g transform=\"translate(572.8367115958433 0)\">\n<text x=\"0\" y=\"-1\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">vpu</text>\n</g>\n</g>\n<g transform=\"translate(0.0 0)\">\n<rect x=\"775.9131597901019\" y=\"-10\" width=\"25.37298075933745\" height=\"10\" fill=\"yellowgreen\" stroke=\"yellowgreen\" />\n<g transform=\"translate(788.5996501697706 0)\">\n<text x=\"0\" y=\"-1\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">rev</text>\n</g>\n</g>\n<g transform=\"translate(0.0 0)\">\n<rect x=\"841.3828583187571\" y=\"-10\" width=\"58.617141681242856\" height=\"10\" fill=\"darkgrey\" stroke=\"darkgrey\" />\n<g transform=\"translate(870.6914291593786 0)\">\n<text x=\"0\" y=\"-1\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">3' LTR</text>\n</g>\n</g>\n</g>\n<g transform=\"translate(0 0.0)\">\n<g transform=\"translate(0.0 0)\">\n<rect x=\"193.07541928181914\" y=\"-10\" width=\"278.8249819940323\" height=\"10\" fill=\"orange\" stroke=\"orange\" />\n<g transform=\"translate(332.4879102788353 0)\">\n<text x=\"0\" y=\"-1\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">pol</text>\n</g>\n</g>\n<g transform=\"translate(0.0 0)\">\n<rect x=\"514.775182631958\" y=\"-10\" width=\"26.94721679185102\" height=\"10\" fill=\"turquoise\" stroke=\"turquoise\" />\n<g transform=\"translate(528.2487910278835 0)\">\n<text x=\"0\" y=\"-1\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">vpr</text>\n</g>\n</g>\n<g transform=\"translate(0.0 0)\">\n<rect x=\"552.8346537709641\" y=\"-10\" width=\"6.945158966971917\" height=\"10\" fill=\"yellowgreen\" stroke=\"yellowgreen\" />\n<g transform=\"translate(556.30723325445 0)\">\n<text x=\"0\" y=\"-1\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">rev</text>\n</g>\n</g>\n<g transform=\"translate(0.0 0)\">\n<rect x=\"576.4481942586687\" y=\"-10\" width=\"237.98744726823747\" height=\"10\" fill=\"salmon\" stroke=\"salmon\" />\n<g transform=\"translate(695.4419178927874 0)\">\n<text x=\"0\" y=\"-1\" font-size=\"10\" font-family=\"monospace\" text-anchor=\"middle\">env</text>\n</g>\n</g>\n</g>\n</svg>"
      },
-     "execution_count": 10,
+     "execution_count": 27,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -461,32 +244,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 28,
    "metadata": {
-    "scrolled": false
+    "scrolled": false,
+    "ExecuteTime": {
+     "end_time": "2023-07-18T23:42:53.919313137Z",
+     "start_time": "2023-07-18T23:42:53.911926703Z"
+    }
    },
    "outputs": [
     {
      "data": {
-      "image/svg+xml": [
-       "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n",
-       "<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\n",
-       "     width=\"400\" height=\"400.0\" viewBox=\"-0.7 -0.7 1.4 1.4\">\n",
-       "<defs>\n",
-       "</defs>\n",
-       "<circle cx=\"0\" cy=\"0\" r=\"0.5\" stroke-width=\"0.005\" stroke=\"lightgrey\" fill-opacity=\"0.0\" />\n",
-       "<path d=\"M-0.08682408883346515,-0.492403876506104 A0.5,0.5,0,0,0,-0.0954044976882724,-0.490813591723832\" stroke-width=\"0.04\" stroke=\"orange\" fill-opacity=\"0.0\" />\n",
-       "<path d=\"M-0.17101007166283436,-0.4698463103929542 A0.5,0.5,0,0,0,0.08682408883346499,0.49240387650610407\" stroke-width=\"0.04\" stroke=\"salmon\" fill-opacity=\"0.0\" />\n",
-       "<path d=\"M-0.32139380484326974,0.38302222155948895 A0.5,0.5,0,0,0,0.043577871373828944,0.4980973490458728\" stroke-width=\"0.04\" stroke=\"firebrick\" fill-opacity=\"0.0\" />\n",
-       "<path d=\"M0.3830222215594889,0.3213938048432698 A0.5,0.5,0,0,0,0.4698463103929542,-0.17101007166283436\" stroke-width=\"0.04\" stroke=\"lightblue\" fill-opacity=\"0.0\" />\n",
-       "<path d=\"M0.4698463103929542,-0.17101007166283436 A0.5,0.5,0,0,0,0.3213938048432697,-0.383022221559489\" stroke-width=\"0.04\" stroke=\"slateblue\" fill-opacity=\"0.0\" />\n",
-       "</svg>"
-      ],
-      "text/plain": [
-       "<drawSvg.drawing.Drawing at 0x7fa7d1558240>"
-      ]
+      "text/plain": "<drawsvg.drawing.Drawing at 0x7fdc8c66b6d0>",
+      "image/svg+xml": "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<svg xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\n     width=\"400\" height=\"400.0\" viewBox=\"-0.7 -0.7 1.4 1.4\">\n<defs>\n</defs>\n<circle cx=\"0\" cy=\"0\" r=\"0.5\" stroke-width=\"0.005\" stroke=\"lightgrey\" fill-opacity=\"0.0\" />\n<path d=\"M-0.0954044976882724,-0.490813591723832 A0.5,0.5,0,0,1,-0.08682408883346515,-0.492403876506104\" stroke-width=\"0.04\" stroke=\"orange\" fill-opacity=\"0.0\" />\n<path d=\"M0.08682408883346499,0.49240387650610407 A0.5,0.5,0,0,1,-0.17101007166283436,-0.4698463103929542\" stroke-width=\"0.04\" stroke=\"salmon\" fill-opacity=\"0.0\" />\n<path d=\"M0.043577871373828944,0.4980973490458728 A0.5,0.5,0,0,1,-0.32139380484326974,0.38302222155948895\" stroke-width=\"0.04\" stroke=\"firebrick\" fill-opacity=\"0.0\" />\n<path d=\"M0.4698463103929542,-0.17101007166283436 A0.5,0.5,0,0,1,0.3830222215594889,0.3213938048432698\" stroke-width=\"0.04\" stroke=\"lightblue\" fill-opacity=\"0.0\" />\n<path d=\"M0.3213938048432697,-0.383022221559489 A0.5,0.5,0,0,1,0.4698463103929542,-0.17101007166283436\" stroke-width=\"0.04\" stroke=\"slateblue\" fill-opacity=\"0.0\" />\n</svg>"
      },
-     "execution_count": 11,
+     "execution_count": 28,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -504,15 +276,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
+   "execution_count": 28,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-07-18T23:42:53.975218686Z",
+     "start_time": "2023-07-18T23:42:53.911985311Z"
+    }
+   },
    "outputs": [],
    "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -526,7 +303,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.6"
+   "version": "3.10.6"
   }
  },
  "nbformat": 4,
diff --git a/genetracks/elements.py b/genetracks/elements.py
index c6d1c0b..83680fe 100644
--- a/genetracks/elements.py
+++ b/genetracks/elements.py
@@ -195,7 +195,7 @@ def __init__(self, track1, track2, connections, text=None, style=None,
         self.w = max(track1.w, track2.w)
 
     def draw(self, x=0, y=0, xscale=1.0):
-        d = draw.Group(transform="translate({} {})".format(x, y))
+        d = draw.Group(transform="translate({} {})".format(x, y-self.gap))
         d.append(self.t1.draw(xscale=xscale))
         d.append(self.t2.draw(y=self.t1.h+self.gap, xscale=xscale))
 
diff --git a/genetracks/plasmid.py b/genetracks/plasmid.py
index 8257b38..1fbe4d7 100644
--- a/genetracks/plasmid.py
+++ b/genetracks/plasmid.py
@@ -30,5 +30,5 @@ def __init__(self, a, b, color='lightgrey'):
         self.b = b
 
     def draw(self, circ):
-        return draw.Arc(0, 0, 0.5, self.a, self.b, stroke_width='0.04',
+        return draw.Arc(0, 0, 0.5, self.b/circ*360, self.a/circ*360, stroke_width='0.04',
                         stroke=self.color, fill_opacity='0.0')
diff --git a/setup.py b/setup.py
index 27295cb..0498372 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="genetracks",
-    version="0.2.dev0",
+    version="0.2.dev1",
     author="jeff-k",
     author_email="jeff_k@fastmail.com",
     description="Generate track diagrams for genomic alignments",