Embeding JBrowse directly didn't work. Instead we are using an iFrame.

theme/css/combination_tracks.css

@@ -1,38 +0,0 @@
-
-.combination_track.empty, .combination_track.empty.pinned {
-    background: #aaa;
-    background: rgba(0,0,0,0.1);
-}
-
-.combinationDialog .formulaPreview {
-    text-align: center;
-    background-color: white;
-    border: 1px solid black;
-    padding: 20px 0;
-    line-height: 25px;
-}
-
-.formulaPreview .tree {
-}
-
-.formulaPreview .leaf {
-    /* background: #A1F0A1; */
-    /* /\* margin: 0 1px; *\/ */
-    padding: 0 4px;
-    text-decoration: underline;
-    /* border: 1px solid #0DCA0D; */
-    /* white-space: nowrap; */
-}
-
-.formulaPreview .leaf.highlighted {
-    background-color: #BBB;
-}
-
-.formulaPreview .op {
-    /* font-weight: bold; */
-    /* color: #FFF; */
-    /* background: #000; */
-    /* /\* padding: 0 7px; *\/ */
-    /* z-index: 10; */
-    /* font-size: 120%; */
-}

theme/css/export_dialog.css

@@ -1,10 +0,0 @@
-.export-view-dialog .dijitDialogPaneContent {
-    background: #fafafa;
-}
-
-.export-view-dialog .save {
-    display: inline-block;
-    border: 1px solid #AFAFAF;
-    padding: 2px 5px 2px 0px;
-}
-

theme/css/faceted_track_selector.css

@@ -1,271 +0,0 @@
-/* Dojo and Dijit stuff */
-
-@import url("src/dojox/grid/resources/tundraGrid.css");
-
-.dojoxGrid table {
-  margin: 0;
-}
-.dojoxGridRowSelectorStatusText {
-    display: none;
-}
-
-/* JBrowse stuff */
-
-#faceted_tracksel {
-    position: fixed;
-    top: 0;
-    left: 0;
-    height: 100%;
-}
-
-#faceted_tracksel.active {
-    -moz-box-shadow: 4px 4px 10px 3px rgba( 30, 30, 50, 0.3 );
-    -webkit-box-shadow: 4px 4px 10px 3px rgba( 30, 30, 50, 0.3 );
-    box-shadow: 4px 4px 10px 3px rgba( 30, 30, 50, 0.3 );
-}
-
-#faceted_tracksel button, #faceted_tracksel input {
-    font-size: 12px;
-}
-
-#faceted_tracksel div.mainContainer {
-    height: 100%;
-    width: 100%;
-}
-.tundra #faceted_tracksel div.mainContainer {
-    border-right: 2px solid #555;
-    background: #e9e9e9;
-}
-
-/* Track grid */
-
-#faceted_tracksel .dojoxGridCellFocus {
-    border-color: transparent;
-    border-color: transparent !important;
-}
-#faceted_tracksel .gridPane .gridControls {
-    padding: 2px 3px;
-    font-size: 110%;
-}
-.tundra #faceted_tracksel .gridPane .gridControls {
-    background: #e9e9e9;
-    border: 1px solid #aaa;
-    border-right: none;
-}
-
-#faceted_tracksel .gridPane .gridControls > * {
-    margin: 2px 3px;
-    display: inline-block;
-    vertical-align: middle;
-}
-#faceted_tracksel .gridPane .gridControls button {
-    height: 2.2em;
-    margin: 4px;
-    white-space: nowrap;
-}
-#faceted_tracksel .gridPane .gridControls button > * {
-    display: inline-block;
-    vertical-align: middle;
-}
-#faceted_tracksel .gridPane .gridControls button img {
-    padding: 0 0.4em 0 0;
-}
-#faceted_tracksel.busy .gridControls .busy_indicator {
-    visibility: visible;
-}
-#faceted_tracksel .gridControls .busy_indicator {
-    z-index: 20;
-    visibility: hidden;
-}
-
-
-#faceted_tracksel label.textFilterControl img.text_filter_clear {
-    display: none;
-}
-#faceted_tracksel label.textFilterControl.selected img.text_filter_clear {
-    display: block;
-}
-#faceted_tracksel label.textFilterControl input {
-    border-top: 3px solid transparent;
-    font-weight: bold;
-    padding: 0.2em;
-}
-#faceted_tracksel label.textFilterControl.selected input {
-    border-top: 3px solid #396494;
-    background: #D2E1F1;
-}
-
-/* Track selector title bar */
-#faceted_tracksel_top {
-    border-bottom: 1px solid #ccc;
-    padding: 5px;
-}
-.tundra #faceted_tracksel_top {
-    background: #396494;
-}
-.tundra #faceted_tracksel_top .topLink {
-    color: white;
-}
-
-#faceted_tracksel_top > * {
-    display: inline-block;
-    vertical-align: middle;
-    margin-left: 5px;
-}
-#faceted_tracksel_top .title {
-    padding: 0;
-    width: 185px;
-
-    font-weight: bold;
-    color: white;
-    font-size: 180%;
-}
-
-#faceted_tracksel .faceted_tracksel_on_off.tab {
-    position: absolute;
-    top: 5em;
-    left: 100%;
-    z-index: 5;
-
-    padding: 5px 0px;
-    white-space: nowrap;
-
-    cursor: pointer;
-
-    -moz-box-shadow: 4px 4px 10px 2px rgba( 80, 80, 80, 0.3 );
-    -webkit-box-shadow: 4px 4px 10px 2px rgba( 80, 80, 80, 0.3 );
-    box-shadow: 4px 4px 10px 2px rgba( 80, 80, 80, 0.3 );
-}
-#faceted_tracksel div.faceted_tracksel_on_off.tab > * {
-    display: inline-block;
-    vertical-align: middle;
-    padding: 0 6px;
-}
-.tundra #faceted_tracksel .faceted_tracksel_on_off.tab {
-    background: #e9e9e9 url("src/dijit/themes/tundra/images/titleBar.png") top repeat-x;
-    border: 2px solid #666;
-
-    border-top-right-radius: 5px;
-    border-bottom-right-radius: 5px;
-}
-
-
-#faceted_tracksel_top div.topLink {
-    position: absolute;
-    top: 0;
-    right: 0;
-
-    background: none;
-    border: none;
-    color: white;
-    padding: 3px 0.6em;
-
-    font-weight: bold;
-}
-
-
-/* Facet selection controls */
-
-#faceted_tracksel .facetSelect {
-    width: 100%;
-    border-spacing: 0;
-}
-#faceted_tracksel .facetSelect .facetValue {
-    padding: 0.1em 0.4em;
-    cursor: pointer;
-}
-#faceted_tracksel .facetSelect .facetValue > * {
-    vertical-align: top;
-}
-#faceted_tracksel .facetSelect .disabled {
-    color: gray;
-}
-
-#faceted_tracksel .facetSelect .facetValue.disabled {
-    display: none;
-}
-#faceted_tracksel .facetSelect .facetValue.disabled.selected {
-    display: table-row;
-}
-
-.tundra #faceted_tracksel .facetSelect .facetValue:hover {
-    background: #D2E1F1;
-}
-
-#faceted_tracksel .facetSelect .facetValue .count {
-    padding: 0 0.7em 0 0.4em;
-    color: #333;
-    text-align: right;
-}
-#faceted_tracksel .facetSelect .facetValue .value {
-    width: 80%;
-}
-
-#faceted_tracksel .facetSelect .selected {
-    background: #b1d3f6;
-}
-.tundra #faceted_tracksel .facetSelect .facetValue.selected,
-.tundra #faceted_tracksel .facetSelect .facetValue.selected:hover {
-    background: #AEC7E3;
-}
-
-
-#faceted_tracksel .dijitContentPane{
-    padding: 0;
-}
-#faceted_tracksel .dijitTitlePane .dijitTitlePaneTitle {
-    padding: 0;
-}
-#faceted_tracksel .dijitTitlePaneTitleFocus {
-    position: relative;
-}
-.tundra #faceted_tracksel .dijitTitlePaneTitleFocus {
-    border-top: 3px solid transparent;
-    padding: 2px 2px 2px 0.6em;
-    color: #1B3047
-}
-#faceted_tracksel .dijitOpen .facetTitle {
-    font-weight: bold;
-    color: black;
-}
-
-#faceted_tracksel .activeFacet .facetTitle {
-    font-weight: bold;
-    color: black;
-}
-.tundra #faceted_tracksel .activeFacet {
-    border-top: 3px solid #396494;
-    background-color: #AEC7E3;
-}
-
-#faceted_tracksel .facetTitle a {
-    position: absolute;
-    top: 2px;
-    right: -4px;
-    visibility: hidden;
-}
-#faceted_tracksel .activeFacet a.clearFacet {
-    visibility: visible;
-    padding: 1px 6px;
-}
-
-#faceted_tracksel .dijitTitlePaneContentInner {
-    padding: 0px;
-}
-
-
-/* styling specifically for the title of the first facet title, which is 'My Tracks' */
-.tundra #faceted_tracksel .myTracks .facetTitle:after {
-    content: url("src/dijit/themes/tundra/images/circleIcon.png");
-    margin-left: 7px;
-}
-#faceted_tracksel .myTracks .facetTitle {
-    color: black;
-    font-weight: bold;
-    padding-bottom: 6px;
-}
-
-/* style the 'empty' and similar messages that show up in the grid master pane */
-#faceted_tracksel .dojoxGridMasterMessages {
-    font-size: 16px;
-}

theme/css/file_dialog.css

@@ -1,141 +0,0 @@
-@import url("src/dojox/form/resources/UploaderFileList.css");
-.fileDialog {
-    color: #333;
-}
-
-.fileDialog label {
-    font-weight: bold;
-    padding: 0 0.5em;
-}
-.fileDialog th {
-    font-weight: bold;
-    border-bottom: 2px solid black;
-}
-.fileDialog .dijitDialogPaneContent > div.intro {
-    width: 27em;
-    text-align: justify;
-    position: relative;
-    left: 12%;
-    margin: 1.4em 0 2.4em 0;
-}
-
-.fileDialog .connector {
-    background: #333;
-    height: 6px;
-    width: 12px;
-    position: absolute;
-
-    bottom: -6px;
-    left: 50%;
-    margin-left: -6px;
-}
-
-.fileDialog h2, .fileDialog h3 {
-    margin: 0;
-    padding: 0;
-    font-size: 125%;
-}
-
-.fileDialog .dijitDialogPaneContent > div {
-    position: relative;
-
-    width: 40em;
-    padding: 0 0 0.75em 0;
-    margin: 6px 0;
-}
-.fileDialog div.aux {
-    text-align: center;
-    margin-bottom: 1em;
-}
-.fileDialog .resourceControls {
-    height: 10em;
-    position: relative;
-}
-.fileDialog .resourceControls > div {
-    width: 19.5em;
-    box-sizing: border-box;
-    height: 100%;
-}
-.fileDialog .resourceControls > div > h3 {
-    height: 19%;
-}
-
-.fileDialog .localFilesControl {
-    position: absolute;
-    top: 0;
-    left: 0;
-}
-
-.fileDialog .dijitUploader {
-    position: absolute;
-    margin: 0;
-}
-
-.fileDialog .remoteURLsControl textarea,
-.fileDialog .localFilesControl .dragArea {
-    height: 81%;
-    position: relative;
-    border: 1px solid #b3b3b3;
-    width: 100%;
-    box-sizing: border-box;
-}
-.fileDialog .localFilesControl .dragArea:hover {
-    border: 1px dashed green;
-}
-
-.fileDialog .localFilesControl .dragArea .dragMessage {
-    height: 2em;
-    position: absolute;
-    top: 60%;
-    font-weight: bold;
-    margin-top: -1em;
-    text-align: center;
-    width: 100%;
-}
-.fileDialog .remoteURLsControl textarea {
-    font-size: 10px;
-    background: #f2f2f2;
-}
-.fileDialog .remoteURLsControl textarea:hover {
-    background: white;
-    border-color: #333;
-}
-
-.fileDialog .remoteURLsControl {
-    position: absolute;
-    top: 0;
-    right: 0;
-}
-
-.fileDialog .resourceList {
-    background: #bcd3ef;
-}
-
-.fileDialog .dijitSelect td.dijitStretch {
-    width: 6em;
-}
-.fileDialog .resourceList > h3, .fileDialog .trackList > h3 {
-     padding: 0 0.6em;
-     line-height: 2.1;
-     margin-bottom: 0.5em;
-}
-
-.fileDialog .emptyMessage {
-    width: 100%;
-    font-size: 110%;
-    color: #686868;
-    font-weight: bold;
-    text-align: center;
-    line-height: 4;
-}
-
-.fileDialog .trackList {
-    background: #8cb1dd;
-}
-
-.fileDialog .resourceList > table, .fileDialog .trackList > table {
-    width: 95%;
-    padding: 0 0.75em 0.5em 0.75em;
-    margin: 0 auto;
-    border-collapse: collapse;
-}

theme/css/genome.css

@@ -1,21 +0,0 @@
-/* main application CSS styles */
-@import url("src/dijit/themes/tundra/tundra.css");
-@import url("src/dojo/resources/dojo.css");
-
-@import url("main.css");
-@import url("sequence.css");
-@import url("menubar.css");
-@import url("icons.css");
-@import url("tristate.css");
-@import url("file_dialog.css");
-@import url("combination_tracks.css");
-@import url("export_dialog.css");
-
-/* CSS styles for the various types of feature glyphs */
-@import url("track_styles.css");
-@import url("hierarchical_track_selector.css");
-@import url("faceted_track_selector.css");
-
-
-/* CSS styles specifically for MAKER output */
-@import url("maker.css");

theme/css/hierarchical_track_selector.css

@@ -1,57 +0,0 @@
-.jbrowseHierarchicalTrackSelector {
-    background: #fafafa;
-    overflow: auto;
-}
-.jbrowseHierarchicalTrackSelector > .header > h2.title {
-    padding: 7px 0 0.5em 6px;
-    margin: 0;
-}
-.jbrowseHierarchicalTrackSelector .trackCount {
-    display: inline-block;
-    float: right;
-}
-
-.jbrowseHierarchicalTrackSelector > .header > .textfilterContainer {
-    padding: 0 5px 5px 5px;
-}
-.jbrowseHierarchicalTrackSelector > .header > .textfilterContainer > .textfilter {
-    margin: 0;
-}
-
-.jbrowseHierarchicalTrackSelector .dijitTitlePaneTitle {
-    padding: 0 4px;
-}
-
-.jbrowseHierarchicalTrackSelector .dijitTitlePaneTitleFocus:focus {
-    outline: none;
-}
-
-.jbrowseHierarchicalTrackSelector label.tracklist-label {
-    display: block;
-}
-.jbrowseHierarchicalTrackSelector > .uncategorized {
-    background: white;
-    padding: 10px;
-    border: 1px solid #bfbfbf;
-}
-.jbrowseHierarchicalTrackSelector label.tracklist-label:hover {
-    background: #D2E1F1;
-}
-.jbrowseHierarchicalTrackSelector label.tracklist-label.collapsed {
-    display: none;
-}
-
-.jbrowseHierarchicalTrackSelector label.tracklist-label input.check {
-    position: relative;
-    top: 2px;
-    margin: 0 4px;
-}
-.dj_safari .jbrowseHierarchicalTrackSelector label.tracklist-label input.check {
-    top: 0;
-}
-
-#hierarchicalTrackPane_splitter {
-    background: #fafafa;
-    width: 5px;
-    border-right: 1px solid #555;
-}

theme/css/icons.css

@@ -1,42 +0,0 @@
-.jbrowseIconHelp,
-.jbrowseIconBusy,
-.jbrowseIconLink,
-.jbrowseIconCancel,
-.jbrowseIconHorizontalResize,
-.jbrowseIconVerticalResize
-{
-    background-image: url('img/commonIconsEnabled.png');
-    width: 16px;
-    height: 16px;
-}
-
-.dijitDisabled .jbrowseIconHelp,
-.dijitDisabled .jbrowseIconBusy,
-.dijitDisabled .jbrowseIconLink,
-.dijitDisabled .jbrowseIconCancel,
-.dijitDisabled .jbrowseIconHorizontalResize,
-.dijitDisabled .jbrowseIconVerticalResize
-{
-    background-image: url('img/commonIconsDisabled.png');
-    width: 16px;
-    height: 16px;
-}
-
-.jbrowseIconHelp {
-    background-position: 0;
-}
-.jbrowseIconLink {
-    background-position: -152px;
-}
-.jbrowseIconCancel {
-    background-position: -170px;
-}
-.jbrowseIconBusy {
-    background-image: url('img/spinner.gif');
-}
-.jbrowseIconHorizontalResize {
-    background-position: -209px;
-}
-.jbrowseIconVerticalResize {
-    background-position: -230px;
-}

theme/css/main.css

@@ -1,1055 +0,0 @@
-html, body {
-    height: 100%;
-    width: 100%;
-    padding: 0;
-    border: 0;
-    font-size: 12px;
-    font-family: Univers,Trebuchet MS,Helvetica,Arial,sans-serif;
-}
-
-
-.tundra .dijitDialogTitleBar {
-    padding-right: 25px;
-}
-
-.jbrowseStandaloneDatasetSelector {
-    margin-left: 2em;
-    font-size: 120%;
-}
-
-/* styles for the about JBrowse dialog */
-.about-dialog .default_about {
-    text-align: center;
-}
-.about-dialog .default_about * {
-    margin: 0.5em 0;
-}
-.about-dialog .default_about h1 {
-    margin-top: 0;
-}
-.about-dialog div.powered_by {
-    margin-top: 0.5em;
-    text-align: center;
-}
-
-/* styles for the highlight-setting dialog */
-.setHighlightDialog label {
-    padding-right: 0.5em;
-}
-
-.track .global_highlight {
-    position: absolute;
-    background: rgba( 255, 255, 0, 0.7 );
-    box-sizing: border-box;
-    -moz-box-sizing: border-box;
-    -webkit-box-sizing: border-box;
-    -ms-box-sizing: border-box;
-
-    border: 1px solid rgb(255, 178, 13);
-    border-width: 0;
-}
-.track .global_highlight.left {
-    border-left-width: 1px;
-}
-.track .global_highlight.right {
-    border-right-width: 1px;
-}
-
-
-.tundra input {
-    outline: none;
-}
-
-.ghosted {
-    color: #aaa;
-}
-
-fieldset {
-    padding-left: 1em;
-    margin: 0.7em 0.5em;
-}
-fieldset > legend {
-    font-weight: bold;
-    margin-left: -1em;
-}
-
-.locString {
-    font-family: Courier New,monospace;
-}
-.fasta {
-    font-family: Courier New,monospace;
-    font-size: 14px;
-}
-
-/* styles for the autocomplete menu */
-.dijitComboBoxMenu .locString, .dijitComboBoxMenu .multipleLocations {
-    margin-left: 1em;
-}
-.dijitComboBoxMenu .multipleLocations {
-    color: #333;
-}
-
-/* location choice dialog */
-.locationChoiceDialog div.prompt {
-    margin: 0.3em 1em 1em 1em;
-}
-.locationChoiceDialog .dgrid-row .dijitButton {
-    margin: 0 0.5em;
-}
-.locationChoiceDialog .goButtonColumn,
-.locationChoiceDialog .showButtonColumn {
-    text-align: center;
-    white-space: nowrap;
-}
-
-
-.tundra .dijitDialogCloseIcon {
-    height: 25px;
-    width:  25px;
-    top:    0px;
-    right:  0px;
-    background: url("img/commonIconsEnabled.png") no-repeat -73px 6px;
-
-    border-left: 1px inset #fcfcfc;
-}
-.tundra .dijitDialogCloseIcon:hover {
-    background-position: -93px 6px;
-    border-left-color: #ccc;
-}
-.dijitDialogCloseIcon:focus {
-    outline: none;
-}
-
-.dijitDialogPaneActionBar {
-    text-align: center;
-    clear: both;
-    padding-top: 1em;
-}
-
-.nav {
-    vertical-align: middle;
-    z-index: 10;
-}
-
-input.icon {
-    display: -moz-inline-stack;
-    display: inline-block;
-    zoom: 1;
-}
-
-div.container {
-    position: absolute;
-    z-index: 0;
-}
-
-div.dragWindow {
-    position:absolute;
-    overflow: hidden;
-    z-index: 1;
-}
-
-div.vertical_scrollbar {
-    width: 6px;
-    background: #eee;
-    background: rgba(235, 235, 235, 0.62);
-    border-left: 1px solid #DDD9D9;
-}
-div.vertical_scrollbar .vertical_position_marker {
-    background: #555;
-    opacity: 0.8;
-    border-radius: 5px;
-    width: 100%;
-    border-right: 1px solid #ccc;
-}
-
-.draggable {
-    cursor: move;
-}
-.rubberBandAvailable {
-    cursor: crosshair;
-}
-
-#navbox {
-    padding-top: 3px;
-    position: relative;
-    text-align: center;
-}
-#navbox .dijitButton, #navbox .dijitToggleButton, #navbox .dijitTextBox, #navbox .dijitSelect, #navbox .dojoxTriStateCheckBox {
-    height: 20px;
-    box-sizing: border-box;
-    -moz-box-sizing: border-box;
-    -webkit-box-sizing: border-box;
-    -ms-box-sizing: border-box;
-}
-
-#navbox .dijitSelectLabel {
-    padding: 0 2px;
-}
-
-#navbox .dijitTextBox .dijitInputField {
-    padding-left: 2px;
-}
-
-#navbox * {
-    font-size: 12px;
-    font-family: sans-serif;
-}
-
-.moreMatches {
-    font-style: italic;
-    color: #aaa;
-}
-.moreMatches.dijitMenuItemSelected {
-    background: none;
-    color: #ccc;
-    cursor: default;
-}
-
-div.locationTrapContainer {
-    position: absolute;
-    z-index: -11;
-    height: 100%;
-    width: 100%;
-    top: 0;
-    left: 0;
-    background-color: white;
-}
-
-div.locationTrap {
-    position: absolute;
-    z-index: -10;
-    height: 0;
-    top: 0;
-    left: 0;
-    border-color: transparent;
-    border-style: solid;
-    border-bottom-color: #A9C6EB;
-    border-top: 0px dotted transparent;
-}
-
-div.locationThumb {
-    position: absolute;
-    top: 0px;
-    /* if you change this border from 2px, change GenomeView.showTrap */
-    border: 2px solid red;
-    margin: 0px -2px 0px -2px;
-    height: 23px;
-    cursor: move;
-    background: rgba(0, 121, 245, 0.1);
-}
-
-div.locationThumb.dojoMoveItem {
-    cursor: move;
-}
-
-div.topLink {
-    position: absolute;
-    right: 0;
-    top: 0;
-    z-index: 50;
-    background: white;
-    border: 1px solid #888;
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-div.textfilter > div.jbrowseIconCancel {
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-
-#trackPane_splitter {
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-div.tracklist-container {
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-.tracklist-container.dojoDndItemAfter {
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-/* styles for feature labels */
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-.rubber-highlight {
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-
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-
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-#zoomOut{
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-
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-.fatal_error {
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-div.error .codecaption {
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-/* styles dealing with popups launched by clicking on features */
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-/* styles for popup feature detail dialogs from tracks */
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-/*styles for vertical line and BP label*/
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theme/css/maker.css

@@ -1,197 +0,0 @@
-/*MAKER CSS with colors for common features*/
-
-/*SNAP*/
-.snap-exon,
-.plus-snap-exon,
-.minus-snap-exon,
-.snap-five_prime_UTR,
-.plus-snap-five_prime_UTR,
-.minus-snap-five_prime_UTR,
-.snap-three_prime_UTR,
-.plus-snap-three_prime_UTR,
-.minus-snap-three_prime_UTR {
-    position: absolute;
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-    border-style: solid;
-    border-color: #D88;
-    border-width: 2px 0px 2px 0px;
-    z-index: 8;
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-    cursor: pointer;
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-
-/*Augustus*/
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-.plus-augustus-exon,
-.minus-augustus-exon,
-.augustus-five_prime_UTR,
-.plus-augustus-five_prime_UTR,
-.minus-augustus-five_prime_UTR,
-.augustus-three_prime_UTR,
-.plus-augustus-three_prime_UTR,
-.minus-augustus-three_prime_UTR {
-    position: absolute;
-    height: 7px;
-    background-color: #FFCCFF;
-    border-style: solid;
-    border-color: #D88;
-    border-width: 2px 0px 2px 0px;
-    z-index: 8;
-    min-width: 1px;
-    cursor: pointer;
-}
-
-/*GeneMark*/
-.genemark-exon,
-.plus-genemark-exon,
-.minus-genemark-exon,
-.genemark-five_prime_UTR,
-.plus-genemark-five_prime_UTR,
-.minus-genemark-five_prime_UTR,
-.genemark-three_prime_UTR,
-.plus-genemark-three_prime_UTR,
-.minus-genemark-three_prime_UTR {
-    position: absolute;
-    height: 7px;
-    background-color: #679B68;
-    border-style: solid;
-    border-color: #D88;
-    border-width: 2px 0px 2px 0px;
-    z-index: 8;
-    min-width: 1px;
-    cursor: pointer;
-}
-
-/*FGENESH*/
-.fgenesh-exon,
-.plus-fgenesh-exon,
-.minus-fgenesh-exon,
-.fgenesh-five_prime_UTR,
-.plus-fgenesh-five_prime_UTR,
-.minus-fgenesh-five_prime_UTR,
-.fgenesh-three_prime_UTR,
-.plus-fgenesh-three_prime_UTR,
-.minus-fgenesh-three_prime_UTR {
-    position: absolute;
-    height: 7px;
-    background-color: #FF99FF;
-    border-style: solid;
-    border-color: #D88;
-    border-width: 2px 0px 2px 0px;
-    z-index: 8;
-    min-width: 1px;
-    cursor: pointer;
-}
-
-/*protein2genome*/
-.protein2genome_part,
-.plus-protein2genome_part,
-.minus-protein2genome_part {
-    position: absolute;
-    height: 4px;
-    margin-top: -2px;
-    background-color: #FFFF00;
-    border-style: solid;
-    border-color: #6E6E6E;
-    border-width: 1px 1px 1px 1px;
-    z-index: 8;
-    min-width: 1px;
-    cursor: pointer;
-}
-
-/*BLASTN*/
-.blastn_part,
-.plus-blastn_part,
-.minus-blastn_part {
-    position: absolute;
-    height: 4px;
-    margin-top: -2px;
-    background-color: #66CC00;
-    border-style: solid;
-    border-color: #6E6E6E;
-    border-width: 1px 1px 1px 1px;
-    z-index: 8;
-    min-width: 1px;
-    cursor: pointer;
-}
-
-/*BLASTX*/
-.blastx_part,
-.plus-blastx_part,
-.minus-blastx_part {
-    position: absolute;
-    height: 4px;
-    margin-top: -2px;
-background-color: #FF00FF;
-    border-style: solid;
-    border-color: #6E6E6E;
-    border-width: 1px 1px 1px 1px;
-    z-index: 8;
-    min-width: 1px;
-    cursor: pointer;
-}
-
-/*TBLASTX*/
-.tblastx_part,
-.plus-tblastx_part,
-.minus-tblastx_part {
-    position: absolute;
-    height: 4px;
-    margin-top: -2px;
-    background-color: #663366;
-    border-style: solid;
-    border-color: #6E6E6E;
-    border-width: 1px 1px 1px 1px;
-    z-index: 8;
-    min-width: 1px;
-    cursor: pointer;
-}
-
-/*est2genome*/
-.est2genome_part,
-.plus-est2genome_part,
-.minus-est2genome_part {
-    position: absolute;
-    height: 4px;
-    margin-top: -2px;
-    background-color: #FAFAD2;
-    border-style: solid;
-    border-color: #6E6E6E;
-    border-width: 1px 1px 1px 1px;
-    z-index: 8;
-    min-width: 1px;
-    cursor: pointer;
-}
-
-/*repeat*/
-.repeat_part,
-.plus-repeat_part,
-.minus-repeat_part {
-    position: absolute;
-    height: 4px;
-    margin-top: -2px;
-    background-color: #FF0000;
-    border-style: solid;
-    border-color: #6E6E6E;
-    border-width: 1px 1px 1px 1px;
-    z-index: 8;
-    min-width: 1px;
-    cursor: pointer;
-}
-
-/*cdna2genome*/
-.cdna2genome_part,
-.plus-cdna2genome_part,
-.minus-cdna2genome_part {
-    position: absolute;
-    height: 4px;
-    margin-top: -2px;
-    background-color: #8C468C;
-    border-style: solid;
-    border-color: #6E6E6E;
-    border-width: 1px 1px 1px 1px;
-    z-index: 8;
-    min-width: 1px;
-    cursor: pointer;
-}

theme/css/menubar.css

@@ -1,140 +0,0 @@
-/* styles for the top menu bar */
-div.menuBar {
-    padding: 1px 0;
-    height: 25px;
-}
-.tundra .menuBar {
-    background: #396494;
-    text-align: right;
-}
-.tundra .menuBar a {
-    color: white;
-}
-div.topLink {
-    position: absolute;
-    right: 0;
-    top: 0;
-    z-index: 50;
-    background: white;
-    border: 1px solid #888;
-    border-width: 0 0 1px 1px;
-}
-div.menuBar a, .topLink a {
-    padding: 0 0.8ex;
-    text-decoration: none;
-}
-.menuBar .powered_by {
-    float: left;
-    font-size: 125%;
-    font-family: 'Helvetica Neue', Arial, Helvetica, 'Nimbus Sans L', sans-serif;
-    font-weight: bold;
-    line-height: 25px; /* note this line-height should be the same as the fixed height of the menuBar */
-    cursor: pointer;
-}
-
-.share .icon {
-    height: 8px;
-    width: 19px;
-    display: inline;
-    display: inline-block;
-    background: url("img/glyphs_white.png") no-repeat -149px -91px;
-    margin-right: 2px;
-    margin-top: -2px;
-}
-a.topLink, a.topLink * {
-    cursor: pointer;
-}
-.topLink .powered_by {
-    padding: 0 0.5em;
-    color: black;
-    text-decoration: none;
-}
-.menuBar * {
-    outline: none;
-}
-.tundra .menuBar .dijitButtonNode {
-    background: transparent;
-}
-
-.tundra .menuBar .dijitButtonNode {
-    border: 2px outset rgba( 120, 120, 120, 0.2 );
-}
-.tundra .menuBar .dijitButtonHover .dijitButtonNode,
-.tundra .menuBar .dijitDropDownButtonHover .dijitButtonNode {
-    background: rgba( 255, 255, 255, 0.07 );
-}
-.tundra .menuBar .dijitButtonActive .dijitButtonNode,
-.tundra .menuBar .dijitDropDownButtonActive .dijitButtonNode {
-    border: 2px inset rgba( 120, 120, 120, 0.2 );
-}
-
-.menuBar .dijitButtonNode {
-    padding: 0 1em;
-}
-
-.menuBar .dijitButtonNode * {
-    color: white;
-}
-.menuBar .config .icon {
-    height: 16px;
-    width: 16px;
-    margin-right: 2px;
-    margin-top: -2px;
-    display: inline;
-    display: inline-block;
-    background: url("img/glyphs_white.png") no-repeat -168px -27px;
-
-}
-
-
-/* dataset selector */
-.menuBar > .menu, .menuBar > .dataset_select {
-    float: left;
-    font-size: 120%;
-    color: white;
-}
-.menuBar > .dataset_select {
-    margin: 1px 0 0 1px;
-    font-weight: bold;
-    height: 100%;
-    background: transparent;
-    border: none;
-}
-.menuBar > .dataset_select .dijitSelectLabel {
-    padding: 0 0.5em;
-}
-.menuBar > .dataset_select.dijitSelectHover td {
-    color: white;
-}
-.menuBar > .dataset_select .dijitButtonContents {
-    background: transparent;
-    border-color: transparent;
-}
-.menuBar > .dataset_select .dijitArrowButtonInner {
-    background: url("img/spriteArrows.png") no-repeat scroll -56px center;
-}
-
-.tundra .globalMenu .dijitMenuItem td {
-    padding: 0.5em 2px 0.5em 5px;
-}
-
-.tundra .menuBar > .menu .dijitButtonNode {
-    border: none;
-}
-.tundra .menuBar > .menu.dijitDropDownButton,
-.tundra .menuBar > .menu.dijitDropDownButton * {
-    margin: 0;
-    padding: 0;
-    line-height: 25px;
-}
-.tundra .menuBar > .menu.dijitDropDownButton .dijitButtonNode {
-    padding: 0 1em 0 0.7em;
-    text-align: left;
-}
-
-.tundra .menuBar > .menu .dijitDropDownButtonHover .dijitButtonNode {
-    background: rgba( 255, 255, 255, 0.07 );
-}
-.tundra .menuBar > .menu .dijitDropDownButtonActive .dijitButtonNode {
-    border: none;
-}

theme/css/sequence.css

@@ -1,124 +0,0 @@
-table.sequence {
-    border-collapse: collapse;
-}
-
-div.sequence_blur {
-    /* background: url('img/sequence_blur.png') #eee repeat-x; */
-    background: #f5f5f5;
-    background: rgba( 50, 50, 50, 0.16 );
-    border: 0;
-    color: #575757;
-    height: 31px;
-    font-size: 12px;
-    text-align: center;
-    position: relative;
-}
-.sequence_blur > span {
-    top: 50%;
-    position: absolute;
-    width: 100%;
-    display: block;
-    left: 0;
-    margin-top: -8px;
-}
-
-table.sequence .highlighted {
-    background: #ff0;
-}
-table.sequence .revcom {
-    color: red;
-}
-table.sequence .base, table.sequence > tr, table.translatedSequence > tr, table.translatedSequence  {
-    height: 14px;
-    line-height: 14px;
-}
-
-table.sequence.big .base {
-    border-right: 1px solid #333;
-}
-
-.translatedSequence {
-    position: relative;
-    border-width: 0px;
-    border-collapse: collapse;
-    overflow: visible;
-}
-.translatedSequence table {
-    z-index: 10;
-}
-
-.translatedSequence.frame0 {
-    background-color: #929292;
-}
-
-.translatedSequence.frame1 {
-    background-color: #B0B0B0;
-}
-
-.translatedSequence.frame2 {
-    background-color: #E0E0E0;
-}
-.translatedSequence td.aminoAcid {
-    text-align: center;
-    z-index: 2000;
-
-    color: black;
-    font-family: Courier New,monospace;
-    font-weight: bold;
-    text-shadow: white 0px 0px 1px;
-}
-.translatedSequence.big, .translatedSequence.big td.aminoAcid {
-    border-right: 1px solid #777;
-}
-
-.translatedSequence.frame2 td.aminoAcid {
-    border-right-color: #979797;
-}
-.translatedSequence.frame1 td.aminoAcid {
-    border-right-color: #6d6d6d;
-}
-.translatedSequence.frame0 td.aminoAcid {
-    border-right-color: #5f5f5f;
-}
-
-.translatedSequence td.aminoAcid_\* {
-    background-color: #FF0000;
-}
-
-.translatedSequence td.aminoAcid_m {
-    background-color: #00FF00;
-}
-
-td.base {
-    text-align: center;
-    z-index: 2000;
-}
-.base {
-    color: black;
-    font-family: Courier New,monospace;
-    font-weight: bold;
-    text-shadow: white 0px 0px 1px;
-}
-
-/* colors for bases must be specified as hex or rgb/hsl strings, no named colors such as 'red' */
-.base_n {
-    background-color: #C6C6C6;
-}
-.base_a {
-    background-color: #00BF00;
-}
-.base_c {
-    background-color: #4747ff;
-}
-.base_t {
-    background-color: #f00;
-}
-.base_g {
-    background-color: #d5bb04;
-}
-.base_reference {
-    background-color: #bbb;
-}
-.base_deletion {
-    background-color: #999; 
-}

theme/css/track_styles.css

@@ -1,516 +0,0 @@
-/*
-  NOTES ON STYLING FEATURES:
-     - avoid using any margins in feature styles. Layout is done
-       by JBrowse.
-
-     - when possible, make all element heights an odd number of
-       pixels, so that vertical centering is possible with
-       pixel-perfect accuracy.
-*/
-
-.basic,
-.plus-basic,
-.minus-basic {
-    position: absolute;
-    cursor: pointer;
-    z-index: 10;
-    min-width: 1px;
-}
-
-.basicSubfeature {
-    position: absolute;
-    cursor: pointer;
-    z-index: 12;
-    min-width: 1px;
-}
-
-div.hist {
-    position: absolute;
-    z-index: 10;
-
-    box-sizing: border-box;
-    -moz-box-sizing: border-box;
-    -webkit-box-sizing: border-box;
-    -ms-box-sizing: border-box;
-}
-
-.feature,
-.plus-feature,
-.minus-feature {
-    position:absolute;
-    height: 7px;
-    background-repeat: repeat-x;
-    cursor: pointer;
-    min-width: 1px;
-    z-index: 10;
-    background-color: #eee;
-
-    box-sizing: border-box;
-    -moz-box-sizing: border-box;
-    -webkit-box-sizing: border-box;
-    -ms-box-sizing: border-box;
-}
-
-.plus-feature { background-image: url('img/plus-chevron3.png'); }
-.minus-feature { background-image: url('img/minus-chevron3.png'); }
-
-.subfeature,
-.plus-subfeature,
-.minus-subfeature {
-    position:absolute;
-    background-color: #dadada;
-    height: 7px;
-    min-width: 1px;
-    z-index: 12;
-
-    box-sizing: border-box;
-    -moz-box-sizing: border-box;
-    -webkit-box-sizing: border-box;
-    -ms-box-sizing: border-box;
-}
-
-.alignment,
-.plus-alignment,
-.minus-alignment {
-    background-color: #ccc;
-
-    /* these should all 3 match */
-    height:      11px;
-    line-height: 11px;
-    font-size:   11px;
-}
-.plus-alignment {
-    background-color: #EC8B8B;
-}
-.minus-alignment {
-    background-color: #898FD8;
-}
-.alignment.missing_mate, .plus-alignment.missing_mate, .minus-alignment.missing_mate {
-    background-image: url('img/red_crosshatch_bg.png');
-}
-
-.alignment > .mismatch, .minus-alignment > .mismatch, .plus-alignment > .mismatch  {
-    height: 100%;
-}
-.alignment > .deletion, .minus-alignment > .deletion, .plus-alignment > .deletion {
-    background-color: black;
-    height: 100%;
-}
-.alignment > .deletion *, .plus-alignment > .deletion *, .minus-alignment > .deletion * {
-    color: white;
-}
-.alignment > .insertion, .plus-alignment > .insertion, .minus-alignment > .insertion {
-    background-color: white;
-    color: black;
-    height: 100%;
-}
-.alignment > .skip, .plus-alignment > .skip, .minus-alignment > .skip {
-    background: url('img/dark_20x3.png') repeat-x 0 50% white;
-    height: 100%;
-    opacity: 0.7;
-}
-
-div.feature-hist {
-    background-color: blue;
-    border-color: #5858C4;
-}
-
-.feature2, .plus-feature2, .minus-feature2 {
-    position:absolute;
-    height: 7px;
-    background-repeat: repeat-x;
-    cursor: pointer;
-    min-width: 1px;
-    z-index: 10;
-    background-color: #62d335;
-}
-
-.Boolean-transparent {
-    opacity: 0.2;
-}
-
-div.feature2-hist {
-    background-color: #9f9;
-    border-color: #ada;
-}
-
-.feature3, .plus-feature3, .minus-feature3 {
-    position:absolute;
-    height: 7px;
-    background-repeat: repeat-x;
-    cursor: pointer;
-    min-width: 1px;
-    z-index: 10;
-    background-color: goldenrod;
-}
-
-div.feature3-hist {
-    background-color: yellow;
-    border-color: black;
-}
-
-.feature4, .plus-feature4, .minus-feature4 {
-    position:absolute;
-    height: 11px;
-    background-repeat: repeat-x;
-    cursor: pointer;
-    min-width: 1px;
-    z-index: 10;
-    background: yellow;
-}
-
-div.feature4-hist {
-    background-color: yellow;
-    border-color: black;
-}
-
-.feature5, .plus-feature5, .minus-feature5 {
-    position:absolute;
-    height: 7px;
-    background-repeat: repeat-x;
-    cursor: pointer;
-    min-width: 1px;
-    z-index: 10;
-    background-color: blue;
-}
-
-div.feature5-hist {
-    background-color: blue;
-    border-color: lightblue;
-}
-
-div.exon-hist {
-    background-color: #4B76E8;
-    border-color: #00f;
-}
-
-.exon,
-.plus-exon,
-.minus-exon {
-    position: absolute;
-    height: 7px;
-    background-color: #4B76E8;
-    border-style: solid;
-    border-color: #00f;
-    border-width: 1px;
-    cursor: pointer;
-    z-index: 10;
-}
-
-div.est-hist {
-    background-color: #ED9185;
-    border-color: #c33;
-}
-
-.est,
-.plus-est,
-.minus-est {
-    position: absolute;
-    height: 7px;
-    background-color: #ED9185;
-}
-
-.dblhelix,
-.plus-dblhelix,
-.minus-dblhelix {
-    position:absolute;
-    height: 11px;
-    background-image: url('img/dblhelix-red.png');
-    background-repeat: repeat-x;
-    min-width: 1px;
-    cursor: pointer;
-    z-index: 10;
-}
-
-div.dblhelix-hist {
-    background-color: #fcc;
-    border-color: #daa;
-}
-
-.plus-helix,
-.minus-helix {
-    position:absolute;
-    height: 11px;
-    background-image: url('img/helix3-green.png');
-    background-repeat: repeat-x;
-    min-width: 1px;
-    cursor: pointer;
-    z-index: 10;
-}
-
-div.helix-hist {
-    background-color: #cfc;
-    border-color: #ada;
-}
-
-.loops, .minus-loops, .plus-loops {
-    position:absolute;
-    height: 13px;
-    background-image: url('img/loops.png');
-    background-repeat: repeat-x;
-    cursor: pointer;
-}
-
-.diamonds, .minus-diamonds, .plus-diamonds {
-
-
-    position:absolute;
-    height: 13px;
-    background-image: url('img/glyph-diamond.png');
-    background-repeat: repeat-x;
-    cursor: pointer;
-}
-
-.plus-cds, .minus-cds {
-    position:absolute;
-    height: 13px;
-    background-repeat: repeat-x;
-    cursor: pointer;
-    min-width: 1px;
-}
-
-.plus-cds_phase0 { background-image: url('img/plus-cds0.png'); }
-.plus-cds_phase1 { background-image: url('img/plus-cds1.png'); }
-.plus-cds_phase2 { background-image: url('img/plus-cds2.png'); }
-.minus-cds_phase0 { background-image: url('img/minus-cds0.png'); }
-.minus-cds_phase1 { background-image: url('img/minus-cds1.png'); }
-.minus-cds_phase2 { background-image: url('img/minus-cds2.png'); }
-
-div.cds-hist {
-    background-color: #fcc;
-    border-color: #daa;
-}
-
-.topbracket {
-    position:absolute;
-    height: 8px;
-    border-style: solid solid none solid;
-    border-width: 2px;
-    border-color: orange;
-    cursor: pointer;
-}
-
-.bottombracket {
-    position:absolute;
-    height: 8px;
-    border-style: none solid solid solid;
-    border-width: 2px;
-    border-color: green;
-    cursor: pointer;
-}
-
-.hourglass, .plus-hourglass, .minus-hourglass {
-    position:absolute;
-    height: 0px;
-    border-style: solid;
-    border-width: 6px 3px 6px 3px;
-    cursor: pointer;
-}
-
-.triangle, .plus-triangle, .minus-triangle {
-    position:absolute;
-    height: 0px;
-    border-style: solid;
-    border-width: 6px 3px 0px 3px;
-    cursor: pointer;
-}
-
-.hgred {
-    border-color: #f99 white #f99 white;
-}
-div.hgred-hist {
-    background-color: #daa;
-    border-color: #d44;
-}
-
-.hgblue {
-    border-color: #99f white #99f white;
-}
-div.hgblue-hist {
-    background-color: #aad;
-    border-color: #99f;
-}
-
-.ibeam, .plus-ibeam, .minus-ibeam {
-    position:absolute;
-    height: 2px;
-    background-color: blue;
-    border-style: solid;
-    border-width: 8px 4px 8px 4px;
-    border-color: white blue white blue;
-    cursor: pointer;
-
-    box-sizing: content-box;
-    -moz-box-sizing: content-box;
-    -webkit-box-sizing: content-box;
-    -ms-box-sizing: content-box;
-
-}
-
-div.transcript-hist {
-    background-color: #ddd;
-    border-color: #FF9185;
-}
-
-.transcript,
-.plus-transcript,
-.minus-transcript {
-    position: absolute;
-    height: 11px;
-    background: url('img/dark_20x3.png') repeat-x 0 4px white;
-    z-index: 6;
-    min-width: 1px;
-    cursor: pointer;
-}
-
-.plus-transcript-arrowhead,
-.plus-arrowhead {
-    position: absolute;
-    width: 9px;
-    height: 5px;
-    background-image: url('img/plus-arrowhead.png');
-    background-repeat: no-repeat;
-    z-index: 100;
-}
-
-.minus-transcript-arrowhead,
-.minus-arrowhead {
-    position: absolute;
-    width: 9px;
-    height: 5px;
-    background-image: url('img/minus-arrowhead.png');
-    background-repeat: no-repeat;
-    z-index: 100;
-}
-
-/* introns are hidden by default */
-.plus-intron, .minus-intron {
-    display: none;
-}
-/* can also set a class of 'hidden' to hide something */
-.hidden, .plus-hidden, .minus-hidden {
-    display: none;
-}
-
-.plus-CDS,
-.plus-transcript-CDS,
-.minus-CDS,
-.minus-transcript-CDS {
-    position: absolute;
-    height: 11px;
-    background: #F09A9A;
-    cursor: pointer;
-    z-index: 10;
-    min-width: 1px;
-}
-
-.plus-exon,
-.minus-exon,
-.plus-UTR,
-.minus-UTR,
-.plus-five_prime_UTR,
-.minus-five_prime_UTR,
-.plus-three_prime_UTR,
-.minus-three_prime_UTR {
-    position: absolute;
-    height: 7px;
-    background-color: #B66;
-    border-style: solid;
-    border-color: #D88;
-    border-width: 2px 0px 2px 0px;
-    z-index: 8;
-    min-width: 1px;
-    cursor: pointer;
-}
-
-.generic_parent,
-.plus-generic_parent,
-.minus-generic_parent {
-    position: absolute;
-    height: 4px;
-    background-color: #AAA;
-    z-index: 6;
-    min-width: 1px;
-    cursor: pointer;
-}
-
-div.generic_parent-hist {
-    background-color: #ddd;
-    border-color: #555;
-}
-
-.match_part,
-.plus-match_part,
-.minus-match_part {
-    position: absolute;
-    height: 4px;
-    background-color: #66B;
-    border-style: solid;
-    border-color: #88D;
-    border-width: 2px 0px 2px 0px;
-    z-index: 8;
-    min-width: 1px;
-    cursor: pointer;
-}
-
-.generic_part_a,
-.plus-generic_part_a,
-.minus-generic_part_a {
-    position: absolute;
-    height: 4px;
-    background-color: #6B6;
-    border-style: solid;
-    border-color: #8D8;
-    border-width: 2px 0px 2px 0px;
-    z-index: 8;
-    min-width: 1px;
-    cursor: pointer;
-}
-
-
-/* floating score display for wiggle tracks */
-.wiggleValueDisplay {
-    background: #FFFEF0;
-    border: 1px solid #aaa;
-    padding: 2px;
-    font-family: Courier New, monospace;
-    font-weight: bold;
-    cursor: default;
-
-    -moz-box-shadow: 4px 4px 10px 2px rgba( 80, 80, 80, 0.3 );
-    -webkit-box-shadow: 4px 4px 10px 2px rgba( 80, 80, 80, 0.3 );
-    box-shadow: 4px 4px 10px 2px rgba( 80, 80, 80, 0.3 );
-}
-.wiggleValueDisplay table {
-    border-spacing: 0;
-}
-.wiggleValueDisplay td {
-    padding: 0.2em 0.4em;
-}
-.wiggleValueDisplay td.count, .wiggleValueDisplay td.pct  {
-    text-align: right;
-}
-.wiggleValueDisplay tr.total > td {
-    border-top: 1px solid #aaa;
-    font-weight: bold;
-}
-
-.wigglePositionIndicator {
-    background: #333;
-    border: none;
-    width: 1px;
-    cursor: default;
-}
-
-.featureTooltip {
-    background: #FFFEF0;
-    border: 1px solid #aaa;
-    padding: 2px;
-    font-family: Courier New, monospace;
-    font-weight: bold;
-    cursor: default;
-
-    -moz-box-shadow: 4px 4px 10px 2px rgba( 80, 80, 80, 0.3 );
-    -webkit-box-shadow: 4px 4px 10px 2px rgba( 80, 80, 80, 0.3 );
-    box-shadow: 4px 4px 10px 2px rgba( 80, 80, 80, 0.3 );
-}

theme/css/tristate.css

@@ -1,130 +0,0 @@
-/* TriStateCheckBox
- * 
- * Styling TriStateCheckBox mainly includes:
- * 
- * 1. Containers
- * 		.dojoxTriStateCheckBox|.dojoxTriStateCheckBoxIcon - for border, padding, width|height and background image
- * 
- * 2. Checked state
- * 		.dojoxTriStateCheckBoxChecked - for checked background-color|image
- * 		.dojoxTriStateCheckBoxMixed - for mixed background-color|image
- * 
- * 3. Hover state
- * 		.dojoxTriStateCheckBoxHover|.dojoxTriStateCheckBoxCheckedHover|.dojoxTriStateCheckBoxMixedHover - for background image
- * 
- * 4. Disabled state
- * 		.dojoxTriStateCheckBoxDisabled|.dojoxTriStateCheckBoxCheckedDisabled|.dojoxTriStateCheckBoxMixedDisabled - for background image
- */
-.tundra .dojoxTriStateCheckBox,  .dojoxTriStateCheckBoxIcon {
-  background-image: url('img/tristate.png');
-  /* checkbox sprite image */
-
-  background-repeat: no-repeat;
-  width: 30px;
-  height: 22px !important;
-  margin: 0 2px 0 0;
-  padding: 5px 5px 5px 5px;
-}
-.dj_ie6 .tundra .dojoxTriStateCheckBox, .dj_ie6  .dojoxTriStateCheckBoxIcon {
-  background-image: url('img/tristate.png');
-  /* checkbox sprite image */
-
-}
-.tundra .dojoxTriStateCheckBox{
-  /* unchecked */
-
-  background-position: -30px;
-}
-.tundra .dojoxTriStateCheckBoxChecked{
-  /* checked */
-  background-position: 0px;
-}
-.tundra .dojoxTriStateCheckBoxMixed {
-  /* mixed */
-
-  background-position: -90px;
-}
-.tundra .dojoxTriStateCheckBoxDisabled {
-  /* disabled and unchecked */
-
-  background-position: -30px;
-}
-.tundra .dojoxTriStateCheckBoxCheckedDisabled {
-  /* disabled and checked */
-
-  background-position: 0px;
-}
-.tundra .dojoxTriStateCheckBoxMixedDisabled {
-  /* disabled and mixed */
-
-  background-position: -90px;
-}
-.tundra .dojoxTriStateCheckBoxHover {
-  /* hovering over and unchecked */
-
-  background-position: -60px;
-}
-.tundra .dojoxTriStateCheckBoxCheckedHover {
-  /* hovering over and checked */
-
-  background-position: 0px;
-}
-.tundra .dojoxTriStateCheckBoxMixedHover {
-  /* hovering over and mixed */
-
-  background-position: -120px;
-}
-
-.dijit_a11y .dojoxTriStateCheckBoxHover .dojoxTriStateCheckBoxInner,
-.dijit_a11y .dojoxTriStateCheckBoxFocused .dojoxTriStateCheckBoxInner{
-  /* focused or hovering over */
-  border: dashed;
-}
-
-.dijit_a11y .dojoxTriStateCheckBoxHover .dojoxTriStateCheckBoxInner,
-.dijit_a11y .dojoxTriStateCheckBoxFocused .dojoxTriStateCheckBoxInner{
-  /* focused or hovering over */
-  border: solid;
-}
-
-.dijit_a11y .dojoxTriStateCheckBoxDisabled .dojoxTriStateCheckBoxInner{
-  /* focused or hovering over */ 
-  opacity: 0.5;
-}
-
-.dj_ie .dijit_a11y .dojoxTriStateCheckBoxDisabled .dojoxTriStateCheckBoxInner{
-  /* disabled */
-}
-
-
-.dojoxTriStateCheckBoxInner{
-  /* inner text */
-
-  visibility: hidden;
-  display: none;
-  position: absolute;
-  text-align: center;
-}
-
-.dijit_a11y .dojoxTriStateCheckBoxInner{
-  /* inner text */
-  
-  visibility: visible;
-  display: block;
-}
-
-.dojoxTriStateCheckBoxInput {
-  /* place the actual input on top, but all-but-invisible */
-  opacity: 0.01;
-  padding: 0;
-  margin: 0;
-  border: 0;
-  width: 30px;
-  height: 22px;
-  background-position:center center;
-  background-repeat:no-repeat;
-}
-
-.dj_ie .dojoxTriStateCheckBoxInput {
-  filter: alpha(opacity=0);
-}

theme/jbrowse_config.js

@@ -1,74 +0,0 @@
-window.onerror=function(msg){
-    if( document.body )
-        document.body.setAttribute("JSError",msg);
-}
-
-        // puts the main Browser object in this for convenience.  feel
-        // free to move it into function scope if you want to keep it
-        // out of the global namespace
-var JBrowse;
-require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
-        function (Browser,ioQuery,JSON) {
-                   // the initial configuration of this JBrowse
-                   // instance
-
-                   // NOTE: this initial config is the same as any
-                   // other JBrowse config in any other file.  this
-                   // one just sets defaults from URL query params.
-                   // If you are embedding JBrowse in some other app,
-                   // you might as well just set this initial config
-                   // to something like { include: '../my/dynamic/conf.json' },
-                   // or you could put the entire
-                   // dynamically-generated JBrowse config here.
-
-                   // parse the query vars in the page URL
-            var queryParams = ioQuery.queryToObject( window.location.search.slice(1) );
-
-            var config = {
-                containerID: "GenomeBrowser",
-
-                dataRoot: '/jbrowse/JBrowse-1.11.5/data',
-                browserRoot: '/jbrowse/JBrowse-1.11.5',
-                queryParams: queryParams,
-                location: queryParams.loc,
-                forceTracks: queryParams.tracks,
-                initialHighlight: queryParams.highlight,
-                show_nav: queryParams.nav,
-                show_tracklist: queryParams.tracklist,
-                show_overview: queryParams.overview,
-                stores: { url: { type: "JBrowse/Store/SeqFeature/FromConfig", features: [] } },
-                makeFullViewURL: function( browser ) {
-
-                           // the URL for the 'Full view' link
-                           // in embedded mode should be the current
-                           // view URL, except with 'nav', 'tracklist',
-                           // and 'overview' parameters forced to 1.
-
-                    return browser.makeCurrentViewURL({ nav: 1, tracklist: 1, overview: 1 });
-                },
-                updateBrowserURL: true
-            };
-
-                   //if there is ?addFeatures in the query params,
-                   //define a store for data from the URL
-            if( queryParams.addFeatures ) {
-                config.stores.url.features = JSON.parse( queryParams.addFeatures );
-            }
-
-                   // if there is ?addTracks in the query params, add
-                   // those track configurations to our initial
-                   // configuration
-            if( queryParams.addTracks ) {
-                config.tracks = JSON.parse( queryParams.addTracks );
-            }
-
-                   // if there is ?addStores in the query params, add
-                   // those store configurations to our initial
-                   // configuration
-            if( queryParams.addStores ) {
-                config.stores = JSON.parse( queryParams.addStores );
-            }
-
-                   // create a JBrowse global variable holding the JBrowse instance
-            JBrowse = new Browser( config );
-        });

theme/jbrowse_config.js~

@@ -1,74 +0,0 @@
-window.onerror=function(msg){
-    if( document.body )
-        document.body.setAttribute("JSError",msg);
-}
-
-        // puts the main Browser object in this for convenience.  feel
-        // free to move it into function scope if you want to keep it
-        // out of the global namespace
-var JBrowse;
-require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
-        function (Browser,ioQuery,JSON) {
-                   // the initial configuration of this JBrowse
-                   // instance
-
-                   // NOTE: this initial config is the same as any
-                   // other JBrowse config in any other file.  this
-                   // one just sets defaults from URL query params.
-                   // If you are embedding JBrowse in some other app,
-                   // you might as well just set this initial config
-                   // to something like { include: '../my/dynamic/conf.json' },
-                   // or you could put the entire
-                   // dynamically-generated JBrowse config here.
-
-                   // parse the query vars in the page URL
-            var queryParams = ioQuery.queryToObject( window.location.search.slice(1) );
-
-            var config = {
-                containerID: "GenomeBrowser",
-
-                dataRoot: '/jbrowse/Medicago/data',
-                browserRoot: '/jbrowse/Medicago',
-                queryParams: queryParams,
-                location: queryParams.loc,
-                forceTracks: queryParams.tracks,
-                initialHighlight: queryParams.highlight,
-                show_nav: queryParams.nav,
-                show_tracklist: queryParams.tracklist,
-                show_overview: queryParams.overview,
-                stores: { url: { type: "JBrowse/Store/SeqFeature/FromConfig", features: [] } },
-                makeFullViewURL: function( browser ) {
-
-                           // the URL for the 'Full view' link
-                           // in embedded mode should be the current
-                           // view URL, except with 'nav', 'tracklist',
-                           // and 'overview' parameters forced to 1.
-
-                    return browser.makeCurrentViewURL({ nav: 1, tracklist: 1, overview: 1 });
-                },
-                updateBrowserURL: true
-            };
-
-                   //if there is ?addFeatures in the query params,
-                   //define a store for data from the URL
-            if( queryParams.addFeatures ) {
-                config.stores.url.features = JSON.parse( queryParams.addFeatures );
-            }
-
-                   // if there is ?addTracks in the query params, add
-                   // those track configurations to our initial
-                   // configuration
-            if( queryParams.addTracks ) {
-                config.tracks = JSON.parse( queryParams.addTracks );
-            }
-
-                   // if there is ?addStores in the query params, add
-                   // those store configurations to our initial
-                   // configuration
-            if( queryParams.addStores ) {
-                config.stores = JSON.parse( queryParams.addStores );
-            }
-
-                   // create a JBrowse global variable holding the JBrowse instance
-            JBrowse = new Browser( config );
-        });

theme/node--jbrowse-instance.tpl.php

@@ -1,92 +1,107 @@
+<?php
+
+/**
+ * @file
+ * Bartik's theme implementation to display a node.
+ *
+ * Available variables:
+ * - $title: the (sanitized) title of the node.
+ * - $content: An array of node items. Use render($content) to print them all,
+ *   or print a subset such as render($content['field_example']). Use
+ *   hide($content['field_example']) to temporarily suppress the printing of a
+ *   given element.
+ * - $user_picture: The node author's picture from user-picture.tpl.php.
+ * - $date: Formatted creation date. Preprocess functions can reformat it by
+ *   calling format_date() with the desired parameters on the $created variable.
+ * - $name: Themed username of node author output from theme_username().
+ * - $node_url: Direct URL of the current node.
+ * - $display_submitted: Whether submission information should be displayed.
+ * - $submitted: Submission information created from $name and $date during
+ *   template_preprocess_node().
+ * - $classes: String of classes that can be used to style contextually through
+ *   CSS. It can be manipulated through the variable $classes_array from
+ *   preprocess functions. The default values can be one or more of the
+ *   following:
+ *   - node: The current template type; for example, "theming hook".
+ *   - node-[type]: The current node type. For example, if the node is a
+ *     "Blog entry" it would result in "node-blog". Note that the machine
+ *     name will often be in a short form of the human readable label.
+ *   - node-teaser: Nodes in teaser form.
+ *   - node-preview: Nodes in preview mode.
+ *   The following are controlled through the node publishing options.
+ *   - node-promoted: Nodes promoted to the front page.
+ *   - node-sticky: Nodes ordered above other non-sticky nodes in teaser
+ *     listings.
+ *   - node-unpublished: Unpublished nodes visible only to administrators.
+ * - $title_prefix (array): An array containing additional output populated by
+ *   modules, intended to be displayed in front of the main title tag that
+ *   appears in the template.
+ * - $title_suffix (array): An array containing additional output populated by
+ *   modules, intended to be displayed after the main title tag that appears in
+ *   the template.
+ *
+ * Other variables:
+ * - $node: Full node object. Contains data that may not be safe.
+ * - $type: Node type; for example, story, page, blog, etc.
+ * - $comment_count: Number of comments attached to the node.
+ * - $uid: User ID of the node author.
+ * - $created: Time the node was published formatted in Unix timestamp.
+ * - $classes_array: Array of html class attribute values. It is flattened
+ *   into a string within the variable $classes.
+ * - $zebra: Outputs either "even" or "odd". Useful for zebra striping in
+ *   teaser listings.
+ * - $id: Position of the node. Increments each time it's output.
+ *
+ * Node status variables:
+ * - $view_mode: View mode; for example, "full", "teaser".
+ * - $teaser: Flag for the teaser state (shortcut for $view_mode == 'teaser').
+ * - $page: Flag for the full page state.
+ * - $promote: Flag for front page promotion state.
+ * - $sticky: Flags for sticky post setting.
+ * - $status: Flag for published status.
+ * - $comment: State of comment settings for the node.
+ * - $readmore: Flags true if the teaser content of the node cannot hold the
+ *   main body content.
+ * - $is_front: Flags true when presented in the front page.
+ * - $logged_in: Flags true when the current user is a logged-in member.
+ * - $is_admin: Flags true when the current user is an administrator.
+ *
+ * Field variables: for each field instance attached to the node a corresponding
+ * variable is defined; for example, $node->body becomes $body. When needing to
+ * access a field's raw values, developers/themers are strongly encouraged to
+ * use these variables. Otherwise they will have to explicitly specify the
+ * desired field language; for example, $node->body['en'], thus overriding any
+ * language negotiation rule that was previously applied.
+ *
+ * @see template_preprocess()
+ * @see template_preprocess_node()
+ * @see template_process()
+ */
+?>
+
+<?php
+  // Determine the URL of the JBrowse based on the node properties
+  $url = $node->field_jburl['und'][0]['url'];
+  $location = (!empty($node->field_jbloc)) ? $node->field_jbloc['und'][0]['safe_value'] : '';
+  $tracks = (!empty($node->field_jbtracks)) ? $node->field_jbtracks['und'][0]['safe_value'] : '';
+
+  $url = "$url/?q=loc=$location&tracks=$tracks";
+?>
 
-<script type="text/javascript" src="/jbrowse/Lentil/src/dojo/dojo.js" data-dojo-config="async: 1, baseUrl: '/jbrowse/Lentil/src'"></script>
-<script type="text/javascript" src="/jbrowse/Lentil/src/JBrowse/init.js"></script>
-
-<script type="text/javascript">
-    window.onerror=function(msg){
-        if( document.body )
-            document.body.setAttribute("JSError",msg);
-    }
-
-    // add this.resolveUrl() on 1537-1538 of src/JBrowse/Browser.js
-    // add /jbrowse/Lentil on 69 of src/dojo/dojo.js
-
-    // puts the main Browser object in this for convenience.  feel
-    // free to move it into function scope if you want to keep it
-    // out of the global namespace
-    var JBrowse;
-    require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
-         function (Browser,ioQuery,JSON) {
-               // the initial configuration of this JBrowse
-               // instance
-
-               // NOTE: this initial config is the same as any
-               // other JBrowse config in any other file.  this
-               // one just sets defaults from URL query params.
-               // If you are embedding JBrowse in some other app,
-               // you might as well just set this initial config
-               // to something like { include: '../my/dynamic/conf.json' },
-               // or you could put the entire
-               // dynamically-generated JBrowse config here.
-
-               // parse the query vars in the page URL
-               var queryParams = ioQuery.queryToObject( window.location.search.slice(1) );
-
-               var config = {
-                   containerID: "JBrowseInstance",
-
-                   dataRoot: '/jbrowse/Lentil/data',
-                   browserRoot: '/jbrowse/Lentil',
-                   queryParams: queryParams,
-                   location: queryParams.loc,
-                   forceTracks: queryParams.tracks,
-                   initialHighlight: queryParams.highlight,
-                   show_nav: queryParams.nav,
-                   show_tracklist: queryParams.tracklist,
-                   show_overview: queryParams.overview,
-                   stores: { url: { type: "JBrowse/Store/SeqFeature/FromConfig", features: [] } },
-                   makeFullViewURL: function( browser ) {
-
-                       // the URL for the 'Full view' link
-                       // in embedded mode should be the current
-                       // view URL, except with 'nav', 'tracklist',
-                       // and 'overview' parameters forced to 1.
-
-                       return browser.makeCurrentViewURL({ nav: 1, tracklist: 1, overview: 1 });
-                   },
-                   updateBrowserURL: true
-               };
-
-               //if there is ?addFeatures in the query params,
-               //define a store for data from the URL
-               if( queryParams.addFeatures ) {
-                   config.stores.url.features = JSON.parse( queryParams.addFeatures );
-               }
-
-               // if there is ?addTracks in the query params, add
-               // those track configurations to our initial
-               // configuration
-               if( queryParams.addTracks ) {
-                   config.tracks = JSON.parse( queryParams.addTracks );
-               }
-
-               // if there is ?addStores in the query params, add
-               // those store configurations to our initial
-               // configuration
-               if( queryParams.addStores ) {
-                   config.stores = JSON.parse( queryParams.addStores );
-               }
-
-               // create a JBrowse global variable holding the JBrowse instance
-               JBrowse = new Browser( config );
-    });
+<div id="node-<?php print $node->nid; ?>" class="<?php print $classes; ?> clearfix"<?php print $attributes; ?>>
 
-</script>
+  <?php if (!$page): ?>
+    <h2<?php print $title_attributes; ?>>
+      <a href="<?php print $node_url; ?>"><?php print $title; ?></a>
+    </h2>
+  <?php endif; ?>
+  <?php print render($title_suffix); ?>
 
-<div id="node-<?php print $node->nid; ?>" class="<?php print $classes; ?> clearfix"<?php print $attributes; ?>>
   <div class="content clearfix"<?php print $content_attributes; ?>>
-    <div id="JBrowse" style="height: 700px;">
-      <div id="JBrowseInstance" ></div>
+    <div id="JBrowseInstance">
+      <iframe src="<?php print $url;?>" width="100%" height="100%">
+      </iframe>
     </div>
   </div>
+
 </div>

tripal_jbrowse.module

@@ -19,32 +19,4 @@ function tripal_jbrowse_theme($existing, $type, $theme, $path) {
   );
 
   return $items;
-}
-
-/**
- * Implements node preprocess hook.
- */
-function tripal_jbrowse_preprocess_node(&$vars) {
-
-  if ($vars['node']->type == 'jbrowse_instance') {
-    $path = $vars['node']->field_jburl['und'][0]['url'];
-
-    $files = array(
-      'combination_tracks.css',
-      'faceted_track_selector.css',
-      'icons.css',
-      'maker.css',
-      'sequence.css',
-      'tristate.css',
-      'export_dialog.css',
-      'file_dialog.css',
-      'hierarchical_track_selector.css',
-      'main.css',
-      'menubar.css',
-      'track_styles.css'
-    );
-    foreach ($files as $filename) {
-      $sheets = drupal_add_css($path . '/' . $filename, array('group' => CSS_THEME, 'type' => 'external'));
-    }
-  }
 }