diff --git a/packages/ove/src/CircularView/Labels/index.js b/packages/ove/src/CircularView/Labels/index.js index 54cba390..9392ca1e 100644 --- a/packages/ove/src/CircularView/Labels/index.js +++ b/packages/ove/src/CircularView/Labels/index.js @@ -416,23 +416,9 @@ function LabelLine(pointArray, options) { }); return ( - {/* */} ); diff --git a/packages/ove/src/Reflex/reflex-styles.css b/packages/ove/src/Reflex/reflex-styles.css index 7f0ce7a7..9d5fdc54 100644 --- a/packages/ove/src/Reflex/reflex-styles.css +++ b/packages/ove/src/Reflex/reflex-styles.css @@ -34,19 +34,19 @@ } .reflex-layout > .reflex-splitter { - background-color: #f5f8fa; + background-color: #f1f1f1; z-index: 100; } .reflex-layout > .reflex-splitter.active, .reflex-layout > .reflex-splitter:hover { - background-color: #f5f8fa; + background-color: #cccccc; transition: all 1s ease; } .reflex-layout.horizontal > .reflex-splitter { - border-bottom: 1px solid #f5f8fa; - border-top: 1px solid #f5f8fa; + border-bottom: 1px solid #f1f1f1; + border-top: 1px solid #f1f1f1; cursor: row-resize; width: 100%; height: 2px; @@ -54,13 +54,13 @@ .reflex-layout.horizontal > .reflex-splitter:hover, .reflex-layout.horizontal > .reflex-splitter.active { - border-bottom: 1px solid #f5f8fa; - border-top: 1px solid #f5f8fa; + border-bottom: 1px solid #cccccc; + border-top: 1px solid #cccccc; } .reflex-layout.vertical > .reflex-splitter { - border-right: 1px solid #f5f8fa; - border-left: 1px solid #f5f8fa; + border-right: 1px solid #f1f1f1; + border-left: 1px solid #f1f1f1; cursor: col-resize; height: 95%; width: 2px; @@ -73,8 +73,8 @@ .reflex-layout.vertical > .reflex-splitter:hover, .reflex-layout.vertical > .reflex-splitter.active { - border-right: 1px solid #f5f8fa; - border-left: 1px solid #f5f8fa; + border-right: 1px solid #cccccc; + border-left: 1px solid #cccccc; } .reflex-layout > .reflex-splitter.reflex-thin { diff --git a/packages/ove/src/RowItem/CutsiteSelectionLayers.js b/packages/ove/src/RowItem/CutsiteSelectionLayers.js index 0adf6fb1..acf3b1cb 100644 --- a/packages/ove/src/RowItem/CutsiteSelectionLayers.js +++ b/packages/ove/src/RowItem/CutsiteSelectionLayers.js @@ -26,10 +26,10 @@ export const CutsiteSelectionLayers = connectToEditor( layer.start > -1 && ( diff --git a/packages/ove/src/RowItem/Translations/Translation.js b/packages/ove/src/RowItem/Translations/Translation.js index 95b028c6..bff76b51 100644 --- a/packages/ove/src/RowItem/Translations/Translation.js +++ b/packages/ove/src/RowItem/Translations/Translation.js @@ -69,6 +69,7 @@ class Translation extends React.Component { nextAaSliver = aminoAcidsForSubrange[index + 2]; return ( exonRange.some(r => isPositionWithinRange(baseIndex, r, sequenceString.length, true, false) @@ -251,28 +250,31 @@ export default function getAminoAcidDataForEachBaseOfDna( let positionInCodon = 0; for (let i = 0; i < basesRead; i++) { const posInCds = i + index; + const sequenceIndex = codonPositionsInCDS.includes(posInCds) + ? absoluteCodonPositions[codonPositionsInCDS.indexOf(posInCds)] + : positionInCdsToPositionInMainSequence( + posInCds, + forward, + translationRange, + originalSequenceStringLength + ); if (codonPositionsInCDS.includes(posInCds)) { aminoAcidDataForEachBaseOfDNA.push({ aminoAcid, positionInCodon, aminoAcidIndex, - sequenceIndex: absoluteCodonPositions[i], + sequenceIndex, codonRange, fullCodon: codonPositionsInCDS.length === 3 }); positionInCodon++; } else { - // TODO: what should we insert here? + // push a null object for intron bases aminoAcidDataForEachBaseOfDNA.push({ aminoAcid: null, positionInCodon: null, aminoAcidIndex: null, - sequenceIndex: positionInCdsToPositionInMainSequence( - posInCds, - forward, - translationRange, - originalSequenceStringLength - ), + sequenceIndex, codonRange: null, fullCodon: null }); diff --git a/packages/ui/src/utils/menuUtils.js b/packages/ui/src/utils/menuUtils.js index 53c4d2ac..8d147da4 100644 --- a/packages/ui/src/utils/menuUtils.js +++ b/packages/ui/src/utils/menuUtils.js @@ -244,7 +244,7 @@ export const DynamicMenuItem = ({ ? item.submenu .filter(ident) .map((def, index) => ( - + )) : undefined} @@ -268,7 +268,7 @@ export const DynamicMenuItem = ({ export const createDynamicMenu = (menuDef, enhancers, context) => { if (menuDef instanceof Array) { return menuDef.map((def, index) => ( - + )); } else { return ; @@ -282,7 +282,7 @@ export const createDynamicBarMenu = (topMenuDef, enhancers, context) => { const def = { ...topLevelItem }; if (def.submenu) { def.submenu = def.submenu.map((subdef, index) => ( - + )); } return def;