fixing more tests

README.md

@@ -362,7 +362,7 @@ They look like this:
 
 # Protein Editor
 OVE can be set up to view and edit proteins (Amino Acid sequences) as first class citizens. 
-The protein editor can be seen here: http://teselagen.github.io/openVectorEditor/#/Editor?isProtein=true 
+The protein editor can be seen here: http://teselagen.github.io/openVectorEditor/#/Editor?moleculeType=Protein
 
 The editor supports Amino Acid sequences as well as DNA sequences!
 Protein sequence mode is enabled by calling updateEditor with a protein sequenceData object: 

cypress/integration/copyPaste.spec.js

@@ -2,20 +2,6 @@ describe("copyPaste", function () {
  beforeEach(() => {
  cy.visit("");
  });
- // it(`isProtein mode - copy via hotkey`, () => {
- // cy.contains(".tg-menu-bar button", "Edit").click();
- // cy.contains(".bp3-menu-item", "Copy").click();
- // cy.window().then(() => {
- // assert(
- // window.Cypress.textToCopy ===
- // "FCILLAAVSGAEGWGYYGCDEELVGPLYARSLGASSYYSLLTAPRFARLHGISGWSPRIGDPNPWLQIDLMKKHRIRAVATQGSFNSWDWVTRYMLLYGDRVDSWTPFYQRGHNSTFFGNVNESAVVRHDLHFHFTARYIRIVPLAWNPRGKIGLRLGLYGCPYKADILYFDGDDAISYRFPRGVSRSLWDVFAFSFKTEEKDGLLLHAEGAQGDYVTLELEGAHLLLHMSLGSSPIQPRPGHTTVSAGGVLNDQHWHYVRVDRFGRDVNFTLDGYVQRFILNGDFERLNLDTEMFIGGLVGAARKNLAYRHNFRGCIENVIFNRVNIADLAVRRHSRITFEGKVAFRCLDPVPHPINFGGPHNFVQVPGFPRRGRLAVSFRFRTWDLTGLLLFSRLGDGLGHVELTLSEGQVNVSIAQSGRKKLQFAAGYRLNDGFWHEVNFVAQENHAVISIDDVEGAEVRVSYPLLIRTGTSYFFGGCPKPASRWDCHSNQTAFHGCMELLKVDGQLVNLTLVEGRRLGFYAEVLFDTCGITDRCSPNMCEHDGRCYQSWDDFICYCELTGYKGETCHTPLYKESCEAYRLSGKTSGNFTIDPDGSGPLKPFVVYCDIRENRAWTVVRHDRLWTTRVTGSSMERPFLGAIQYWNASWEEVSALANASQHCEQWIEFSCYNSRLLNTAGGYPYSFWIGRNEEQHFYWGGSQPGIQRCACGLDRSCVDPALYCNCDADQPQWRTDKGLLTFVDHLPVTQVVIGDTNRSTSEAQFFLRPLRCYGDRNSWNTISFHTGAALRFPPIRANHSLDVSFYFRTSAPSGVFLENMGGPYCQWRRPYVRVELNTSRDVVFAFDVGNGDENLTVHSDDFEFNDDEWHLVRAEINVK"
- // );
- // assert(
- // window.Cypress.seqDataToCopy.proteinSequence ===
- // "fcillaavsgaegwgyygcdeelvgplyarslgassyyslltaprfarlhgisgwsprigdpnpwlqidlmkkhriravatqgsfnswdwvtrymllygdrvdswtpfyqrghnstffgnvnesavvrhdlhfhftaryirivplawnprgkiglrlglygcpykadilyfdgddaisyrfprgvsrslwdvfafsfkteekdglllhaegaqgdyvtlelegahlllhmslgsspiqprpghttvsaggvlndqhwhyvrvdrfgrdvnftldgyvqrfilngdferlnldtemfigglvgaarknlayrhnfrgcienvifnrvniadlavrrhsritfegkvafrcldpvphpinfggphnfvqvpgfprrgrlavsfrfrtwdltglllfsrlgdglghveltlsegqvnvsiaqsgrkklqfaagyrlndgfwhevnfvaqenhavisiddvegaevrvsypllirtgtsyffggcpkpasrwdchsnqtafhgcmellkvdgqlvnltlvegrrlgfyaevlfdtcgitdrcspnmcehdgrcyqswddficyceltgykgetchtplykesceayrlsgktsgnftidpdgsgplkpfvvycdirenrawtvvrhdrlwttrvtgssmerpflgaiqywnasweevsalanasqhceqwiefscynsrllntaggypysfwigrneeqhfywggsqpgiqrcacgldrscvdpalycncdadqpqwrtdkglltfvdhlpvtqvvigdtnrstseaqfflrplrcygdrnswntisfhtgaalrfppiranhsldvsfyfrtsapsgvflenmggpycqwrrpyvrvelntsrdvvfafdvgngdenltvhsddfefnddewhlvraeinvk"
- // );
- // });
- // });
  it(`isProtein mode - copy genbank of protein`, () => {
  cy.get(`[data-test="moleculeType"]`).select("Protein");
 

cypress/integration/demo.spec.js

@@ -1,9 +1,13 @@
 describe("demo", function () {
  it(`users should be able to search the options in the demo`, () => {
  cy.visit("");
- cy.contains(`.toggle-button-holder`, "isProtein").should("exist");
+ cy.contains(`.toggle-button-holder`, "Show Rotate Circular View").should(
+ "exist"
+ );
  cy.get(`[placeholder="Search Options.."]`).type("Custom");
- cy.contains(`.toggle-button-holder`, "isProtein").should("not.exist");
+ cy.contains(`.toggle-button-holder`, "Show Rotate Circular View").should(
+ "not.exist"
+ );
  cy.contains(`.toggle-button-holder`, "Customize property tabs").should(
  "exist"
  );

cypress/integration/rna.spec.js

@@ -4,17 +4,17 @@ describe("rna editing in OVE", function () {
  });
 
  it(`should support rna editing`, () => {
- cy.tgToggle(`isRna`);
+ cy.get(`[data-test="moleculeType"]`).select("RNA");
  cy.contains("uuaugacaacuugacggcuacaucauucacuuuuucuuca");
  cy.selectRange(10, 11);
- cy.get(".veSelectionLayer").first().rightclick();
+ cy.get(".veSelectionLayer").first().rightclick({ force: true });
  cy.contains(".bp3-menu-item", "Replace").click();
  cy.focused().type("tguugttuuuuuuuuuuuuuuuaa{enter}");
  cy.contains("Selecting 21 bps from 10 to 30"); //the t's should be filtered out
  cy.contains("guuguuuuuuuuuuuuuuuaa");
  });
  it(`should support mixed rna and dna editing`, () => {
- cy.tgToggle(`isMixedRnaAndDna`);
+ cy.get(`[data-test="moleculeType"]`).select("mixedRnaAndDna");
  cy.contains("uuaugacaacuugacggcuacaucauucacuuuuucuuca").should("not.exist");
  cy.contains("uuuugacgt");
  cy.selectRange(10, 11);

demo/src/EditorDemo/index.js

@@ -437,7 +437,7 @@ updateEditor(store, "DemoEditor", {
  })}
  {renderToggle({
  isSelect: true,
- options: ["DNA", "RNA", "Protein"],
+ options: ["DNA", "RNA", "Protein", "mixedRnaAndDna"],
  that: this,
  label: "Molecule Type:",
  type: "moleculeType",
@@ -504,6 +504,18 @@ certain dna specific tools and annotations are automatically disabled when isPro
  readOnly: false,
  sequenceData: { ...exampleSequenceData, isRna: true }
  });
+ } else if (val === "mixedRnaAndDna") {
+ updateEditor(store, "DemoEditor", {
+ readOnly: false,
+ sequenceData: tidyUpSequenceData(
+ {
+ ...exampleSequenceData,
+ sequence: "uuuu" + exampleSequenceData.sequence,
+ isMixedRnaAndDna: true
+ },
+ {}
+ )
+ });
  } else {
  updateEditor(store, "DemoEditor", {
  readOnly: false,

src/updateEditor.js

@@ -66,7 +66,7 @@ export default function updateEditor(
  },
  annotationVisibility: {
  caret: true,
- sequence: false,
+ sequence: true,
  reverseSequence: false,
  ...annotationVisibility, //we spread this here to allow the user to override this .. if they must!
  translations: false,