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dhusondhuson
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working on generating documentation
1 parent 6ba53e7 commit ff25983

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2 files changed

+113
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‎src/main/java/splitstree6/xtra/latex/MenusToLaTeX.java

Lines changed: 7 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -23,15 +23,21 @@
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import javafx.scene.control.MenuBar;
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import javafx.scene.control.SeparatorMenuItem;
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import static splitstree6.xtra.latex.IOToLaTeX.FOOTER;
27+
import static splitstree6.xtra.latex.IOToLaTeX.HEADER;
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/**
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* write out all items in the menu bar in LaTeX
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*/
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public class MenusToLaTeX {
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public static String apply(MenuBar menuBar) {
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var buf = new StringBuilder("\\section{The main menu bar}\n\n");
34+
var buf = new StringBuilder();
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buf.append(HEADER);
36+
buf.append("\\section{The main menu bar}\n\n");
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for (var menu : menuBar.getMenus()) {
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buf.append(applyRec(menu, 0));
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}
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buf.append(FOOTER);
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return buf.toString();
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}
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‎src/main/resources/splitstree6/window/MainWindow.fxml

Lines changed: 106 additions & 60 deletions
Original file line numberDiff line numberDiff line change
@@ -207,7 +207,7 @@
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</accelerator>
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</CheckMenuItem>
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<MenuItem fx:id="findAgainMenuItem" text="Find Again"
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userData="Find next match int the current tab">
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userData="Find next match in the current tab">
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<accelerator>
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<KeyCodeCombination alt="UP" code="G" control="UP" meta="UP" shift="UP"
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shortcut="DOWN"/>
@@ -372,84 +372,130 @@
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<CheckMenuItem fx:id="logDetMenuItem" text="Log Det"
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userData="Compute distances using the Log-Det method"/>
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<SeparatorMenuItem mnemonicParsing="false"/>
375-
<CheckMenuItem fx:id="hky85MenuItem" text="HKY 85"/>
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<CheckMenuItem fx:id="jukesCantorMenuItem" text="Jukes Cantor"/>
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<CheckMenuItem fx:id="k2pMenuItem" text="K2P"/>
378-
<CheckMenuItem fx:id="k3stMenuItem" text="K3ST"/>
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<CheckMenuItem fx:id="f81MenuItem" text="F81"/>
380-
<CheckMenuItem fx:id="f84MenuItem" text="F84"/>
381-
<SeparatorMenuItem mnemonicParsing="false"/>
382-
<CheckMenuItem fx:id="proteinMLDistanceMenuItem" text="Protein ML Dist"/>
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<SeparatorMenuItem mnemonicParsing="false"/>
384-
<CheckMenuItem fx:id="geneContentDistanceMenuItem" text="Gene Content Distance"/>
375+
<CheckMenuItem fx:id="hky85MenuItem" text="HKY 85"
376+
userData="Compute distances using the Hasegawa-Kishino-Yano model"/>
377+
<CheckMenuItem fx:id="jukesCantorMenuItem" text="Jukes Cantor"
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userData="Compute distances using the Jukes-Cantor model"/>
379+
<CheckMenuItem fx:id="k2pMenuItem" text="K2P"
380+
userData="Compute distances using the Kimura-2P model"/>
381+
<CheckMenuItem fx:id="k3stMenuItem" text="K3ST"
382+
userData="Compute distances using the Kimura-3ST model"/>
383+
<CheckMenuItem fx:id="f81MenuItem" text="F81"
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userData="Compute distances using the Felsenstein-1981 model"/>
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<CheckMenuItem fx:id="f84MenuItem" text="F84"
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userData="Compute distances using the Felsenstein-1984 model"/>
387+
<SeparatorMenuItem mnemonicParsing="false"/>
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<CheckMenuItem fx:id="proteinMLDistanceMenuItem" text="Protein ML Dist"
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userData="Compute distances for proteins using maximum-likelihood estimation"/>
390+
<SeparatorMenuItem mnemonicParsing="false"/>
391+
<CheckMenuItem fx:id="geneContentDistanceMenuItem" text="Gene Content Distance"
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userData="Compute distances based on the presence/absence of genes"/>
385393
</Menu>
386394
<Menu text="Tree">
387-
<CheckMenuItem fx:id="njMenuItem" text="NJ"/>
388-
<CheckMenuItem fx:id="bioNJMenuItem" text="BioNJ"/>
389-
<CheckMenuItem fx:id="upgmaMenuItem" text="UPGMA"/>
390-
<SeparatorMenuItem mnemonicParsing="false"/>
391-
<CheckMenuItem fx:id="bunemanTreeMenuItem" text="Buneman Tree"/>
392-
<SeparatorMenuItem mnemonicParsing="false"/>
393-
<CheckMenuItem fx:id="consensusTreeMenuItem" text="Consensus Tree"/>
394-
<SeparatorMenuItem mnemonicParsing="false"/>
395-
<CheckMenuItem fx:id="minSpanningTreeMenuItem" text="Minimum Spanning Tree"/>
396-
<SeparatorMenuItem mnemonicParsing="false"/>
397-
<CheckMenuItem fx:id="rerootOrReorderTreesMenuItem" text="Reroot Or Reorder Trees"/>
398-
<SeparatorMenuItem mnemonicParsing="false"/>
399-
<CheckMenuItem fx:id="viewSingleTreeMenuItem" text="Show Single Tree"/>
400-
<CheckMenuItem fx:id="viewTreePagesMenuItem" text="Show Tree Pages"/>
401-
<SeparatorMenuItem mnemonicParsing="false"/>
402-
<CheckMenuItem fx:id="viewTanglegramMenuItem" text="Show Tanglegram"/>
403-
<CheckMenuItem fx:id="viewDensiTreeMenuItem" text="Show DensiTree"/>
395+
<CheckMenuItem fx:id="njMenuItem" text="NJ"
396+
userData="Compute a tree from distances using the Neighbor-Joining method"/>
397+
<CheckMenuItem fx:id="bioNJMenuItem" text="BioNJ"
398+
userData="Compute a tree from distances using the Bio-NJ method"/>
399+
<CheckMenuItem fx:id="upgmaMenuItem" text="UPGMA"
400+
userData="Compute a rooted tree from distances using the UPGMA method"/>
401+
<SeparatorMenuItem mnemonicParsing="false"/>
402+
<CheckMenuItem fx:id="bunemanTreeMenuItem" text="Buneman Tree"
403+
userData="Compute a tree from distances using the Buneman tree method"/>
404+
<SeparatorMenuItem mnemonicParsing="false"/>
405+
<CheckMenuItem fx:id="consensusTreeMenuItem" text="Consensus Tree"
406+
userData="Compute a consensus tree"/>
407+
<SeparatorMenuItem mnemonicParsing="false"/>
408+
<CheckMenuItem fx:id="minSpanningTreeMenuItem" text="Minimum Spanning Tree"
409+
userData="Compute a minimum spanning tree from distances"/>
410+
<SeparatorMenuItem mnemonicParsing="false"/>
411+
<CheckMenuItem fx:id="rerootOrReorderTreesMenuItem" text="Reroot Or Reorder Trees"
412+
userData="Open the reroot or reorder tab"/>
413+
<SeparatorMenuItem mnemonicParsing="false"/>
414+
<CheckMenuItem fx:id="viewSingleTreeMenuItem" text="Show Single Tree"
415+
userData="Show a single tree in a tab"/>
416+
<CheckMenuItem fx:id="viewTreePagesMenuItem" text="Show Tree Pages"
417+
userData="Show multiple trees in a tab"/>
418+
<SeparatorMenuItem mnemonicParsing="false"/>
419+
<CheckMenuItem fx:id="viewTanglegramMenuItem" text="Show Tanglegram"
420+
userData="Show two trees as a tanglegram"/>
421+
<CheckMenuItem fx:id="viewDensiTreeMenuItem" text="Show DensiTree"
422+
userData="Show a Bayesian chain of trees as a densi-tree"/>
404423
</Menu>
405424
<Menu text="Network">
406-
<CheckMenuItem fx:id="neighborNetMenuItem" text="Neighbor Net"/>
407-
<CheckMenuItem fx:id="splitDecompositionMenuItem" text="Split Decomposition"/>
408-
<CheckMenuItem fx:id="parsimonySplitsMenuItem" text="Parsimony Splits"/>
409-
<SeparatorMenuItem mnemonicParsing="false"/>
410-
<CheckMenuItem fx:id="consensusSplitsMenuItem" text="Consensus Splits"/>
411-
<CheckMenuItem fx:id="consensusNetworkMenuItem" text="Consensus Network"/>
412-
<CheckMenuItem fx:id="consensusOutlineMenuItem" text="Consensus Outline"/>
413-
<CheckMenuItem fx:id="superNetworkMenuItem" text="Super Network"/>
414-
<SeparatorMenuItem mnemonicParsing="false"/>
415-
<CheckMenuItem fx:id="medianJoiningMenuItem" text="Median Joining Network"/>
416-
<CheckMenuItem fx:id="minSpanningNetworkMenuItem" text="Min Spanning Network"/>
417-
<SeparatorMenuItem mnemonicParsing="false"/>
418-
<CheckMenuItem fx:id="hybridizationNetworkMenuItem" text="Hybridization Network"/>
419-
<CheckMenuItem fx:id="clusterNetworkMenuItem" text="Cluster Network"/>
425+
<CheckMenuItem fx:id="neighborNetMenuItem" text="Neighbor Net"
426+
userData="Compute a planar split network from distances using the Neighbor-Net method"/>
427+
<CheckMenuItem fx:id="splitDecompositionMenuItem" text="Split Decomposition"
428+
userData="Compute a split network from distances using the split-decomposition method"/>
429+
<CheckMenuItem fx:id="parsimonySplitsMenuItem" text="Parsimony Splits"
430+
userData="Compute a split network from DNA sequences using the parsimony-splits method"/>
431+
<SeparatorMenuItem mnemonicParsing="false"/>
432+
<CheckMenuItem fx:id="consensusSplitsMenuItem" text="Consensus Splits"
433+
userData="Open the consensus splits tab"/>
434+
<CheckMenuItem fx:id="consensusNetworkMenuItem" text="Consensus Network"
435+
userData="Compute a consensus network from trees"/>
436+
<CheckMenuItem fx:id="consensusOutlineMenuItem" text="Consensus Outline"
437+
userData="Compute a consensus outline from trees"/>
438+
<CheckMenuItem fx:id="superNetworkMenuItem" text="Super Network"
439+
userData="Compute a super network from trees on unequal taxon sets"/>
440+
<SeparatorMenuItem mnemonicParsing="false"/>
441+
<CheckMenuItem fx:id="medianJoiningMenuItem" text="Median Joining Network"
442+
userData="Compute a haplotype network from DNA sequences using the median-joining algorithm"/>
443+
<CheckMenuItem fx:id="minSpanningNetworkMenuItem" text="Min Spanning Network"
444+
userData="Compute a minimum spanning network from distances"/>
445+
<SeparatorMenuItem mnemonicParsing="false"/>
446+
<CheckMenuItem fx:id="hybridizationNetworkMenuItem" text="Hybridization Network"
447+
userData="Compute a minimum hybridization network for two rooted trees using the autumn algorithm"/>
448+
<CheckMenuItem fx:id="clusterNetworkMenuItem" text="Cluster Network"
449+
userData="Compute a cluster network from trees"/>
420450

421451
</Menu>
422452
<Menu text="Analysis">
423-
<CheckMenuItem fx:id="bootStrapTreeMenuItem" text="Bootstrap Tree..."/>
424-
<CheckMenuItem fx:id="bootstrapTreeAsNetworkMenuItem" text="Bootstrap Tree as Network..."/>
425-
<CheckMenuItem fx:id="bootStrapNetworkMenuItem" text="Bootstrap Splits Network..."/>
426-
<SeparatorMenuItem mnemonicParsing="false"/>
427-
<MenuItem fx:id="estimateInvariableSitesMenuItem" text="Estimate Invariable Sites"/>
428-
<MenuItem fx:id="computeDeltaScoreMenuItem" text="Compute Delta Score"/>
429-
<MenuItem fx:id="phiTestMenuItem" text="Conduct Phi Test for Recombination"/>
453+
<CheckMenuItem fx:id="bootStrapTreeMenuItem" text="Bootstrap Tree..."
454+
userData="Perform bootstrapping on a tree calculation from sequences"/>
455+
<CheckMenuItem fx:id="bootstrapTreeAsNetworkMenuItem" text="Bootstrap Tree as Network..."
456+
userData="Perform bootstrapping on a tree calculation from sequences, producing a network"/>
457+
<CheckMenuItem fx:id="bootStrapNetworkMenuItem" text="Bootstrap Splits Network..."
458+
userData="Perform bootstrapping on a split network calculation from sequences"/>
459+
<SeparatorMenuItem mnemonicParsing="false"/>
460+
<MenuItem fx:id="estimateInvariableSitesMenuItem" text="Estimate Invariable Sites"
461+
userData="Estimate the proportion of invariable sites"/>
462+
<MenuItem fx:id="computeDeltaScoreMenuItem" text="Compute Delta Score"
463+
userData="Compute the delta score from distances"/>
464+
<MenuItem fx:id="phiTestMenuItem" text="Conduct Phi Test for Recombination"
465+
userData="Run the Phi Test to detect recombination in sequences"/>
430466
<SeparatorMenuItem mnemonicParsing="false"/>
431467
<MenuItem fx:id="computeSplitsPhylogeneticDiversityMenuItem"
432-
text="Splits Phylogenetic Diversity"/>
433-
<MenuItem fx:id="computeSplitsShapleyValuesMenuItem" text="Splits Shapley Values"/>
468+
text="Splits Phylogenetic Diversity"
469+
userData="Computes the phylogenetic diversity for selected taxa on splits"/>
470+
<MenuItem fx:id="computeSplitsShapleyValuesMenuItem" text="Splits Shapley Values"
471+
userData="Computes Shapely values on splits"/>
434472
<SeparatorMenuItem mnemonicParsing="false"/>
435-
<MenuItem fx:id="computeTreePhylogeneticDiversityMenuItem" text="Tree Phylogenetic Diversity"/>
473+
<MenuItem fx:id="computeTreePhylogeneticDiversityMenuItem" text="Tree Phylogenetic Diversity"
474+
userData="Computes the phylogenetic diversity for selected taxa on trees"/>
436475
<MenuItem fx:id="computeRootedTreeFairProportionMenuItem"
437-
text="Rooted Tree Fair Proportion Diversity Index"/>
476+
text="Rooted Tree Fair Proportion Diversity Index"
477+
userData="Compute rooted-tree fair-proportion diversity index"/>
438478
<MenuItem fx:id="computeRootedTreeEqualSplitsMenuItem"
439-
text="Rooted Tree Equal Splits Diversity Index"/>
440-
<MenuItem fx:id="computeUnrootedTreeShapleyMenuItem" text="Unrooted Tree Shapley Values"/>
479+
text="Rooted Tree Equal Splits Diversity Index"
480+
userData="Compute rooted-tree equal-splits diversity index"/>
481+
<MenuItem fx:id="computeUnrootedTreeShapleyMenuItem" text="Unrooted Tree Shapley Values"
482+
userData="Computes Shapely values on unrooted trees"/>
441483
<SeparatorMenuItem mnemonicParsing="false"/>
442-
<CheckMenuItem fx:id="pcoaMenuItem" text="PCoA"/>
484+
<CheckMenuItem fx:id="pcoaMenuItem" text="PCoA"
485+
userData="Perform principal coordinate analysis on distances"/>
443486
<SeparatorMenuItem mnemonicParsing="false"/>
444-
<MenuItem fx:id="showWorkflowMenuItem" text="Show Workflow"/>
487+
<MenuItem fx:id="showWorkflowMenuItem" text="Show Workflow" userData="Show the workflow tab"/>
445488
</Menu>
446489
<Menu fx:id="windowMenu" text="Window">
447-
<CheckMenuItem fx:id="showMessageWindowMenuItem" text="Show Message Window..."/>
448-
<MenuItem fx:id="setWindowSizeMenuItem" text="Set Window Size..."/>
490+
<CheckMenuItem fx:id="showMessageWindowMenuItem" text="Show Message Window..."
491+
userData="Show or hide the message window"/>
492+
<MenuItem fx:id="setWindowSizeMenuItem" text="Set Window Size..."
493+
userData="Set the window size"/>
449494
<SeparatorMenuItem mnemonicParsing="false"/>
450495
</Menu>
451496
<Menu fx:id="helpMenu" text="Help">
452-
<MenuItem fx:id="checkForUpdatesMenuItem" text="Check For Updates..."/>
497+
<MenuItem fx:id="checkForUpdatesMenuItem" text="Check For Updates..."
498+
userData="Check whether an update is available for download"/>
453499
<SeparatorMenuItem mnemonicParsing="false"/>
454500
<MenuItem fx:id="aboutMenuItem" text="About...">
455501
<accelerator>

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