Merge pull request #29 from wmaddisn/master

3.0 beta 3

Resources/examples/Ancestral_States/02-TreeWindow.nex

@@ -427,7 +427,7 @@ Begin MESQUITE;
 					setFont SanSerif;
 					setFontSize 10;
 					setActive;
-				setExplanation 'This is the Tree Window^n^nTo show graphically a reconstruction of ancestral states, select Trace Character History under the Analysis menu of the tree window.  You may be asked what method to use (parsimony or likelihood) and what source of characters.';
+				setExplanation 'This is the Tree Window^n^nTo show graphically a reconstruction of ancestral states, select Trace Character History under the Analysis:Tree menu of the tree window.  You may be asked what method to use (parsimony or likelihood) and what source of characters.';
 				toggleFileNames off;
 				setPrevButtonName Previous;
 				setNextButtonName Next;

Resources/examples/Ancestral_States/15ab-xiphStochCharMap.nex

@@ -319,7 +319,7 @@ Begin MESQUITE;
 				toggleFileNames off;
 				setPrevButtonName Previous;
 				setNextButtonName Next;
-				addWebLink Show_Manual  'docs/mesquite/CharacterEvolution/AncestralStates.html#scm';
+				addWebLink Show_Manual  'http://mesquiteproject.wikispaces.com/Ancestral+States#scm';
 			endTell;
 			showWindow;
 		endTell;

Resources/examples/Ancestral_States/16c-TraceAllChars.nex

@@ -387,12 +387,12 @@ Begin MESQUITE;
 					getToolPalette;
 					tell It;
 					endTell;
-				setExplanation 'Trace All Characters (available in the Analysis menu) summarizes ancestral states in many characters.  A text window shows a crude table listing states at different nodes for all the characters.^n^nBy default the table lists reconstructions only for those nodes selected in the tree, and for all selected characters.  You can adjust these options using items in the Trace_All menu of the Tree Window.  There you can also change the specifications of the reconstruction.';
+				setExplanation 'Trace All Characters (available in the Analysis:Tree menu) summarizes ancestral states in many characters.  A text window shows a crude table listing states at different nodes for all the characters.^n^nBy default the table lists reconstructions only for those nodes selected in the tree, and for all selected characters.  You can adjust these options using items in the Trace_All menu of the Tree Window.  There you can also change the specifications of the reconstruction.';
 				setTitle Trace_All_Characters;
 				toggleFileNames off;
 				setPrevButtonName Previous;
 				setNextButtonName Next;
-				addWebLink Manual_page  'mesquite:docs/mesquite/AncestralStates/AncestralStates.html#tac';
+				addWebLink Manual_page  'http://mesquiteproject.wikispaces.com/Ancestral+States#tac';
 			endTell;
 			showWindow;
 		endTell;

Resources/examples/Ancestral_States/17-TraceOverTrees.nex

@@ -659,12 +659,12 @@ Begin MESQUITE;
 					setFont SanSerif;
 					setFontSize 10;
 					setActive;
-				setExplanation 'In this tree window is shown the "Trace Over Trees" feature, available in the Analysis menu of a Tree Window.  This reconstructs ancestral states over a series of selected trees, and attempts to summarize them on a single tree.  Usually you would use this by first displaying some sort of consensus tree in the tree window, then selecting a series of trees from which the consensus was derived.  Trace over Trees does NOT calculate the consensus tree automatically, but instead summarizes states on whatever tree you have in the Tree Window.^n^nIn this example the tree is a strict consensus of some most parsimonious trees, on which the character''s evolution was reconstructed.^n^nThe method shows, at each node in your consensus tree, the ancestral states reconstructed in the various other trees that happened to have that same clade.  If the other tree doesn''t have that clade, its state at that node is not (of course) recorded for that node.^n^nIf you hold the cursor over the node, the Trace over Trees legend will show details like how many of the trees show each of the character states at the node, and how many of the trees total have the node (i.e. the clade).^n';
+				setExplanation 'In this tree window is shown the "Trace Over Trees" feature, available in the Analysis:Tree menu of a Tree Window.  This reconstructs ancestral states over a series of selected trees, and attempts to summarize them on a single tree.  Usually you would use this by first displaying some sort of consensus tree in the tree window, then selecting a series of trees from which the consensus was derived.  Trace over Trees does NOT calculate the consensus tree automatically, but instead summarizes states on whatever tree you have in the Tree Window.^n^nIn this example the tree is a strict consensus of some most parsimonious trees, on which the character''s evolution was reconstructed.^n^nThe method shows, at each node in your consensus tree, the ancestral states reconstructed in the various other trees that happened to have that same clade.  If the other tree doesn''t have that clade, its state at that node is not (of course) recorded for that node.^n^nIf you hold the cursor over the node, the Trace over Trees legend will show details like how many of the trees show each of the character states at the node, and how many of the trees total have the node (i.e. the clade).^n';
 				setTitle Trace_over_trees;
 				toggleFileNames off;
 				setPrevButtonName Previous;
 				setNextButtonName Next;
-				addWebLink Manual_page  'mesquite:docs/mesquite/AncestralStates/AncestralStates.html#tcot';
+				addWebLink Manual_page  'http://mesquiteproject.wikispaces.com/Ancestral+States#tcot';
 			endTell;
 			showWindow;
 		endTell;

Resources/examples/Ancestral_States/17a-TraceOverTrees.nex

@@ -1324,12 +1324,12 @@ Begin MESQUITE;
 					setFont SanSerif;
 					setFontSize 10;
 					setActive;
-				setExplanation 'In this tree window is shown the "Trace Over Trees" feature, available in the Analysis menu of a Tree Window.  This reconstructs ancestral states over a series of selected trees, and attempts to summarize them on a single tree.  Usually you would use this by first displaying some sort of consensus tree in the tree window, then selecting a series of trees from which the consensus was derived.  Trace over Trees does NOT calculate the consensus tree automatically, but instead summarizes states on whatever tree you have in the Tree Window.^n^nIn this example the tree is a strict consensus of some most parsimonious trees, on which the character''s evolution was reconstructed.^n^nThe method shows, at each node in your consensus tree, the ancestral states reconstructed in the various other trees that happened to have that same clade.  If the other tree doesn''t have that clade, its state at that node is not (of course) recorded for that node.^n^nIf you hold the cursor over the node, the Trace over Trees legend will show details like how many of the trees show each of the character states at the node, and how many of the trees total have the node (i.e. the clade).^n';
+				setExplanation 'In this tree window is shown the "Trace Over Trees" feature, available in the Analysis:Tree menu of a Tree Window.  This reconstructs ancestral states over a series of selected trees, and attempts to summarize them on a single tree.  Usually you would use this by first displaying some sort of consensus tree in the tree window, then selecting a series of trees from which the consensus was derived.  Trace over Trees does NOT calculate the consensus tree automatically, but instead summarizes states on whatever tree you have in the Tree Window.^n^nIn this example the tree is a strict consensus of some most parsimonious trees, on which the character''s evolution was reconstructed.^n^nThe method shows, at each node in your consensus tree, the ancestral states reconstructed in the various other trees that happened to have that same clade.  If the other tree doesn''t have that clade, its state at that node is not (of course) recorded for that node.^n^nIf you hold the cursor over the node, the Trace over Trees legend will show details like how many of the trees show each of the character states at the node, and how many of the trees total have the node (i.e. the clade).^n';
 				setTitle Trace_over_trees;
 				toggleFileNames off;
 				setPrevButtonName Previous;
 				setNextButtonName Next;
-				addWebLink Manual_page  'mesquite:docs/mesquite/AncestralStates/AncestralStates.html#tcot';
+				addWebLink Manual_page  'http://mesquiteproject.wikispaces.com/Ancestral+States#tcot';
 			endTell;
 			showWindow;
 		endTell;

Resources/examples/Basic_Examples/basic_operation/02-standardMenus.nex

@@ -119,7 +119,7 @@ Begin MESQUITE;
 				toggleFileNames off;
 				setPrevButtonName Previous;
 				setNextButtonName Next;
-				addWebLink Menu_documentation  'mesquite:docs/mesquite/menus.html';
+				addWebLink Menu_documentation  'http://mesquiteproject.wikispaces.com/Menus';
 			endTell;
 			showWindow;
 		endTell;

Resources/examples/Basic_Examples/basic_operation/04-treeWindow.nex

@@ -211,7 +211,7 @@ Begin MESQUITE;
 					setLocation 21 22;
 					setFont SanSerif;
 					setFontSize 10;
-				setExplanation 'This file shows the tree window in which trees can be viewed and edited.  At left is a tool palette, whose tools can be used for manipulating the tree.  There is also a control with blue arrows to scroll from one tree to another from the current source of trees.  ^n^nThe Tree Window has  a Tree menu in which you can control the trees appearance, and choose the source of trees.  There is also an Analysis menu from which you can initiate analyses with the tree.^n^nThe tree window also has an annotation and explanation area at the bottom for communicating with the user.^n^nFor more information about viewing and editing trees, follow the "Go" button below beside "Viewing trees".  For more information about manipulating trees, follow the "Go" button beside "Manipulating trees".  Otherwise, go to the next example via the Next button.';
+				setExplanation 'This file shows the tree window in which trees can be viewed and edited.  At left is a tool palette, whose tools can be used for manipulating the tree.  There is also a control with blue arrows to scroll from one tree to another from the current source of trees.  ^n^nThe Tree Window has  a Tree menu in which you can control the trees appearance, and choose the source of trees.  There is also an Analysis:Tree menu from which you can initiate analyses with the tree.^n^nThe tree window also has an annotation and explanation area at the bottom for communicating with the user.^n^nFor more information about viewing and editing trees, follow the "Go" button below beside "Viewing trees".  For more information about manipulating trees, follow the "Go" button beside "Manipulating trees".  Otherwise, go to the next example via the Next button.';
 				setTitle Tree_window;
 				toggleFileNames off;
 				setPrevButtonName Previous;

Resources/examples/Basic_Examples/basic_operation/05-windowModes.nex

@@ -472,7 +472,7 @@ Begin MESQUITE;
 					setFont SanSerif;
 					setFontSize 10;
 					setActive;
-				setExplanation 'Most windows have several modes for viewing, controlled by the information bar at the top.  The information bar has five tabs, "Graphics", "Text", "Parameters", "Modules" and "Citations".  If the information bar does not appear at the top of a window, it may be turned on using the "Show Information Bar" menu item in the Windows menu.^n^nThe four windows shown here are all tree windows, being show in each of four different modes.  The "Graphics" mode is the standard mode in which you''re likely to work.  The "Text" mode gives an alternative, text-based view of the window.  The "Parameters" mode shows important parameter settings of the various modules participating in the window.  This can be useful to see what are the parameters values or assumptions for an analysis.  The "Modules" mode shows the hierarchy of Mesquite modules involved in making the window.  If you pass the cursor over the names of the modules, information about each module will appear in the explanation area at the bottom of the window.  Touching on the name of the module also gives information.  The "Citations" mode shows citations of any modules involved in the calculations that consider themselves citable in the sense of producing substantive results.';
+				setExplanation 'Most windows have several modes for viewing, controlled by the View Mode submenu of the window''s Window menu.  The menu has 5 choices, "Graphics (Standard)", "Text", "Parameters", "Modules" and "Citations".  ^n^nThe four windows shown here are all tree windows, being show in each of four different modes.  The "Graphics" mode is the standard mode in which you''re likely to work.  The "Text" mode gives an alternative, text-based view of the window.  The "Parameters" mode shows important parameter settings of the various modules participating in the window.  This can be useful to see what are the parameters values or assumptions for an analysis.  The "Modules" mode shows the hierarchy of Mesquite modules involved in making the window.  If you pass the cursor over the names of the modules, information about each module will appear in the explanation area at the bottom of the window.  Touching on the name of the module also gives information.  The "Citations" mode shows citations of any modules involved in the calculations that consider themselves citable in the sense of producing substantive results.';
 				setTitle Window_modes;
 				toggleFileNames off;
 				setPrevButtonName Previous;

Resources/examples/Basic_Examples/basic_operation/06-helpMenu.nex

@@ -211,12 +211,12 @@ Begin MESQUITE;
 					setLocation 14 22;
 					setFont SanSerif;
 					setFontSize 10;
-				setExplanation 'An important first step in learning Mesquite is to discover where to find instructions and information.  Because Mesquite is modular, there are many challenges in providing documentation, since what options are available depend on what is installed.  Mesquite may also be confusing at times, since its interface changes with what is installed and what calculations are being done.  ^n^nTo overcome these challenges, there are various features designed to give you information and instructions, which are described in this example file and the next.^n^nHere are the primary tools to learn Mesquite:^n^n1. These example files.^n^n2. The manual.  Go to the Help menu and select Mesquite Manual.  (You may find other items in the Help menu helpful)^n^n3. The search system.  Note the little text box at the top of this window with "Search Features" or "Search Data" beside it.  If it says "Search Data", touch on the blue d until it says "Search Features".  Enter text in the box and hit return; it will find features that match that search string.^n^n4. See the Mesquite manual page on learning Mesquite (link below). ^n^n';
+				setExplanation 'An important first step in learning Mesquite is to discover where to find instructions and information.  Because Mesquite is modular, there are many challenges in providing documentation, since what options are available depend on what is installed.  Mesquite may also be confusing at times, since its interface changes with what is installed and what calculations are being done.  ^n^nTo overcome these challenges, there are various features designed to give you information and instructions, which are described in this example file and the next.^n^nHere are the primary tools to learn Mesquite:^n^n1. These example files.^n^n2. The manual.  Go to the Help menu and select Mesquite Documentation.  (You may find other items in the Help menu helpful)^n^n3. The search system.  Note the little text box at the top of this window with "Search Features" or "Search Data" beside it.  If it says "Search Data", touch on the blue d until it says "Search Features".  Enter text in the box and hit return; it will find features that match that search string.^n^n4. See the Mesquite manual page on learning Mesquite (link below). ^n^n';
 				setTitle Help;
 				toggleFileNames off;
 				setPrevButtonName Previous;
 				setNextButtonName Next;
-				addWebLink Page_on_learning_Mesquite  'mesquite:docs/mesquite/help.html';
+				addWebLink Page_on_learning_Mesquite  'http://mesquiteproject.wikispaces.com/Learning+how+to+use+Mesquite';
 			endTell;
 			showWindow;
 		endTell;

Resources/examples/Basic_Examples/basic_operation/07-moreHelp.nex

@@ -211,12 +211,12 @@ Begin MESQUITE;
 					setLocation 13 25;
 					setFont SanSerif;
 					setFontSize 10;
-				setExplanation 'You can learn what different menu items and tools do by using several features:^n^n-- if you hold down the Shift key as you select a menu item, an explanation of the menu item will appear in the explanation area of the window associated with the menu (try this with menus of the Tree Window -- you can''t do it for this note, since this note has no explanation area)^n^n-- if you touch on a button for a tool in a tool palette, like the one at the left of the tree window, an explanation for the tool will appear in the window''s explanation area.^n^n-- if you select the Menu & Control Explanations menu item in the Window menu, Mesquite will compose a web page listing all the menu items of the current window (i.e. the one associated with the menu), and what the menu items do.  The page also includes a listing of any buttons and other controls in the window, and explains what they do.^n^nTo learn more about Mesquite''s Help system hit the Show button below, to go to the documentation on the topic.';
+				setExplanation 'You can learn what different menu items and tools do by using several features:^n^n-- if you hold down the Shift key as you select a menu item, an explanation of the menu item will appear in the explanation area of the window associated with the menu (try this with menus of the Tree Window -- you can''t do it for this note, since this note has no explanation area)^n^n-- if you touch on a button for a tool in a tool palette, like the one at the left of the tree window, an explanation for the tool will appear in the window''s explanation area.^n^n-- if you select the Menu & Control Explanations menu item in the View menu, Mesquite will compose a web page listing all the menu items of the current window (i.e. the one associated with the menu), and what the menu items do.  The page also includes a listing of any buttons and other controls in the window, and explains what they do.^n^nTo learn more about Mesquite''s Help system hit the Show button below, to go to the documentation on the topic.';
 				setTitle More_help;
 				toggleFileNames off;
 				setPrevButtonName Previous;
 				setNextButtonName Next;
-				addWebLink Page_on_Learning_Mesquite  'mesquite:docs/mesquite/help.html';
+				addWebLink Page_on_Learning_Mesquite  'http://mesquiteproject.wikispaces.com/Learning+how+to+use+Mesquite';
 			endTell;
 			showWindow;
 		endTell;

Resources/examples/Basic_Examples/basic_operation/08-logFile.nex

@@ -122,7 +122,7 @@ Begin MESQUITE;
 					setFont SanSerif;
 					setFontSize 10;
 					setActive;
-				setExplanation 'Mesquite maintains a log file ("Mesquite log") automatically that records commands given.  You can see it by selecting the Mesquite Log menu item in the Windows menu.^n^nMesquite saves the current log file and the previous five log files automatically in the Mesquite_Support_Files on your hard disk.  If you wish to save a log file, you can copy it from that directory or rename it so that Mesquite won''t overwrite it.';
+				setExplanation 'Mesquite maintains a log file ("Mesquite log") automatically that records commands given.  You can see it by selecting the Mesquite Log menu item in the View menu.^n^nMesquite saves the current log file and the previous five log files automatically in the Mesquite_Support_Files on your hard disk.  If you wish to save a log file, you can copy it from that directory or rename it so that Mesquite won''t overwrite it.';
 				setTitle Log_file;
 				toggleFileNames off;
 				setPrevButtonName Previous;