Merge branch 'master' into use-original-ada-grammar

.gitmodules

@@ -656,3 +656,6 @@
 [submodule "vendor/grammars/ada.tmbundle"]
 	path = vendor/grammars/ada.tmbundle
 	url = https://github.com/textmate/ada.tmbundle
+[submodule "vendor/grammars/api-blueprint-sublime-plugin"]
+	path = vendor/grammars/api-blueprint-sublime-plugin
+	url = https://github.com/apiaryio/api-blueprint-sublime-plugin

grammars.yml

@@ -156,6 +156,9 @@ vendor/grammars/antlr.tmbundle:
 vendor/grammars/apache.tmbundle:
 - source.apache-config
 - source.apache-config.mod_perl
+vendor/grammars/api-blueprint-sublime-plugin/:
+- text.html.markdown.source.gfm.apib
+- text.html.markdown.source.gfm.mson
 vendor/grammars/applescript.tmbundle:
 - source.applescript
 vendor/grammars/asciidoc.tmbundle/:

lib/linguist/languages.yml

@@ -59,6 +59,14 @@ ANTLR:
   - .g4
   ace_mode: text
 
+API Blueprint:
+  type: markup
+  color: "#2ACCA8"
+  ace_mode: markdown
+  extensions:
+  - .apib
+  tm_scope: text.html.markdown.source.gfm.apib
+
 APL:
   type: programming
   color: "#5A8164"
@@ -1349,6 +1357,13 @@ Hy:
   - hylang
   tm_scope: source.hy
 
+HyPhy:
+  type: programming
+  ace_mode: text
+  extensions:
+  - .bf
+  tm_scope: none
+  
 IDL:
   type: programming
   color: "#a3522f"

samples/API Blueprint/actions.apib

@@ -0,0 +1,55 @@
+FORMAT: 1A
+
+# Advanced Action API
+A resource action is – in fact – a state transition. This API example demonstrates an action - state transition - to another resource.
+
+## API Blueprint
++ [Previous: Resource Model](11.%20Resource%20Model.md)
++ [This: Raw API Blueprint](https://raw.github.com/apiaryio/api-blueprint/master/examples/11.%20Advanced%20Action.md)
+
+# Tasks [/tasks/tasks{?status,priority}]
+
++ Parameters
+    + status (string)
+    + priority (number)
+
+## List All Tasks [GET]
+
++ Response 200 (application/json)
+
+        [
+            {
+                "id": 123,
+                "name": "Exercise in gym",
+                "done": false,
+                "type": "task"
+            },
+            {
+                "id": 124,
+                "name": "Shop for groceries",
+                "done": true,
+                "type": "task"
+            }
+        ]
+
+## Retrieve Task [GET /task/{id}]
+This is a state transition to another resource
+
++ Parameters
+    + id (string)
+
++ Response 200 (application/json)
+
+        {
+            "id": 123,
+            "name": "Go to gym",
+            "done": false,
+            "type": "task"
+        }
+
+## Delete Task [DELETE /task/{id}]
+
++ Parameters
+    + id (string)
+
++ Response 204

samples/API Blueprint/attributes.apib

@@ -0,0 +1,39 @@
+FORMAT: 1A
+
+# Attributes API
+This API example demonstrates how to describe body attributes of a request or response message.
+
+In this case, the description is complementary (and duplicate!) to the provided JSON example in the body section. The [Advanced Attributes](09.%20Advanced%20Attributes.md) API example will demonstrate how to avoid duplicates and how to reuse attributes descriptions.
+
+## API Blueprint
++ [Previous: Parameters](07.%20Parameters.md)
++ [This: Raw API Blueprint](https://raw.github.com/apiaryio/api-blueprint/master/examples/08.%20Attributes.md)
++ [Next: Advanced Attributes](09.%20Advanced%20Attributes.md)
+
+# Group Coupons
+
+## Coupon [/coupons/{id}]
+A coupon contains information about a percent-off or amount-off discount you might want to apply to a customer.
+
+### Retrieve a Coupon [GET]
+Retrieves the coupon with the given ID.
+
++ Response 200 (application/json)
+
+    + Attributes (object)
+        + id: 250FF (string)
+        + created: 1415203908 (number) - Time stamp
+        + percent_off: 25 (number)
+
+            A positive integer between 1 and 100 that represents the discount the coupon will apply.
+
+        + redeem_by (number) - Date after which the coupon can no longer be redeemed
+
+    + Body
+
+            {
+                "id": "250FF",
+                "created": 1415203908,
+                "percent_off": 25,
+                "redeem_by:" null
+            }

samples/API Blueprint/simple.apib

@@ -0,0 +1,18 @@
+FORMAT: 1A
+
+# The Simplest API
+This is one of the simplest APIs written in the **API Blueprint**.
+One plain resource combined with a method and that's it! We will explain what is going on in the next installment - [Resource and Actions](02.%20Resource%20and%20Actions.md).
+
+**Note:** As we progress through the examples, do not also forget to view the [Raw](https://raw.github.com/apiaryio/api-blueprint/master/examples/01.%20Simplest%20API.md) code to see what is really going on in the API Blueprint, as opposed to just seeing the output of the Github Markdown parser.
+
+Also please keep in mind that every single example in this course is a **real API Blueprint** and as such you can **parse** it with the [API Blueprint parser](https://github.com/apiaryio/drafter) or one of its [bindings](https://github.com/apiaryio/drafter#bindings).
+
+## API Blueprint
++ [This: Raw API Blueprint](https://raw.github.com/apiaryio/api-blueprint/master/examples/01.%20Simplest%20API.md)
++ [Next: Resource and Actions](02.%20Resource%20and%20Actions.md)
+
+# GET /message
++ Response 200 (text/plain)
+
+        Hello World!

samples/HyPhy/AAModelComparison.bf

@@ -0,0 +1,252 @@
+if (Rows (modelMatrixList) == 0)
+{
+	modelMatrixList = 
+	{
+	{"Equal Input", "EIAA.mdl", "19"}
+	{"Dayhoff","Dayhoff.mdl","0"}
+	{"Dayhoff+F","Dayhoff_F.mdl","19"}
+	{"JTT", "Jones.mdl", "0"}
+	{"JTT+F", "Jones_F.mdl", "19"}
+	{"WAG", "WAG.mdl", "0"}
+	{"WAG+F", "WAG_F.mdl", "19"}
+	{"rtREV", "rtREV.mdl", "0"}
+	{"rtREV+F", "rtREV_F.mdl", "19"}
+	{"mtMAM", 		  "mtMAM.mdl", "0"}
+	{"mtMAM+F", 	  "mtMAM_F.mdl", "19"}
+	{"mtREV 24",      "mtREV_24.mdl", "0"}
+	{"mtREV 24+F",    "mtREV_24_F.mdl", "19"}
+	{"HIV within",    "HIVwithin.mdl", "0"}
+	{"HIV within+F",  "HIVwithin+F.mdl", "19"}
+	{"HIV between",   "HIVbetween.mdl", "0"}
+	{"HIV between+F", "HIVbetween+F.mdl", "19"}
+	{"REV-1 step", "reducedREV.mdl", "19"}
+	{"REV",   "mtREV.mdl",    "19"}
+	};
+}
+
+/*___________________________________________________________________________________________________________*/
+
+function runAModel (modelID, fileName, xtraP, midx)
+{
+	ExecuteCommands ("#include \"TemplateModels/"+fileName+"\";"); 
+	Tree 					givenTree 			= treeString;
+	LikelihoodFunction 		lf 					= (filteredData,givenTree);
+	
+	GetString (lf_info, lf, -1);
+	locals = lf_info["Local Independent"];
+
+	if (Columns (branchLengthStash))
+	{
+		USE_LAST_RESULTS = 1;
+		for (_iv = 0; _iv < Columns (locals); _iv = _iv+1)
+		{
+			ExecuteCommands (locals[_iv] + "=1;\n");
+		}
+		currentBL = BranchLength (givenTree,0);
+		currentBN = BranchName	 (givenTree,-1);
+		for (_iv = 0; _iv < Columns (currentBN); _iv = _iv+1)
+		{
+			ExecuteCommands ("givenTree."+currentBN[_iv]+".t="+branchLengthStash[_iv]/currentBL+";");
+			
+		}
+	}
+	else
+	{
+		for (_iv = 0; _iv < Columns (locals); _iv = _iv+1)
+		{
+			ExecuteCommands (locals[_iv] + "=0.1;\n");
+		}
+		USE_LAST_RESULTS = 1;
+	}
+
+	Optimize (res,lf);
+	
+	fprintf (stdout, "| ", modelID);
+	for (k=0; k<maxModelWidth-Abs(modelID)-1; k=k+1)
+	{
+		fprintf (stdout, " ");
+	}
+
+	params = res[1][1]+xtraP;
+	AIC    =  2(-res[1][0]+params);
+	
+	if (filteredData.sites-params>1)
+	{
+		cAIC   = 2(-res[1][0]+params*(filteredData.sites/(filteredData.sites-params-1)));
+	}
+	else
+	{
+		cAIC = 0;
+	}
+	
+	branchLengths = BranchLength (givenTree,-1);
+	TL = 0;
+	for (k=Rows(branchLengths)*Columns(branchLengths)-1; k>=0; k=k-1)				  
+	{
+		TL = TL + branchLengths[k];
+	}
+
+	fprintf (stdout, "| ", Format (res[1][0],14,3), " | ", Format (params,5,0), " | ",
+						   Format (AIC, 9,3), " | ",);
+					
+	if (cAIC > 0)
+	{
+		 fprintf (stdout, Format (cAIC,11,3), " | ");
+	}
+	else
+	{
+		 fprintf (stdout, "    N/A     | ");
+	}
+		   
+	fprintf (stdout, Format (TL,11,3), " |\n", sepString);
+	
+	resultMatrix[midx][0] = res[1][0];
+	resultMatrix[midx][1] = params;
+	resultMatrix[midx][2] = AIC;
+	resultMatrix[midx][3] = cAIC;
+	resultMatrix[midx][4] = TL;
+	
+	if (AIC < bestAIC)
+	{
+		bestAIC 	= AIC;
+		bestAICidx  = midx;
+		branchLengthStash = BranchLength (givenTree,-1);
+	}
+	
+	if (cAIC > 0)
+	{
+		if (bestCAIC > cAIC)
+		{
+			bestCAIC = cAIC;
+			bestCAICidx = midx;
+			
+		}
+	}
+	
+	return 0;
+}
+
+
+/*___________________________________________________________________________________________________________*/
+
+
+
+maxModelWidth = 7;
+skipCodeSelectionStep = 0;
+
+ChoiceList (doREV, "Include REV?", 1, SKIP_NONE, "Yes", "Include REV and reduced REV models. CAUTION: these models take a long time to fit.",
+												 "No", "Only use empirical models");
+												 
+if (doREV < 0)
+{
+	return 0;
+}
+
+if (doREV == 0)
+{
+	#include "TemplateModels/chooseGeneticCode.def";
+	skipCodeSelectionStep = 1;
+}
+
+modelCount    = Rows (modelMatrixList) - 2*doREV;
+
+for (k=0; k<modelCount; k=k+1)
+{
+	maxModelWidth = Max(maxModelWidth,Abs (modelMatrixList[k][0])+2);
+}
+
+sepString = "";
+capString = "";
+sepString * 256;
+sepString * "+";
+
+capString * 256;
+capString * "| Model";
+
+for (k=0; k<maxModelWidth; k=k+1)
+{
+	sepString * "-";
+}
+
+for (k=0; k<maxModelWidth-6; k=k+1)
+{
+	capString * " ";
+}
+
+capString * "| Log Likelihood | #prms | AIC Score | c-AIC Score | Tree Length |\n";
+sepString * "+----------------+-------+-----------+-------------+-------------+\n";
+sepString * 0;
+capString * 0;
+
+branchLengthStash = 0;
+
+SKIP_MODEL_PARAMETER_LIST = 0;
+
+#include "TemplateModels/modelParameters2.mdl";
+if (modelType == 1)
+{
+	#include "TemplateModels/defineGamma.mdl";
+}
+
+if (modelType == 2)
+{
+	#include "TemplateModels/defineHM.mdl";
+}
+SKIP_MODEL_PARAMETER_LIST = 1;
+
+SetDialogPrompt ("Please load an amino-acid data file:");
+
+DataSet ds = ReadDataFile (PROMPT_FOR_FILE);
+DataSetFilter filteredData = CreateFilter (ds,1);
+
+fprintf (stdout,"\nRunning aminoacid model comparisons on ", LAST_FILE_PATH, "\n\nThe alignment has ",ds.species, " sequences and ", ds.sites, " sites\n");
+
+_DO_TREE_REBALANCE_ = 1;
+
+#include "queryTree.bf";
+
+resultMatrix = {modelCount, 5};
+
+fprintf (stdout, "\n",sepString,capString,sepString);
+
+bestAIC 	= 1e100;
+bestCAIC	= 1e100;
+bestAICidx	= 0;
+bestCAICidx = -1;
+
+for (mid=0; mid<modelCount; mid=mid+1)
+{
+	runAModel (modelMatrixList[mid][0], modelMatrixList[mid][1], 0+modelMatrixList[mid][2], mid);
+}	
+
+fprintf (stdout, "\n\nBest AIC model:\n\t", modelMatrixList[bestAICidx][0], " with the score of ", bestAIC);
+
+if (bestCAICidx>=0)
+{
+	fprintf (stdout, "\n\nBest c-AIC model:\n\t", modelMatrixList[bestCAICidx][0], " with the score of ", bestCAIC);
+}
+
+labelMatrix  = {{"Log-likelihood","Parameters","AIC","c-AIC","Total tree length",""}};
+
+aaString = "Model";
+
+for (fC = 0; fC < modelCount; fC = fC+1)
+{
+	aaString = aaString + ";" + modelMatrixList[fC][0];
+}
+
+USE_LAST_RESULTS = 0;
+
+labelMatrix[5] = aaString;
+skipCodeSelectionStep = 0;
+OpenWindow (CHARTWINDOW,{{"Model Fits"}
+						   {"labelMatrix"},
+						   {"resultMatrix"},
+						   {"Bar Chart"},
+						   {"Index"},
+						   {"c-AIC"},
+						   {"Model Index"},
+						   {""},
+						   {"AIC"}
+						   },
+						   "SCREEN_WIDTH-60;SCREEN_HEIGHT-60;30;30");

samples/HyPhy/MatrixIndexing.bf

@@ -0,0 +1 @@
+fprintf (stdout, "\n1). Spawning a zero-populated 5x6 matrix and setting it's values to random numbers in [0,1].\n");

samples/HyPhy/MolecularClock.bf

@@ -0,0 +1,147 @@
+#include "molclockBootstrap.bf";
+
+RESTORE_GLOBALS 	= 1;
+_DO_TREE_REBALANCE_ = 0;
+VERBOSITY_LEVEL     = -1;
+
+function RestoreGlobalValues (lfIndex)
+{
+	if (lfIndex==0)
+	{
+		for (i=0;i<SAVE_GLOBALS;i=i+1)
+		{
+			SetParameter (lf,i,globalSpoolMatrix[i]);
+		}
+	}
+	if (lfIndex==1)
+	{
+		for (i=0;i<SAVE_GLOBALS2;i=i+1)
+		{
+			SetParameter (lfConstrained,i,globalSpoolMatrix2[i]);
+		}
+	}
+	return 0;
+}
+
+
+
+fprintf(stdout,"\n ---- RUNNING MOLECULAR CLOCK ANALYSIS ---- \n");
+
+ChoiceList (dataType,"Data type",1,SKIP_NONE,"Nucleotide/Protein","Nucleotide or amino-acid (protein).",
+				     "Codon","Codon (several available genetic codes).");
+
+if (dataType<0) 
+{
+	return;
+}
+if (dataType)
+{
+	NICETY_LEVEL = 3;
+	#include "TemplateModels/chooseGeneticCode.def";
+}
+
+SetDialogPrompt ("Choose the data file:");
+
+DataSet ds = ReadDataFile (PROMPT_FOR_FILE);
+
+fprintf (stdout,"The following data was read:\n",ds,"\n");
+
+if (dataType)
+{
+	DataSetFilter filteredData = CreateFilter (ds,3,"","",GeneticCodeExclusions);
+}
+else
+{
+	DataSetFilter filteredData = CreateFilter (ds,1);
+}
+
+SelectTemplateModel(filteredData);
+
+#include "queryTree.bf";
+
+global RelRatio;
+
+RelRatio = 1.0;
+
+relationString = ":=RelRatio*";
+
+parameter2Constrain = 0;
+
+if (Rows("LAST_MODEL_PARAMETER_LIST")>1)
+{
+	ChoiceList (parameter2Constrain, "Parameter(s) to constrain:",1,SKIP_NONE,LAST_MODEL_PARAMETER_LIST);
+
+	if (parameter2Constrain<0)
+	{
+		return;
+	}
+	if (parameter2Constrain==0)
+	{
+		parameter2ConstrainString = "";
+		for (parameter2Constrain=Rows("LAST_MODEL_PARAMETER_LIST")-1; parameter2Constrain; parameter2Constrain = parameter2Constrain-1)
+		{
+			GetString (funnyString,LAST_MODEL_PARAMETER_LIST,parameter2Constrain);
+			parameter2ConstrainString = parameter2ConstrainString + funnyString + ",";
+		}
+		GetString (funnyString,LAST_MODEL_PARAMETER_LIST,0);
+		parameter2ConstrainString = parameter2ConstrainString + funnyString;
+	}
+	else
+	{
+		GetString (parameter2ConstrainString,LAST_MODEL_PARAMETER_LIST,parameter2Constrain-1);
+	}
+}
+else
+{
+	GetString (parameter2ConstrainString,LAST_MODEL_PARAMETER_LIST,0);
+}
+
+timer = Time(0);
+
+LikelihoodFunction lf = (filteredData,givenTree);
+
+Optimize (res,lf);
+
+separator = "*-----------------------------------------------------------*";
+
+fprintf (stdout, "\n", separator, "\nRESULTS WITHOUT THE CLOCK:\n",lf);
+
+fullModelLik = res[1][0];
+
+fullVars = res[1][1];
+
+/* now specify the constraint */
+
+Tree clockTree = treeString;
+
+ExecuteCommands ("MolecularClock (clockTree,"+parameter2ConstrainString+");");
+
+LikelihoodFunction lfConstrained = (filteredData, clockTree);
+
+USE_LAST_RESULTS = 1;
+Optimize (res1,lfConstrained);
+USE_LAST_RESULTS = 0;
+
+SAVE_GLOBALS = res1[1][2];
+
+if (SAVE_GLOBALS)
+{
+	globalSpoolMatrix = {1,SAVE_GLOBALS};
+
+	for (i=0;i<SAVE_GLOBALS;i=i+1)
+	{
+		globalSpoolMatrix[i]=res1[0][i];
+	}
+}
+
+fprintf (stdout, "\n", separator,"\n\nRESULTS WITH THE CLOCK:\n",lfConstrained);
+
+lnLikDiff = 2(fullModelLik-res1[1][0]);
+
+degFDiff = fullVars - res1[1][1];
+
+fprintf (stdout, "\n", separator,"\n\n-2(Ln Likelihood Ratio)=",lnLikDiff,"\n","Constrained parameters:",Format(degFDiff,0,0));
+
+fprintf (stdout, "\nP-Value:",1-CChi2(lnLikDiff,degFDiff));
+
+fprintf (stdout, "\nCPU time taken: ", Time(0)-timer, " seconds.\n");

samples/HyPhy/profile_test.bf

@@ -0,0 +1 @@
+#profile START;

script/travis/before_install

@@ -17,6 +17,9 @@ else
   bundle config build.charlock_holmes --with-icu-dir=$(pwd)/vendor/debs
 fi
 
+# Replace SSH links to submodules by HTTPS links.
+sed -i 's/git@github.com:/https:\/\/github.com\//' .gitmodules
+
 git submodule init
 git submodule sync --quiet
 script/fast-submodule-update