Merge pull request #33 from Gaius-Augustus/fix_typos

Fix typos

HISTORY.TXT

@@ -42,7 +42,7 @@ List of changes from version 3.2 to 3.2.1 (until October 23rd, 2015)
      - comparative gene prediction (CGP): make the parameters from the GCB proceedings paper match again
      - new CGP default parameters (tested on 5 clades)
      - CGP version penalizes very long introns equivalently to a geometric distribution
-     - code now under artistic licence only
+     - code now under artistic license only
 List of changes from version 3.1 to 3.2 (until September 25th, 2015)
      - comparative gene prediction (CGP option) has sensible default parameters of the logistic regression model
      - new tool hal2maf_split.pl for splitting an alignment for parallel comparative prediction
@@ -85,10 +85,10 @@ List of changes from version 3.0.2 to 3.0.3 (until August 28th, 2014)
      - other bugfixes in comparative mode
      - removal of mysql++ code from package: this is available as Debian/Ubuntu package
 List of changes from version 3.0 to 3.0.2 (until February 22nd, 2014)
-     - inclusion of scanner and parser code for Newick tree format (GPL licence), easier installation of 
+     - inclusion of scanner and parser code for Newick tree format (GPL license), easier installation of 
        comparative augustus functionality
-     - therefore release under more restrictive GPL licence (the plan is to replace this later
-       and switch back to the more permissive and non-viral artistic open source licence)
+     - therefore release under more restrictive GPL license (the plan is to replace this later
+       and switch back to the more permissive and non-viral artistic open source license)
      - drop requirement to set environment variable AUGUSTUS_CONFIG_PATH
      - bugfixes (etraining: "not Genbank format", gtf2gff.pl, compilation warning)
 List of changes from version 2.7 to 3.0 (until January 8th, 2014)
@@ -153,7 +153,7 @@ List of changes from version 2.4 to 2.5 (until Nov 13th, 2010)
      - new species pneumocystis (fungus), user contributed by Marco Pagni
 List of changes from version 2.3.1 to 2.4 (until July 27, 2010)
      - improved human parameter set: roughly 13 percent points better on CDS exon level
-     - improved fly paramter set
+     - improved fly parameter set
      - added new species 'lamprey', contributed by Falk Hildebrand and Shigehiro Kuraku
      - added new species Leishmania tarentolae, Trichinella spiralis
      - added maize5 parameter set, better than 'maize' and with UTR model
@@ -274,7 +274,7 @@ List of changes from version 1.6 to version 1.7 (until October 5th, 2005):
 
 List of changes from version 1.5 to version 1.6 (until August 3rd, 2005):
 
-     - The source code is now freely available (Artistic Licence).
+     - The source code is now freely available (Artistic License).
      - New species: Tribolium castaneum, Aedes aegypti, Coprinus cinereus
      - Bugfix: Wrong interpretation of reading frame for reverse strand exon hints.
      - Training of hints possible with nested genes.

README-cgp.md

@@ -10,7 +10,7 @@
    (not needed unless you run into compiler errors related to 'parse.cc' or 'lex.cc')  
 [AUTHORS AND CONTACT](docs/CONTACT.md)  
 [REFERENCES](README.md#references)  
-[LICENCES](README.md#licenses)  
+[LICENSES](README.md#licenses)  
 
 # INTRODUCTION
 

README.md

@@ -8,7 +8,7 @@
 [WEB-SERVER](#web-server)  
 [AUTHORS AND CONTACT](docs/CONTACT.md)  
 [REFERENCES](#references)  
-[LICENCES](#licenses)  
+[LICENSES](#licenses)  
 
 # INTRODUCTION
 

augustus-training/dynamic/about.html

@@ -35,7 +35,7 @@ <h3>Gene prediction with AUGUSTUS</h3>
 <p align="center"><a href="images/AUG.cDNA.gif"><img src="images/AUG.cDNA.gif"  alt="with cDNA" width="70%"></a><br><i>Click on image to enlarge!</i></p>
 </li>
 
-<li> AUGUSTUS ususally belongs to the most accurate programs for the species it is trained
+<li> AUGUSTUS usually belongs to the most accurate programs for the species it is trained
 for. Often it is the most accurate <i>ab initio</i> program. For example, at the independent gene finder
 assessment (EGASP) on the human ENCODE regions AUGUSTUS was the most accurate gene finder among the
 tested <i>ab initio</i> programs. At the more recent nGASP (worm), it was among the best in the <i>ab initio</i>
@@ -67,7 +67,7 @@ <h3>Gene prediction with AUGUSTUS</h3>
 
 <li> AUGUSTUS can report a large number of alternative genes, including probabilities for the
 transcripts and each exon and intron. You can make AUGUSTUS predict suboptimal gene structures (<a
-href="images/alternative-sampling.png">example</a>) and you can adjust command line paramters to regulate
+href="images/alternative-sampling.png">example</a>) and you can adjust command line parameters to regulate
 the number of reported alternatives.
 </li>
 

augustus-training/grails-app/views/about.gsp

@@ -152,7 +152,7 @@
                         </li>
                         <li> AUGUSTUS can report a large number of alternative genes, including probabilities for the
                            transcripts and each exon and intron. You can make AUGUSTUS predict suboptimal gene structures (<a
-                              href="images/alternative-sampling.png">example</a>) and you can adjust command line paramters to regulate
+                              href="images/alternative-sampling.png">example</a>) and you can adjust command line parameters to regulate
                            the number of reported alternatives.
                         </li>
                      </ul>

augustus-training/grails-app/views/help.gsp

@@ -799,7 +799,7 @@ HS04636 anchor  intronpart      7631    7633    0       +       0       source=M
 # Setting 1group1gene for E.
 # Sources of extrinsic information: M E 
 # Have extrinsic information about 1 sequences (in the specified range). 
-# Initialising the parameters ...
+# Initializing the parameters ...
 # human version. Use default transition matrix.
 # Looks like /var/tmp/augustus/AUG-1855139717/input.fa is in fasta format.
 # We have hints for 1 sequence and for 1 of the sequences in the input set.

augustus-training/grails-app/views/predictiontutorial.gsp

@@ -1065,7 +1065,7 @@ HS04636 anchor  intronpart      7631    7633    0       +       0       source=M
 # Setting 1group1gene for E.
 # Sources of extrinsic information: M E
 # Have extrinsic information about 1 sequences (in the specified range).
-# Initialising the parameters ...
+# Initializing the parameters ...
 # human version. Use default transition matrix.
 # Looks like /var/tmp/augustus/AUG-1855139717/input.fa is in fasta format.
 # We have hints for 1 sequence and for 1 of the sequences in the input set.

augustus-training/plugins/plugins-list-default.xml

@@ -31822,7 +31822,7 @@ It integrates nicely with the resources plugin.
       <title>Git Plugin</title>
       <author>Peter Ledbrook</author>
       <authorEmail>[email protected]</authorEmail>
-      <description>Integrates git, the distributed version control system, into Grails projects. It can initialise a local git repository for your project, add a .gitignore file and commit the first version of your source code.
+      <description>Integrates git, the distributed version control system, into Grails projects. It can initialize a local git repository for your project, add a .gitignore file and commit the first version of your source code.
 </description>
       <file>http://plugins.grails.org/grails-git/tags/RELEASE_1_0-SNAPSHOT/grails-git-1.0-SNAPSHOT.zip</file>
     </release>

auxprogs/bam2hints/bam2hints.cc

@@ -820,7 +820,7 @@ int main(int argc, char* argv[])
       // check if there is a proper old target
       if(OldTargetID >= 0) // -1 <-> "*"(unknown reference), -2 <-> uninitialized
       {
-  	// check previous occurence of that target
+  	// check previous occurrence of that target
   	if(seenRefSet.find(TargetName) != seenRefSet.end())
   	{
   	  if(IntOnly && Mult)
@@ -1069,7 +1069,7 @@ int main(int argc, char* argv[])
     // TASK: else store alignment pointer into map
     // TASK: set new or reuse "pal"
 
-  } // end while (parsing through bam aligment lines)
+  } // end while (parsing through bam alignment lines)
 
 
   // newline after display of the line count

auxprogs/bam2wig/bam2wig.c

@@ -91,7 +91,7 @@ int main(int argc, char *argv[])
 	  }
 
 
-	// Initialising auxiliary data structures
+	// Initializing auxiliary data structures
 	data = calloc(1, sizeof(void*)); // data[0] is array for just one BAM file
 	// set the default region. left-shift "end" by appending 30 zeros (i.e. end=1073741824) 
 	beg = 0; end = 1<<30; tid = -1;  

auxprogs/filterBam/src/filterBam.cc

@@ -149,7 +149,7 @@ int main(int argc, char *argv[])
   optionalCounters.outPaired = outPaired;
   optionalCounters.outUniq = outUniq;
   optionalCounters.outBest = outBest;
-  // Initialising options
+  // Initializing options
   struct globalOptions_t globalOptions;
   globalOptions = initOptions(argc, argv);
   bool best = globalOptions.best;

auxprogs/filterBam/src/functions/MatePairs.cc

@@ -55,15 +55,15 @@ MatePairs::MatePairs(const MatePairs &copyin)   // Copy constructor to handle pa
 	this->score = copyin.score; 	               
 }
 
-// Initialisation method
+// Initialization method
 MatePairs::MatePairs(int it, int jit, float score)
 {
 	this->alIt = it;
 	this->alJit = jit;
 	this->score = score;
 }
 
-// Initialisation method
+// Initialization method
 void MatePairs::setValues(int it, int jit, float score)
 {
 	this->alIt = it;

auxprogs/filterBam/src/functions/PairednessCoverage.cc

@@ -51,7 +51,7 @@ PairednessCoverage::PairednessCoverage(const PairednessCoverage &copyin)   // Co
 	this->chr = copyin.chr; 	               
 }
 
-// Initialisation method
+// Initialization method
 PairednessCoverage::PairednessCoverage(int coord, int label, string chr)
 {
 	this->coord = coord; 	               
@@ -60,7 +60,7 @@ PairednessCoverage::PairednessCoverage(int coord, int label, string chr)
 }
 
 
-// Initialisation method
+// Initialization method
 void PairednessCoverage::setValues(int coord, int label, string chr)
 {
 	this->coord = coord;

auxprogs/filterBam/src/functions/SingleAlignment.cc

@@ -75,7 +75,7 @@ SingleAlignment::SingleAlignment(BamAlignment *al, float coverage, float percId,
 }
 
 
-// Initialisation method
+// Initialization method
 void SingleAlignment::setValues(BamAlignment *al, float coverage, float percId, const RefVector *refData)
 {
 	this->al = al; 	               

auxprogs/filterBam/src/functions/initOptions.cc

@@ -146,7 +146,7 @@ void displayUsage(int argc, char *argv[])
 }
 
 
-// Options initialisation
+// Options initialization
 globalOptions_t initOptions(int argc, char *argv[])
 {
   	int opt = 0, longIndex;

auxprogs/filterBam/src/headers/filterBam.h

@@ -32,7 +32,7 @@ uint32_t sumMandIOperations(vector<CigarOp> cigar, string printFlag);
 uint32_t sumDandIOperations(vector<CigarOp> cigar, string printFlag);
 int printElapsedTime(int tEnd, int tStart); 
 
-// For option initialisation
+// For option initialization
 struct globalOptions_t {
 	bool best;
 	bool help;

auxprogs/homGeneMapping/include/bitmasking.hh

@@ -1,6 +1,6 @@
  /**********************************************************************
  * file:    bitmasking.hh
- * licence: Artistic Licence, see file LICENCE.TXT or 
+ * license: Artistic License, see file LICENSE.TXT or 
  *          http://www.opensource.org/licenses/artistic-license.php
  * descr.:  usage of bit masks to pack multiple values into a
             single integer

auxprogs/homGeneMapping/include/gene.hh

@@ -1,6 +1,6 @@
  /**********************************************************************
  * file:    gene.hh
- * licence: Artistic Licence, see file LICENCE.TXT or 
+ * license: Artistic License, see file LICENSE.TXT or 
  *          http://www.opensource.org/licenses/artistic-license.php
  * descr.:  
  * authors: Stefanie Koenig, [email protected]

auxprogs/homGeneMapping/include/genome.hh

@@ -1,6 +1,6 @@
 /**********************************************************************
  * file:    genome.hh
- * licence: Artistic Licence, see file LICENCE.TXT or 
+ * license: Artistic License, see file LICENSE.TXT or 
  *          http://www.opensource.org/licenses/artistic-license.php
  * descr.:  
  * authors: Stefanie Koenig, [email protected]

auxprogs/homGeneMapping/include/projectio.hh

@@ -1,6 +1,6 @@
  /**********************************************************************
  * file:    projectio.hh
- * licence: Artistic Licence, see file LICENCE.TXT or 
+ * license: Artistic License, see file LICENSE.TXT or 
  *          http://www.opensource.org/licenses/artistic-license.php
  * descr.:  
  * authors: Stefanie Koenig, [email protected]
@@ -69,7 +69,7 @@ inline std::string exec(const char* cmd) {
  */
 inline std::string expandDir(std::string filename){
     if(filename.length()>0 && filename[filename.size()-1] != '/')
-	filename += '/';                     // append slash if neccessary 
+	filename += '/';                     // append slash if necessary 
     filename = expandHome(filename);         // replace "~" by "$HOME
     return filename;
 }

auxprogs/homGeneMapping/include/sqliteDB.hh

@@ -1,6 +1,6 @@
 /**********************************************************************
  * file:    sqliteDB.hh
- * licence: Artistic Licence, see file LICENCE.TXT or 
+ * license: Artistic License, see file LICENSE.TXT or 
  *          http://www.opensource.org/licenses/artistic-license.php
  * descr.:  wrapper class around the SQLite interface
  * authors: Stefanie Koenig

auxprogs/homGeneMapping/src/gene.cc

@@ -1,6 +1,6 @@
 /**********************************************************************
  * file:    gene.cc
- * licence: Artistic Licence, see file LICENCE.TXT or 
+ * license: Artistic License, see file LICENSE.TXT or 
  *          http://www.opensource.org/licenses/artistic-license.php
  * descr.:  
  * authors: Stefanie Koenig, [email protected]

auxprogs/homGeneMapping/src/genome.cc

@@ -1,6 +1,6 @@
 /**********************************************************************
  * file:    genome.cc
- * licence: Artistic Licence, see file LICENCE.TXT or 
+ * license: Artistic License, see file LICENSE.TXT or 
  *          http://www.opensource.org/licenses/artistic-license.php
  * descr.:  
  * authors: Stefanie Koenig, [email protected]

auxprogs/homGeneMapping/src/main.cc

@@ -1,6 +1,6 @@
 /**********************************************************************
  * file:    main.cc
- * licence: Artistic Licence, see file LICENCE.TXT or 
+ * license: Artistic License, see file LICENSE.TXT or 
  *          http://www.opensource.org/licenses/artistic-license.php
  *
  * authors: Stefanie Koenig

auxprogs/homGeneMapping/src/sqliteDB.cc

@@ -1,6 +1,6 @@
 /**********************************************************************
  * file:    sqliteDB.cc
- * licence: Artistic Licence, see file LICENCE.TXT or 
+ * license: Artistic License, see file LICENSE.TXT or 
  *          http://www.opensource.org/licenses/artistic-license.php
  * descr.:  wrapper class around the SQLite interface
  * authors: Stefanie Koenig

config/model/constraints_shadow_partial.txt

@@ -51,7 +51,7 @@
 # This section is for seting constraints between transition probabilities,
 # such as suggested by symmetry such as strand symmetry (or by treating transitions in
 # all reading frames the same). Theoretically, i.e. with infinite and
-# representative traininig data, this should not be neccessary. However, in the real finite
+# representative traininig data, this should not be necessary. However, in the real finite
 # world this is a little safeguard against overfitting.
 #
 [BINDINGS]

config/model/constraints_shadow_partial_utr.txt

@@ -63,10 +63,10 @@
 32
 36
 # --------------------------------------------------------------------
-# This section is for seting constraints between transition probabilities,
+# This section is for setting constraints between transition probabilities,
 # such as suggested by symmetry such as strand symmetry (or by treating transitions in
 # all reading frames the same). Theoretically, i.e. with infinite and
-# representative traininig data, this should not be neccessary. However, in the real finite
+# representative training data, this should not be necessary. However, in the real finite
 # world this is a little safeguard against overfitting.
 #
 [BINDINGS]

config/model/trans_shadow_atleastone.pbl

@@ -8,7 +8,7 @@
 # Date: 19.05.2003
 
 # Initial probabilities (a priori probs for a state ending at a
-# certain position, e.g. the position before the first nukleotide in
+# certain position, e.g. the position before the first nucleotide in
 # the sequence or the last position.
 # only non-zero probabilities
 [Initial]
@@ -20,7 +20,7 @@
 
 # Terminal probabilities (a priori probs for a state ending at
 # the last position.
-# only non-zero probabilities neccessary
+# only non-zero probabilities necessary
 [Terminal]
 # number of states where terminating is possible
 1

config/model/trans_shadow_bacterium.pbl

@@ -21,7 +21,7 @@
 
 # Terminal probabilities (a priori probs for a state ending at
 # the last position.
-# only non-zero probabilities neccessary
+# only non-zero probabilities necessary
 [Terminal]
 # number of states where terminating is possible
 3

config/model/trans_shadow_complete.pbl

@@ -8,7 +8,7 @@
 # Date: 19.05.2003
 
 # Initial probabilities (a priori probs for a state ending at a
-# certain position, e.g. the position before the first nukleotide in
+# certain position, e.g. the position before the first nucleotide in
 # the sequence or the last position.
 # only non-zero probabilities
 [Initial]
@@ -20,7 +20,7 @@
 
 # Terminal probabilities (a priori probs for a state ending at
 # the last position.
-# only non-zero probabilities neccessary
+# only non-zero probabilities necessary
 [Terminal]
 # number of states where terminating is possible
 1

config/model/trans_shadow_complete_utr.pbl

@@ -18,7 +18,7 @@
 
 # Terminal probabilities (a priori probs for a state ending at
 # the last position.
-# only non-zero probabilities neccessary
+# only non-zero probabilities necessary
 [Terminal]
 # number of states where terminating is possible
 1

config/model/trans_shadow_exactlyone.pbl

@@ -8,7 +8,7 @@
 # Date: 19.05.2003
 
 # Initial probabilities (a priori probs for a state ending at a
-# certain position, e.g. the position before the first nukleotide in
+# certain position, e.g. the position before the first nucleotide in
 # the sequence or the last position.
 # only non-zero probabilities
 [Initial]
@@ -20,7 +20,7 @@
 
 # Terminal probabilities (a priori probs for a state ending at
 # the last position.
-# only non-zero probabilities neccessary
+# only non-zero probabilities necessary
 [Terminal]
 # number of states where terminating is possible
 1

config/model/trans_shadow_intronless.pbl

@@ -21,7 +21,7 @@
 
 # Terminal probabilities (a priori probs for a state ending at
 # the last position.
-# only non-zero probabilities neccessary
+# only non-zero probabilities necessary
 [Terminal]
 # number of states where terminating is possible
 3