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r205 - trunk/src/main/java/org/nuiton/j2r/types
by jcouteau＠users.nuiton.org April 19, 2010

April 19, 2010

Author: jcouteau Date: 2010-04-19 16:44:30 +0200 (Mon, 19 Apr 2010) New Revision: 205 Log: Deal with autocommit mode in DataFrame getData() method Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-19 13:20:43 UTC (rev 204) +++ trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-19 14:44:30 UTC (rev 205) @@ -499,13 +499,38 @@ } /** - * Method to get the ArrayLists of the R data.frame (there is no - * synchronizing with R). + * Method to get the ArrayLists of the R data.frame. Synchronize with R only + * if in autocommit mode and variable set. * - * @return a ArrayList containing the ArrayLists of the R data.frame + * @return the data of the data.frame */ public List<List<?>> getData() { - //TODO JC manage the autocommit mode here. + if (this.engine.isAutoCommit()){ + + int rowNumber; + int columnNumber; + + try { + checkVariable(); + int[] dim = dim(); + rowNumber = dim[0]; + columnNumber = dim[1]; + } catch (RException eee) { + return data; + } + + try { + for(int i=0;i<columnNumber;i++){ + for(int j=0;j<rowNumber;j++){ + get(i,j); + } + } + + } catch (RException eee) { + log.error("An error occurred while trying to contact R"); + } + + } return data; }

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r204 - in trunk/src: main/java/org/nuiton/j2r/types test/java/org/nuiton/j2r
by jcouteau＠users.nuiton.org April 19, 2010

April 19, 2010

Author: jcouteau Date: 2010-04-19 15:20:43 +0200 (Mon, 19 Apr 2010) New Revision: 204 Log: Improve attributes management Modified: trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java trunk/src/test/java/org/nuiton/j2r/ListTest.java Modified: trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java 2010-04-19 10:50:13 UTC (rev 203) +++ trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java 2010-04-19 13:20:43 UTC (rev 204) @@ -25,10 +25,8 @@ package org.nuiton.j2r.types; -import java.util.Arrays; -import java.util.List; -import java.util.Map; -import java.util.Set; +import java.util.*; + import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.nuiton.j2r.REngine; @@ -65,54 +63,9 @@ @Override public void setAttributes(Map<String, Object> attributes) throws RException { - //TODO JC should be useful to test the validity of attributes before assigning it. - this.attributes = attributes; - - if ((this.attributes != null) && (!this.attributes.isEmpty())) { - Set<String> keyset = attributes.keySet(); - for (String key : keyset) { - //foreach type of attribute, adapt the R instruction. - if (this.attributes.get(key) instanceof String) { - engine.eval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, key, - "\"" + this.attributes.get(key) + "\"")); - //String, value between quotes - } else if (this.attributes.get(key) instanceof Double) { - engine.eval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, - key, this.attributes.get(key))); - } else if (this.attributes.get(key) instanceof Integer) { - engine.eval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, - key, String.format(RInstructions.AS_INTEGER, - this.attributes.get(key)))); - //Integer, value formated by the R function : as.integer() - } else if (this.attributes.get(key) instanceof Boolean) { - if ((Boolean) this.attributes.get(key)) { - engine.eval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, - key, RInstructions.TRUE)); - //Boolean true replaced by TRUE - } else { - engine.eval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, - key, RInstructions.FALSE)); - //Boolean false replaced by REPLACE - } - } else if (this.attributes.get(key) instanceof REXP) { - engine.eval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, - key, - ((REXP) this.attributes.get(key)).toRString())); - //REXP replaced by the result of their toRString() method. - } else { - if (log.isWarnEnabled()) { - log.warn("This attribute is not valid : " + key + - " ; " + this.attributes.get(key) + - ". It will not be sent to R"); - //if the attribute is not recognised. - } - } + if (attributes!=null){ + for(Map.Entry<String, Object> entry : attributes.entrySet()){ + setAttribute(entry.getKey(),entry.getValue()); } } } @@ -166,7 +119,7 @@ if (returnedAttribute != null) { if (attributes.containsKey(attribute)) { //if the attribute already exists, remove it first (or you - //will have too times the same attribubte with different + //will have too times the same attribute with different //values) attributes.remove(attribute); attributes.put(attribute, returnedAttribute); @@ -186,45 +139,63 @@ /** {@inheritDoc} */ @Override public void setAttribute(String attribute, Object value) throws RException { - //variable to check if the attribute is valid before setting it. - boolean isOK = false; if (value instanceof String) { - isOK = true; - engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, attribute, "\"" + value + "\"")); - //if String, between quotes + setAttribute(attribute, (String)value); } else if (value instanceof Double) { - isOK = true; - engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, attribute, value)); + setAttribute(attribute, (Double)value); } else if (value instanceof Integer) { - isOK = true; - engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, attribute, String.format( - RInstructions.AS_INTEGER, value))); - //If integer in the R function : as.integer() + setAttribute(attribute, (Integer)value); } else if (value instanceof Boolean) { - isOK = true; - //R boolean is upper case - engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, attribute, value.toString().toUpperCase())); + setAttribute(attribute,(Boolean)value); } else if (value instanceof REXP) { - isOK = true; - engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, - this.variable, attribute, ((REXP) value).toRString())); - //if REXP, use its method toRString() + setAttribute(attribute, (REXP)value); } else { log.warn("This attribute is not valid : " + attribute + " ; " + value + ". It will not be processed"); } - //if attribute is valid, out it in the attribute list. - if (isOK) { - if (attributes.containsKey(attribute)) { - attributes.remove(attribute); - attributes.put(attribute, value); - } else { - attributes.put(attribute, value); - } + } + + public void setAttribute(String attribute, Double value) throws RException { + engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, + this.variable, attribute, value)); + putAttributeInData(attribute,value); + } + + public void setAttribute(String attribute, Integer value) throws RException { + //If integer in the R function : as.integer() + engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, + this.variable, attribute, String.format( + RInstructions.AS_INTEGER, value))); + putAttributeInData(attribute,value); + } + + public void setAttribute(String attribute, Boolean value) throws RException { + //R boolean is upper case + engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, + this.variable, attribute, value.toString().toUpperCase())); + putAttributeInData(attribute,value); + } + + public void setAttribute(String attribute, String value) throws RException { + //if String, between quotes + engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, + this.variable, attribute, "\"" + value + "\"")); + putAttributeInData(attribute,value); + } + + public void setAttribute(String attribute, REXP value) throws RException { + //if REXP, use its method toRString() + engine.voidEval(String.format(RInstructions.SET_ATTRIBUTE, + this.variable, attribute, value.toRString())); + putAttributeInData(attribute,value); + } + + private void putAttributeInData(String attribute, Object value){ + if (attributes.containsKey(attribute)) { + attributes.remove(attribute); + attributes.put(attribute, value); + } else { + attributes.put(attribute, value); } } Modified: trunk/src/test/java/org/nuiton/j2r/ListTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/ListTest.java 2010-04-19 10:50:13 UTC (rev 203) +++ trunk/src/test/java/org/nuiton/j2r/ListTest.java 2010-04-19 13:20:43 UTC (rev 204) @@ -134,8 +134,7 @@ assertEquals("c", list1.getNames().get(2)); assertEquals("d", list1.getNames().get(3)); - engine - .voidEval("a<-list(a=as.integer(1),b=\"toto\",c=3.6,d=TRUE,e=FALSE)"); + engine.voidEval("a<-list(a=as.integer(1),b=\"toto\",c=3.6,d=TRUE,e=FALSE)"); try { list1.getNames(); Assert.fail("Error was not thrown although it should have been");

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r203 - trunk/src/main/java/org/nuiton/j2r/types
by jcouteau＠users.nuiton.org April 19, 2010

April 19, 2010

Author: jcouteau Date: 2010-04-19 12:50:13 +0200 (Mon, 19 Apr 2010) New Revision: 203 Log: Split the set method in a method per authorized type Modified: trunk/src/main/java/org/nuiton/j2r/types/RList.java Modified: trunk/src/main/java/org/nuiton/j2r/types/RList.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-04-19 10:40:21 UTC (rev 202) +++ trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-04-19 10:50:13 UTC (rev 203) @@ -46,8 +46,6 @@ //Content of the list (eg elements of the list in R) private List<Object> data; private Log log = LogFactory.getLog(RDataFrame.class); - - //TODO JC implement the logger use ! /** * Create a default RList linked to a R engine (the List is not initialized * in R.) @@ -166,6 +164,11 @@ returnString = returnString.substring(0, returnString.length() - 1); } returnString += ")"; + + + + System.out.println(returnString); + return returnString; } @@ -179,8 +182,106 @@ * @throws RException * if no variable name has been given to the list */ - public void set(int x, Object data) throws RException { + public void set(int x, Double data) throws RException { checkVariable(); + + setInData(x,data); + + //in R, all data is numeric, no need to transformation, simple + //assignation + engine.voidEval(String.format(RInstructions.SET_LIST_ITEM, + this.variable, x + 1, data)); + } + + /** + * Method to set the xth object of the list to a value. + * + * @param x + * x coordinate (from 0 to size-1) + * @param data + * value to set + * @throws RException + * if no variable name has been given to the list + */ + public void set(int x, Integer data) throws RException { + checkVariable(); + + setInData(x,data); + + //transform the data in R integer + String asInteger = String.format(RInstructions.AS_INTEGER, data); + //assign the transformed data + engine.voidEval(String.format(RInstructions.SET_LIST_ITEM, + this.variable, x + 1, asInteger)); + } + + /** + * Method to set the xth object of the list to a value. + * + * @param x + * x coordinate (from 0 to size-1) + * @param data + * value to set + * @throws RException + * if no variable name has been given to the list + */ + public void set(int x, Boolean data) throws RException { + checkVariable(); + + setInData(x,data); + + if (data) { + engine.voidEval(String.format(RInstructions.SET_LIST_ITEM, + this.variable, x + 1, RInstructions.TRUE)); + } else { + engine.voidEval(String.format(RInstructions.SET_LIST_ITEM, + this.variable, x + 1, RInstructions.FALSE)); + } + } + + /** + * Method to set the xth object of the list to a value. + * + * @param x + * x coordinate (from 0 to size-1) + * @param data + * value to set + * @throws RException + * if no variable name has been given to the list + */ + public void set(int x, String data) throws RException { + checkVariable(); + + setInData(x,data); + + engine.voidEval(String.format(RInstructions.SET_LIST_ITEM, + this.variable, x + 1, "\"" + data + "\"")); + } + + /** + * Method to set the xth object of the list to a value. + * + * @param x + * x coordinate (from 0 to size-1) + * @param data + * value to set + * @throws RException + * if no variable name has been given to the list + */ + public void set(int x, REXP data) throws RException { + checkVariable(); + + setInData(x,data); + + //Send the REXP to R + engine.voidEval(data.toRString()); + //Set the REXP as list item + engine.voidEval(String.format(RInstructions.SET_LIST_ITEM, + this.variable, x + 1, data.getVariable())); + } + + + private void setInData(int x, Object data){ for (int i = 0; i <= x; i++) { try { this.data.get(i); @@ -194,37 +295,7 @@ this.data.add(null); } } - } - if (data instanceof Double) { - //in R, all data is numeric, no need to transformation, simple - //assignation - engine.voidEval(String.format(RInstructions.SET_LIST_ITEM, - this.variable, x + 1, data)); - } else if (data instanceof Integer) { - //transform the data in R integer - String asInteger = String.format(RInstructions.AS_INTEGER, data); - //assign the transformed data - engine.voidEval(String.format(RInstructions.SET_LIST_ITEM, - this.variable, x + 1, asInteger)); - } else if (data instanceof Boolean) { - if ((Boolean) data) { - engine.voidEval(String.format(RInstructions.SET_LIST_ITEM, - this.variable, x + 1, RInstructions.TRUE)); - } else { - engine.voidEval(String.format(RInstructions.SET_LIST_ITEM, - this.variable, x + 1, RInstructions.FALSE)); - } - } else if (data instanceof String) { - engine.voidEval(String.format(RInstructions.SET_LIST_ITEM, - this.variable, x + 1, "\"" + data + "\"")); - } else if (data instanceof REXP) { - //Send the REXP to R - engine.voidEval(((REXP) data).toRString()); - //Set the REXP as list item - engine.voidEval(String.format(RInstructions.SET_LIST_ITEM, - this.variable, x + 1, ((REXP) data).getVariable())); - } } /**

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r202 - trunk/src/main/java/org/nuiton/j2r/types
by jcouteau＠users.nuiton.org April 19, 2010

April 19, 2010

Author: jcouteau Date: 2010-04-19 12:40:21 +0200 (Mon, 19 Apr 2010) New Revision: 202 Log: Remove system.out.println() Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-19 09:28:53 UTC (rev 201) +++ trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-19 10:40:21 UTC (rev 202) @@ -397,7 +397,9 @@ returnString += "stringsAsFactors=FALSE)"; } - System.out.println(returnString); + if(log.isDebugEnabled()){ + log.debug(returnString); + } return returnString; }

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r201 - trunk/src/main/java/org/nuiton/j2r/types
by jcouteau＠users.nuiton.org April 19, 2010

April 19, 2010

Author: jcouteau Date: 2010-04-19 11:28:53 +0200 (Mon, 19 Apr 2010) New Revision: 201 Log: Add a toString method to RDataFrame to represent it as in R. (under a table form with column and row names). Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-16 18:12:42 UTC (rev 200) +++ trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-19 09:28:53 UTC (rev 201) @@ -57,8 +57,6 @@ //Vector containing the vectors of the data.frame private List<List<?>> data; - //TODO JC 20100415 Create a toString method that displays the DataFrame - /** * Constructor * @@ -720,7 +718,7 @@ //get the first line of the file BufferedReader br = new BufferedReader(new FileReader(inputFile)); tmp = br.readLine(); - String[] splitted = tmp.split("\\;"); + String[] splitted = tmp.split(";"); //get the data size (number of columns) if (rowNames) { @@ -762,7 +760,7 @@ while ((tmp = br.readLine()) != null) { //parse each line - splitted = tmp.split("\\;"); + splitted = tmp.split(";"); //to determine the data index on the line. int index = 0; @@ -814,20 +812,10 @@ br.close(); this.data = tempData; - if (log.isDebugEnabled()){ //Display the imported data.frame in debug mode - - log.debug("Imported DataFrame : "); - - for(List<?> column:this.data){ - String debugLine="Column " + this.data.indexOf(column)+ " : "; - for(Object obj:column){ - debugLine += obj + " ,"; - } - log.debug(debugLine); - } + log.debug("Imported DataFrame : \n"+toString()); } } @@ -866,4 +854,124 @@ return (new int[]{x,y}); } + + /** + * Method that returns a string representing the DataFrame. The output + * String should looks like the dataframe in R. + * @return a string representing the dataframe as in R. + */ + @Override + public String toString(){ + + List<String> linesToDisplay = new ArrayList<String>(); + + Boolean displayRowNames = !rowNames.isEmpty(); + + Boolean displayNames = !names.isEmpty(); + + Integer numberOfLines = 0; + + //Calculate the number of lines to display + if (!this.data.isEmpty()) { + if (!this.data.get(0).isEmpty()){ + numberOfLines = this.data.get(0).size(); + } + } + if (displayNames){ + numberOfLines += 1; + } + + // fill the lines with empty strings + for (int i=0;i<numberOfLines;i++){ + linesToDisplay.add(i,""); + } + + // Add the row names if necessary + if (displayRowNames){ + + // calculate the column size + int columnSize = 0; + for (String name:rowNames){ + if (name.length()>columnSize){ + columnSize = name.length(); + } + } + columnSize +=2; + + // add the row name to each line, complete with spaces to have next + // column aligned + if (displayNames) { + String line = linesToDisplay.get(0); + String str = String.format("%-"+columnSize+"s", ""); + line +=str ; + linesToDisplay.set(0, line); + } + for (int i=0;i<rowNames.size();i++){ + String str = String.format("%-"+columnSize+"s", rowNames.get(i)); + + if(displayNames) { + String line = linesToDisplay.get(i+1); + line += str; + linesToDisplay.set(i+1, line); + } else { + String line = linesToDisplay.get(i); + line += str; + linesToDisplay.set(i, line); + } + + } + + } + + // for each column, calculate the column size, add the value to each + // line, complete with spaces to have next column aligned + for (List<?> column:this.data){ + + String columnName=""; + + // calculate the column size + int columnSize = 0; + if(displayNames){ + columnName = names.get(this.data.indexOf(column)); + columnSize = columnName.length(); + } + for (Object obj:column){ + String toString = obj.toString(); + if (toString.length()>columnSize){ + columnSize = toString.length(); + } + } + columnSize +=2; + + if(displayNames){ + String str = String.format("%-"+columnSize+"s", columnName); + String line = linesToDisplay.get(0); + line += str; + linesToDisplay.set(0, line); + } + + for (int i=0;i<column.size();i++){ + + String str = String.format("%-"+columnSize+"s", column.get(i)); + + if(displayNames) { + String line = linesToDisplay.get(i+1); + line += str; + linesToDisplay.set(i+1, line); + } else { + String line = linesToDisplay.get(i); + line += str; + linesToDisplay.set(i, line); + } + } + } + + String returnString = ""; + + for (String str:linesToDisplay){ + returnString+= str +"\n"; + } + + return returnString; + } }

1 0

r200 - trunk
by tchemit＠users.nuiton.org April 16, 2010

April 16, 2010

Author: tchemit Date: 2010-04-16 20:12:42 +0200 (Fri, 16 Apr 2010) New Revision: 200 Log: Utilisation de mavenpom4redmine 2.1.1 Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2010-04-15 14:29:08 UTC (rev 199) +++ trunk/pom.xml 2010-04-16 18:12:42 UTC (rev 200) @@ -1,5 +1,5 @@ <?xml version="1.0"?> -  -<project xmlns="http://maven.apache.org/POM/4.0.0" - xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" - xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"> +<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"> <modelVersion>4.0.0</modelVersion> @@ -36,7 +34,7 @@ <parent> <groupId>org.nuiton</groupId> <artifactId>mavenpom4redmine</artifactId> - <version>2.1</version> + <version>2.1.1</version> </parent> <artifactId>nuiton-j2r</artifactId>

1 0

r199 - in trunk: . src/license src/main/java/org/nuiton/j2r src/main/java/org/nuiton/j2r/jni src/main/java/org/nuiton/j2r/net src/main/java/org/nuiton/j2r/types src/site src/site/rst src/test/java/org/nuiton/j2r
by tchemit＠users.nuiton.org April 15, 2010

April 15, 2010

Author: tchemit Date: 2010-04-15 16:29:08 +0200 (Thu, 15 Apr 2010) New Revision: 199 Log: remove redundant svn keywords on header Modified: trunk/pom.xml trunk/src/license/project.xml trunk/src/main/java/org/nuiton/j2r/REngine.java trunk/src/main/java/org/nuiton/j2r/REngineAbstract.java trunk/src/main/java/org/nuiton/j2r/RException.java trunk/src/main/java/org/nuiton/j2r/RInstructions.java trunk/src/main/java/org/nuiton/j2r/RProxy.java trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java trunk/src/main/java/org/nuiton/j2r/net/RNetEngine.java trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java trunk/src/main/java/org/nuiton/j2r/types/REXP.java trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java trunk/src/main/java/org/nuiton/j2r/types/RList.java trunk/src/site/rst/etude.rst trunk/src/site/rst/index.rst trunk/src/site/rst/installation.rst trunk/src/site/rst/module.rst trunk/src/site/site.xml trunk/src/test/java/org/nuiton/j2r/DataframeTest.java trunk/src/test/java/org/nuiton/j2r/JNITest.java trunk/src/test/java/org/nuiton/j2r/JPurTest.java trunk/src/test/java/org/nuiton/j2r/ListTest.java trunk/src/test/java/org/nuiton/j2r/LutinTimer.java trunk/src/test/java/org/nuiton/j2r/NetTest.java trunk/src/test/java/org/nuiton/j2r/TestConstants.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/pom.xml 2010-04-15 14:29:08 UTC (rev 199) @@ -3,7 +3,6 @@ #%L Nuiton Java-2-R library - $Author$ $Id$ $HeadURL$ %% Modified: trunk/src/license/project.xml =================================================================== --- trunk/src/license/project.xml 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/license/project.xml 2010-04-15 14:29:08 UTC (rev 199) @@ -3,7 +3,6 @@ #%L Nuiton Java-2-R library - $Author: tchemit $ $Id$ $HeadURL$ %% Modified: trunk/src/main/java/org/nuiton/j2r/REngine.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/REngine.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/main/java/org/nuiton/j2r/REngine.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/REngineAbstract.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/REngineAbstract.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/main/java/org/nuiton/j2r/REngineAbstract.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/RException.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/RException.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/main/java/org/nuiton/j2r/RException.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/RInstructions.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/RInstructions.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/main/java/org/nuiton/j2r/RInstructions.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/RProxy.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/RProxy.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/main/java/org/nuiton/j2r/RProxy.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/net/RNetEngine.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/net/RNetEngine.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/main/java/org/nuiton/j2r/net/RNetEngine.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/types/REXP.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/REXP.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/main/java/org/nuiton/j2r/types/REXP.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/types/RList.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/site/rst/etude.rst =================================================================== --- trunk/src/site/rst/etude.rst 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/site/rst/etude.rst 2010-04-15 14:29:08 UTC (rev 199) @@ -9,7 +9,6 @@ .. * #%L .. * Nuiton Java-2-R library .. * -.. * $Author$ .. * $Id$ .. * $HeadURL$ .. * %% Modified: trunk/src/site/rst/index.rst =================================================================== --- trunk/src/site/rst/index.rst 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/site/rst/index.rst 2010-04-15 14:29:08 UTC (rev 199) @@ -6,7 +6,6 @@ .. * #%L .. * Nuiton Java-2-R library .. * -.. * $Author$ .. * $Id$ .. * $HeadURL$ .. * %% Modified: trunk/src/site/rst/installation.rst =================================================================== --- trunk/src/site/rst/installation.rst 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/site/rst/installation.rst 2010-04-15 14:29:08 UTC (rev 199) @@ -11,7 +11,6 @@ .. * #%L .. * Nuiton Java-2-R library .. * -.. * $Author$ .. * $Id$ .. * $HeadURL$ .. * %% Modified: trunk/src/site/rst/module.rst =================================================================== --- trunk/src/site/rst/module.rst 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/site/rst/module.rst 2010-04-15 14:29:08 UTC (rev 199) @@ -13,7 +13,6 @@ .. * #%L .. * Nuiton Java-2-R library .. * -.. * $Author$ .. * $Id$ .. * $HeadURL$ .. * %% Modified: trunk/src/site/site.xml =================================================================== --- trunk/src/site/site.xml 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/site/site.xml 2010-04-15 14:29:08 UTC (rev 199) @@ -3,7 +3,6 @@ #%L Nuiton Java-2-R library - $Author$ $Id$ $HeadURL$ %% Modified: trunk/src/test/java/org/nuiton/j2r/DataframeTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/DataframeTest.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/test/java/org/nuiton/j2r/DataframeTest.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/test/java/org/nuiton/j2r/JNITest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/JNITest.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/test/java/org/nuiton/j2r/JNITest.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% @@ -33,8 +32,7 @@ * @version $Revision$ * * Mise a jour: $Date$ - * par : $Author$ - */ + * par : */ package org.nuiton.j2r; import static org.nuiton.j2r.TestConstants.S_NB_LOOPS; Modified: trunk/src/test/java/org/nuiton/j2r/JPurTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/JPurTest.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/test/java/org/nuiton/j2r/JPurTest.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/test/java/org/nuiton/j2r/ListTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/ListTest.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/test/java/org/nuiton/j2r/ListTest.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/test/java/org/nuiton/j2r/LutinTimer.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/LutinTimer.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/test/java/org/nuiton/j2r/LutinTimer.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/test/java/org/nuiton/j2r/NetTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/NetTest.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/test/java/org/nuiton/j2r/NetTest.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %% @@ -33,8 +32,7 @@ * @version $Revision$ * * Mise a jour: $Date$ - * par : $Author$ - */ + * par : */ package org.nuiton.j2r; import static org.nuiton.j2r.TestConstants.S_NB_LOOPS; Modified: trunk/src/test/java/org/nuiton/j2r/TestConstants.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/TestConstants.java 2010-04-15 11:10:09 UTC (rev 198) +++ trunk/src/test/java/org/nuiton/j2r/TestConstants.java 2010-04-15 14:29:08 UTC (rev 199) @@ -2,7 +2,6 @@ * #%L * Nuiton Java-2-R library * - * $Author$ * $Id$ * $HeadURL$ * %%

1 0

r198 - in trunk: . src/license src/main/java/org/nuiton/j2r src/main/java/org/nuiton/j2r/jni src/main/java/org/nuiton/j2r/net src/main/java/org/nuiton/j2r/types src/site src/site/rst src/test/java/org/nuiton/j2r
by tchemit＠users.nuiton.org April 15, 2010

April 15, 2010

Author: tchemit Date: 2010-04-15 13:10:09 +0200 (Thu, 15 Apr 2010) New Revision: 198 Log: remove Date and Rev svn keywords Modified: trunk/pom.xml trunk/src/license/project.xml trunk/src/main/java/org/nuiton/j2r/REngine.java trunk/src/main/java/org/nuiton/j2r/REngineAbstract.java trunk/src/main/java/org/nuiton/j2r/RException.java trunk/src/main/java/org/nuiton/j2r/RInstructions.java trunk/src/main/java/org/nuiton/j2r/RProxy.java trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java trunk/src/main/java/org/nuiton/j2r/net/RNetEngine.java trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java trunk/src/main/java/org/nuiton/j2r/types/REXP.java trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java trunk/src/main/java/org/nuiton/j2r/types/RList.java trunk/src/site/rst/etude.rst trunk/src/site/rst/index.rst trunk/src/site/rst/installation.rst trunk/src/site/rst/module.rst trunk/src/site/site.xml trunk/src/test/java/org/nuiton/j2r/DataframeTest.java trunk/src/test/java/org/nuiton/j2r/JNITest.java trunk/src/test/java/org/nuiton/j2r/JPurTest.java trunk/src/test/java/org/nuiton/j2r/ListTest.java trunk/src/test/java/org/nuiton/j2r/LutinTimer.java trunk/src/test/java/org/nuiton/j2r/NetTest.java trunk/src/test/java/org/nuiton/j2r/TestConstants.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/pom.xml 2010-04-15 11:10:09 UTC (rev 198) @@ -4,8 +4,6 @@ Nuiton Java-2-R library $Author$ - $LastChangedDate$ - $LastChangedRevision$ $Id$ $HeadURL$ %% Modified: trunk/src/license/project.xml =================================================================== --- trunk/src/license/project.xml 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/license/project.xml 2010-04-15 11:10:09 UTC (rev 198) @@ -1,4 +1,29 @@ <?xml version='1.0' encoding='UTF-8'?> +  <project xmlns="http://maven-site.nuiton.org/maven-license-plugin/1.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven-site.nuiton.org/maven-license-plugin/1.0.0 http://maven-site.nuiton.org/maven-license-plugin/licenseProjectDescriptor-…"> Modified: trunk/src/main/java/org/nuiton/j2r/REngine.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/REngine.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/main/java/org/nuiton/j2r/REngine.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/REngineAbstract.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/REngineAbstract.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/main/java/org/nuiton/j2r/REngineAbstract.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/RException.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/RException.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/main/java/org/nuiton/j2r/RException.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/RInstructions.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/RInstructions.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/main/java/org/nuiton/j2r/RInstructions.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/RProxy.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/RProxy.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/main/java/org/nuiton/j2r/RProxy.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% @@ -52,7 +50,7 @@ * <li><code>-DR.type=...</code></li> * </ul> * It is possible to parametrize the network solution, for that, see the - * {@link org.nuiton.j2r.net.RNetEngine} documentation. + * {@link RNetEngine} documentation. */ public class RProxy implements REngine { @@ -153,7 +151,7 @@ * * @return the result of the R instruction. * - * @see org.nuiton.j2r.REngine#eval(java.lang.String) + * @see REngine#eval(String) */ @Override public Object eval(String expr) throws RException { @@ -168,7 +166,7 @@ /** * Get back the R engine type options to initialize the REngine. * - * @see org.nuiton.j2r.REngine#init() + * @see REngine#init() */ @Override public boolean init() { @@ -190,7 +188,7 @@ /** * Terminate the R engine. * - * @see org.nuiton.j2r.REngine#terminate() + * @see REngine#terminate() */ @Override public void terminate() throws RException { @@ -207,7 +205,7 @@ * * @param expr the R instruction to send. * - * @see org.nuiton.j2r.REngine#voidEval(java.lang.String) + * @see REngine#voidEval(String) */ @Override public void voidEval(String expr) throws RException { @@ -226,8 +224,8 @@ * directory where the .RData file is located * @throws RException if an error occcur while loading the R session. * - * @see org.nuiton.j2r.REngine#loadRData(java.io.File) - * @see org.nuiton.j2r.REngineAbstract#loadRData(java.io.File) + * @see REngine#loadRData(File) + * @see REngineAbstract#loadRData(File) */ @Override public void loadRData(File directory) throws RException { @@ -247,8 +245,8 @@ * where the .RData file will be saved * @throws RException if an error occur while saving the R session. * - * @see org.nuiton.j2r.REngine#saveRData(java.io.File) - * @see org.nuiton.j2r.REngineAbstract#saveRData(java.io.File) + * @see REngine#saveRData(File) + * @see REngineAbstract#saveRData(File) */ @Override public void saveRData(File directory) throws RException { @@ -268,8 +266,8 @@ * * @throws RException if an error occur while setting the R working directory. * - * @see org.nuiton.j2r.REngine#setwd(java.io.File) - * @see org.nuiton.j2r.REngineAbstract#setwd(java.io.File) + * @see REngine#setwd(File) + * @see REngineAbstract#setwd(File) */ @Override public void setwd(File directory) throws RException { @@ -289,8 +287,8 @@ * * @throws RException if an error occur while getting the R working directory. * - * @see org.nuiton.j2r.REngine#getwd() - * @see org.nuiton.j2r.REngineAbstract#getwd() + * @see REngine#getwd() + * @see REngineAbstract#getwd() */ @Override public File getwd() throws RException { @@ -313,8 +311,8 @@ * @throws RException if an error occur while saving the content of the * object. * - * @see org.nuiton.j2r.REngine#dput(java.lang.String, java.lang.String) - * @see org.nuiton.j2r.REngineAbstract#dput(java.lang.String, java.lang.String) + * @see REngine#dput(String, String) + * @see REngineAbstract#dput(String, String) */ @Override public void dput(String rObject, String outputFileName) throws RException { @@ -339,8 +337,8 @@ * @throws RException if an error occur while trying to perform this * operation. * - * @see org.nuiton.j2r.REngine#dget(java.lang.String, java.lang.String) - * @see org.nuiton.j2r.REngineAbstract#dget(java.lang.String, java.lang.String) + * @see REngine#dget(String, String) + * @see REngineAbstract#dget(String, String) */ @Override public void dget(String rObject, String inputFileName) throws RException { @@ -363,8 +361,8 @@ * the file to save * @throws RException if an error occur while performing the operation. * - * @see org.nuiton.j2r.REngine#dput(java.lang.String, java.io.File) - * @see org.nuiton.j2r.REngineAbstract#dput(java.lang.String, java.io.File) + * @see REngine#dput(String, File) + * @see REngineAbstract#dput(String, File) */ @Override public void dput(String rObject, File outputFile) throws RException { @@ -391,8 +389,8 @@ * file to load * @throws RException if an eroor occur while performing the operation. * - * @see org.nuiton.j2r.REngine#dget(java.lang.String, java.io.File) - * @see org.nuiton.j2r.REngineAbstract#dget(java.lang.String, java.io.File) + * @see REngine#dget(String, File) + * @see REngineAbstract#dget(String, File) */ @Override public void dget(String rObject, File inputFile) throws RException { @@ -414,11 +412,11 @@ * * @param rObject name of the R object to remove. * - * @throws org.nuiton.j2r.RException if an error occur while removing the R + * @throws RException if an error occur while removing the R * object. * - * @see org.nuiton.j2r.REngine#remove(java.lang.String) - * @see org.nuiton.j2r.REngineAbstract#remove(java.lang.String) + * @see REngine#remove(String) + * @see REngineAbstract#remove(String) */ @Override public void remove(String rObject) throws RException { @@ -437,11 +435,11 @@ * * @param destination the destination R object name * - * @throws org.nuiton.j2r.RException if an error occur while renaming the R + * @throws RException if an error occur while renaming the R * object. * - * @see org.nuiton.j2r.REngine#mv(java.lang.String, java.lang.String) - * @see org.nuiton.j2r.REngineAbstract#mv(java.lang.String, java.lang.String) + * @see REngine#mv(String, String) + * @see REngineAbstract#mv(String, String) */ @Override public void mv(String source, String destination) throws RException { @@ -461,11 +459,11 @@ * * @param outputObject the destination R object name * - * @throws org.nuiton.j2r.RException if an error occur while copying the R + * @throws RException if an error occur while copying the R * object. * - * @see org.nuiton.j2r.REngine#cp(java.lang.String, java.lang.String) - * @see org.nuiton.j2r.REngineAbstract#cp(java.lang.String, java.lang.String) + * @see REngine#cp(String, String) + * @see REngineAbstract#cp(String, String) */ @Override public void cp(String inputObject, String outputObject) throws RException { @@ -483,11 +481,11 @@ * * @return a table containing all the R objects present in session. * - * @throws org.nuiton.j2r.RException if an error occur while getting back + * @throws RException if an error occur while getting back * the objects list. * - * @see org.nuiton.j2r.REngine#ls() - * @see org.nuiton.j2r.REngineAbstract#ls() + * @see REngine#ls() + * @see REngineAbstract#ls() */ @Override public String[] ls() throws RException { @@ -502,11 +500,11 @@ /** * Method to remove all objects from the R session. * - * @throws org.nuiton.j2r.RException if an error occur while clearing the R + * @throws RException if an error occur while clearing the R * session. * - * @see org.nuiton.j2r.REngine#clearSession() - * @see org.nuiton.j2r.REngineAbstract#clearSession() + * @see REngine#clearSession() + * @see REngineAbstract#clearSession() */ @Override public void clearSession() throws RException { @@ -522,11 +520,11 @@ * Method to launch the evaluation of all the R expressions stored when in * non-autocommit mode. * - * @throws org.nuiton.j2r.RException if an error occur while evaluating one + * @throws RException if an error occur while evaluating one * of the R expressions. * - * @see org.nuiton.j2r.REngine#commit() - * @see org.nuiton.j2r.REngineAbstract#commit() + * @see REngine#commit() + * @see REngineAbstract#commit() */ @Override public void commit() throws RException { @@ -545,11 +543,11 @@ * * @param autocommit the autocommit mode * - * @throws org.nuiton.j2r.RException if an error occur while switching + * @throws RException if an error occur while switching * modes. * - * @see org.nuiton.j2r.REngine#setAutoCommit(java.lang.Boolean) - * @see org.nuiton.j2r.REngine#setAutoCommit(java.lang.Boolean) + * @see REngine#setAutoCommit(Boolean) + * @see REngine#setAutoCommit(Boolean) */ @Override public void setAutoCommit(Boolean autocommit) throws RException { @@ -568,8 +566,8 @@ * * @return the autocommit mode * - * @see org.nuiton.j2r.REngine#isAutoCommit() - * @see org.nuiton.j2r.REngineAbstract#isAutoCommit() + * @see REngine#isAutoCommit() + * @see REngineAbstract#isAutoCommit() */ @Override public Boolean isAutoCommit() { @@ -589,11 +587,11 @@ * @param fileName name of the file to save (will save in the fileName.RData * file) * - * @throws org.nuiton.j2r.RException if an error occur while saving the R + * @throws RException if an error occur while saving the R * session. * - * @see org.nuiton.j2r.REngine#saveRData(java.io.File, java.lang.String) - * @see org.nuiton.j2r.REngineAbstract#saveRData(java.io.File, java.lang.String) + * @see REngine#saveRData(File, String) + * @see REngineAbstract#saveRData(File, String) */ @Override public void saveRData(File directory, String fileName) throws RException { @@ -613,11 +611,11 @@ * @param fileName name of the file to load (will load the fileName.RData * file) * - * @throws org.nuiton.j2r.RException if an error occur while loading the R + * @throws RException if an error occur while loading the R * session file. * - * @see org.nuiton.j2r.REngine#loadRData(java.io.File, java.lang.String) - * @see org.nuiton.j2r.REngineAbstract#loadRData(java.io.File, java.lang.String) + * @see REngine#loadRData(File, String) + * @see REngineAbstract#loadRData(File, String) */ @Override public void loadRData(File directory, String fileName) throws RException { Modified: trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/net/RNetEngine.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/net/RNetEngine.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/main/java/org/nuiton/j2r/net/RNetEngine.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/types/REXP.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/REXP.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/main/java/org/nuiton/j2r/types/REXP.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/main/java/org/nuiton/j2r/types/RList.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/site/rst/etude.rst =================================================================== --- trunk/src/site/rst/etude.rst 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/site/rst/etude.rst 2010-04-15 11:10:09 UTC (rev 198) @@ -10,8 +10,6 @@ .. * Nuiton Java-2-R library .. * .. * $Author$ -.. * $LastChangedDate$ -.. * $LastChangedRevision$ .. * $Id$ .. * $HeadURL$ .. * %% Modified: trunk/src/site/rst/index.rst =================================================================== --- trunk/src/site/rst/index.rst 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/site/rst/index.rst 2010-04-15 11:10:09 UTC (rev 198) @@ -7,8 +7,6 @@ .. * Nuiton Java-2-R library .. * .. * $Author$ -.. * $LastChangedDate$ -.. * $LastChangedRevision$ .. * $Id$ .. * $HeadURL$ .. * %% Modified: trunk/src/site/rst/installation.rst =================================================================== --- trunk/src/site/rst/installation.rst 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/site/rst/installation.rst 2010-04-15 11:10:09 UTC (rev 198) @@ -2,7 +2,6 @@ Installation ============ - Le présent document a pour but de faciliter les différentes installations nécessaires en vue d'utiliser la librairie LutinJ2R. @@ -13,8 +12,6 @@ .. * Nuiton Java-2-R library .. * .. * $Author$ -.. * $LastChangedDate$ -.. * $LastChangedRevision$ .. * $Id$ .. * $HeadURL$ .. * %% Modified: trunk/src/site/rst/module.rst =================================================================== --- trunk/src/site/rst/module.rst 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/site/rst/module.rst 2010-04-15 11:10:09 UTC (rev 198) @@ -2,7 +2,6 @@ Documentation du module ======================= - .. contents:: @@ -15,8 +14,6 @@ .. * Nuiton Java-2-R library .. * .. * $Author$ -.. * $LastChangedDate$ -.. * $LastChangedRevision$ .. * $Id$ .. * $HeadURL$ .. * %% Modified: trunk/src/site/site.xml =================================================================== --- trunk/src/site/site.xml 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/site/site.xml 2010-04-15 11:10:09 UTC (rev 198) @@ -4,8 +4,6 @@ Nuiton Java-2-R library $Author$ - $LastChangedDate$ - $LastChangedRevision$ $Id$ $HeadURL$ %% Modified: trunk/src/test/java/org/nuiton/j2r/DataframeTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/DataframeTest.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/test/java/org/nuiton/j2r/DataframeTest.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/test/java/org/nuiton/j2r/JNITest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/JNITest.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/test/java/org/nuiton/j2r/JNITest.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/test/java/org/nuiton/j2r/JPurTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/JPurTest.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/test/java/org/nuiton/j2r/JPurTest.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/test/java/org/nuiton/j2r/ListTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/ListTest.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/test/java/org/nuiton/j2r/ListTest.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/test/java/org/nuiton/j2r/LutinTimer.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/LutinTimer.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/test/java/org/nuiton/j2r/LutinTimer.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/test/java/org/nuiton/j2r/NetTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/NetTest.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/test/java/org/nuiton/j2r/NetTest.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %% Modified: trunk/src/test/java/org/nuiton/j2r/TestConstants.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/TestConstants.java 2010-04-15 09:21:38 UTC (rev 197) +++ trunk/src/test/java/org/nuiton/j2r/TestConstants.java 2010-04-15 11:10:09 UTC (rev 198) @@ -3,8 +3,6 @@ * Nuiton Java-2-R library * * $Author$ - * $LastChangedDate$ - * $LastChangedRevision$ * $Id$ * $HeadURL$ * %%

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r197 - trunk/src/main/java/org/nuiton/j2r/types
by jcouteau＠users.nuiton.org April 15, 2010

April 15, 2010

Author: jcouteau Date: 2010-04-15 11:21:38 +0200 (Thu, 15 Apr 2010) New Revision: 197 Log: Clean code, improve toRString method for RDataFrames (deal with empty dataframe) Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java trunk/src/main/java/org/nuiton/j2r/types/REXP.java trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java trunk/src/main/java/org/nuiton/j2r/types/RList.java Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-15 07:44:34 UTC (rev 196) +++ trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-04-15 09:21:38 UTC (rev 197) @@ -60,6 +60,8 @@ //Vector containing the vectors of the data.frame private List<List<?>> data; + //TODO JC 20100415 Create a toString method that displays the DataFrame + /** * Constructor * @@ -336,42 +338,54 @@ @Override public String toRString() throws RException { checkVariable(); + String returnString = this.variable + "<-data.frame("; - if (!(this.data.isEmpty())) { - for (int i = 0; i < data.size(); i++) { + + for (List<?> column:this.data){ + + if (!column.isEmpty()){ + if (!(this.names.isEmpty())) { - returnString += this.names.get(i) + "=c("; + int index = this.data.indexOf(column); + returnString += this.names.get(index) + "=c("; } else { returnString += "c("; } - if (data.get(i).get(0) instanceof String) { - for (int j = 0; j < data.get(i).size(); j++) { - returnString += "\"" + data.get(i).get(j) + "\","; + + Object firstElement = column.get(0); + + + if (firstElement instanceof String) { + for (Object obj:column) { + returnString += "\"" + obj + "\","; } - } else if (data.get(i).get(0) instanceof Boolean) { - for (int j = 0; j < data.get(i).size(); j++) { - if ((Boolean) data.get(i).get(j)) { + } else if (firstElement instanceof Boolean) { + for (Object obj:column) { + if ((Boolean) obj) { returnString += RInstructions.TRUE + ","; } else { returnString += RInstructions.FALSE + ","; } } - } else if (data.get(i).get(0) instanceof Integer) { - for (int j = 0; j < data.get(i).size(); j++) { + } else if (firstElement instanceof Integer) { + for (Object obj:column) { returnString += String.format(RInstructions.AS_INTEGER, - data.get(i).get(j)) + ","; + obj) + ","; } } else { - for (int j = 0; j < data.get(i).size(); j++) { - returnString += data.get(i).get(j) + ","; + for (Object obj:column) { + returnString += obj + ","; } } + returnString = returnString.substring(0, returnString.length() - 1); returnString = returnString + "),"; + + } - } + } if (!(this.rowNames.isEmpty())) { returnString += "row.names=c("; @@ -387,6 +401,9 @@ } else { returnString += "stringsAsFactors=FALSE)"; } + + System.out.println(returnString); + return returnString; } @@ -491,7 +508,7 @@ * @return a ArrayList containing the ArrayLists of the R data.frame */ public List<List<?>> getData() { - //TODO manage the autocommit mode here. + //TODO JC manage the autocommit mode here. return data; } @@ -697,88 +714,125 @@ */ public void importCsv(File inputFile, boolean rowNames, boolean names, List<Object> importTypes) throws IOException { + //temporary String to read lines. String tmp; + Integer dataSize; + //get the first line of the file BufferedReader br = new BufferedReader(new FileReader(inputFile)); tmp = br.readLine(); String[] splitted = tmp.split("\\;"); + //get the data size (number of columns) if (rowNames) { dataSize = splitted.length - 1; } else { dataSize = splitted.length; } + //if data has already been initialized, clear it. if (this.data != null) { this.data.clear(); } - if ((rowNames) && (this.rowNames != null)) { + + //Clear rowNames + if ((this.rowNames != null)) { this.rowNames.clear(); + } + //if names has already been initialized, clear it. + if (this.names != null) { + this.names.clear(); } + if (names) { //if names are present in the file, parse the first line to get //the names. - if (this.names != null) { - //if names has already been initialized, clear it. - this.names.clear(); - } - //get every name from the first line this.names.addAll(Arrays.asList(splitted).subList(1, splitted.length)); } //temporary data list. - List<List<?>> tempData = - new ArrayList<List<?>>(); + List<List<?>> tempData = new ArrayList<List<?>>(); - //Initialize all the data columns + //Initialize all the data columns with empty lists for (int i = 0; i < dataSize; i++) { List<Object> column = new ArrayList<Object>(); tempData.add(column); } while ((tmp = br.readLine()) != null) { + //parse each line splitted = tmp.split("\\;"); + //to determine the data index on the line. int index = 0; + + //if there are row names, extract the first item as the row name if (rowNames) { - //if there are row names, extract the first item as the row name this.rowNames.add(splitted[0]); index = 1; } + for (int i = index; i < splitted.length; i++) { //cast the data imported to the specified type. //test the size of the inputType list. If 1 import all the //columns as the type of the first element. - if (importTypes.size() == 1) { - if (importTypes.get(0) instanceof String) { - ((ArrayList<Object>) tempData.get(i - index)).add( - splitted[i]); - } else if (importTypes.get(0) instanceof Double) { - ((ArrayList<Object>) tempData.get(i - index)).add(Double.valueOf( - splitted[i])); - } else if (importTypes.get(0) instanceof Integer) { - ((ArrayList<Object>) tempData.get(i - index)).add(Integer.valueOf( - splitted[i])); - } - } else if (importTypes.get(i - index) instanceof String) { - ((ArrayList<Object>) tempData.get(i - index)).add( - splitted[i]); - } else if (importTypes.get(i - index) instanceof Double) { - ((ArrayList<Object>) tempData.get(i - index)).add(Double.valueOf( - splitted[i])); - } else if (importTypes.get(i - index) instanceof Integer) { - ((ArrayList<Object>) tempData.get(i - index)).add(Integer.valueOf( - splitted[i])); + //Get the column for index + ArrayList<Object> objects = (ArrayList<Object>)tempData.get(i - index); + + //add to the column the converted value. If importTypes contains + //only one element, cast into this type, else cast into the + //column type. + if (((importTypes.size() == 1) && + (importTypes.get(0) instanceof String) ) || + ((importTypes.size() > (i -index )) && + (importTypes.get(i - index) instanceof String)) ) { + + //We import strings so no cast in case of string + objects.add(splitted[i]); + + } else if (((importTypes.size() == 1) && + (importTypes.get(0) instanceof Double) ) || + ((importTypes.size() > (i -index )) && + (importTypes.get(i - index) instanceof Double))) { + + //in case of Double + objects.add(Double.valueOf(splitted[i])); + + } else if (((importTypes.size() == 1) && + (importTypes.get(0) instanceof Integer) ) || + ((importTypes.size() > (i -index )) && + (importTypes.get(i - index) instanceof Integer))) { + + //in case of Integer + objects.add(Integer.valueOf(splitted[i])); + } } } br.close(); this.data = tempData; + + + if (log.isDebugEnabled()){ + + //Display the imported data.frame in debug mode + + log.debug("Imported DataFrame : "); + + for(List<?> column:this.data){ + String debugLine="Column " + this.data.indexOf(column)+ " : "; + for(Object obj:column){ + debugLine += obj + " ,"; + } + log.debug(debugLine); + } + } + } private void checkY(int y) { Modified: trunk/src/main/java/org/nuiton/j2r/types/REXP.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/REXP.java 2010-04-15 07:44:34 UTC (rev 196) +++ trunk/src/main/java/org/nuiton/j2r/types/REXP.java 2010-04-15 09:21:38 UTC (rev 197) @@ -51,8 +51,6 @@ * * @param variable * name of the data.frame in R - * @param engine - * a REngine where the R session is located. * @throws RException */ void getFrom(String variable) throws RException; Modified: trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java 2010-04-15 07:44:34 UTC (rev 196) +++ trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java 2010-04-15 09:21:38 UTC (rev 197) @@ -68,7 +68,7 @@ @Override public void setAttributes(Map<String, Object> attributes) throws RException { - //TODO should be useful to test the validity of attributes before assigning it. + //TODO JC should be useful to test the validity of attributes before assigning it. this.attributes = attributes; if ((this.attributes != null) && (!this.attributes.isEmpty())) { Modified: trunk/src/main/java/org/nuiton/j2r/types/RList.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-04-15 07:44:34 UTC (rev 196) +++ trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-04-15 09:21:38 UTC (rev 197) @@ -29,6 +29,7 @@ package org.nuiton.j2r.types; import java.util.ArrayList; +import java.util.Arrays; import java.util.HashMap; import java.util.List; @@ -49,7 +50,7 @@ private List<Object> data; private Log log = LogFactory.getLog(RDataFrame.class); - //TODO implement the logger use ! + //TODO JC implement the logger use ! /** * Create a default RList linked to a R engine (the List is not initialized * in R.) @@ -79,7 +80,7 @@ String variable) throws RException { super(); this.names = names; - this.data = (ArrayList<Object>) data; + this.data = data; this.variable = variable; this.attributes = new HashMap<String, Object>(); this.engine = engine; @@ -102,12 +103,19 @@ */ public RList(String[] names, List<Object> data, REngine engine, String variable) throws RException { + super(); + + String[] tempNames = {}; + + if(names!=null){ + tempNames = names.clone(); + } + + this.names = new ArrayList<String>(); - for (int i = 0; i < names.length; i++) { - this.names.add(names[i]); - } - this.data = (ArrayList<Object>) data; + this.names.addAll(Arrays.asList(tempNames)); + this.data = data; this.variable = variable; this.attributes = new HashMap<String, Object>(); this.engine = engine; @@ -237,13 +245,13 @@ Object returnObject = engine.eval(String.format( RInstructions.GET_LIST_ITEM, this.variable, x + 1)); if (returnObject instanceof String) { - this.data.set(x, (String) returnObject); + this.data.set(x, returnObject); } else if (returnObject instanceof Double) { - this.data.set(x, (Double) returnObject); + this.data.set(x, returnObject); } else if (returnObject instanceof Integer) { - this.data.set(x, (Integer) returnObject); + this.data.set(x, returnObject); } else if (returnObject instanceof Boolean) { - this.data.set(x, (Boolean) returnObject); + this.data.set(x, returnObject); } } return this.data.get(x); @@ -264,7 +272,7 @@ * * @param data * a List of Objects, containing each element of the R list - * @throws RException + * @throws RException if cannot communicate with R */ public void setData(List<Object> data) throws RException { this.data = data; @@ -300,9 +308,7 @@ //update names String[] namesArray = (String[]) engine.eval(String.format( RInstructions.GET_NAMES, this.variable)); - for (int i = 0; i < namesArray.length; i++) { - names.add(namesArray[i]); - } + names.addAll(Arrays.asList(namesArray)); //update data int length = (Integer) engine.eval(String.format(RInstructions.LENGTH,

1 0

r196 - trunk
by tchemit＠users.nuiton.org April 15, 2010

April 15, 2010

Author: tchemit Date: 2010-04-15 09:44:34 +0200 (Thu, 15 Apr 2010) New Revision: 196 Log: do EVER commit idea files Modified: trunk/ Property changes on: trunk ___________________________________________________________________ Modified: svn:ignore - target .classpath .project .settings *.iml *.ipr + target .classpath .project .settings *.iml *.ipr nbactions.xml nb-configuration.xml

1 0