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Conflicts: net.bioclipse.target.platform/target-platform.target plugins/net.bioclipse.core.tests/src/net/bioclipse/core/tests/AbstractManagerTest.java
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plugins/net.bioclipse.core/src/net/bioclipse/core/domain/IDataset.java
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| package net.bioclipse.core.domain; | ||
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| public interface IDataset { | ||
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| public static final String CSV_SEPARATOR = "\t"; | ||
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| public String getFileExtension(); | ||
| public String getFileContents(); | ||
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| } |
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plugins/net.bioclipse.core/src/net/bioclipse/core/domain/SparseDataset.java
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| /* ****************************************************************************** | ||
| * Copyright (c) 2011 Ola Spjuth <ola@bioclipse.net> | ||
| * | ||
| * All rights reserved. This program and the accompanying materials | ||
| * are made available under the terms of the Eclipse Public License v1.0 | ||
| * which accompanies this distribution, and is available at | ||
| * http://www.eclipse.org/legal/epl-v10.html | ||
| * | ||
| * Contact: http://www.bioclipse.net/ | ||
| ******************************************************************************/ | ||
| package net.bioclipse.core.domain; | ||
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| import java.awt.Point; | ||
| import java.io.FileWriter; | ||
| import java.util.HashMap; | ||
| import java.util.LinkedHashMap; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.TreeMap; | ||
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| /** | ||
| * A dataset contains a matrix of values (Float) with headers and | ||
| * an optional response variable. | ||
| * | ||
| * @author ola | ||
| * | ||
| */ | ||
| public class SparseDataset implements IDataset{ | ||
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| private static final String DEFAULT_SEPARATOR = " "; | ||
| protected List<String> colHeaders; | ||
| protected List<String> rowHeaders; | ||
| protected String responseProperty; | ||
| protected List<String> responseValues; | ||
| protected LinkedHashMap<Point, Integer> values; | ||
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| public LinkedHashMap<Point, Integer> getValues() { | ||
| return values; | ||
| } | ||
| public void setValues(LinkedHashMap<Point, Integer> values) { | ||
| this.values = values; | ||
| } | ||
| public String getResponseProperty() { | ||
| return responseProperty; | ||
| } | ||
| public void setResponseProperty(String responseProperty) { | ||
| this.responseProperty = responseProperty; | ||
| } | ||
| public List<String> getResponseValues() { | ||
| return responseValues; | ||
| } | ||
| public void setResponseValues(List<String> responseValues) { | ||
| this.responseValues = responseValues; | ||
| } | ||
| public List<String> getColHeaders() { | ||
| return colHeaders; | ||
| } | ||
| public void setColHeaders(List<String> colHeaders) { | ||
| this.colHeaders = colHeaders; | ||
| } | ||
| public List<String> getRowHeaders() { | ||
| return rowHeaders; | ||
| } | ||
| public void setRowHeaders(List<String> rowHeaders) { | ||
| this.rowHeaders = rowHeaders; | ||
| } | ||
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| public SparseDataset() { | ||
| super(); | ||
| } | ||
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| public SparseDataset(List<String> colHeaders, List<String> rowHeaders, | ||
| LinkedHashMap<Point, Integer> values) { | ||
| super(); | ||
| this.colHeaders = colHeaders; | ||
| this.rowHeaders = rowHeaders; | ||
| this.values = values; | ||
| } | ||
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| public SparseDataset(List<String> colHeaders, List<String> rowHeaders, | ||
| String responseProperty, List<String> responseValues, | ||
| LinkedHashMap<Point, Integer> values) { | ||
| super(); | ||
| this.colHeaders = colHeaders; | ||
| this.rowHeaders = rowHeaders; | ||
| this.responseProperty = responseProperty; | ||
| this.responseValues = responseValues; | ||
| this.values = values; | ||
| } | ||
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| // [,1] [,2] [,3] [,4] | ||
| //[1,] 0.000000 0.000000 -0.7161187 0.0000000 | ||
| //[2,] 0.000000 1.749898 -1.2605905 -1.5254161 | ||
| //[3,] -2.012254 1.033870 0.0000000 -0.9921068 | ||
| //[4,] 0.000000 0.000000 1.7928275 0.0000000 | ||
| //[5,] 0.000000 -1.897589 1.7793862 -1.0933724 | ||
| // | ||
| //> write.matrix.csr(tmp, file = "tmp.dat") | ||
| // | ||
| // ola$ cat tmp.dat | ||
| // 3:-0.7161187 | ||
| // 2:1.749898 3:-1.260590 4:-1.525416 | ||
| // 1:-2.012254 2:1.03387 4:-0.9921068 | ||
| // 3:1.792828 | ||
| // 2:-1.897589 3:1.779386 4:-1.093372 | ||
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| @Override | ||
| public String getFileExtension() { | ||
| return "csr"; | ||
| } | ||
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| @Override | ||
| public String getFileContents() { | ||
| return toSparseString(DEFAULT_SEPARATOR); | ||
| } | ||
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| public String toSparseString(String separator) { | ||
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| StringBuffer buf = new StringBuffer(50000); | ||
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| int c=0; //line number | ||
| for (Point p : values.keySet()){ | ||
| if (p.x==c) | ||
| buf.append(separator + p.y+":"+values.get(p)); | ||
| else if (p.x==(c+1)){ | ||
| //next line | ||
| if (c!=0) //not first line | ||
| buf.append("\n"); | ||
| c++; | ||
| buf.append(p.y+":"+values.get(p)); | ||
| } | ||
| } | ||
| buf.append("\n"); //last newline | ||
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| System.out.println(buf.toString()); | ||
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| return buf.toString(); | ||
| } | ||
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| /** | ||
| * Convenience method to just return the response values. | ||
| * Remove leading and trailing '[' and ']'. | ||
| * | ||
| * @return | ||
| */ | ||
| public String getResponseValuesRaw() { | ||
| return responseValues.toString().substring(1, responseValues.toString().length()-1)+"\n"; | ||
| } | ||
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| } |
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