RubyGems - toxtree - Versions diffs - 0.0.1 - Mend

toxtree 0.0.1

Files changed (1384) hide show

data/Toxtree-v2.6.13/src/toxTree/tree/ReportTreePrinter.java ADDED

@@ -0,0 +1,271 @@
+package toxTree.tree;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.OutputStream;
+import toxTree.core.IDecisionCategories;
+import toxTree.core.IDecisionCategory;
+import toxTree.core.IDecisionMethod;
+import toxTree.core.IDecisionRule;
+import toxTree.core.IDecisionRuleList;
+import toxTree.core.IImplementationDetails;
+import toxTree.core.IProcessRule;
+import toxTree.exceptions.DecisionMethodIOException;
+public class ReportTreePrinter extends AbstractTreeWriter implements IProcessRule {
+    protected String folder="";
+	public ReportTreePrinter() {
+		super(System.out);
+	}
+	public ReportTreePrinter(OutputStream outputStream) {
+		super(outputStream);
+	}
+    public ReportTreePrinter(File file) throws FileNotFoundException {
+        super(new FileOutputStream(file));
+        File dir = file.getParentFile();
+        if (dir != null) folder = dir.getAbsolutePath();
+    }
+	public void init(IDecisionMethod tree) throws DecisionMethodIOException {
+		try {
+			writer.write("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\" \"http://www.w3.org/TR/html4/loose.dtd\">");
+			writer.write("<html>");
+			writer.write("<head>");
+			writer.write("<meta http-equiv=\"Content-Type\" content=\"text/html;charset=UTF-8\">");
+			writer.write("<title>");
+			writer.write(tree.getTitle());
+			writer.write("</title>");
+			writer.write("</head>");
+			writer.write("<body>");
+			writer.write("<h2>");
+			writer.write(tree.getTitle());
+			writer.write("</h2>");
+			writer.write("<h4>");
+			writer.write(tree.getExplanation());
+			writer.write("</h4>");
+            IDecisionCategories c = tree.getCategories();
+            writer.write("<h3>");
+            writer.write("Categories assigned:");
+            writer.write("</h3>");
+            writer.write("<table width='95%'>");
+            for (int i=0; i < c.size(); i++) {
+                writer.write("<tr>");
+                writer.write("<th align='left' width='50%'>");
+                writer.write("<a name=\"");
+                writer.write(c.get(i).getName());
+                writer.write("\">");
+                writer.write(c.get(i).getName());
+                writer.write("</a>");
+                writer.write("</th>");
+                writer.write("<td>");
+                writer.write(c.get(i).getExplanation());
+                writer.write("</td>");
+                writer.write("</td>");
+                writer.write("</tr>");
+            }
+            writer.write("</table>");
+            writer.write("<h3>");
+            writer.write("Rules:");
+            writer.write("</h3>");
+            writer.write("<table width=\"95%\">");
+            writer.write("<tr><td>");
+            IDecisionRuleList rules = tree.getRules();
+            for (int i=0; i < rules.size(); i++) {
+                writer.write("<a href=\"#");
+                writer.write(rules.get(i).getNum());
+                writer.write("\" title=\"");
+                writer.write(rules.get(i).getTitle());
+                writer.write("\">");
+                writer.write(rules.get(i).getID());
+                writer.write("</a>");
+                writer.write(" ");
+            }
+            writer.write("</td></tr>");
+            writer.write("</table>");
+			writer.write("<table border=\"0\" frame=\"box\" rules=\"groups\">");
+		} catch (Exception x) {
+			throw new DecisionMethodIOException(x);
+		}
+	}
+	@Override
+	public void done() throws DecisionMethodIOException {
+		try {
+			writer.write("</table>");
+			writer.write("</body>");
+			writer.write("</html>");
+		} catch (Exception x) {
+			throw new DecisionMethodIOException(x);
+		} finally {
+			super.done();
+		}
+	}
+	public Object process(IDecisionMethod method, IDecisionRule rule) throws DecisionMethodIOException {
+		try {
+			writer.write("<tr><td colspan=2></td></tr>");
+            writer.write("<thead>");
+			writer.write("<tr bgcolor='#DDDDDD'>");
+			writer.write("<td>");
+			writer.write("<h4>");
+			writer.write("Rule ID");
+			writer.write("</h4>");
+			writer.write("</td>");
+			writer.write("<td>");
+			writer.write("<h4>");
+			writer.write("<a name=\"");
+			writer.write(rule.getNum());
+			writer.write("\">");
+			writer.write(rule.getID());
+			writer.write("</a>");
+			writer.write("</h4>");
+			writer.write("</td>");
+			writer.write("</tr>");
+            writer.write("</thead>");
+            writer.write("<tbody>");
+			writer.write("<tr>");
+			writer.write("<td>");
+			writer.write("<h4>");
+			writer.write("Title:");
+			writer.write("</h4>");
+			writer.write("</td>");
+			writer.write("<td>");
+			writer.write("<h4>");
+			writer.write(rule.getTitle());
+			writer.write("</h4>");
+			writer.write("</td>");
+			writer.write("</tr>");
+	    	final boolean[] answers = {true,false};
+	    	for (int i=0; i < answers.length;i++) {
+	    		IDecisionCategory category = method.getCategory(rule, answers[i]);
+	    		IDecisionRule nextrule = method.getBranch(rule, answers[i]);
+				writer.write("<tr>");
+				writer.write("<td>");
+				writer.write("If ");
+				if (answers[i])
+					writer.write("YES");
+				else
+					writer.write("NO");
+				writer.write("</td>");
+				writer.write("<td>");
+				if (category != null) {
+					writer.write("ASSIGN ");
+                    writer.write("<a href=\"#");
+                    writer.write(category.getName());
+                    writer.write("\">");
+                    writer.write("<b>");
+                    writer.write(category.toString());
+                    writer.write("</b>");
+                    writer.write("</a>");
+					writer.write("<br>");
+				}
+				if (nextrule != null) {
+					writer.write("GO TO Rule ID ");
+					writer.write("<b>");
+					writer.write("<a href=\"#");
+					writer.write(nextrule.getNum());
+                    writer.write("\" title=\"");
+                    writer.write(nextrule.getTitle());
+					writer.write("\">");
+					writer.write(nextrule.getID());
+					writer.write("</a>");
+					writer.write("</b>");
+					writer.write("<br>");
+				}
+				//rule.getExampleMolecule(ruleResult)
+				writer.write("</td>");
+				writer.write("</tr>");
+	    	}
+			writer.write("<tr>");
+			writer.write("<th align=\"left\" valign=\"top\">");
+			writer.write("Explanation");
+			writer.write("</th>");
+			writer.write("<td>");
+			writer.write(rule.getExplanation());
+            writer.write("</td>");
+			writer.write("</tr>");
+            writer.write("<tr>");
+            writer.write("<tr>");
+            writer.write("<th align=\"left\" valign=\"top\">");
+            writer.write("Examples");
+            writer.write("</th>");
+            writer.write("<td>");
+            writer.write("YES");
+            try {
+                String url = writeMolecule(rule, true);
+                writer.write("<img src=\"");
+                writer.write(url);
+                writer.write("\" title=\"a hit\">");
+            } catch (Exception x) {
+                writer.write("N/A");
+            }
+            writer.write("NO");
+            try {
+                String url = writeMolecule(rule, false);
+                writer.write("<img src=\"");
+                writer.write(url);
+                writer.write("\" title=\"not a hit\">");
+            } catch (Exception x) {
+                writer.write("N/A");
+            }
+            //
+            writer.write("</td>");
+            writer.write("</tr>");
+			IImplementationDetails details = null;
+			if (rule instanceof IImplementationDetails)
+				details =(IImplementationDetails) rule;
+			if ((rule instanceof DecisionNode) &&
+					(((DecisionNode)rule).getRule() instanceof IImplementationDetails)
+					) {
+				details = (IImplementationDetails) ((DecisionNode)rule).getRule();
+			}
+			if (details != null)  {
+				writer.write("<tr>");
+				writer.write("<td align=\"left\" valign=\"top\">");
+				writer.write("<i>Implementation details<i>");
+				writer.write("</td>");
+				writer.write("<td>");
+				writer.write("<i>");
+				writer.write(details.getImplementationDetails().replaceAll("\n", "<br>"));
+				writer.write("</i>");
+				writer.write("</td>");
+				writer.write("</tr>");
+			}
+			writer.write("</td>");
+			writer.write("<td>");
+			writer.write("</tr>");
+            writer.write("</tbody>");
+            return null;
+		} catch (Exception x) {
+			throw new DecisionMethodIOException(x);
+		}
+	}
+	protected String writeMolecule(IDecisionRule rule, boolean answer) throws Exception  {
+        String url =  rule.getID()+Boolean.toString(answer)+".png";
+        File file = new File(folder+"/"+url);
+        FileOutputStream out = new FileOutputStream(file);
+        writeMolecule(rule,answer, out);
+        out.close();
+        return url;
+    }
+}

data/Toxtree-v2.6.13/src/toxTree/tree/RuleResult.java ADDED

@@ -0,0 +1,240 @@
+/*
+Copyright Ideaconsult Ltd. (C) 2005-2007
+Contact: nina@acad.bg
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+of the License, or (at your option) any later version.
+All we ask is that proper credit is given for our work, which includes
+- but is not limited to - adding the above copyright notice to the beginning
+of your source code files, and to any copyright notice that you may distribute
+with programs based on this work.
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+*/
+package toxTree.tree;
+import java.io.Serializable;
+import net.idea.modbcum.i.processors.IProcessor;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.renderer.selection.IChemObjectSelection;
+import toxTree.core.IDecisionCategory;
+import toxTree.core.IDecisionRule;
+/**
+ * Stores the result of {@link IDecisionRule} application,
+ * which contains the rule applied, the boolean result and the category assigned (if any).
+ * @author Nina Jeliazkova
+ * <b>Modified</b> 2005-9-2
+ */
+public class RuleResult implements Serializable {
+	/**
+	 * Comment for <code>serialVersionUID</code>
+	 */
+	private static final long serialVersionUID = -7844039700306791740L;
+	public static final String prefix = "http://localhost" ;
+	public static final String ruleURL = String.format("%s/rule/",prefix);
+	public static final String categoryURL = String.format("%s/category/",prefix);
+	public static final String alertURL = String.format("%s?alerts=",prefix);
+	public static final String resultURL = String.format("%s?parameters=",prefix);
+	protected IDecisionRule rule = null;
+	protected boolean result = false;
+	protected IDecisionCategory category = null;
+	protected transient IAtomContainer molecule = null;
+	protected boolean silent = false;
+	protected boolean web = false;
+	public boolean isWeb() {
+		return web;
+	}
+	public void setWeb(boolean web) {
+		this.web = web;
+	}
+	public RuleResult() {
+		super();
+	}
+	public RuleResult(IDecisionRule rule, boolean result) {
+		super();
+		this.rule = rule;
+		this.result = result;
+	}
+	public RuleResult(IDecisionRule rule, boolean result, IDecisionCategory category) {
+		super();
+		this.rule = rule;
+		this.result = result;
+		this.category = category;
+	}
+	/**
+	 * @return Returns the result.
+	 */
+	public boolean isResult() {
+		return result;
+	}
+	/**
+	 * @param result The result to set.
+	 */
+	public void setResult(boolean result) {
+		this.result = result;
+	}
+	/**
+	 * @return Returns the category.
+	 */
+	public synchronized IDecisionCategory getCategory() {
+		return category;
+	}
+	/**
+	 * @param category The category to set.
+	 */
+	public synchronized void setCategory(IDecisionCategory category) {
+		this.category = category;
+	}
+	/**
+	 * @return Returns the rule.
+	 */
+	public synchronized IDecisionRule getRule() {
+		return rule;
+	}
+	/**
+	 * @param rule The rule to set.
+	 */
+	public synchronized void setRule(IDecisionRule rule) {
+		this.rule = rule;
+	}
+	public StringBuffer explain(boolean verbose) {
+		return explain(verbose,-1);
+	}
+	protected static final String wwwAlertFormat = "%s.%s";
+	public StringBuffer explain(boolean verbose,int ruleIndex) {
+		StringBuffer b = new StringBuffer();
+		String space = web?" ":"&nbsp;";
+		if (!silent)
+			if (verbose) {
+				if (web)  {
+					if (result && (rule.isImplemented()) && (rule.getSelector()!=null))
+						b.append(String.format(wwwAlertFormat,rule.getID(),rule.getTitle()));
+					else
+						b.append(rule.toString());
+					b.append(space);
+					if (web)
+						b.append(result?"Yes":"No");
+					else
+						b.append(String.format("<span style='color:%s;position:relative;font-weight: bold;'>%s</span>", result?"green":"red",result?"Yes":"No"));
+					b.append(space);
+					if (category != null) {
+						if (web)
+							b.append(String.format("Class %s",category.toString()));
+						else
+							b.append(String.format("Class&nbsp;<span style='color:black'>%s</span>",category.toString()));
+					} else b.append(space);
+				} else {
+					b.append(String.format("<a href=\"%s%s\" title='Show rule'><img src='%s' border='0' alt='Show rule' title='Show rule'></a>",
+							ruleURL,rule.getTitle(),this.getClass().getResource("/toxTree/ui/tree/images/find.png").toString()));
+					b.append(space);
+					if (result && (rule.isImplemented()) && (rule.getSelector()!=null))
+						if (ruleIndex<0)
+							b.append(String.format("<a href=\"%s%s\"  title='Hilight structure alert'>%s</a>",alertURL,rule.getTitle(),rule.toString()));
+						else
+							b.append(String.format("<a href=\"%s%d\"  title='Hilight structure alert'>%s</a>",resultURL,ruleIndex,rule.toString()));
+					else
+						b.append(rule.toString());
+					b.append(space);
+					if (web)
+						b.append(String.format(result?"Yes":"No"));
+					else {
+						b.append(String.format("<span style='color:%s;position:relative;font-weight: bold;'>%s</span>", result?"green":"red",result?"Yes":"No"));
+						b.append(space);
+					}
+					if (category != null) {
+						if (web)
+							b.append(String.format(category.toString()));
+						else
+							b.append(String.format("Class&nbsp;<span style='color:orange'><a href=\"%s%s\">%s</a></span>",categoryURL,category.getID(),category.toString()));
+					} else b.append(space);
+					if ((molecule != null) && (molecule.getID() != null)) {
+						b.append("\t");
+						b.append(molecule.getID());
+					} else b.append("\t");
+				}
+			} else {
+				b.append(rule.getID());
+				if (result) b.append("Y");
+				else b.append("N");
+			}
+		return b;
+	}
+	/**
+	 * @return Returns the molecule.
+	 */
+	public synchronized IAtomContainer getMolecule() {
+		return molecule;
+	}
+	/**
+	 * @param molecule The molecule to set.
+	 */
+	public synchronized void setMolecule(IAtomContainer molecule) {
+		this.molecule = molecule;
+	}
+	/**
+	 * @return Returns the silent.
+	 */
+	public synchronized boolean isSilent() {
+		return silent;
+	}
+	/**
+	 * @param silent The silent to set.
+	 */
+	public synchronized void setSilent(boolean silent) {
+		this.silent = silent;
+	}
+	/* (non-Javadoc)
+	 * @see java.lang.Object#equals(java.lang.Object)
+	 */
+	@Override
+	public boolean equals(Object obj) {
+		try {
+			RuleResult r = (RuleResult) obj;
+			return (result == r.result) &&
+				   (rule.equals(r.rule)) &&
+				   (
+				   	((category == null) && (r.category==null))
+					|| category.equals(r.category));
+		} catch (Exception x) {
+			return false;
+		}
+	}
+	/* (non-Javadoc)
+	 * @see java.lang.Object#toString()
+	 */
+	@Override
+	public String toString() {
+		return explain(true).toString();
+	}
+	IProcessor<IAtomContainer, IChemObjectSelection> getSelector() {
+		return getRule().getSelector();
+	}
+}