diff --git a/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java b/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
index ad0da2b687a659ab717e21ff0b50c70a17d498cb..d899d2ab3abfd01a5f44b19e559a4f72e87b7323 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
@@ -1,7 +1,5 @@
package lcsb.mapviewer.run;
-import static org.junit.Assert.fail;
-
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.PrintWriter;
@@ -44,364 +42,366 @@ import lcsb.mapviewer.reactome.utils.comparators.MatchResult.MatchStatus;
*/
public class ReactomeComparison {
- /**
- * Number of nanoseconds in second :).
- */
- private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
-
- /**
- * Local model used for comparison.
- */
- private Model model;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ReactomeComparison.class);
-
- /**
- * Comparator of reactions between our model and reactome.
- */
- @Autowired
- private ReactionComparator reactionComparator;
-
- /**
- * Class used for accessing reactome data.
- */
- @Autowired
- private DataSourceUpdater rc;
-
- /**
- * Util class used for manipulating information in reactome objects.
- */
- @Autowired
- private ReactomeQueryUtil rcu;
-
- /**
- * Formatter used for reaction comparison.
- */
- @Autowired
- private DataFormatter dataFormatter;
-
- /**
- * Static main method used to run this stand alone code.
- *
- * @param args
- * command line arguments
- */
- public static void main(String[] args) {
- long startTime = System.nanoTime();
- PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
- ReactomeComparison main = new ReactomeComparison();
- ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
- ApplicationContextLoader.injectDependencies(main);
- main.run();
- long endTime = System.nanoTime();
-
- long duration = endTime - startTime;
- double sec = duration / NANOSECONDS_IN_SECOND;
- System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
- }
-
- /**
- * Executes comparison between model and reactome representation.
- */
- public void run() {
- try {
- model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
-
- Set<String> list = new HashSet<String>();
-
- for (Species element : model.getSpeciesList()) {
- list.add(element.getName());
- }
- logger.debug("Species: " + list.size());
-
- List<String> ids = new ArrayList<String>();
- for (Reaction reaction : model.getReactions()) {
- ids.add(reaction.getIdReaction());
- }
- Collections.sort(ids);
- List<MatchResult> results = new ArrayList<MatchResult>();
-
- printHeader();
- int i = 0;
- for (String string : ids) {
- Reaction reaction = model.getReactionByReactionId(string);
- logger.info("Reaction: " + string + "; " + (i++) + "/" + ids.size());
- if (rcu.getReactomeIdentifierForReaction(reaction) != null) {
- MatchResult result = checkReaction(string);
- if (result != null) {
- results.add(result);
- printResult(result);
- }
- } else {
- ReactomeReactionlikeEvent reactomReaction = rcu.getSimilarReaction(reaction);
- if (reactomReaction != null) {
- MatchResult matchResult = new MatchResult();
- matchResult.setStatus(MatchStatus.SIMILAR_REACTION_FOUND);
- matchResult.setLocalReaction(reaction);
- matchResult.setReactomeReaction(reactomReaction);
- results.add(matchResult);
- printResult(matchResult);
-
- }
- }
- }
- printFooter(results);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
-
- }
-
- /**
- * Prints report footer.
- *
- * @param results
- * results used in the report
- */
- private void printFooter(List<MatchResult> results) {
- writer.println("</table>");
-
- int ok = 0;
- int mismatch = 0;
- int severe = 0;
- int similar = 0;
- for (MatchResult matchResult : results) {
- if (matchResult.getStatus() == MatchStatus.OK) {
- ok++;
- } else if (matchResult.getStatus() == MatchStatus.MISMATCH) {
- mismatch++;
- } else if (matchResult.getStatus() == MatchStatus.SIMILAR_REACTION_FOUND) {
- similar++;
- } else {
- severe++;
- }
- }
- writer.println("<p>Reactions checked: " + (results.size()) + "</p>");
- writer.println("<p>OK: " + ok + "</p>");
- writer.println("<p>MISMATCH: " + mismatch + "</p>");
- writer.println("<p>SEVERE PROBLEMS: " + severe + "</p>");
- writer.println("<p>SIMILAR: " + similar + "</p>");
-
- writer.println("</body></html>");
- writer.close();
-
- }
-
- /**
- * Object to which the report is written.
- */
- private PrintWriter writer;
-
- /**
- * Creates report stream and prints header of the report.
- *
- * @throws FileNotFoundException
- * if there is a problem with creating report file
- * @throws UnsupportedEncodingException
- * thrown when there are problems with encoding
- */
- private void printHeader() throws FileNotFoundException, UnsupportedEncodingException {
- writer = new PrintWriter("out/report/report.html", "UTF-8");
- writer.println("<html><head></head><body>");
- writer.println("<table cellspacing=\"0\">");
-
- String resultString = "<tr>";
- resultString += "<td" + style + ">Reaction</td>";
- resultString += "<td" + style + ">REACTOME ID</td>";
- resultString += "<td" + style + ">Status</td>";
- resultString += "<td" + style + ">Similarity</td>";
- resultString += "<td" + style + ">Unknown reaction input</td>";
- resultString += "<td" + style + ">Unknown reaction modifier</td>";
- resultString += "<td" + style + ">Unknown reaction output</td>";
- resultString += "<td" + style + ">Unknown reactome input</td>";
- resultString += "<td" + style + ">Unknown reactome modifier</td>";
- resultString += "<td" + style + ">Unknown reactome output</td>";
- resultString += "</tr>";
- writer.println(resultString);
-
- }
-
- /**
- * Formatter of decimal numbers.
- */
- private DecimalFormat df = new DecimalFormat("#.##");
-
- /**
- * Style used by report cells.
- */
- private String style = " style=\"border-width:1;border-style:solid;border-color:#000000;\" ";
-
- /**
- * Prints result row.
- *
- * @param result
- * result to be printed
- * @throws AnnotatorException
- * thrown when there is a problem accessing external annotation
- * service
- */
- private void printResult(MatchResult result) throws AnnotatorException {
- String color = "#000000";
- String status = "";
- String error = "";
- switch (result.getStatus()) {
- case OK:
- color = "#52D017";
- status = "OK";
- error = "<td colspan=\"6\" " + style + "></td>";
- return;
- case SIMILAR_REACTION_FOUND:
- color = "#5757E0";
- status = "SIMILAR";
- error = "<td colspan=\"6\" " + style + "></td>";
- return;
- case MISMATCH:
- color = "#FFFF00";
- status = "MISMATCH";
- error += "<td" + style + ">" + dataFormatter.getInvalidLocalInputString(result) + " </td>";
- error += "<td" + style + ">" + dataFormatter.getInvalidLocalModifierString(result) + " </td>";
- error += "<td" + style + ">" + dataFormatter.getInvalidLocalOutputString(result) + " </td>";
- error += "<td" + style + ">" + dataFormatter.getInvalidReactomeInputString(result) + " </td>";
- error += "<td" + style + ">" + dataFormatter.getInvalidReactomeModifierString(result) + " </td>";
- error += "<td" + style + ">" + dataFormatter.getInvalidReactomeOutputString(result) + " </td>";
- break;
- case INVALID_REACTOME_ID:
- color = "#FF0000";
- status = "REACTOME id does not point to reaction";
- error = "<td colspan=\"6\" " + style + "></td>";
- return;
- case INVALID_REACTION_WITH_PHEONTYPE:
- color = "#FF0000";
- status = "Impossible to map reaction to reactome - reaction contains Phenotype";
- error = "<td colspan=\"6\" " + style + "></td>";
- return;
- default:
- return;
- }
- String resultString = "<tr bgcolor = \"" + color + "\">";
- String reactionId = result.getLocalReaction().getIdReaction();
- String reactomId = null;
- reactomId = rcu.getReactomeIdentifierForReaction(result.getLocalReaction());
-
- resultString += "<td" + style + "><a target=\"_blank\" href=\"" + PdMapAnnotations.getLinkForReaction(result.getLocalReaction()) + "\">" + reactionId
- + "</a> ";
- resultString += "<a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">" + reactomId + "</a></td>";
-
- if (result.getReactomeReaction() != null) {
- reactomId = result.getReactomeReaction().getStableIdentifier().getIdentifier() + "."
- + result.getReactomeReaction().getStableIdentifier().getIdentifierVersion();
- } else {
- reactomId = rcu.getReactomeIdentifierForReaction(result.getLocalReaction());
- }
-
- resultString += "<td" + style + "><a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">" + reactomId + "</a></td>";
- resultString += "<td" + style + ">" + status + "</td>";
- resultString += "<td" + style + ">" + df.format(result.getScore() * IProgressUpdater.MAX_PROGRESS) + "%</td>";
- resultString += error;
- resultString += "</tr>";
- writer.println(resultString);
- System.out.println(resultString);
- }
-
- /**
- * Compares our model reaction to reactome representation.
- *
- * @param id
- * identifier of our reaction
- * @return result of reaction comparison
- * @throws IOException
- * thrown whene there are problems accessing reactome reaction
- * @throws ComparatorException
- * thrown when there is a problem with comparison {@link Reaction}
- * with Reactome object
- *
- */
- private MatchResult checkReaction(String id) throws IOException, ComparatorException {
- return checkReaction(model.getReactionByReactionId(id));
- }
-
- /**
- * Compares our model reaction to reactome representation.
- *
- * @param reaction
- * our reaction
- * @return result of reaction comparison
- * @throws IOException
- * thrown whene there are problems accessing reactome reaction
- * @throws ComparatorException
- * thrown when there is a problem with comparison {@link Reaction}
- * with Reactome object
- */
- private MatchResult checkReaction(Reaction reaction) throws IOException, ComparatorException {
- String stableIdentifier = rcu.getReactomeIdentifierForReaction(reaction);
- if (stableIdentifier != null) {
- String identifier = stableIdentifier.split("\\.")[0];
- String version = stableIdentifier.split("\\.")[1];
-
- ReactomeDatabaseObject object = rc.getFullObjectForStableIdentifier(identifier, version);
- if (object != null && object instanceof ReactomeReactionlikeEvent) {
- return reactionComparator.compareReactions(reaction, (ReactomeReactionlikeEvent) object);
-
- } else {
- MatchResult result = new MatchResult();
- result.setLocalReaction(reaction);
- result.setStatus(MatchStatus.INVALID_REACTOME_ID);
- return result;
- }
- }
- return null;
- }
-
- /**
- * @return the reactionComparator
- */
- public ReactionComparator getReactionComparator() {
- return reactionComparator;
- }
-
- /**
- * @param reactionComparator
- * the reactionComparator to set
- */
- public void setReactionComparator(ReactionComparator reactionComparator) {
- this.reactionComparator = reactionComparator;
- }
-
- /**
- * @return the dataFormatter
- */
- public DataFormatter getDataFormatter() {
- return dataFormatter;
- }
-
- /**
- * @param dataFormatter
- * the dataFormatter to set
- */
- public void setDataFormatter(DataFormatter dataFormatter) {
- this.dataFormatter = dataFormatter;
- }
-
- /**
- * @return the rc
- * @see #rc
- */
- public DataSourceUpdater getRc() {
- return rc;
- }
-
- /**
- * @param rc
- * the rc to set
- * @see #rc
- */
- public void setRc(DataSourceUpdater rc) {
- this.rc = rc;
- }
+ /**
+ * Number of nanoseconds in second :).
+ */
+ private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
+
+ /**
+ * Local model used for comparison.
+ */
+ private Model model;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ReactomeComparison.class);
+
+ /**
+ * Comparator of reactions between our model and reactome.
+ */
+ @Autowired
+ private ReactionComparator reactionComparator;
+
+ /**
+ * Class used for accessing reactome data.
+ */
+ @Autowired
+ private DataSourceUpdater rc;
+
+ /**
+ * Util class used for manipulating information in reactome objects.
+ */
+ @Autowired
+ private ReactomeQueryUtil rcu;
+
+ /**
+ * Formatter used for reaction comparison.
+ */
+ @Autowired
+ private DataFormatter dataFormatter;
+
+ /**
+ * Static main method used to run this stand alone code.
+ *
+ * @param args
+ * command line arguments
+ */
+ public static void main(String[] args) {
+ long startTime = System.nanoTime();
+ PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
+ ReactomeComparison main = new ReactomeComparison();
+ ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+ ApplicationContextLoader.injectDependencies(main);
+ main.run();
+ long endTime = System.nanoTime();
+
+ long duration = endTime - startTime;
+ double sec = duration / NANOSECONDS_IN_SECOND;
+ System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
+ }
+
+ /**
+ * Executes comparison between model and reactome representation.
+ */
+ public void run() {
+ try {
+ model = new CellDesignerXmlParser()
+ .createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
+
+ Set<String> list = new HashSet<String>();
+
+ for (Species element : model.getSpeciesList()) {
+ list.add(element.getName());
+ }
+ logger.debug("Species: " + list.size());
+
+ List<String> ids = new ArrayList<String>();
+ for (Reaction reaction : model.getReactions()) {
+ ids.add(reaction.getIdReaction());
+ }
+ Collections.sort(ids);
+ List<MatchResult> results = new ArrayList<MatchResult>();
+
+ printHeader();
+ int i = 0;
+ for (String string : ids) {
+ Reaction reaction = model.getReactionByReactionId(string);
+ logger.info("Reaction: " + string + "; " + (i++) + "/" + ids.size());
+ if (rcu.getReactomeIdentifierForReaction(reaction) != null) {
+ MatchResult result = checkReaction(string);
+ if (result != null) {
+ results.add(result);
+ printResult(result);
+ }
+ } else {
+ ReactomeReactionlikeEvent reactomReaction = rcu.getSimilarReaction(reaction);
+ if (reactomReaction != null) {
+ MatchResult matchResult = new MatchResult();
+ matchResult.setStatus(MatchStatus.SIMILAR_REACTION_FOUND);
+ matchResult.setLocalReaction(reaction);
+ matchResult.setReactomeReaction(reactomReaction);
+ results.add(matchResult);
+ printResult(matchResult);
+
+ }
+ }
+ }
+ printFooter(results);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ }
+
+ /**
+ * Prints report footer.
+ *
+ * @param results
+ * results used in the report
+ */
+ private void printFooter(List<MatchResult> results) {
+ writer.println("</table>");
+
+ int ok = 0;
+ int mismatch = 0;
+ int severe = 0;
+ int similar = 0;
+ for (MatchResult matchResult : results) {
+ if (matchResult.getStatus() == MatchStatus.OK) {
+ ok++;
+ } else if (matchResult.getStatus() == MatchStatus.MISMATCH) {
+ mismatch++;
+ } else if (matchResult.getStatus() == MatchStatus.SIMILAR_REACTION_FOUND) {
+ similar++;
+ } else {
+ severe++;
+ }
+ }
+ writer.println("<p>Reactions checked: " + (results.size()) + "</p>");
+ writer.println("<p>OK: " + ok + "</p>");
+ writer.println("<p>MISMATCH: " + mismatch + "</p>");
+ writer.println("<p>SEVERE PROBLEMS: " + severe + "</p>");
+ writer.println("<p>SIMILAR: " + similar + "</p>");
+
+ writer.println("</body></html>");
+ writer.close();
+
+ }
+
+ /**
+ * Object to which the report is written.
+ */
+ private PrintWriter writer;
+
+ /**
+ * Creates report stream and prints header of the report.
+ *
+ * @throws FileNotFoundException
+ * if there is a problem with creating report file
+ * @throws UnsupportedEncodingException
+ * thrown when there are problems with encoding
+ */
+ private void printHeader() throws FileNotFoundException, UnsupportedEncodingException {
+ writer = new PrintWriter("out/report/report.html", "UTF-8");
+ writer.println("<html><head></head><body>");
+ writer.println("<table cellspacing=\"0\">");
+
+ String resultString = "<tr>";
+ resultString += "<td" + style + ">Reaction</td>";
+ resultString += "<td" + style + ">REACTOME ID</td>";
+ resultString += "<td" + style + ">Status</td>";
+ resultString += "<td" + style + ">Similarity</td>";
+ resultString += "<td" + style + ">Unknown reaction input</td>";
+ resultString += "<td" + style + ">Unknown reaction modifier</td>";
+ resultString += "<td" + style + ">Unknown reaction output</td>";
+ resultString += "<td" + style + ">Unknown reactome input</td>";
+ resultString += "<td" + style + ">Unknown reactome modifier</td>";
+ resultString += "<td" + style + ">Unknown reactome output</td>";
+ resultString += "</tr>";
+ writer.println(resultString);
+
+ }
+
+ /**
+ * Formatter of decimal numbers.
+ */
+ private DecimalFormat df = new DecimalFormat("#.##");
+
+ /**
+ * Style used by report cells.
+ */
+ private String style = " style=\"border-width:1;border-style:solid;border-color:#000000;\" ";
+
+ /**
+ * Prints result row.
+ *
+ * @param result
+ * result to be printed
+ * @throws AnnotatorException
+ * thrown when there is a problem accessing external annotation
+ * service
+ */
+ private void printResult(MatchResult result) throws AnnotatorException {
+ String color = "#000000";
+ String status = "";
+ String error = "";
+ switch (result.getStatus()) {
+ case OK:
+ color = "#52D017";
+ status = "OK";
+ error = "<td colspan=\"6\" " + style + "></td>";
+ return;
+ case SIMILAR_REACTION_FOUND:
+ color = "#5757E0";
+ status = "SIMILAR";
+ error = "<td colspan=\"6\" " + style + "></td>";
+ return;
+ case MISMATCH:
+ color = "#FFFF00";
+ status = "MISMATCH";
+ error += "<td" + style + ">" + dataFormatter.getInvalidLocalInputString(result) + " </td>";
+ error += "<td" + style + ">" + dataFormatter.getInvalidLocalModifierString(result) + " </td>";
+ error += "<td" + style + ">" + dataFormatter.getInvalidLocalOutputString(result) + " </td>";
+ error += "<td" + style + ">" + dataFormatter.getInvalidReactomeInputString(result) + " </td>";
+ error += "<td" + style + ">" + dataFormatter.getInvalidReactomeModifierString(result) + " </td>";
+ error += "<td" + style + ">" + dataFormatter.getInvalidReactomeOutputString(result) + " </td>";
+ break;
+ case INVALID_REACTOME_ID:
+ color = "#FF0000";
+ status = "REACTOME id does not point to reaction";
+ error = "<td colspan=\"6\" " + style + "></td>";
+ return;
+ case INVALID_REACTION_WITH_PHEONTYPE:
+ color = "#FF0000";
+ status = "Impossible to map reaction to reactome - reaction contains Phenotype";
+ error = "<td colspan=\"6\" " + style + "></td>";
+ return;
+ default:
+ return;
+ }
+ String resultString = "<tr bgcolor = \"" + color + "\">";
+ String reactionId = result.getLocalReaction().getIdReaction();
+ String reactomId = null;
+ reactomId = rcu.getReactomeIdentifierForReaction(result.getLocalReaction());
+
+ resultString += "<td" + style + "><a target=\"_blank\" href=\""
+ + PdMapAnnotations.getLinkForReaction(result.getLocalReaction()) + "\">" + reactionId + "</a> ";
+ resultString += "<a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">"
+ + reactomId + "</a></td>";
+
+ if (result.getReactomeReaction() != null) {
+ reactomId = result.getReactomeReaction().getStableIdentifier().getIdentifier() + "."
+ + result.getReactomeReaction().getStableIdentifier().getIdentifierVersion();
+ } else {
+ reactomId = rcu.getReactomeIdentifierForReaction(result.getLocalReaction());
+ }
+
+ resultString += "<td" + style + "><a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId)
+ + "\">" + reactomId + "</a></td>";
+ resultString += "<td" + style + ">" + status + "</td>";
+ resultString += "<td" + style + ">" + df.format(result.getScore() * IProgressUpdater.MAX_PROGRESS) + "%</td>";
+ resultString += error;
+ resultString += "</tr>";
+ writer.println(resultString);
+ System.out.println(resultString);
+ }
+
+ /**
+ * Compares our model reaction to reactome representation.
+ *
+ * @param id
+ * identifier of our reaction
+ * @return result of reaction comparison
+ * @throws IOException
+ * thrown whene there are problems accessing reactome reaction
+ * @throws ComparatorException
+ * thrown when there is a problem with comparison {@link Reaction}
+ * with Reactome object
+ *
+ */
+ private MatchResult checkReaction(String id) throws IOException, ComparatorException {
+ return checkReaction(model.getReactionByReactionId(id));
+ }
+
+ /**
+ * Compares our model reaction to reactome representation.
+ *
+ * @param reaction
+ * our reaction
+ * @return result of reaction comparison
+ * @throws IOException
+ * thrown whene there are problems accessing reactome reaction
+ * @throws ComparatorException
+ * thrown when there is a problem with comparison {@link Reaction}
+ * with Reactome object
+ */
+ private MatchResult checkReaction(Reaction reaction) throws IOException, ComparatorException {
+ String stableIdentifier = rcu.getReactomeIdentifierForReaction(reaction);
+ if (stableIdentifier != null) {
+ String identifier = stableIdentifier.split("\\.")[0];
+ String version = stableIdentifier.split("\\.")[1];
+
+ ReactomeDatabaseObject object = rc.getFullObjectForStableIdentifier(identifier, version);
+ if (object != null && object instanceof ReactomeReactionlikeEvent) {
+ return reactionComparator.compareReactions(reaction, (ReactomeReactionlikeEvent) object);
+
+ } else {
+ MatchResult result = new MatchResult();
+ result.setLocalReaction(reaction);
+ result.setStatus(MatchStatus.INVALID_REACTOME_ID);
+ return result;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * @return the reactionComparator
+ */
+ public ReactionComparator getReactionComparator() {
+ return reactionComparator;
+ }
+
+ /**
+ * @param reactionComparator
+ * the reactionComparator to set
+ */
+ public void setReactionComparator(ReactionComparator reactionComparator) {
+ this.reactionComparator = reactionComparator;
+ }
+
+ /**
+ * @return the dataFormatter
+ */
+ public DataFormatter getDataFormatter() {
+ return dataFormatter;
+ }
+
+ /**
+ * @param dataFormatter
+ * the dataFormatter to set
+ */
+ public void setDataFormatter(DataFormatter dataFormatter) {
+ this.dataFormatter = dataFormatter;
+ }
+
+ /**
+ * @return the rc
+ * @see #rc
+ */
+ public DataSourceUpdater getRc() {
+ return rc;
+ }
+
+ /**
+ * @param rc
+ * the rc to set
+ * @see #rc
+ */
+ public void setRc(DataSourceUpdater rc) {
+ this.rc = rc;
+ }
}