Changeset 1303

Timestamp:

09/02/13 18:10:07 (11 years ago)

Author:

rkrimmel

Message:

Adding Match class, Smith Waterman algorithm and Substitution Matrix class

Location:

trunk/autoquest-plugin-guitar/src/main/java/de/ugoe/cs/autoquest/plugin

Files:

• alignment/Match.java (added)
• alignment/SmithWaterman.java (added)
• alignment/SubstitutionMatrix.java (added)
• alignment/commands (copied) (copied from trunk/autoquest-plugin-guitar/src/main/java/de/ugoe/cs/autoquest/plugin/guitar/commands)
• alignment/commands/CMDbinaryAligment.java (copied) (copied from trunk/autoquest-plugin-guitar/src/main/java/de/ugoe/cs/autoquest/plugin/guitar/commands/CMDefgTestCasesToSequences.java) (7 diffs)
• alignment/commands/CMDefgTestCasesToSequences.java (deleted)
• alignment/commands/CMDefgToDFA.java (deleted)
• alignment/commands/CMDefgToMM.java (deleted)
• guitar (deleted)

trunk/autoquest-plugin-guitar/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAligment.java

@@ -13 +13 @@
 //   limitations under the License.
 
-package de.ugoe.cs.autoquest.plugin.guitar.commands;
+package de.ugoe.cs.autoquest.plugin.alignment.commands;
 
 import java.io.File;
@@ -24 +24 @@
 import de.ugoe.cs.autoquest.CommandHelpers;
 import de.ugoe.cs.autoquest.eventcore.Event;
-import de.ugoe.cs.autoquest.plugin.guitar.GUITARTestCaseParser;
 import de.ugoe.cs.util.console.Command;
 import de.ugoe.cs.util.console.Console;
@@ -31 +30 @@
 /**
  * <p>
- * Command to load a set of sequences from a set of GUITAR test cases.
+ * Command to generate a binary alignment of two sequences
  * </p>
  * 
@@ -37 +36 @@
  * @version 1.0
  */
-public class CMDefgTestCasesToSequences implements Command {
+public class CMDbinaryAligment implements Command {
 
         /*
@@ -46 +45 @@
         @Override
         public void run(List<Object> parameters) {
-                String foldername;
                 String sequencesName;
-                String efgFileName = null;
+                String algorithm;
                 try {
-                        foldername = (String) parameters.get(0);
-                        sequencesName = (String) parameters.get(1);
-                        if (parameters.size() >= 3) {
-                                efgFileName = (String) parameters.get(2);
+                        sequencesName = (String) parameters.get(0);
+                        if (parameters.size() > 1) {
+                                algorithm = (String) parameters.get(1);
                         }
                 } catch (Exception e) {
@@ -59 +56 @@
                 }
 
-                File folder = new File(foldername);
                 
-                File[] testcaseFiles = folder.listFiles( new FilenameFilter() {
-                        @Override
-                        public boolean accept(File dir, String name) {
-                                return name.endsWith(".tst");
-                        }
-                });
                 Collection<List<Event>> sequences = new LinkedList<List<Event>>();
-                GUITARTestCaseParser parser;
-                if (efgFileName == null) {
-                        parser = new GUITARTestCaseParser();
-                } else {
-                        parser = new GUITARTestCaseParser(efgFileName);
-                }
-                for (File testcaseFile : testcaseFiles) {
-                        Console.traceln(Level.INFO, "Loading from file "
-                                        + testcaseFile.getAbsolutePath());
-                        sequences.add(parser.parseTestCaseFile(testcaseFile));
-                }
-                if (GlobalDataContainer.getInstance().addData(sequencesName, sequences)) {
-                        CommandHelpers.dataOverwritten(sequencesName);
-                }
+                
 
         }
@@ -92 +69 @@
         @Override
         public String help() {
-                return "efgTestCasesToSequences <directory> <sequencesName> {<guiFileName>}";
+                return "binaryAlignment <sequencesName> {<algorithm>}";
         }