Changeset 1542 for trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java

Timestamp:

05/07/14 15:59:10 (10 years ago)

Author:

rkrimmel

Message:

pre-catastraphic-changes-commit

File:

• trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java (modified) (5 diffs)

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

@@ -15 +15 @@
 package de.ugoe.cs.autoquest.plugin.alignment.commands;
 
-
 import java.util.Collection;
 import java.util.LinkedList;
@@ -22 +21 @@
 import de.ugoe.cs.autoquest.eventcore.Event;
 import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman;
+import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SequenceGenerator;
 import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SimpleSequenceGenerator;
 import de.ugoe.cs.autoquest.plugin.alignment.substitution.NearbySubstitutionMatrix;
@@ -46 +46 @@
         @SuppressWarnings("unchecked")
         public void run(List<Object> parameters) {
-                String sequencesName = "sequences";
-                String algorithm;
+                String sequencesName = "numberSequences";
+                String substitutionName = "substitutionMatrix";
+                String algorithm = "smithwaterman";
                 try {
                         sequencesName = (String) parameters.get(0);
-                        if (parameters.size() > 1) {
-                                algorithm = (String) parameters.get(1);
+                        substitutionName = (String) parameters.get(1);
+                        if (parameters.size() > 2) {
+                                algorithm = (String) parameters.get(2);
                         }
                 } catch (Exception e) {
@@ -57 +59 @@
                 }
 
-                Collection<List<Event>> sequences = new LinkedList<List<Event>>();
+                SimpleSequenceGenerator gen;
                 Object obj = GlobalDataContainer.getInstance().getData(sequencesName);
-                if(obj != null) {
-                        
-                        if(obj.getClass().equals(sequences.getClass())) {
-                                sequences = (Collection<List<Event>>) obj;
-                        }
-                 
+                if (obj != null) {
+                        if (obj.getClass().equals(SimpleSequenceGenerator.class)) {
+                                gen = (SimpleSequenceGenerator) obj;
+                                Console.println("Number of sequences: " + gen.sequenceCount());
+
+                                int[] seq1 = gen.get(0).getSequence();
+                                int[] seq2 = gen.get(0).getSequence();
                                 
-                                        Console.println("Number of sequences: " + sequences.size());
+                                ObjectDistanceSubstitionMatrix submat = new
+                                ObjectDistanceSubstitionMatrix();
+                                submat.generate(sequences);
+                                // SmithWaterman sw = new SmithWaterman(seq1, seq2,
+                                // new NearbySubstitutionMatrix(seq1, seq2, 10));
+                                // sw.printDPMatrix();
+                                // System.out.println();
+                                // sw.printAlignments();
+                                // sw.getMatches();
+                                System.out.println("foo");
 
-                                        SimpleSequenceGenerator gen = new SimpleSequenceGenerator();
-                                        gen.generate(sequences);
-                                        int[] seq1 = gen.get(0).getSequence();
-                                        int[] seq2 = gen.get(0).getSequence();
-                                        //ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix();
-                                        //submat.generate(sequences);
-                                        //SmithWaterman sw = new SmithWaterman(seq1, seq2,
-                                        //              new NearbySubstitutionMatrix(seq1, seq2, 10));
-
-                                //sw.printDPMatrix();
-                                //System.out.println();
-                                //sw.printAlignments();
-                                // sw.getMatches();
-                                        System.out.println("foo");
-                                }
+                        } else {
+                                Console.printerr("No number sequences generated. Please run the generateNumberSequences before.");
+                                
                         }
 
+                                        }
+
+        }
 
         /*
@@ -93 +96 @@
         @Override
         public String help() {
-                return "binaryAlignment <sequencesName> {<algorithm>}";
+                return "binaryAlignment <sequencesName> <substitutionMatrixname> {<algorithm>}";
         }