Fixed several issues related to analyzing sequences containing only the

randomized region. Added batch mode, allowing the user to import
multiplexed, pools without primers.

src/main/java/gui/core/aptamer/pool/AptamerPoolRootController.java

@@ -987,8 +987,6 @@ private void computeIndexOrder(ProgressPaneController pp) {
 			// Temporarily store the counts in an array as random access to mapdb is slow but sequential access is fast
 			int[] counts = new int[aptamer_ids.length];
 
-			System.out.println("here");
-
 			// Provide a progress bar for this operation
 			pp.setShowProgressBar(true);
 
@@ -1019,9 +1017,6 @@ public void run() {
 					pp.setProgress(items_to_sort.doubleValue()/cycle_to_sort_by.getUniqueSize() );
 					pp.setProgressLabel(String.format("Retrieved %s/%s items (%.2f%%)", items_to_sort.get(), cycle_to_sort_by.getUniqueSize(), (items_to_sort.doubleValue()/cycle_to_sort_by.getUniqueSize())*100.0) );
 
-					System.out.println(items_to_sort.get() + "  " + cycle_to_sort_by.getUniqueSize());
-					System.out.flush();
-
 					// Once every half a second should suffice
 					Thread.sleep(500);
 

src/main/java/gui/wizards/newexperiment/DataModel.java

@@ -79,6 +79,8 @@ public class DataModel {
 	private SimpleIntegerProperty aptaplexParserPrimerTolerance = new SimpleIntegerProperty( Configuration.getDefaults().containsKey("AptaplexParser.PrimerTolerance") ? Configuration.getDefaults().getInt("AptaplexParser.PrimerTolerance") : Configuration.getParameters().getInt("AptaplexParser.PrimerTolerance") );
 
 	private File lastSelectedDirectory = null;
+
+	private BooleanProperty noPrimers = new SimpleBooleanProperty(false); 
 
 
 	/**
@@ -438,6 +440,19 @@ public SimpleIntegerProperty getAptaplexParserPrimerTolerance() {
 	public void setAptaplexParserPrimerTolerance(SimpleIntegerProperty aptaplexParserPrimerTolerance) {
 		this.aptaplexParserPrimerTolerance = aptaplexParserPrimerTolerance;
 	}
-
+
+	/**
+	 * @return the noPrimers
+	 */
+	public BooleanProperty getNoPrimers() {
+		return noPrimers;
+	}
+
+	/**
+	 * @param aptaplexParserPrimerTolerance the aptaplexParserPrimerTolerance to set
+	 */
+	public void setNoPrimers(BooleanProperty noPrimers) {
+		this.noPrimers = noPrimers;
+	}
 
 }

src/main/java/gui/wizards/newexperiment/Wizard1Controller.java

@@ -98,6 +98,9 @@ public class Wizard1Controller{
 	@FXML
 	private CheckBox rangeLengthCheckBox;	
 
+	@FXML
+	private CheckBox noPrimersCheckbox;
+
 
     private List<SelectionCycleDetailsController> selectionCycleDetailsControllers = new ArrayList<SelectionCycleDetailsController>();
 
@@ -141,6 +144,28 @@ public void init() {
     	randomizedRegionSizeLowerSpinner.getValueFactory().valueProperty().bindBidirectional(getDataModel().getRandomizedRegionSizeLower());
     	randomizedRegionSizeUpperSpinner.getValueFactory().valueProperty().bindBidirectional(getDataModel().getRandomizedRegionSizeUpper());
 
+    	noPrimersCheckbox.selectedProperty().bindBidirectional(getDataModel().getNoPrimers());
+
+    	// Prevent access to "No primer" checkbox if data is not demultiplexed or paired end.
+    	noPrimersCheckbox.disableProperty().bind(Bindings.or(getDataModel().getIsDemultiplexed().not(), getDataModel().getIsPairedEnd()));
+
+    	// Disable primer input if user has selected the noPrimerCheckbox
+    	primer5TextField.disableProperty().bind(noPrimersCheckbox.selectedProperty());
+    	primer3TextField.disableProperty().bind(noPrimersCheckbox.selectedProperty());
+
+    	// Clear the primer text fields if the user checks the "No Primer" checkbox
+    	noPrimersCheckbox.selectedProperty().addListener((obs, wasSelected, isNowSelected) -> {
+    	    if (isNowSelected) {
+    	    	primer5TextField.clear();
+    	    	primer3TextField.clear();
+    	    }
+    	});
+
+    	// If the checkbox is disabled, we need to unselect it
+    	if (noPrimersCheckbox.isDisabled()) {
+    		getDataModel().getNoPrimers().set(false);
+    	}
+
     	// Make sure that either only the exact size or the range or non of them is selected
     	exactLengthCheckBox.selectedProperty().addListener((obs, wasSelected, isNowSelected) -> {
     	    if (isNowSelected) {
@@ -210,8 +235,8 @@ public boolean validateData() {
 
     	// First the trivial things:
 
-    	// Make sure the 5' primer is present
-    	if (primer5TextField.textProperty().isEmpty().get()) {
+    	// Make sure the 5' primer is present, but only if we are not in batch mode
+    	if (primer5TextField.textProperty().isEmpty().get() && noPrimersCheckbox.selectedProperty().not().get()) {
 
     		ControlFXValidatorFactory.setTemporaryValidation(
     				primer5TextField, 
@@ -225,8 +250,9 @@ public boolean validateData() {
 
     	}
 
-    	// Make sure that either the 3' primer is present or the  randomized region size is not 0 
-    	if (primer3TextField.textProperty().isEmpty().get() && randomizedRegionSizeSpinner.getValueFactory().getValue().equals(0)) {
+
+    	// Make sure that either the 3' primer is present or the  randomized region size is not 0 and we are not in batch mode 
+    	if (primer3TextField.textProperty().isEmpty().get() && randomizedRegionSizeSpinner.getValueFactory().getValue().equals(0) && noPrimersCheckbox.selectedProperty().not().get()) {
 
     		ControlFXValidatorFactory.setTemporaryValidation(
         			primer3TextField, 
@@ -248,6 +274,36 @@ public boolean validateData() {
 
     	}
 
+    	// Make sure that if we are in batch mode we have either a fixed randomized region size or a range 
+    	if (noPrimersCheckbox.selectedProperty().get() &&  exactLengthCheckBox.selectedProperty().not().get() && this.rangeLengthCheckBox.selectedProperty().not().get()) {
+
+    		ControlFXValidatorFactory.setTemporaryValidation(
+    				exactLengthCheckBox, 
+        			ControlFXValidatorFactory.AllwaysWrongValidator("Either an exact randomized region or a range must be specified."), 
+        			this.validationSupport, 
+        			ControlFXValidatorFactory.AllwaysCorrectValidator,
+        			false
+        			);
+
+    		is_valid = false;
+
+    	}    	
+
+    	// Make sure that if an exact length is specified it must be greater than 0
+    	if (this.exactLengthCheckBox.isSelected() && randomizedRegionSizeSpinner.getValueFactory().getValue() <= 0) {
+
+			ControlFXValidatorFactory.setTemporaryValidation(
+    				randomizedRegionSizeSpinner, 
+        			ControlFXValidatorFactory.AllwaysWrongValidator("Randomized region size must be greater than zero."), 
+        			this.validationSupport, 
+        			ControlFXValidatorFactory.AllwaysCorrectValidator,
+        			false
+        			);
+
+			is_valid = false;
+
+    	}
+
     	// Make sure that if a range for the randomized region size is specified, it is a valid one
     	if (this.rangeLengthCheckBox.isSelected()) {
 
@@ -757,6 +813,12 @@ public boolean validateData() {
 
     		}
 
+    		if (getDataModel().getNoPrimers().get()) {
+
+    			utilities.Configuration.getParameters().setProperty("AptaplexParser.BatchMode", true);
+
+    		}
+
     		// Save to file 
     		utilities.Configuration.writeConfiguration();
 

src/main/java/gui/wizards/newexperiment/Wizard2Controller.java

@@ -122,7 +122,7 @@ public void init() {
 
 
     /**
-     * Instaniates a new Experiment and starts AptaPLEX
+     * Instantiates a new Experiment and starts AptaPLEX
      * @param event
      */
     @FXML

src/main/java/gui/wizards/newexperiment/wizard1.fxml

@@ -14,7 +14,7 @@
 <?import javafx.scene.layout.VBox?>
 <?import javafx.scene.text.Font?>
 
-<BorderPane fx:id="rootBorderPane" prefHeight="620.0" prefWidth="800.0" xmlns="http://javafx.com/javafx/9" xmlns:fx="http://javafx.com/fxml/1" fx:controller="gui.wizards.newexperiment.Wizard1Controller">
+<BorderPane fx:id="rootBorderPane" prefHeight="620.0" prefWidth="800.0" xmlns="http://javafx.com/javafx/16" xmlns:fx="http://javafx.com/fxml/1" fx:controller="gui.wizards.newexperiment.Wizard1Controller">
     <bottom>
         <fx:include fx:id="actionBar" source="actionBar.fxml" />
     </bottom>
@@ -72,6 +72,11 @@
                   </TextField>
                </children>
             </HBox>
+            <HBox>
+               <children>
+                  <CheckBox fx:id="noPrimersCheckbox" mnemonicParsing="false" text="Batch Mode (reads are assumed to contain only the randomized region)" />
+               </children>
+            </HBox>
             <Label text="Randomized Region Size">
                <font>
                   <Font name="System Bold" size="14.0" />

src/main/java/gui/wizards/structureprofileprediction/StructureProfilePredictionWizardController.java

@@ -92,7 +92,7 @@ public void run() {
 
 				// now that we have the data, set any file backed implementations 
 				// of StructurePool to read only. Do this only if the prediction has not 
-				// been cancled by the user.
+				// been canceled by the user.
 				experiment.getStructurePool().setReadOnly();
 
 				closeButton.setDisable(false);

src/main/java/lib/parser/aptaplex/AptaPlexConsumer.java

@@ -49,6 +49,13 @@
  *         from the queue, processes them and adds them to the aptamer pool.
  */
 public class AptaPlexConsumer implements Runnable {
+
+	/**
+	 * True AptaPlex should run in batch mode. No primer or barcode checks will be performed
+	 * and AptaPlex assumes the reads are preprocessed randomized regions only. In contrast to
+	 * onlyRandomizedRegtionInData, batchMode will not add any primers back to these sequences.
+	 */	
+	private boolean batchMode = Configuration.getParameters().getBoolean("AptaplexParser.BatchMode");	
 
 	/**
 	 * The queue to consume from
@@ -101,9 +108,9 @@ public class AptaPlexConsumer implements Runnable {
 	private byte[] primer5reverse = Configuration.getParameters().getString("Experiment.primer5").getBytes();
 
 	/**
-	 * Access to the 5 prime primer
+	 * Access to the 3 prime primer
 	 */
-	private byte[] primer3 = Configuration.getParameters().getString("Experiment.primer3").getBytes();
+	private byte[] primer3 = batchMode ? "".getBytes() : Configuration.getParameters().getString("Experiment.primer3").getBytes();
 
 	/**
 	 * True if the sequences have previously been demultiplexed
@@ -112,6 +119,7 @@ public class AptaPlexConsumer implements Runnable {
 
 	/**
 	 * True if the sequences have previously been stripped of their primers and barcodes
+	 * Note that primers will be added again by AptaPlex
 	 */
 	private boolean onlyRandomizedRegionInData = Configuration.getParameters().getBoolean("AptaplexParser.OnlyRandomizedRegionInData");
 
@@ -275,15 +283,20 @@ public void run() {
 				contig = getContig(queueElement);
 
 				// ...check for undetermined nucleotides and fail if present...
-				if (!isValidSequence(contig)) {
+				// getContig returns null if invalid nucleotides are present.
+				if (contig == null) {
 					progress.totalInvalidContigs.incrementAndGet();
 					continue;
 				}
 
 
+				// Batch mode
+				if (this.batchMode) {
+					this.processBatchMode(contig);
+				}
 				// we need to differentiate between randomized region only mode, 
 				// and fully parsable data
-				if (this.onlyRandomizedRegionInData) {
+				else if (this.onlyRandomizedRegionInData) {
 
 					this.processReadRandomizedRegionOnly(contig);
 
@@ -365,9 +378,6 @@ private byte[] getContig(Object queueElement) {
 		// keep taking elements from the queue
 		byte[] contig = null;
 
-		// Update the progress in a thread-safe manner
-		// progress.totalProcessedReads.incrementAndGet(); TODO: Move this to the end of run();
-
 		// process queueElement
 		read = (Read) queueElement;
 
@@ -394,6 +404,103 @@ private byte[] getContig(Object queueElement) {
 
 	}
 
+	/**
+	 * Processes the current queueElement in batch mode. Assumes that the read consists only of the randomized region 
+	 * @param queueElement the element to be processed 
+	 * @return the error progress counter that was incremented in the last call of this function. null if success.  
+	 */
+	private AtomicInteger processBatchMode(byte[] contig) {
+
+		 // check if the contig conforms to the size restrictions 
+		if (this.randomizedRegionSizeExactBound != null) {
+
+			if (contig.length != this.randomizedRegionSizeExactBound) {
+
+				progress.totalContigAssemblyFails.getAndIncrement();
+				return progress.totalContigAssemblyFails;
+
+			}
+
+		}
+
+		// otherwise we must have a bound
+		else {
+
+			if (this.randomizedRegionSizeLowerBound <= contig.length &&  this.randomizedRegionSizeUpperBound >= contig.length){
+
+				progress.totalContigAssemblyFails.getAndIncrement();
+				return progress.totalContigAssemblyFails;
+
+			}
+
+		}
+
+		 // and add it to the selection cycle	 
+		 if (!storeReverseComplement) { // Do we have to compute the reverse complement?
+
+			read.selection_cycle.addToSelectionCycle(
+				 contig,
+				 0,
+				 contig.length
+				 );
+
+		 	// Add metadata information
+			addAcceptedNucleotideDistributions(read.selection_cycle, contig, 0, contig.length);
+
+		 } else { // We do!
+
+			// compute the complement...
+			for (int x = 0; x < contig.length; x++) {
+
+				switch (contig[x]) {
+				case 65:
+					contig[x] = 84;
+					break;
+
+				case 67:
+					contig[x] = 71;
+					break;
+
+				case 71:
+					contig[x] = 67;
+					break;
+
+				case 84:
+					contig[x] = 65;
+					break;
+				}
+			}
+
+			// ...and reverse it
+			for(int i = 0; i < contig.length / 2; i++)
+			{
+			    byte temp = contig[i];
+			    contig[i] = contig[contig.length - i - 1];
+			    contig[contig.length - i - 1] = temp;
+			}
+
+			read.selection_cycle.addToSelectionCycle(
+					 contig,
+					 0,
+					 contig.length
+					 );
+
+			 // Add metadata information
+			 addAcceptedNucleotideDistributions(read.selection_cycle, contig, 0, contig.length);
+
+		 }
+
+	 	 // Store nucleotide distribution and quality score
+	 	 addNuceotideDistributions();
+		 addQualityScores();
+
+		 progress.totalAcceptedReads.incrementAndGet();
+
+		 // if we are here, all went well and we can go home.
+		 return null;
+
+	}	
+
 	/**
 	 * Processes the current queueElement. Assumes that the read consists only of the randomized region 
 	 * @param queueElement the element to be processed 

src/main/java/lib/parser/aptaplex/AptaPlexProducer.java

@@ -145,7 +145,7 @@ public void run() {
 
 					reverse_export_path = Paths.get(exportPath.toString(), "undetermined_"+current_reverse_file_path.getFileName().toString() + (Configuration.getParameters().getBoolean("Export.compress") ? ".gz" : "" )); 
 					ExportWriter reverse_export_writer = Configuration.getParameters().getBoolean("Export.compress") ? new CompressedExportWriter() : new UncompressedExportWriter();
-					reverse_export_writer.open(reverse_export_path); 
+					reverse_export_writer.open(reverse_export_path);
 
 				}
 

src/main/java/utilities/Configuration.java

@@ -109,6 +109,9 @@ public class Configuration {
 																			// In addition, it is assumed that the data has already been demultiplexed.		
 		defaults.put("AptaplexParser.UndeterminedToFile", false); 	// If set to true, AptaPlex will dump all read which failed processing for any reason to a fastq file located
 																	// in the export folder of the project and named undetermined.fastq.gz
+		defaults.put("AptaplexParser.BatchMode", false);            //If true, AptaPlex will parse all files without looking for primers and blindly 
+																	//accept every read that fits the specified size
+
 
 		// AptaSIM Options
 		defaults.put("Aptasim.HmmDegree", 2); // Degree of the Markov model