Examples of org.moltools.apps.probemaker.seq.ProbeMakerTarget

Package org.moltools.apps.probemaker.seq

Examples of org.moltools.apps.probemaker.seq.ProbeMakerTarget

org.moltools.apps.probemaker.seq.ProbeMakerTarget

The Target interface is central to the probe design task performed by ProbeMaker. Each target for which a probe is to be designed is described by an object of a class implementing this interface.
The Target class controls the probe design by defining two template sequences of class for TSSTemplate for the construction of the two (five- and three-prime) TargetSpecificSequences to be put into the Probe.
In addition to the methods defined by the ChangeableNucleotideSequence interface, a Target should contain methods for getting and setting the TargetGroup that the target belongs to. Furthermore, the methods getTemplateForFivePrime and getTemplateForThreePrime define the TSSTemplates.
Before probe design starts, all Targets are validated by calling their isValidTarget method, which may return OK or INVALID. A response other than OK will abort the probe design.
A target is also a plug-in extension, which requires it to define the following methods:

getSequenceBuilder

a public static method that returns a SequenceBuilder object for creating targets of this class. Should take a SequenceConverter as argument to provide the possibility to parse the sequence data prior to building the sequence.
public static SequenceBuilder getSequenceBuilder()
This method is not enforced by the interface (since it should be a static method), but a runtime error will occur if it is not present.

getBriefDescription

A public static method that returns a short description of the target type for display in the UI. public static String getBriefDescription()
This method is not enforced by the interface (since it should be a static method)

getLongDescription

A public static method that returns a longer description of the target type for display in the UI. The string may be in HTML. public static String getLongDescription()
This method is not enforced by the interface (since it should be a static method).

Parameterless constructor

A no-argument constructor to be able to create an empty target object when loading target data from a project file.

@author Johan Stenberg

    
    //Put groupname - group of each target group in a map
    Map<String, TargetGroup> targetGroups = new LinkedHashMap<String, TargetGroup>();
    //Create target groups and add targets to them
    for (S seq : targets.getSequenceCollection()) {
      ProbeMakerTarget t = (ProbeMakerTarget) seq;
      //Create group names on first word (before " ") of target name
      String groupName = t.getID().split(" ")[0]; //$NON-NLS-1$
              
      if (targetGroups.containsKey(groupName)) {
        TargetGroup tg = targetGroups.get(groupName);
        tg.addMember(t);
      }
      else {
        TargetGroup tg = new TargetGroup(t.getID());
        tg.addMember(t);
        targetGroups.put(groupName,tg);
      }
    }

View Full Code Here

    
    //Put groupname - group of each target group in a map
    Map<String, TargetGroup> targetGroups = new HashMap<String, TargetGroup>();
    //Create target groups and add targets to them
    for (int i = 0;i<targets.size();i++) {
      ProbeMakerTarget t = (ProbeMakerTarget) targets.getSequenceAt(i);
      //Create group names on first word (before " ") of target name
      String groupName = t.getID().split(" ")[0]; //$NON-NLS-1$
              
      if (targetGroups.containsKey(groupName)) {
        TargetGroup tg = targetGroups.get(groupName);
        tg.addMember(t);
      }
      else {
        TargetGroup tg = new TargetGroup(t.getID());
        tg.addMember(t);
        targetGroups.put(groupName,tg);
      }
    }

View Full Code Here

      h4.addContent(CoreMessages.getString("ProbeMakerHTMLRenderer.TEXT_GROUPED_WITH")); //$NON-NLS-1$
      
      Element list = new Element(HTMLWriter.UL.getTag());
      
      for (Iterator<? extends Target> i = targetGroup.getMembers().iterator(); i.hasNext(); ) {
        ProbeMakerTarget other = (ProbeMakerTarget) i.next();
        if (t != other) {
          Element li = new Element(HTMLWriter.LI.getTag());
          li.addContent(other.getID());
          list.addContent(li);
        }
      }      
      root.addContent(h4);
      root.addContent(list);

View Full Code Here

   * padlock probes and gap-fill probes*/
  public boolean checkTemplatingByTarget(Probe p) {
    boolean found = false;
    //Check that target is template in correct position only
    //Can't check ligation on target if no target!
    ProbeMakerTarget t = (ProbeMakerTarget) p.getTarget();    
    if (t != null) {
      boolean correct = false;
      int[] results = isLigationTemplate(t, p, false, true);
      if (results != null) {
        for (int i = 0; i < results.length; i++) {

View Full Code Here

0 1 2

TOP

Related Classes of org.moltools.apps.probemaker.seq.ProbeMakerTarget

org.moltools.apps.probemaker.calculators.PadlockLigationCalculator

org.moltools.apps.probemaker.design.Analyzer

org.moltools.apps.probemaker.design.DefaultProbeDesigner

org.moltools.apps.probemaker.design.TargetHandler

org.moltools.apps.probemaker.ext.dbb.SelectorGrouper

org.moltools.apps.probemaker.ext.dbb.SelectorGroupSorter

org.moltools.apps.probemaker.ext.mod.DefaultHybInterferenceModule

org.moltools.apps.probemaker.ext.mod.FalsePrimingModule

org.moltools.apps.probemaker.ProbeMakerHTMLRenderer

org.moltools.apps.probemaker.project.ProjectIOTask

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.