Package org.moltools.design.data

Examples of org.moltools.design.data.ValidatingTarget

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      setStatus(CoreMessages.getString("ProbeDesignTask.MESSAGE_VALIDATING")); //$NON-NLS-1$
      //Check the validity of validatable targets
      for (Iterator<ProbeMakerTarget> ti = targets.iterator(); ti.hasNext(); ) {
        Target target = ti.next();
        if (target instanceof ValidatingTarget) {
          ValidatingTarget vt = (ValidatingTarget) target;
          switch (vt.isValidTarget()) {
            case ValidatingTarget.OK:
              break;
            case ValidatingTarget.INVALID:
              throw new UnsupportedOperationException(target.getID() +
                  CoreMessages.getString("ProbeDesignTask.MESSAGE_INVALID")); //$NON-NLS-1$
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      setStatus(CoreMessages.getString("ProbeDesignTask.MESSAGE_VALIDATING")); //$NON-NLS-1$
      //Check the validity of validatable targets
      for (Iterator<ProbeMakerTarget> ti = targets.iterator(); ti.hasNext(); ) {
        Target target = ti.next();
        if (target instanceof ValidatingTarget) {
          ValidatingTarget vt = (ValidatingTarget) target;
          switch (vt.isValidTarget()) {
          case ValidatingTarget.OK:
            break;
          case ValidatingTarget.INVALID:
            throw new UnsupportedOperationException(target.getID() +
                CoreMessages.getString("ProbeDesignTask.MESSAGE_INVALID")); //$NON-NLS-1$
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      setStatus(CoreMessages.getString("ProbeDesignTask.MESSAGE_VALIDATING")); //$NON-NLS-1$
      //Check the validity of validatable targets
      for (Iterator<ProbeMakerTarget> ti = targets.iterator(); ti.hasNext(); ) {
        Target target = ti.next();
        if (target instanceof ValidatingTarget) {
          ValidatingTarget vt = (ValidatingTarget) target;
          switch (vt.isValidTarget()) {
          case ValidatingTarget.OK:
            break;
          case ValidatingTarget.INVALID:
            throw new UnsupportedOperationException(target.getID() +
                CoreMessages.getString("ProbeDesignTask.MESSAGE_INVALID")); //$NON-NLS-1$
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                ": " + other.getName(), //$NON-NLS-1$
                SELECTOR_LIGATION_OTHER_3, Message.WARNING));
          }
        }
        if (tests[7].perform() && sel5 != null) {
          ValidatingTarget t = (ValidatingTarget) other.getTarget();
          if (t != null) {
            if (t instanceof SelectorTarget) {
              SelectorTarget it = (SelectorTarget) t;
              if (isMatch(it, sel5, true, FIVE_PRIME_END)) {
                ProbeMakerPropertyUtils.addMessage(p.getTSSPair(),new Message(SELECTOR_TARGET_LIGATION_OTHER_5.
                    getDescription() + ": " + //$NON-NLS-1$
                    other.getName(),
                    SELECTOR_TARGET_LIGATION_OTHER_5,
                    Message.WARNING));
              }
            }
            else {
              ProbeMakerPropertyUtils.addMessage(p.getTSSPair(),new Message(
                  "Could not perform ligation to target test: Incompatible target", //$NON-NLS-1$
                  SELECTOR_TARGET_LIGATION_OTHER_5, Message.ALERT));
            }
          }
          else {
            ProbeMakerPropertyUtils.addMessage(p.getTSSPair(),new Message(
                "Could not perform ligation to target test: No target", //$NON-NLS-1$
                SELECTOR_TARGET_LIGATION_OTHER_5, Message.ALERT));

          }
        }
        if (tests[8].perform() && sel3 != null) {
          //Selector 3' end ligates to 3' end of other target
          ValidatingTarget t = (ValidatingTarget) other.getTarget();
          if (t != null) {
            if (t instanceof SelectorTarget) {
              SelectorTarget it = (SelectorTarget) t;
              if (isMatch(it, sel3, true, THREE_PRIME_END)) {
                ProbeMakerPropertyUtils.addMessage(p.getTSSPair(),new Message(SELECTOR_TARGET_LIGATION_OTHER_3.
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Related Classes of org.moltools.design.data.ValidatingTarget

  • org.moltools.apps.probemaker.ext.mod.SelectorLigationModule
  • org.moltools.apps.probemaker.ProbeDesignTask
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