Package org.moltools.lib.seq.io

Examples of org.moltools.lib.seq.io.SequenceDBDataReader

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            }
          }
        }
        System.out.println("  Selector is: " + selector.getClass().getName());   //$NON-NLS-1$

        SequenceDBDataReader format = (SequenceDBDataReader) Class.forName(formatClassName).newInstance();
        if (format instanceof ParameterPlugIn) {
          ParameterPlugIn paFormat = (ParameterPlugIn) selector;
          DataDescriptor[] dds = paFormat.getDataDescriptors();
          if (dds != null) {
            for (int d = 0;d<dds.length;d++) {
              DataDescriptor dd = dds[d];
              String string = props.getProperty("probemaker.targetInputFormat." + dd.getKey());
              paFormat.setData(dd.getKey(), string);
            }
          }
        }

        if (outputClassName == null) {
          outputClassName = DefaultTextTableFormatter.class.getName();
        }
        Class<?> outputClass = Class.forName(outputClassName);
        TextTableFormatter<Probe> outputformatter = (TextTableFormatter<Probe>) outputClass.newInstance();
       
        if (targetClassName == null) {
          System.err.println("ERROR: Must specify a probemaker.targetType"); //$NON-NLS-1$
          return;
        }
        Class<?> targetClass = Class.forName(targetClassName);
        SequenceBuilder<? extends ProbeMakerTarget> seqBuilder = (SequenceBuilder<? extends ProbeMakerTarget>) targetClass.getMethod("getSequenceBuilder",(Class[])null).invoke(null,(Object[]) null); //$NON-NLS-1$

        System.out.println("  Format is: " + format.getClass().getName()); //$NON-NLS-1$
        System.out.println("  Target type is: " + targetClass.getName()); //$NON-NLS-1$
        System.out.println("  Output format is: " + outputClass.getName()); //$NON-NLS-1$

        TargetInputFormat<? extends ProbeMakerTarget> tif = new DefaultTargetInputFormat("Input format",format,null,seqBuilder,ListSequenceDB.getDefaultBuilder()); //$NON-NLS-1$
       
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  protected void importTargets() {
    TargetInputFormat tif = null;

    Class<?> targetClass = null;
    SequenceBuilder<? extends ProbeMakerTarget> seqBuilder;
    SequenceDBDataReader format;
    Transformer conv = null;
    SequenceDBBuilder dbBuilder = null;
    try {
      if (template == null) {
        //Target type
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    if (!platform.getUI().inputData(importProbesData,CoreMessages.getString("ProbeMakerPlugIn.TITLE_IMPORT_PROBES"))) { //$NON-NLS-1$
      return;
    }

    final Class<?> formatClass = (Class) importProbesData.getData("FORMAT"); //$NON-NLS-1$
    SequenceDBDataReader format = null;
    try {
      format = (SequenceDBDataReader) formatClass.newInstance();
    }
    catch (final InstantiationException e) {
      platform.handleError(e.getMessage(),e);
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            }
          }
        }
        System.out.println("  Selector is: " + selector.getClass().getName());   //$NON-NLS-1$

        SequenceDBDataReader format = (SequenceDBDataReader) Class.forName(formatClassName).newInstance();
        if (format instanceof ParameterPlugIn) {
          ParameterPlugIn paFormat = (ParameterPlugIn) selector;
          DataDescriptor[] dds = paFormat.getDataDescriptors();
          if (dds != null) {
            for (int d = 0;d<dds.length;d++) {
              DataDescriptor dd = dds[d];
              String string = props.getProperty("probemaker.targetInputFormat." + dd.getKey());
              paFormat.setData(dd.getKey(), string);
            }
          }
        }

        if (outputClassName == null) {
          outputClassName = DefaultTextTableFormatter.class.getName();
        }
        Class<?> outputClass = Class.forName(outputClassName);
        TextTableFormatter<Probe> outputformatter = (TextTableFormatter<Probe>) outputClass.newInstance();
       
        if (targetClassName == null) {
          System.err.println("ERROR: Must specify a probemaker.targetType"); //$NON-NLS-1$
          return;
        }
        Class<?> targetClass = Class.forName(targetClassName);
        SequenceBuilder<? extends ProbeMakerTarget> seqBuilder = (SequenceBuilder<? extends ProbeMakerTarget>) targetClass.getMethod("getSequenceBuilder",(Class[])null).invoke(null,(Object[]) null); //$NON-NLS-1$

        System.out.println("  Format is: " + format.getClass().getName()); //$NON-NLS-1$
        System.out.println("  Target type is: " + targetClass.getName()); //$NON-NLS-1$
        System.out.println("  Output format is: " + outputClass.getName()); //$NON-NLS-1$

        TargetInputFormat<? extends ProbeMakerTarget> tif = new DefaultTargetInputFormat("Input format",format,null,seqBuilder,ListSequenceDB.getDefaultBuilder()); //$NON-NLS-1$
       
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    javax.swing.filechooser.FileFilter filter = useFormat ? null : libFilter;
   
    File[] tagFiles = platform.getUI().selectFiles(filter,SwingUIMessages.getString("TagPanel.CAPTION_SELECT_FILES")); //$NON-NLS-1$
   
    //Select default filter
    SequenceDBDataReader format = new FastaDBFormat<NucleotideSequence>();

    //Check if file open was successfull
    if (tagFiles != null) {

      //If import, choose a plugin file format
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  protected void importTargets() {
    TargetInputFormat tif = null;

    Class<?> targetClass = null;
    SequenceBuilder<? extends ProbeMakerTarget> seqBuilder;
    SequenceDBDataReader format;
    Transformer conv = null;
    SequenceDBBuilder dbBuilder = null;
    try {
      if (template == null) {
        //Target type
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    if (!platform.getUI().inputData(importProbesData,CoreMessages.getString("ProbeMakerPlugIn.TITLE_IMPORT_PROBES"))) { //$NON-NLS-1$
      return;
    }

    final Class<?> formatClass = (Class) importProbesData.getData("FORMAT"); //$NON-NLS-1$
    SequenceDBDataReader format = null;
    try {
      format = (SequenceDBDataReader) formatClass.newInstance();
    }
    catch (final InstantiationException e) {
      platform.handleError(e.getMessage(),e);
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  protected void importTargets() {
    TargetInputFormat tif = null;

    Class<?> targetClass = null;
    SequenceBuilder<? extends ProbeMakerTarget> seqBuilder;
    SequenceDBDataReader format;
    Transformer conv = null;
    SequenceDBBuilder dbBuilder = null;
    try {
      if (template == null) {
        //Target type
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    if (!platform.getUI().inputData(importProbesData,CoreMessages.getString("ProbeMakerPlugIn.TITLE_IMPORT_PROBES"))) { //$NON-NLS-1$
      return;
    }

    final Class<?> formatClass = (Class) importProbesData.getData("FORMAT"); //$NON-NLS-1$
    SequenceDBDataReader format = null;
    try {
      format = (SequenceDBDataReader) formatClass.newInstance();
    }
    catch (final InstantiationException e) {
      platform.handleError(e.getMessage(),e);
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  protected void importTargets() {
    TargetInputFormat tif = null;

    Class<?> targetClass = null;
    SequenceBuilder<? extends ProbeMakerTarget> seqBuilder;
    SequenceDBDataReader format;
    Transformer conv = null;
    SequenceDBBuilder dbBuilder = null;
    try {
      if (template == null) {
        //Target type
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Related Classes of org.moltools.lib.seq.io.SequenceDBDataReader

  • org.moltools.apps.probemaker.ProbeMakerLauncher
  • org.moltools.apps.probemaker.ProbeMakerPlugIn
  • org.moltools.apps.probemaker.swingui.TagSetupPanel
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