Package org.moltools.apps.probemaker.design

Examples of org.moltools.apps.probemaker.design.DefaultTagLibrary

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          File libFile = new File(libFileName);
          if (!libFile.getAbsolutePath().equals(libFile.getPath())) {
            libFile = new File(settingsFile.getAbsoluteFile().getParentFile(),libFile.getPath());
          }
          DefiniteSequenceDB<NucleotideSequence> tagseqs = SequenceIO.readSequenceDB(new FileReader(libFile), new FastaDBFormat<NucleotideSequence>(), null, ListSequenceDB.getDefaultBuilder(),new SimpleDNASequenceBuilder());
          TagLibrary lib = new DefaultTagLibrary(tagseqs,"taglib"+ti); //$NON-NLS-1$
          lib.setMode(mode);
          libs.add(lib);
          ti++;
        }
        TagLibrary[] libraries = libs.toArray(new TagLibrary[libs.size()]);
        int[] order = new int[libraries.length];
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          File libFile = new File(libFileName);
          if (!libFile.getAbsolutePath().equals(libFile.getPath())) {
            libFile = new File(settingsFile.getAbsoluteFile().getParentFile(),libFile.getPath());
          }
          DefiniteSequenceDB<NucleotideSequence> tagseqs = SequenceIO.readSequenceDB(new FileReader(libFile), new FastaDBFormat<NucleotideSequence>(), null, ListSequenceDB.getDefaultBuilder(),new SimpleDNASequenceBuilder());
          TagLibrary lib = new DefaultTagLibrary(tagseqs,"taglib"+ti); //$NON-NLS-1$
          lib.setMode(mode);
          libs.add(lib);
          ti++;
        }
        TagLibrary[] libraries = libs.toArray(new TagLibrary[libs.size()]);
        int[] order = new int[libraries.length];
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  @Override
  protected void setUp() throws Exception {
   
    t1 = new AlleleSpecificPadlockTarget("T1","CCCCCCCCCCCCCCCCCCCCCCCCC|AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA","Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
   
    tags = new DefaultTagLibrary(new ListSequenceDB<NucleotideSequence>(),"Tag library 10"); //$NON-NLS-1$
    tags.setMode(TagLibrary.USE_UNIQUE_TAG);
    tags.addSequence(new SimpleNucleotideSequence("Tag1","GAAAAAAAAAAAAAAAAAAT", NucleotideSequence.DNA)); //$NON-NLS-1$ //$NON-NLS-2$
   
    proj = new Project("Test project"); //$NON-NLS-1$
    proj.getSettings().addDesignerProperties(GreedyTagAllocator.defaultParameters);
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    tags1.addSequence(new SimpleNucleotideSequence("ZIP|1","ACTAGCACGGACGAC")); //$NON-NLS-1$ //$NON-NLS-2$
    tags1.addSequence(new SimpleNucleotideSequence("ZIP|2","ACTAGCACGGACGAC")); //$NON-NLS-1$ //$NON-NLS-2$
    tags1.addSequence(new SimpleNucleotideSequence("ZIP|3","ACTAGCACGGACGAC")); //$NON-NLS-1$ //$NON-NLS-2$
    tags2.addSequence(new SimpleNucleotideSequence("PRIMER|1","ACTAGCACGGACGAC")); //$NON-NLS-1$ //$NON-NLS-2$
    project.getSettings().getDesignParameters().put("UPSTREAM_BLOCKS","1"); //$NON-NLS-1$ //$NON-NLS-2$
    TagLibrary lib1 = new DefaultTagLibrary(tags1,"Lib 1"); //$NON-NLS-1$
    TagLibrary lib2 = new DefaultTagLibrary(tags2,"Lib 2"); //$NON-NLS-1$
    lib1.setMode(TagLibrary.USE_UNIQUE_TAG);
    lib2.setMode(TagLibrary.USE_SAME_TAG);
    project.setTagSettings(new DefaultTagSettings(new TagLibrary[] { lib1, lib2 }));
  }
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    pm.getProject().getTargets().addSequence(t1);
   
    ListSequenceDB<NucleotideSequence> db = new ListSequenceDB<NucleotideSequence>();
    db.addSequence(new SimpleNucleotideSequence("Tag 1","AAAAAAAAAA")); //$NON-NLS-1$ //$NON-NLS-2$
    db.addSequence(new SimpleNucleotideSequence("Tag 2","TTTTTTTTTT")); //$NON-NLS-1$ //$NON-NLS-2$
    TagLibrary tl = new DefaultTagLibrary(db,"Unique"); //$NON-NLS-1$
    tl.setMode(TagLibrary.USE_UNIQUE_TAG);
   
    pm.getProject().setTagSettings(new DefaultTagSettings(new TagLibrary[] {tl}));
   
    //Design
    ProbeDesigner pd = new DefaultProbeDesigner(new PairwiseTagAllocator());
    pm.getProbeDesignTask(false, false, null, new DefaultNamingScheme(), new AllAcceptor(),new NoSelector(), pd, new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true)).run();
       
//  Store to project file
    File f = new File("temp.pmp"); //$NON-NLS-1$
    f.deleteOnExit();
    new ProjectXMLIOTask(pm,null,new FileWriter(f)).run();
   
    //Read project
    new ProjectXMLIOTask(pm,null,new FileReader(f)).run();
   
    //Add new target
    pm.getProject().getTargets().clear();
    pm.getProject().getTargets().addSequence(t2);
   
//  Design with append       
    pm.getProbeDesignTask(true, false, null, new DefaultNamingScheme(), new AllAcceptor(), new NoSelector(), pd, new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true)).run();
   
        
//  Store to project file
    f = new File("temp2.pmp"); //$NON-NLS-1$
    f.deleteOnExit();
    new ProjectXMLIOTask(pm,eh,new FileWriter(f)).run();
   
    //Read project
    new ProjectXMLIOTask(pm,eh,new FileReader(f)).run();
      
    pm.getProject().getTargets().clear();
    pm.getProject().getTargets().addSequence(t1);
    pm.getProject().getTargets().addSequence(t2);
   
    db = new ListSequenceDB<NucleotideSequence>();
    db.addSequence(new SimpleNucleotideSequence("Tag 1","AAAAAAAAAA")); //$NON-NLS-1$ //$NON-NLS-2$
    db.addSequence(new SimpleNucleotideSequence("Tag 2","TTTTTTTTTT")); //$NON-NLS-1$ //$NON-NLS-2$
    db.addSequence(new SimpleNucleotideSequence("Tag 3","AAAAAAAAAA")); //$NON-NLS-1$ //$NON-NLS-2$
    db.addSequence(new SimpleNucleotideSequence("Tag 4","TTTTTTTTTT")); //$NON-NLS-1$ //$NON-NLS-2$
    tl = new DefaultTagLibrary(db,"Unique"); //$NON-NLS-1$
    tl.setMode(TagLibrary.USE_PER_GROUP);
   
    pm.getProject().setTagSettings(new DefaultTagSettings(new TagLibrary[] {tl, tl}));
   
//  Design
    pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new AllAcceptor(), new NoSelector(), pd, new DefaultTSSPairDesigner(new DefaultTSSConstructor()), eh).run();   
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    //Create the tagPane
    JPanel tagPane = new JPanel(new GridBagLayout());

    //Create the available-list and listPane
    availableList = new TagLibraryDragList(availableModel);
    availableList.setPrototypeCellValue(new LibraryLabel(new DefaultTagLibrary(new
        ListSequenceDB<NucleotideSequence>(), "Prototype library"))); //$NON-NLS-1$
    availableList.setCellRenderer(new LibraryLabel());
    availableList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);

    JPanel listPane = new JPanel(new GridBagLayout());
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      //Get the next position to use
      boolean gotlib = false;
      while (!gotlib) {
        if (tagLibFields[pos].isSelected()) {
          //Use a new TagLibrary with the SAME tags in it (not just copies).
          tagLibraries[libno] = new DefaultTagLibrary(tagLibFields[pos].getLibrary(),tagLibFields[pos].getLibrary().getName());
          tagLibraries[libno].setMode(new Integer(tagUsageBoxes[pos].
                                                  getSelectedIndex()).byteValue());
          gotlib = true;
        }
        else {
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              SwingUIMessages.getString("Common.TITLE_IO_ERROR"), //$NON-NLS-1$
              JOptionPane.ERROR_MESSAGE);
          return;
        }
        //Add a label with the taglibrary to the available list
        TagLibrary temptl = new DefaultTagLibrary(temp, tagFiles[i].getName());
        availableModel.addElement(new LibraryLabel(temptl));
      }
    }
  }
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  @Override
  protected void setUp() throws Exception {
   
    t1 = new AlleleSpecificPadlockTarget("T1","CCCCCCCCCCCCCCCCCCCCCCCCC|AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA","Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
   
    tags = new DefaultTagLibrary(new ListSequenceDB<NucleotideSequence>(),"Tag library 10"); //$NON-NLS-1$
    tags.setMode(TagLibrary.USE_UNIQUE_TAG);
    tags.addSequence(new SimpleNucleotideSequence("Tag1","GAAAAAAAAAAAAAAAAAAT", NucleotideSequence.DNA)); //$NON-NLS-1$ //$NON-NLS-2$
   
    proj = new Project("Test project"); //$NON-NLS-1$
    proj.getSettings().addDesignerProperties(GreedyTagAllocator.defaultParameters);
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    t1.setVariant(t1.getVariants()[0]);
    t2.setVariant(t2.getVariants()[0]);


    //Make tag library with ten tags
    TagLibrary tags10 = new DefaultTagLibrary(new ListSequenceDB<NucleotideSequence>(),"Tag library 10"); //$NON-NLS-1$
    tags10.setMode(TagLibrary.USE_UNIQUE_TAG);
    for (int i = 1;i <= 10;i++) {
      tags10.addSequence(new SimpleNucleotideSequence("Tag" + i,"AAAAAAAAAAAAAAAAAAAA", NucleotideSequence.DNA)); //$NON-NLS-1$ //$NON-NLS-2$
    }   

    //Make tag library with one tag
    TagLibrary tags1 = new DefaultTagLibrary(new ListSequenceDB<NucleotideSequence>(),"Tag library 1"); //$NON-NLS-1$
    tags1.setMode(TagLibrary.USE_UNIQUE_TAG);
    tags1.addSequence(new SimpleNucleotideSequence("Tag1","AAAAAAAAAAAAAAAAAAAA", NucleotideSequence.DNA)); //$NON-NLS-1$ //$NON-NLS-2$

    TagLibrary tags1b = new DefaultTagLibrary(new ListSequenceDB<NucleotideSequence>(),"Tag library 1b"); //$NON-NLS-1$
    tags1b.setMode(TagLibrary.USE_UNIQUE_TAG);
    tags1b.addSequence(new SimpleNucleotideSequence("Tag1b","AAAAAAAAAAAAAAAAAAAA", NucleotideSequence.DNA)); //$NON-NLS-1$ //$NON-NLS-2$

    libraries1_10 = new TagLibrary[] { tags10 };
    libraries1_1 = new TagLibrary[] { tags1 };
    libraries2_1_1 = new TagLibrary[] { tags1, tags1b };
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Related Classes of org.moltools.apps.probemaker.design.DefaultTagLibrary

  • org.moltools.apps.probemaker.ProbeMakerLauncher
  • org.moltools.apps.probemaker.project.ProjectIOTask
  • org.moltools.apps.probemaker.project.ProjectXMLIOTask
  • org.moltools.apps.probemaker.swingui.TagSetupPanel
  • org.moltools.apps.probemaker.test.HybInterferenceModuleTest
  • org.moltools.apps.probemaker.test.ProjectIOTest
  • org.moltools.apps.probemaker.test.TagAllocationTableTest
  • org.moltools.apps.probemaker.test.TagAllocationTest
  • org.moltools.apps.probemaker.test.TagSelectorTest
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