Package org.moltools.apps.probemaker.design

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

266
267
268
269
270
271
272
273
274
275
276
277
          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];
View Full Code Here
193
194
195
196
197
198
199
200
201
202
203
        throw new IllegalArgumentException("Invalid spacer position"); //$NON-NLS-1$
      }
      spacerPosition = spacerPos;

      //Create and set up a spacer library
      TagLibrary spacerLib = new SpacerLibrary(0, NucleotideSequence.DNA);

      //parse the spacer string and check that its valid
      spacerSequence = ""; //$NON-NLS-1$
      for (int i = 0; i < spacerString.length(); i++) {
        Nucleotide nt = NucleotideSequenceHandler.getNucleotide(spacerString.
View Full Code Here
264
265
266
267
268
269
270
271
272
273
274
275
          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];
View Full Code Here
93
94
95
96
97
98
99
100
101
102
103
    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 }));
  }
View Full Code Here
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
    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();   
View Full Code Here
401
402
403
404
405
406
407
408
409
410
              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));
      }
    }
  }
View Full Code Here
509
510
511
512
513
514
515
516
517
518
519
520
521
    }

    public Component getListCellRendererComponent(JList list, Object value,
                                                  int index, boolean isSelected,
                                                  boolean cellHasFocus) {
      TagLibrary lib = ( (LibraryLabel) value).getLibrary();
      setText(lib.getName());
      setToolTipText(lib.size() + (lib.size() == 1 ? SwingUIMessages.getString("TagPanel.LIBRARY_SIZE_SINGLE") : SwingUIMessages.getString("TagPanel.LIBRARY_SIZE_ZERO_OR_MULTIPLE"))); //$NON-NLS-1$ //$NON-NLS-2$
      setBackground(isSelected ? Color.blue : Color.white);
      setForeground(isSelected ? Color.white : Color.black);

      return this;
    }
View Full Code Here
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
    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 };
View Full Code Here
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
    proj.getTargets().addSequence(t1);
    proj.getTargets().addSequence(t2);
    TargetHandler.expandTargets(pm.getProject().getTargets());
    pm.setProject(proj);
  
    TagLibrary lib = libraries1_10[0];

    Probe[] probes = performModeTest(TagLibrary.USE_ANY_TAG);

    assertEquals(lib.getSequenceAt(0),probes[0].getTagAt(0));
    assertEquals(lib.getSequenceAt(0),probes[1].getTagAt(0));
    assertEquals(lib.getSequenceAt(0),probes[2].getTagAt(0));
    assertEquals(lib.getSequenceAt(0),probes[3].getTagAt(0));
    assertEquals(lib.getSequenceAt(0),probes[4].getTagAt(0));

    probes = performModeTest(TagLibrary.USE_UNIQUE_TAG);

    assertEquals(lib.getSequenceAt(0),probes[0].getTagAt(0));
    assertEquals(lib.getSequenceAt(1),probes[1].getTagAt(0));
    assertEquals(lib.getSequenceAt(2),probes[2].getTagAt(0));
    assertEquals(lib.getSequenceAt(3),probes[3].getTagAt(0));
    assertEquals(lib.getSequenceAt(4),probes[4].getTagAt(0));
   
    probes = performModeTest(TagLibrary.USE_PER_GROUP);

    assertEquals(lib.getSequenceAt(0),probes[0].getTagAt(0));
    assertEquals(lib.getSequenceAt(0),probes[1].getTagAt(0));
    assertEquals(lib.getSequenceAt(1),probes[2].getTagAt(0));
    assertEquals(lib.getSequenceAt(1),probes[3].getTagAt(0));
    assertEquals(lib.getSequenceAt(1),probes[4].getTagAt(0));

    probes = performModeTest(TagLibrary.USE_SAME_TAG);

    assertEquals(lib.getSequenceAt(0),probes[0].getTagAt(0));
    assertEquals(lib.getSequenceAt(0),probes[1].getTagAt(0));
    assertEquals(lib.getSequenceAt(0),probes[2].getTagAt(0));
    assertEquals(lib.getSequenceAt(0),probes[3].getTagAt(0));
    assertEquals(lib.getSequenceAt(0),probes[4].getTagAt(0));
   
    probes = performModeTest(TagLibrary.USE_UNIQUE_IN_GROUP);

    assertEquals(lib.getSequenceAt(0),probes[0].getTagAt(0));
    assertEquals(lib.getSequenceAt(1),probes[1].getTagAt(0));
    assertEquals(lib.getSequenceAt(0),probes[2].getTagAt(0));
    assertEquals(lib.getSequenceAt(1),probes[3].getTagAt(0));
    assertEquals(lib.getSequenceAt(2),probes[4].getTagAt(0));   
  
  }
View Full Code Here
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
public class TagLibraryViewFactory
    implements HTMLRenderer {

  public String renderHTML(Object obj) {
    TagLibrary library;
    if (obj instanceof TagLibrary) {
      library = (TagLibrary) obj;
    }
    else {
      throw new IllegalArgumentException("Expected tag library, got " + //$NON-NLS-1$
                                         obj.getClass());
    }

    StringBuffer html = new StringBuffer();

    for (Iterator<NucleotideSequence> i = library.iterator(); i.hasNext(); ) {
      NucleotideSequence t = i.next();
      HTMLWriter.appendEnclosed(html,t.getID(),HTMLWriter.B);
      html.append("<br>\n"); //$NON-NLS-1$
      html.append("<tt>" + SequenceHTMLRenderer.getHardWrappedString(t.seqString(),60) + "</tt><br>\n"); //$NON-NLS-1$ //$NON-NLS-2$
    }
View Full Code Here
TOP

Related Classes of org.moltools.apps.probemaker.design.TagLibrary

  • org.moltools.apps.probemaker.ext.mod.DefaultTagOccurrenceModule
  • org.moltools.apps.probemaker.ext.ta.GreedyTagAllocator
  • org.moltools.apps.probemaker.ProbeMakerLauncher
  • org.moltools.apps.probemaker.project.ProjectIOTask
  • org.moltools.apps.probemaker.project.ProjectXMLIOTask
  • org.moltools.apps.probemaker.swingui.TagLibraryViewFactory
  • org.moltools.apps.probemaker.swingui.TagSetupPanel
  • org.moltools.apps.probemaker.swingui.TagSetupPanel$LibraryLabel
  • org.moltools.apps.probemaker.test.ProjectIOTest
  • org.moltools.apps.probemaker.test.TagAllocationTest
    • Copyright © 2018 www.massapicom. All rights reserved.
    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.