(The additional project https://secure.bioinfweb.info/Code/svn/LibrAlign / trunk / main / info.bioinfweb.libralign.biojava1 needs to be in the workspace from now on.)
eu.etaxonomy.taxeditor.editor/icons/pherogram-insert-right-16x16.png -text
eu.etaxonomy.taxeditor.editor/icons/pherogram-insert-right-disabled-16x16.png -text
eu.etaxonomy.taxeditor.editor/icons/xper64.png -text
-eu.etaxonomy.taxeditor.editor/lib/biojava3-alignment-3.0.7.jar -text
-eu.etaxonomy.taxeditor.editor/lib/biojava3-core-3.0.7.jar -text
eu.etaxonomy.taxeditor.editor/lib/commons-lang3-3.1.jar -text
eu.etaxonomy.taxeditor.editor/lib/core-1.8.5.jar -text
eu.etaxonomy.taxeditor.editor/lib/sequencing-1.8.5.jar -text
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/RefreshNodeNumberingOperation.java -text
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java -text
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditorInput.java -text
-eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/CDMAlignmentObjectPlaceholder.java -text
-eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ContigSequenceDataProvider.java -text
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramMouseListener.java -text
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramViewPart.java -text
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/TaxonNameEditor.java -text
<classpathentry including="**/*.java" kind="src" path="src/main/java"/>\r
<classpathentry including="**/*.java" kind="src" path="src/test/java"/>\r
<classpathentry excluding="**/*.java" kind="src" path="src/main/resources"/>\r
- <classpathentry exported="true" kind="lib" path="lib/biojava3-alignment-3.0.7.jar"/>\r
- <classpathentry exported="true" kind="lib" path="lib/biojava3-core-3.0.7.jar"/>\r
<classpathentry exported="true" kind="lib" path="lib/core-1.8.5.jar"/>\r
<classpathentry exported="true" kind="lib" path="lib/sequencing-1.8.5.jar"/>\r
<classpathentry exported="true" kind="lib" path="lib/bioinfweb.commons"/>\r
<classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.libralign.swt"/>\r
<classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.tic.core"/>\r
<classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.tic.swt"/>\r
+ <classpathentry exported="true" kind="lib" path="lib/info.bioinfweb.libralign.biojava1"/>\r
<classpathentry kind="output" path="target/classes"/>\r
</classpath>\r
<type>2</type>\r
<locationURI>WORKSPACE_LOC/_Lib/bin</locationURI>\r
</link>\r
+ <link>\r
+ <name>lib/info.bioinfweb.libralign.biojava1</name>\r
+ <type>2</type>\r
+ <locationURI>WORKSPACE_LOC/info.bioinfweb.libralign.biojava1/bin</locationURI>\r
+ </link>\r
<link>\r
<name>lib/info.bioinfweb.libralign.core</name>\r
<type>2</type>\r
pdebuild.jar,
compatibility.jar,
junit.jar,
- lib/biojava3-alignment-3.0.7.jar,
- lib/biojava3-core-3.0.7.jar,
lib/core-1.8.5.jar,
lib/sequencing-1.8.5.jar,
lib/bioinfweb.commons/,
lib/info.bioinfweb.libralign.core/,
lib/info.bioinfweb.libralign.swt/,
lib/info.bioinfweb.tic.core/,
- lib/info.bioinfweb.tic.swt/
+ lib/info.bioinfweb.tic.swt/,
+ lib/info.bioinfweb.libralign.biojava1/
p2.inf,\
OSGI-INF/l10n/plugin.properties,\
OSGI-INF/l10n/plugin_de.properties,\
- lib/biojava3-alignment-3.0.7.jar,\
- lib/biojava3-core-3.0.7.jar,\
lib/core-1.8.5.jar,\
lib/sequencing-1.8.5.jar,\
lib/bioinfweb.commons/,\
lib/info.bioinfweb.libralign.core/,\
lib/info.bioinfweb.libralign.swt/,\
lib/info.bioinfweb.tic.core/,\
- lib/info.bioinfweb.tic.swt/
+ lib/info.bioinfweb.tic.swt/,\
+ lib/info.bioinfweb.libralign.biojava1/
package eu.etaxonomy.taxeditor.editor.molecular;
-import info.bioinfweb.jphyloio.events.TokenSetType;
import info.bioinfweb.libralign.alignmentarea.AlignmentArea;
import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel;
import info.bioinfweb.libralign.alignmentarea.tokenpainter.NucleotideTokenPainter;
import info.bioinfweb.libralign.model.events.SequenceRenamedEvent;
import info.bioinfweb.libralign.model.events.TokenChangeEvent;
import info.bioinfweb.libralign.model.implementations.PackedAlignmentModel;
-import info.bioinfweb.libralign.model.tokenset.BioJavaTokenSet;
+import info.bioinfweb.libralign.model.tokenset.CharacterTokenSet;
import info.bioinfweb.libralign.model.tokenset.TokenSet;
import info.bioinfweb.libralign.multiplealignments.AlignmentAreaList;
import info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer;
import org.biojava.bio.chromatogram.ChromatogramFactory;
import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;
-import org.biojava3.core.sequence.compound.DNACompoundSet;
-import org.biojava3.core.sequence.compound.NucleotideCompound;
import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.swt.SWT;
import org.eclipse.swt.widgets.Composite;
AlignmentArea result = new AlignmentArea(container);
result.setAllowVerticalScrolling(allowVerticalScrolling);
- TokenSet<NucleotideCompound> tokenSet = new BioJavaTokenSet<NucleotideCompound>(
- TokenSetType.DNA, new DNACompoundSet(), true); //TODO Should NUCLEOTIDE be used instead?
- AlignmentModel<NucleotideCompound> provider = new PackedAlignmentModel<NucleotideCompound>(tokenSet);
+ CharacterTokenSet tokenSet = CharacterTokenSet.newDNAInstance(); //TODO Should NUCLEOTIDE be used instead?
+ AlignmentModel<Character> provider = new PackedAlignmentModel<Character>(tokenSet);
result.setAlignmentModel(provider, false);
provider.getChangeListeners().add(DIRTY_LISTENER);
result.getPaintSettings().getTokenPainterList().set(0, new NucleotideTokenPainter());
AlignmentModel consensusModel = getEditableConsensusArea().getAlignmentModel();
int id = consensusModel.addSequence(CONSENSUS_NAME);
Collection<Object> tokens = new ArrayList<Object>(); // First save tokens in a collection to avoid GUI updated for each token.
- tokens.add(consensusModel.getTokenSet().tokenByKeyChar('A'));
- tokens.add(consensusModel.getTokenSet().tokenByKeyChar('C'));
- tokens.add(consensusModel.getTokenSet().tokenByKeyChar('G'));
- tokens.add(consensusModel.getTokenSet().tokenByKeyChar('T'));
+ tokens.add(consensusModel.getTokenSet().tokenByRepresentation("A"));
+ tokens.add(consensusModel.getTokenSet().tokenByRepresentation("C"));
+ tokens.add(consensusModel.getTokenSet().tokenByRepresentation("G"));
+ tokens.add(consensusModel.getTokenSet().tokenByRepresentation("T"));
consensusModel.insertTokensAt(id, 0, tokens);
}
catch (Exception e) {
public void addRead(URI pherogramURI, boolean reverseComplemented) throws IOException, UnsupportedChromatogramFormatException {
- addRead(newReadName(), pherogramURI, reverseComplemented, null, 0, 0, 0, null); // Position values will be ignored, if shifts == null.
+ addRead(newReadName(), pherogramURI, reverseComplemented, null, null, null, null, null);
}
else if (pherogramProvider != null) { // Copy base call sequence into alignment:
tokens = new ArrayList<Object>();
for (int i = 0; i < pherogramProvider.getSequenceLength(); i++) {
- tokens.add(provider.getTokenSet().tokenByKeyChar(
- pherogramProvider.getBaseCall(i).getUpperedBase().charAt(0)));
+ tokens.add(provider.getTokenSet().tokenByRepresentation(
+ Character.toString(pherogramProvider.getBaseCall(i))));
}
setDirty();
}
+++ /dev/null
-package eu.etaxonomy.taxeditor.editor.molecular;\r
-\r
-\r
-import info.bioinfweb.libralign.pherogram.model.ShiftChange;\r
-\r
-import java.util.ArrayList;\r
-import java.util.List;\r
-import java.util.Map;\r
-import java.util.TreeMap;\r
-\r
-import org.biojava3.core.sequence.compound.NucleotideCompound;\r
-import org.biojava3.core.sequence.template.Sequence;\r
-\r
-\r
-\r
-/**\r
- * This class is used as a replacement for a class representing the CMD objects storing an contig alignment during early\r
- * development phase.\r
- *\r
- * @author Ben Stöver\r
- * @date 06.08.2014\r
- */\r
-public class CDMAlignmentObjectPlaceholder {\r
- /**\r
- * Represents information in the contig alignment describing a single read sequence and the relation to its associated\r
- * pherogram.\r
- *\r
- * @author Ben Stöver\r
- * @date 06.08.2014\r
- */\r
- public static class Read {\r
- private long pherogramObjectID = Long.MIN_VALUE; // The ID used in the CMD to identify the object storing the pherogram URL. (Dont' know if this is long, just as an example-)\r
- private final Sequence<NucleotideCompound> editableSequence = null; // Could also be of type String, if helpful for CDM architecture.\r
- private final List<ShiftChange> shiftChangeList = new ArrayList<ShiftChange>();\r
- private String readName = "";\r
- private boolean reverseComplemeted = false;\r
-\r
-\r
- public Read(long pherogramObjectID) {\r
- super();\r
- this.pherogramObjectID = pherogramObjectID;\r
- }\r
-\r
-\r
- public long getPherogramObjectID() {\r
- return pherogramObjectID;\r
- }\r
-\r
-\r
- public void setPherogramObjectID(long pherogramObjectID) {\r
- this.pherogramObjectID = pherogramObjectID;\r
- }\r
-\r
-\r
- public List<ShiftChange> getShiftChangeList() {\r
- return shiftChangeList;\r
- }\r
-\r
-\r
- public Sequence<NucleotideCompound> getEditableSequence() {\r
- return editableSequence;\r
- }\r
-\r
-\r
- public String getReadName() {\r
- return readName;\r
- }\r
-\r
-\r
- public void setReadName(String readName) {\r
- this.readName = readName;\r
- }\r
-\r
-\r
- public boolean isReverseComplemeted() {\r
- return reverseComplemeted;\r
- }\r
-\r
-\r
- public void setReverseComplemeted(boolean reverseComplemeted) {\r
- this.reverseComplemeted = reverseComplemeted;\r
- }\r
- }\r
-\r
-\r
- private final Map<String, Sequence<NucleotideCompound>> consensusSequences = new TreeMap<String, Sequence<NucleotideCompound>>(); // Could also be of type Map<String, String>, if helpful for CDM architecture.\r
- private final Map<Long, Read> readSequences = new TreeMap<Long, Read>();\r
-\r
-\r
- public Map<String, Sequence<NucleotideCompound>> getConsensusSequences() {\r
- return consensusSequences;\r
- }\r
-\r
-\r
- public Map<Long, Read> getReadSequences() {\r
- return readSequences;\r
- }\r
-}\r
+++ /dev/null
-// $Id$\r
-/**\r
-* Copyright (C) 2014 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.taxeditor.editor.molecular;\r
-\r
-\r
-import org.biojava3.core.sequence.compound.NucleotideCompound;\r
-\r
-import info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityDNACompoundSet;\r
-import info.bioinfweb.jphyloio.events.TokenSetType;\r
-import info.bioinfweb.libralign.model.AlignmentModel;\r
-import info.bioinfweb.libralign.model.implementations.PackedAlignmentModel;\r
-import info.bioinfweb.libralign.model.tokenset.BioJavaTokenSet;\r
-\r
-\r
-\r
-/**\r
- * The LibrAlign sequence data provider used to edit contig alignments with the {@link AlignmentEditor}.\r
- * \r
- * @author Ben Stöver\r
- * @date 04.08.2014\r
- */\r
-public class ContigSequenceDataProvider extends PackedAlignmentModel<NucleotideCompound> \r
- implements AlignmentModel<NucleotideCompound> {\r
-\r
- \r
- public ContigSequenceDataProvider() {\r
- super(new BioJavaTokenSet<NucleotideCompound>(TokenSetType.NUCLEOTIDE, \r
- AlignmentAmbiguityDNACompoundSet.getAlignmentAmbiguityDNACompoundSet(), true));\r
- }\r
- \r
- \r
- public void saveToCMD() { //TODO Add cmd node as parameter \r
- //TODO impl.\r
- }\r
- \r
- \r
- public void loadFromCMD() { //TODO Add cmd node as parameter\r
- //TODO impl.\r
- }\r
-}\r
BGBM BDI Projects / taxeditor.git / commitdiff