Molecular plugin adjusted to recent changes in JPhyloIO.

diff --git a/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/CDMSequenceMatrixAdapter.java b/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/CDMSequenceMatrixAdapter.java
index cfe36a674977743e10bfa3535d7a229475631546..9cf44e70f35d0ef7ae73ba1c8534b4d076ac8099 100644 (file)
--- a/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/CDMSequenceMatrixAdapter.java
+++ b/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/CDMSequenceMatrixAdapter.java
@@ -13,10 +13,11 @@ package eu.etaxonomy.taxeditor.molecular.io;
 import info.bioinfweb.commons.bio.CharacterStateSetType;\r
 import info.bioinfweb.commons.text.StringUtils;\r
 import info.bioinfweb.jphyloio.ReadWriteConstants;\r
+import info.bioinfweb.jphyloio.ReadWriteParameterMap;\r
 import info.bioinfweb.jphyloio.dataadapters.JPhyloIOEventReceiver;\r
 import info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter;\r
 import info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter;\r
-import info.bioinfweb.jphyloio.dataadapters.implementations.NoSetsMatrixDataAdapter;\r
+import info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter;\r
 import info.bioinfweb.jphyloio.dataadapters.implementations.readtowriteadapter.StoreObjectListDataAdapter;\r
 import info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent;\r
 import info.bioinfweb.jphyloio.events.SequenceTokensEvent;\r
@@ -36,7 +37,7 @@ import eu.etaxonomy.cdm.model.molecular.Sequence;
  * @author Ben Stöver\r
  * @date 29.04.2016\r
  */\r
-public class CDMSequenceMatrixAdapter extends NoSetsMatrixDataAdapter implements ReadWriteConstants {\r
+public class CDMSequenceMatrixAdapter extends NoCharDefsNoSetsMatrixDataAdapter implements ReadWriteConstants {\r
     public static final String MATRIX_ID = DEFAULT_MATRIX_ID_PREFIX + "ContigAlignment";\r
     public static final String SINGLE_READ_SEQUENCE_ID_PREFIX = DEFAULT_SEQUENCE_ID_PREFIX + "SingleRead";\r
     public static final String CONSENSUS_SEQUENCE_ID= DEFAULT_SEQUENCE_ID_PREFIX + "Consensus";\r
@@ -90,38 +91,38 @@ public class CDMSequenceMatrixAdapter extends NoSetsMatrixDataAdapter implements
 \r
 \r
     @Override\r
-    public LinkedLabeledIDEvent getStartEvent() {\r
+    public LinkedLabeledIDEvent getStartEvent(ReadWriteParameterMap parameters) {\r
         return new LinkedLabeledIDEvent(EventContentType.ALIGNMENT, MATRIX_ID, "Contig alignment", null);\r
                 //TODO Use label according to derivate and markers.\r
     }\r
 \r
 \r
     @Override\r
-    public boolean containsLongTokens() {\r
+    public boolean containsLongTokens(ReadWriteParameterMap parameters) {\r
         return false;\r
     }\r
 \r
 \r
     @Override\r
-    public long getColumnCount() {\r
+    public long getColumnCount(ReadWriteParameterMap parameters) {\r
         return getCDMSequence().getSequenceString().length();  //TODO Consider that parts of single reads may lie outside of the current consensus sequence. Possibly return -1 in the future.\r
     }\r
 \r
 \r
     @Override\r
-    public long getSequenceCount() {\r
+    public long getSequenceCount(ReadWriteParameterMap parameters) {\r
         return /*sequence.getSingleReadAlignments().size() +*/ 1;\r
     }\r
 \r
 \r
     @Override\r
-    public Iterator<String> getSequenceIDIterator() {\r
+    public Iterator<String> getSequenceIDIterator(ReadWriteParameterMap parameters) {\r
         return new SequenceIDIterator(getCDMSequence().getSingleReadAlignments().size());\r
     }\r
 \r
 \r
     @Override\r
-    public long getSequenceLength(String sequenceID) throws IllegalArgumentException {\r
+    public long getSequenceLength(ReadWriteParameterMap parameters, String sequenceID) throws IllegalArgumentException {\r
         int singleReadIndex = extractSingleReadIndexFromID(sequenceID);\r
         if (singleReadIndex >= 0) {\r
             //TODO Determine single read length. (Current problem: Reads are not ordered in the set of the Sequence object.)\r
@@ -137,7 +138,7 @@ public class CDMSequenceMatrixAdapter extends NoSetsMatrixDataAdapter implements
 \r
 \r
     @Override\r
-    public LinkedLabeledIDEvent getSequenceStartEvent(String sequenceID) {\r
+    public LinkedLabeledIDEvent getSequenceStartEvent(ReadWriteParameterMap parameters, String sequenceID) {\r
         int singleReadIndex = extractSingleReadIndexFromID(sequenceID);\r
         if (singleReadIndex >= 0) {\r
             return new LinkedLabeledIDEvent(EventContentType.SEQUENCE, sequenceID, "singleRead" + singleReadIndex, null);\r
@@ -153,7 +154,7 @@ public class CDMSequenceMatrixAdapter extends NoSetsMatrixDataAdapter implements
 \r
 \r
     @Override\r
-    public void writeSequencePartContentData(JPhyloIOEventReceiver receiver, String sequenceID, long startColumn,\r
+    public void writeSequencePartContentData(ReadWriteParameterMap parameters, JPhyloIOEventReceiver receiver, String sequenceID, long startColumn,\r
             long endColumn) throws IOException, IllegalArgumentException {\r
 \r
         int singleReadIndex = extractSingleReadIndexFromID(sequenceID);\r
@@ -178,7 +179,7 @@ public class CDMSequenceMatrixAdapter extends NoSetsMatrixDataAdapter implements
      * @see info.bioinfweb.jphyloio.dataadapters.implementations.NoSetsMatrixDataAdapter#getTokenSets()\r
      */\r
     @Override\r
-    public ObjectListDataAdapter<TokenSetDefinitionEvent> getTokenSets() {\r
+    public ObjectListDataAdapter<TokenSetDefinitionEvent> getTokenSets(ReadWriteParameterMap parameters) {\r
         return tokenSetList;\r
     }\r
 }\r