Example object demonstrating pherogram and alignment data to be stored in CDM added.

diff --git a/.gitattributes b/.gitattributes
index 2c5d2340d4d380b39495a818d69388f19e8ee956..817258fa912600c6ab8eca801b9e28352361b032 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -420,6 +420,7 @@ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/po
 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/CMDAlignmentObjectPlaceholder.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/TaxonNameEditor.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroup.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroupedContainer.java -text

diff --git a/eu.etaxonomy.taxeditor.editor/.classpath b/eu.etaxonomy.taxeditor.editor/.classpath
index 1b2ee01870a0f3101361da87643d0fd792e18868..c633e345613f3cf7207b7e00166ef846a8430394 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/.classpath
+++ b/eu.etaxonomy.taxeditor.editor/.classpath
@@ -1,15 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>\r
 <classpath>\r
-       <classpathentry exported="true" kind="lib" path="lib/LibrAlign/"/>\r
-       <classpathentry exported="true" kind="lib" path="lib/bioinfweb.commons/"/>\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/biojava3-alignment-3.0.7.jar"/>\r
        <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>\r
        <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>\r
        <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/LibrAlign" sourcepath="lib/LibrAlign"/>\r
        <classpathentry kind="output" path="target/classes"/>\r
 </classpath>\r

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/CMDAlignmentObjectPlaceholder.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/CMDAlignmentObjectPlaceholder.java
new file mode 100644 (file)
index 0000000..589b1c2
--- /dev/null
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/CMDAlignmentObjectPlaceholder.java
@@ -0,0 +1,76 @@
+package eu.etaxonomy.taxeditor.editor.molecular;\r
+\r
+\r
+import info.bioinfweb.libralign.dataarea.implementations.pherogram.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 CMDAlignmentObjectPlaceholder {\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 Sequence<NucleotideCompound> editableSequence = null;  // Could also be of type String, if helpful for CDM architecture.\r
+               private List<ShiftChange> shiftChangeList = new ArrayList<ShiftChange>();\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
+       \r
+       private 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 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