Bug fix: CDMSequenceMatrixAdapter now defines valid columns for its character set.

Draft for ExportSingleReadAlignmentWizard added.

diff --git a/.gitattributes b/.gitattributes
index b777e5c2d3624bc23e675dc42b58c032d616db92..177934b63a27ee3cd514cd06d3ab13d923d976ae 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -1989,8 +1989,9 @@ eu.etaxonomy.taxeditor.cdmlib/.classpath merge=ours
 eu.etaxonomy.taxeditor.cdmlib/build.properties merge=ours
 eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ExportSequenceToFileHandler.java -text
 eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/CDMSequenceMatrixAdapter.java -text
-eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/ExportSingleReadAlignmentWizardPage.java -text
 eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/SequenceIDIterator.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/ExportSingleReadAlignmentWizard.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/ExportSingleReadAlignmentWizardPage.java -text
 eu.etaxonomy.taxeditor.molecular/src/test/java/eu/etaxonomy/taxeditor/molecular/io/SequenceIDIteratorTest.java -text
 eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product merge=ours
 eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product.with.jre merge=ours

diff --git a/eu.etaxonomy.taxeditor.molecular/.gitignore b/eu.etaxonomy.taxeditor.molecular/.gitignore
index 29eb2f8cf13938350b6fb67ad0869eddce05a473..af75effc7a466ebd53bebd025e7ef9bd73b54454 100644 (file)
--- a/eu.etaxonomy.taxeditor.molecular/.gitignore
+++ b/eu.etaxonomy.taxeditor.molecular/.gitignore
@@ -48,3 +48,9 @@
 !src/test/.directory
 !src/test/hibernate.log
 !src/test/.settings
+!src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/.project
+!src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/integration-test.log
+!src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/target
+!src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/.directory
+!src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/hibernate.log
+!src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/.settings

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 9cf44e70f35d0ef7ae73ba1c8534b4d076ac8099..41175772f9233a6bb5ab3567e14d535dc0ebc8a5 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
@@ -19,6 +19,7 @@ import info.bioinfweb.jphyloio.dataadapters.MatrixDataAdapter;
 import info.bioinfweb.jphyloio.dataadapters.ObjectListDataAdapter;\r
 import info.bioinfweb.jphyloio.dataadapters.implementations.NoCharDefsNoSetsMatrixDataAdapter;\r
 import info.bioinfweb.jphyloio.dataadapters.implementations.readtowriteadapter.StoreObjectListDataAdapter;\r
+import info.bioinfweb.jphyloio.events.CharacterSetIntervalEvent;\r
 import info.bioinfweb.jphyloio.events.LinkedLabeledIDEvent;\r
 import info.bioinfweb.jphyloio.events.SequenceTokensEvent;\r
 import info.bioinfweb.jphyloio.events.TokenSetDefinitionEvent;\r
@@ -65,8 +66,9 @@ public class CDMSequenceMatrixAdapter extends NoCharDefsNoSetsMatrixDataAdapter
 \r
     private ObjectListDataAdapter<TokenSetDefinitionEvent> createTokenSetList() {\r
         StoreObjectListDataAdapter<TokenSetDefinitionEvent> result = new StoreObjectListDataAdapter<TokenSetDefinitionEvent>();\r
-        result.setObjectStartEvent(new TokenSetDefinitionEvent(CharacterStateSetType.DNA,\r
-                ReadWriteConstants.DEFAULT_TOKEN_SET_ID_PREFIX, null));\r
+        final String id = ReadWriteConstants.DEFAULT_TOKEN_SET_ID_PREFIX;\r
+        result.setObjectStartEvent(new TokenSetDefinitionEvent(CharacterStateSetType.DNA, id, null));\r
+        result.getObjectContent(id).add(new CharacterSetIntervalEvent(0, getColumnCount(null)));  //TODO Change this expression, if column count should return -1 in the future.\r
         return result;\r
     }\r
 \r
@@ -141,7 +143,7 @@ public class CDMSequenceMatrixAdapter extends NoCharDefsNoSetsMatrixDataAdapter
     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
+            return new LinkedLabeledIDEvent(EventContentType.SEQUENCE, sequenceID, "Single read " + singleReadIndex, null);\r
                     //TODO Use name displayed in derivate hierarchy or specified name as label instead?\r
         }\r
         else if (CONSENSUS_SEQUENCE_ID.equals(sequenceID)) {\r

diff --git a/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/ExportSingleReadAlignmentWizard.java b/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/ExportSingleReadAlignmentWizard.java
new file mode 100644 (file)
index 0000000..8f9c1c2
--- /dev/null
+++ b/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/ExportSingleReadAlignmentWizard.java
@@ -0,0 +1,39 @@
+// $Id$\r
+/**\r
+* Copyright (C) 2016 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.molecular.io.wizard;\r
+\r
+\r
+import org.eclipse.jface.wizard.Wizard;\r
+\r
+\r
+\r
+/**\r
+ * A wizard to export a single read alignment from <i>CDM</i> using <i>JPhyloIO</i>.\r
+ *\r
+ * @author Ben Stöver\r
+ * @date 23.06.2016\r
+ */\r
+public class ExportSingleReadAlignmentWizard extends Wizard {\r
+    public ExportSingleReadAlignmentWizard() {\r
+        setWindowTitle("Export single read alignment");  //TODO Use multi languange message\r
+    }\r
+\r
+\r
+    @Override\r
+    public void addPages() {\r
+        addPage(new ExportSingleReadAlignmentWizardPage());\r
+    }\r
+\r
+\r
+    @Override\r
+    public boolean performFinish() {\r
+        return true;  //TODO Check inputs\r
+    }\r
+}\r

diff --git a/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/ExportSingleReadAlignmentWizardPage.java b/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/ExportSingleReadAlignmentWizardPage.java
similarity index 96%
rename from eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/ExportSingleReadAlignmentWizardPage.java
rename to eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/ExportSingleReadAlignmentWizardPage.java
index ddc149a5f3a894a7a240164c19b69c08c9fb8ec8..cd7c35c4ac2162d7de03c237cfafeab36725e5fd 100644 (file)
--- a/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/ExportSingleReadAlignmentWizardPage.java
+++ b/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/wizard/ExportSingleReadAlignmentWizardPage.java
@@ -7,7 +7,7 @@
 * 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.molecular.io;\r
+package eu.etaxonomy.taxeditor.molecular.io.wizard;\r
 \r
 \r
 import org.eclipse.jface.wizard.WizardPage;\r