PherogramView renamed to PherogramViewPart to avoid name conflict with LibrAlign...

Adjustments to recent changes in LibrAlign on pherogram view components.

diff --git a/.gitattributes b/.gitattributes
index 52d0b6230dc9d1703b5fb68943c2edd563d9a6e8..f1d14482d52b1835be2066c0aab90e8dfee45dee 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -427,7 +427,7 @@ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecu
 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/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/PherogramView.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/molecular/ToggleInsertOverwriteButton.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ToggleLeftRightInsertionButton.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/TaxonNameEditor.java -text

diff --git a/eu.etaxonomy.taxeditor.editor/plugin.xml b/eu.etaxonomy.taxeditor.editor/plugin.xml
index 1fdf2b517425979d001b956dc22b96ef267e501e..acadd517e55414639bb3326ec9900d4d5152e435 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/plugin.xml
+++ b/eu.etaxonomy.taxeditor.editor/plugin.xml
@@ -153,7 +153,7 @@
          </view>
          <view
                allowMultiple="true"
-               class="eu.etaxonomy.taxeditor.editor.molecular.PherogramView"
+               class="eu.etaxonomy.taxeditor.editor.molecular.PherogramViewPart"
                id="eu.etaxonomy.taxeditor.editor.molecular.PherogramView"
                name="PherogramView"
                restorable="true">

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java
index 9812a2f7085c24d71443926de4afb023e41c2fa1..12424c22ceb5d803c212f172df793605b2261e0a 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java
@@ -115,7 +115,7 @@ public class AlignmentEditor extends EditorPart {
 
                // Just for testing:
                try {
-                       addRead(new File("D:/Users/BenStoever/Documents/Studium/Projekte/Promotion/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1").toURI());
+                       addRead(new File("D:/Users/BenStoever/Documents/Studium/Projekte/Promotion/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1").toURI());
                        addRead(new File("D:/Users/BenStoever/Documents/Studium/Projekte/Promotion/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1").toURI());
                }
                catch (Exception e) {

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramMouseListener.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramMouseListener.java
index 4f393db9e790d5107cfaaaf40930efe586d2cd31..2fce3dfb1dbeff2546da97dd5b5754291cb1c93b 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramMouseListener.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramMouseListener.java
@@ -39,7 +39,7 @@ public class PherogramMouseListener extends TICMouseAdapter {
        public void mousePressed(TICMouseEvent event) {\r
                if (event.getClickCount() == 2) {  // Double click\r
                        try {\r
-                               PherogramView.createView(uri);\r
+                               PherogramViewPart.createView(uri);\r
                        }\r
                        catch (Exception e) {\r
                                MessagingUtils.errorDialog("Error", this, e.getLocalizedMessage(), "eu.etaxonomy.taxeditor.editor", e, false);  //TODO set pluginID\r

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramView.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramViewPart.java
similarity index 57%
rename from eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramView.java
rename to eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramViewPart.java
index 0b4e166cccb88332ce6a01c0e4ad46f4cb11dbe8..485ed4c8710eb855e709d22ee6ecb080b9b4481c 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramView.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramViewPart.java
@@ -13,7 +13,8 @@ import java.io.IOException;
 import java.net.MalformedURLException;\r
 import java.net.URI;\r
 \r
-import info.bioinfweb.libralign.pherogram.PherogramTraceCurveView;\r
+import info.bioinfweb.libralign.pherogram.PherogramFormats.QualityOutputType;\r
+import info.bioinfweb.libralign.pherogram.view.PherogramView;\r
 \r
 import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;\r
 import org.eclipse.swt.SWT;\r
@@ -31,25 +32,30 @@ import org.eclipse.ui.part.ViewPart;
  * @author Ben Stöver\r
  * @date Nov 20, 2014\r
  */\r
-public class PherogramView extends ViewPart {\r
+public class PherogramViewPart extends ViewPart {\r
     public static final String ID = "eu.etaxonomy.taxeditor.editor.molecular.PherogramView";\r
 \r
     private URI uri = null;\r
-    private PherogramTraceCurveView pherogramView = null;\r
+    private PherogramView pherogramView = null;\r
        \r
        \r
-    public static PherogramView createView(URI uri) throws PartInitException, MalformedURLException, \r
+    public static PherogramViewPart createView(URI uri) throws PartInitException, MalformedURLException, \r
                UnsupportedChromatogramFormatException, IOException {\r
        \r
-       PherogramView view = (PherogramView)PlatformUI.getWorkbench().getActiveWorkbenchWindow().getActivePage().showView(ID);\r
+       PherogramViewPart view = (PherogramViewPart)PlatformUI.getWorkbench().getActiveWorkbenchWindow().getActivePage().showView(ID);\r
        view.setURI(uri);\r
        return view;\r
     }\r
     \r
     \r
-       public PherogramTraceCurveView getPherogramView() {\r
+       public PherogramView getPherogramView() {\r
                if (pherogramView == null) {\r
-                       pherogramView = new PherogramTraceCurveView();\r
+                       pherogramView = new PherogramView();\r
+                       pherogramView.getTraceCurveView().getFormats().setShowProbabilityValues(true);\r
+                       pherogramView.getTraceCurveView().setHorizontalScale(1);                        \r
+                       pherogramView.getTraceCurveView().setVerticalScale(100);\r
+                       pherogramView.getTraceCurveView().getFormats().setQualityOutputType(QualityOutputType.ALL);\r
+                       pherogramView.getTraceCurveView().getFormats().setShowProbabilityValues(true);\r
                }\r
                return pherogramView;\r
        }\r
@@ -62,7 +68,8 @@ public class PherogramView extends ViewPart {
 \r
        protected void setURI(URI uri) throws MalformedURLException, IOException, UnsupportedChromatogramFormatException {\r
                this.uri = uri;\r
-               getPherogramView().setProvider(AlignmentEditor.readPherogram(uri));\r
+               getPherogramView().getTraceCurveView().setProvider(AlignmentEditor.readPherogram(uri));\r
+               getPherogramView().assignSize();\r
        }\r
 \r
 \r