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Merge branch 'features/JAL-4034_improve_3dbeacons_button_and_ux' into develop
authorJim Procter <j.procter@dundee.ac.uk>
Mon, 8 Aug 2022 13:47:31 +0000 (14:47 +0100)
committerJim Procter <j.procter@dundee.ac.uk>
Mon, 8 Aug 2022 13:47:31 +0000 (14:47 +0100)
RELEASE patch | blob | history
build.gradle patch | blob | history
doc/building.md patch | blob | history
help/markdown/releases/release-2_11_2_3.md patch | blob | history
help/markdown/releases/release-2_11_2_4.md [new file with mode: 0644] patch | blob
help/templates/whatsNew.html patch | blob | history
src/jalview/gui/RotatableCanvas.java patch | blob | history

diff --git a/RELEASE b/RELEASE
index 557e9d9..c63eaef 100644 (file)
--- a/RELEASE
+++ b/RELEASE
@@ -1,2 +1,2 @@
 jalview.release=releases/Release_2_11_2_Branch
-jalview.version=2.11.2.3
+jalview.version=2.11.2.4
diff --git a/build.gradle b/build.gradle
index 4f9798c..a62e85a 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -1561,6 +1561,7 @@ task releasesTemplates {
       whatsnewHtml = whatsnewTemplateFile.text.replaceAll("__WHATS_NEW__", whatsnewHtml)
       whatsnewHtmlFile.text = hugoTemplateSubstitutions(whatsnewHtml,
         [
+            VERSION: JALVIEW_VERSION,
           DISPLAY_DATE: wnDisplayDate
         ]
       )
diff --git a/doc/building.md b/doc/building.md
index 8e21d57..34d5d67 100644 (file)
--- a/doc/building.md
+++ b/doc/building.md
@@ -6,7 +6,7 @@
 # download
 git clone http://source.jalview.org/git/jalview.git
 # compile
-cd jalview
+cd ./jalview
 gradle shadowJar
 # run
 java -jar build/libs/jalview-all-*-j11.jar
@@ -14,7 +14,7 @@ java -jar build/libs/jalview-all-*-j11.jar
 # and/or create launcher
 gradle getdown
 # use launcher
-cd getdown/files
+cd ./build/getdown/files/11
 java -jar getdown-launcher.jar . jalview
 ```
 
diff --git a/help/markdown/releases/release-2_11_2_3.md b/help/markdown/releases/release-2_11_2_3.md
index f78868f..e229cb0 100644 (file)
--- a/help/markdown/releases/release-2_11_2_3.md
+++ b/help/markdown/releases/release-2_11_2_3.md
@@ -1,6 +1,6 @@
 ---
 version: 2.11.2.3
-date: 2022-07-05
+date: 2022-07-06
 channel: "release"
 ---
 
diff --git a/help/markdown/releases/release-2_11_2_4.md b/help/markdown/releases/release-2_11_2_4.md
new file mode 100644 (file)
index 0000000..4f1e8d7
--- /dev/null
+++ b/help/markdown/releases/release-2_11_2_4.md
@@ -0,0 +1,15 @@
+---
+version: 2.11.2.4
+date: 2022-08-04
+channel: "release"
+---
+
+## New Features
+
+- <!-- JAL-4036 --> Migrated Uniprot Free Text Search to latest Uniprot search API
+
+
+
+## Issues Resolved
+
+- <!-- JAL-4045 --> buggy PCA plot axes rendering can make them appear to be non-orthogonal
diff --git a/help/templates/whatsNew.html b/help/templates/whatsNew.html
index 52df728..70deea4 100755 (executable)
--- a/help/templates/whatsNew.html
+++ b/help/templates/whatsNew.html
@@ -24,12 +24,11 @@
 </head>
 <body>
   <p>
-    <strong>Welcome to Jalview Version $$Version-Rel$$ !!</strong><br/>
+    <strong>Welcome to Jalview Version __VERSION__ (released __DISPLAY_DATE__)!!</strong><br/>
   </p>
-  <p><em>__DISPLAY_DATE__</em></p>
 __WHATS_NEW__
   <p>
-    This release series provides support for two popular 3D
+    The 2.11.2 release series provides support for two popular 3D
     structure visualisation tools, new features for discovery of 3D
     structures, improved platform integration and a new command line
     tool allowing Jalview to be more easily called from scripts.</p>
@@ -79,7 +78,7 @@ __WHATS_NEW__
 
   <p>
       For the full details, see <a
-        href="releases.html#Jalview.2.11.2.1">the Jalview 2.11.2.1
+        href="releases.html#Jalview.2.11.2">the Jalview 2.11.2 series
         release notes</a>.
     </p>
   <p>
diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index d695ebb..ef0b2aa 100755 (executable)
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -20,17 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.api.RotatableCanvasI;
-import jalview.datamodel.Point;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.SequencePoint;
-import jalview.math.RotatableMatrix;
-import jalview.math.RotatableMatrix.Axis;
-import jalview.util.ColorUtils;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Font;
@@ -53,6 +42,17 @@ import java.util.List;
 import javax.swing.JPanel;
 import javax.swing.ToolTipManager;
 
+import jalview.api.RotatableCanvasI;
+import jalview.datamodel.Point;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequencePoint;
+import jalview.math.RotatableMatrix;
+import jalview.math.RotatableMatrix.Axis;
+import jalview.util.ColorUtils;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
 /**
  * Models a Panel on which a set of points, and optionally x/y/z axes, can be
  * drawn, and rotated or zoomed with the mouse
@@ -322,16 +322,16 @@ public class RotatableCanvas extends JPanel
 
     int midX = getWidth() / 2;
     int midY = getHeight() / 2;
-    float maxWidth = Math.max(Math.abs(seqMax[0] - seqMin[0]),
-            Math.abs(seqMax[1] - seqMin[1]));
+    // float maxWidth = Math.max(Math.abs(seqMax[0] - seqMin[0]),
+    // Math.abs(seqMax[1] - seqMin[1]));
     int pix = Math.min(getWidth(), getHeight());
-    float scaleBy = pix * getScaleFactor() / (2f * maxWidth);
+    float scaleBy = pix * getScaleFactor() / (2f);
 
     for (int i = 0; i < DIMS; i++)
     {
       g.drawLine(midX, midY,
-              midX + (int) (getAxisEndPoints()[i].x * scaleBy * seqMax[0]),
-              midY + (int) (getAxisEndPoints()[i].y * scaleBy * seqMax[1]));
+              midX + (int) (getAxisEndPoints()[i].x * scaleBy * 0.25),
+              midY + (int) (getAxisEndPoints()[i].y * scaleBy * 0.25));
     }
   }