From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 29 Jul 2024 16:35:38 +0000 (+0100)
Subject: JAL-4443 patch out pasimap in GUI for JalviewJS and note some lines causing java2scri... 
X-Git-Tag: Release_2_11_4_0~18
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a44044c64799bb880c652ebad6ad98332c4b28f8;p=jalview.git

JAL-4443 patch out pasimap in GUI for JalviewJS and note some lines causing java2script issues
---

diff --git a/help/markdown/releases/release-2_11_4_0.md b/help/markdown/releases/release-2_11_4_0.md
index 43ad48a..0db5bd8 100644
--- a/help/markdown/releases/release-2_11_4_0.md
+++ b/help/markdown/releases/release-2_11_4_0.md
@@ -35,5 +35,5 @@ channel: "develop"
 - <!-- JAL-4358 --> 	Getdown splash screen should disappear as soon as the Jalview Desktop is created/visible
 
 ### New Known Issues
-
+- <!-- JAL-4443 -->     PaSiMap not available in JalviewJS
 
diff --git a/src/jalview/analysis/ccAnalysis.java b/src/jalview/analysis/ccAnalysis.java
index 4922a54..b8ed4e2 100755
--- a/src/jalview/analysis/ccAnalysis.java
+++ b/src/jalview/analysis/ccAnalysis.java
@@ -288,6 +288,7 @@ public class ccAnalysis
 
     int iterationCount = 0;
 
+    // FIXME JAL-4443 - spliterators could be coded out or patched with j2s annotation
     // repeat unitl values of h do not significantly change anymore
     while (true)
     {
diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index f8986b6..4d5823a 100644
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -28,6 +28,7 @@ import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
 import jalview.datamodel.SequenceGroup;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.viewmodel.AlignmentViewport;
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -261,12 +262,17 @@ public class CalculationChooser extends JPanel
     pasimapBorderless.setOpaque(false); // false -> stops every pixel inside
                                         // border from being painted
     pasimapBorderless.add(pasimap, FlowLayout.LEFT); // add pasimap button to
-                                                     // the JPanel
-    calcChoicePanel.add(pasimapBorderless, FlowLayout.LEFT); // add button with
-                                                             // border and
-                                                             // everything to
-                                                             // the overall
-                                                             // ChoicePanel
+    // the JPanel
+    if (!Platform.isJS())
+    {
+      // FIXME JAL-4443
+      calcChoicePanel.add(pasimapBorderless, FlowLayout.LEFT); // add button
+                                                               // with
+      // border and
+      // everything to
+      // the overall
+      // ChoicePanel
+    }
 
     treePanel.add(neighbourJoining);
     treePanel.add(averageDistance);
@@ -276,7 +282,10 @@ public class CalculationChooser extends JPanel
 
     ButtonGroup calcTypes = new ButtonGroup();
     calcTypes.add(pca);
-    calcTypes.add(pasimap);
+    if (!Platform.isJS()) {
+      // FIXME JAL-4443
+      calcTypes.add(pasimap);
+    }
     calcTypes.add(neighbourJoining);
     calcTypes.add(averageDistance);
     calcTypes.add(pairwise);