Retain only Juicer Tools code; rebuild with Java straw; Code cleanup;…

… Remove all Juicebox and other redundant code
aidenlab · Dec 19, 2021 · a49bb8a · a49bb8a
1 parent 1bf3dfb
commit a49bb8a
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Showing 393 changed files with 1,356 additions and 88,491 deletions.
diff --git a/.idea/artifacts/Juicebox.xml b/.idea/artifacts/Juicebox.xml
diff --git a/.idea/artifacts/JuicerTools.xml b/.idea/artifacts/JuicerTools.xml
diff --git a/README.md b/README.md
@@ -39,7 +39,7 @@ The former turns on all warnings, the latter gives some flexibility since some p
 * Set the main class by clicking the little `...` button next to the text box for main class
 
         MainWindow.java is the main method class for the visualization/GUI portion of the software.
-        HiCTools.java is the main method class for the analysis/CLT portion.
+        juicebox.HiCTools.java is the main method class for the analysis/CLT portion.
 
 * For the GUI under VM Options:
 

diff --git a/build.xml b/build.xml
@@ -2,7 +2,7 @@
 <!--
   ~ The MIT License (MIT)
   ~
-  ~ Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine
+  ~ Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine
   ~
   ~ Permission is hereby granted, free of charge, to any person obtaining a copy
   ~ of this software and associated documentation files (the "Software"), to deal
@@ -16,7 +16,7 @@
   ~
   ~  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   ~  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-  ~  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+  ~  FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE
   ~  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
   ~  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
   ~  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
@@ -331,8 +331,8 @@
         <property name="artifact.temp.output.juicer_tools:jar" value="${artifacts.temp.dir}/juicer_tools_jar"/>
         <mkdir dir="${artifact.temp.output.juicer_tools:jar}"/>
         <jar destfile="${temp.jar.path.juicer_tools.jar}" duplicate="preserve"
-             manifest="${basedir}/src/resources/manifests/juicer_tools_jar/META-INF/MANIFEST.MF">
-            <zipfileset file="${basedir}/src/resources/manifests/juicer_tools_jar/META-INF/MANIFEST.MF"
+             manifest="/resources/MANIFEST.MF">
+            <zipfileset file="/resources/MANIFEST.MF"
                         prefix="META-INF"/>
             <zipfileset dir="${juicebox.output.dir}"/>
             <zipfileset src="${basedir}/lib/general/jsi1.1.jar" excludes="META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA"/>

diff --git a/lib/general/java-straw.1.8.1.jar b/lib/general/java-straw.1.8.1.jar
diff --git a/src/images/Folder-icon.png b/src/images/Folder-icon.png
diff --git a/src/images/assembly/small-ne-invert.png b/src/images/assembly/small-ne-invert.png
diff --git a/src/images/assembly/small-ne-paste.png b/src/images/assembly/small-ne-paste.png
diff --git a/src/images/assembly/small-nw-paste.png b/src/images/assembly/small-nw-paste.png
diff --git a/src/images/assembly/small-scissors.png b/src/images/assembly/small-scissors.png
diff --git a/src/images/assembly/small-se-paste.png b/src/images/assembly/small-se-paste.png
diff --git a/src/images/assembly/small-sw-invert.png b/src/images/assembly/small-sw-invert.png
diff --git a/src/images/assembly/small-sw-paste.png b/src/images/assembly/small-sw-paste.png
diff --git a/src/images/center.png b/src/images/center.png
diff --git a/src/images/close.png b/src/images/close.png
diff --git a/src/images/collapseall.gif b/src/images/collapseall.gif
diff --git a/src/images/crystal/fileclose.png b/src/images/crystal/fileclose.png
diff --git a/src/images/cursor-fist.png b/src/images/cursor-fist.png
diff --git a/src/images/cursor-openhand-arrow.png b/src/images/cursor-openhand-arrow.png
diff --git a/src/images/cursor-openhand-dot.png b/src/images/cursor-openhand-dot.png
diff --git a/src/images/cursor-openhand.png b/src/images/cursor-openhand.png
diff --git a/src/images/dragNdrop.png b/src/images/dragNdrop.png
diff --git a/src/images/dsliderbar.png b/src/images/dsliderbar.png
diff --git a/src/images/dsliderbottom.png b/src/images/dsliderbottom.png
diff --git a/src/images/dslidertop.png b/src/images/dslidertop.png
diff --git a/src/images/east.png b/src/images/east.png
diff --git a/src/images/expandall.gif b/src/images/expandall.gif
diff --git a/src/images/file-document.png b/src/images/file-document.png
diff --git a/src/images/genomespacelogo.png b/src/images/genomespacelogo.png
diff --git a/src/images/info.gif b/src/images/info.gif
diff --git a/src/images/info2.gif b/src/images/info2.gif
diff --git a/src/images/juicebox.png b/src/images/juicebox.png
diff --git a/src/images/juicebox256.png b/src/images/juicebox256.png
diff --git a/src/images/layer/color.png b/src/images/layer/color.png
diff --git a/src/images/layer/copy.png b/src/images/layer/copy.png
diff --git a/src/images/layer/down.png b/src/images/layer/down.png
diff --git a/src/images/layer/enlarge_clicked.png b/src/images/layer/enlarge_clicked.png
diff --git a/src/images/layer/enlarge_clicked_down.png b/src/images/layer/enlarge_clicked_down.png
diff --git a/src/images/layer/enlarge_clicked_up.png b/src/images/layer/enlarge_clicked_up.png
diff --git a/src/images/layer/erase.png b/src/images/layer/erase.png
diff --git a/src/images/layer/export_icon.png b/src/images/layer/export_icon.png
diff --git a/src/images/layer/export_icon_green.png b/src/images/layer/export_icon_green.png
diff --git a/src/images/layer/eye_clicked.png b/src/images/layer/eye_clicked.png
diff --git a/src/images/layer/eye_clicked_green.png b/src/images/layer/eye_clicked_green.png
diff --git a/src/images/layer/full_clicked.png b/src/images/layer/full_clicked.png
diff --git a/src/images/layer/hiclogo.png b/src/images/layer/hiclogo.png
diff --git a/src/images/layer/import_icon.png b/src/images/layer/import_icon.png
diff --git a/src/images/layer/import_icon_green.png b/src/images/layer/import_icon_green.png
diff --git a/src/images/layer/ll_clicked.png b/src/images/layer/ll_clicked.png
diff --git a/src/images/layer/pencil.png b/src/images/layer/pencil.png
diff --git a/src/images/layer/pencil_gray.png b/src/images/layer/pencil_gray.png
diff --git a/src/images/layer/sparse.png b/src/images/layer/sparse.png
diff --git a/src/images/layer/trans_clicked.png b/src/images/layer/trans_clicked.png
diff --git a/src/images/layer/trans_clicked_green.png b/src/images/layer/trans_clicked_green.png
diff --git a/src/images/layer/trash.png b/src/images/layer/trash.png
diff --git a/src/images/layer/undo.png b/src/images/layer/undo.png
diff --git a/src/images/layer/up.png b/src/images/layer/up.png
diff --git a/src/images/layer/ur_clicked.png b/src/images/layer/ur_clicked.png
diff --git a/src/images/left-arrow.gif b/src/images/left-arrow.gif
diff --git a/src/images/lock.png b/src/images/lock.png
diff --git a/src/images/lock_open.png b/src/images/lock_open.png
diff --git a/src/images/manifest.mf b/src/images/manifest.mf
diff --git a/src/images/no-tooltip.png b/src/images/no-tooltip.png
diff --git a/src/images/north.png b/src/images/north.png
diff --git a/src/images/regionTool.png b/src/images/regionTool.png
diff --git a/src/images/right-arrow.gif b/src/images/right-arrow.gif
diff --git a/src/images/roi_image.png b/src/images/roi_image.png
diff --git a/src/images/slider.png b/src/images/slider.png
diff --git a/src/images/south.png b/src/images/south.png
diff --git a/src/images/tooltip.png b/src/images/tooltip.png
diff --git a/src/images/west.png b/src/images/west.png
diff --git a/src/images/zoom-minus.png b/src/images/zoom-minus.png
diff --git a/src/images/zoom-plus.png b/src/images/zoom-plus.png
diff --git a/src/images/zoom.png b/src/images/zoom.png
diff --git a/src/images/zoomin.gif b/src/images/zoomin.gif
diff --git a/src/juicebox/CommandBroadcaster.java b/src/juicebox/CommandBroadcaster.java
diff --git a/src/juicebox/CommandExecutor.java b/src/juicebox/CommandExecutor.java