From fbd682c00e543eadb48074ac354ade57c04c20cb Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Mon, 30 Oct 2023 11:24:07 +0000
Subject: [PATCH] JAL-4315 allow feature settings to be loaded from a file or
 input stream without the dialog being open

---
 src/jalview/gui/FeatureSettings.java |  121 +++++++++++++++++++++-------------
 1 file changed, 77 insertions(+), 44 deletions(-)

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 4d31805..3eccdf0 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -45,6 +45,7 @@ import java.io.FileOutputStream;
 import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
+import java.io.Reader;
 import java.util.Arrays;
 import java.util.Comparator;
 import java.util.HashMap;
@@ -103,6 +104,8 @@ import jalview.datamodel.features.FeatureMatcherSet;
 import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.gui.Help.HelpId;
 import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.schemes.FeatureColour;
@@ -955,6 +958,65 @@ public class FeatureSettings extends JPanel
     chooser.showOpenDialog(this);
   }
 
+  public static boolean loadFeatureSettingsFile(FeatureRenderer fr,
+          File file) throws Exception
+  {
+    InputStreamReader in = new InputStreamReader(new FileInputStream(file),
+            "UTF-8");
+    return loadFeatureSettingsFile(fr, in);
+  }
+
+  public static void loadFeatureSettingsFile(
+          FeatureRenderer featureRenderer, Object fileObject,
+          DataSourceType sourceType) throws Exception
+  {
+    FileParse fp = new FileParse(fileObject, sourceType);
+    loadFeatureSettingsFile(featureRenderer, fp.getReader());
+  }
+
+  private static boolean loadFeatureSettingsFile(FeatureRenderer fr,
+          Reader in) throws Exception
+  {
+    JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.jalview");
+    javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+    XMLStreamReader streamReader = XMLInputFactory.newInstance()
+            .createXMLStreamReader(in);
+    JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader,
+            JalviewUserColours.class);
+    JalviewUserColours jucs = jbe.getValue();
+
+    // JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
+
+    /*
+     * load feature colours
+     */
+    for (int i = jucs.getColour().size() - 1; i >= 0; i--)
+    {
+      Colour newcol = jucs.getColour().get(i);
+      FeatureColourI colour = jalview.project.Jalview2XML
+              .parseColour(newcol);
+      fr.setColour(newcol.getName(), colour);
+      fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size());
+    }
+
+    /*
+     * load feature filters; loaded filters will replace any that are
+     * currently defined, other defined filters are left unchanged 
+     */
+    for (int i = 0; i < jucs.getFilter().size(); i++)
+    {
+      Filter filterModel = jucs.getFilter().get(i);
+      String featureType = filterModel.getFeatureType();
+      FeatureMatcherSetI filter = jalview.project.Jalview2XML
+              .parseFilter(featureType, filterModel.getMatcherSet());
+      if (!filter.isEmpty())
+      {
+        fr.setFeatureFilter(featureType, filter);
+      }
+    }
+    return true;
+  }
+
   /**
    * Loads feature colours and filters from XML stored in the given file
    * 
@@ -962,50 +1024,21 @@ public class FeatureSettings extends JPanel
    */
   void load(File file)
   {
+    load(file, DataSourceType.FILE);
+  }
+
+  /**
+   * Loads feature colours and filters from XML at a specified source
+   * 
+   * @param file
+   *          - string or file or other object that allows FileParse to be
+   *          created
+   */
+  void load(Object file, DataSourceType sourceType)
+  {
     try
     {
-      InputStreamReader in = new InputStreamReader(
-              new FileInputStream(file), "UTF-8");
-
-      JAXBContext jc = JAXBContext
-              .newInstance("jalview.xml.binding.jalview");
-      javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
-      XMLStreamReader streamReader = XMLInputFactory.newInstance()
-              .createXMLStreamReader(in);
-      JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader,
-              JalviewUserColours.class);
-      JalviewUserColours jucs = jbe.getValue();
-
-      // JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
-
-      /*
-       * load feature colours
-       */
-      for (int i = jucs.getColour().size() - 1; i >= 0; i--)
-      {
-        Colour newcol = jucs.getColour().get(i);
-        FeatureColourI colour = jalview.project.Jalview2XML
-                .parseColour(newcol);
-        fr.setColour(newcol.getName(), colour);
-        fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size());
-      }
-
-      /*
-       * load feature filters; loaded filters will replace any that are
-       * currently defined, other defined filters are left unchanged 
-       */
-      for (int i = 0; i < jucs.getFilter().size(); i++)
-      {
-        Filter filterModel = jucs.getFilter().get(i);
-        String featureType = filterModel.getFeatureType();
-        FeatureMatcherSetI filter = jalview.project.Jalview2XML
-                .parseFilter(featureType, filterModel.getMatcherSet());
-        if (!filter.isEmpty())
-        {
-          fr.setFeatureFilter(featureType, filter);
-        }
-      }
-
+      loadFeatureSettingsFile(fr, file, sourceType);
       /*
        * update feature settings table
        */
@@ -1019,7 +1052,8 @@ public class FeatureSettings extends JPanel
       }
     } catch (Exception ex)
     {
-      jalview.bin.Console.outPrintln("Error loading User Colour File\n" + ex);
+      jalview.bin.Console
+              .outPrintln("Error loading User Colour File\n" + ex);
     }
   }
 
@@ -2119,7 +2153,6 @@ public class FeatureSettings extends JPanel
     refreshDisplay();
   }
 }
-
 class FeatureIcon implements Icon
 {
   FeatureColourI gcol;
-- 
1.7.10.2