X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=3eccdf00a8112419890a1b22dab9b94c6cfaa3bd;hb=fbd682c00e543eadb48074ac354ade57c04c20cb;hp=ebd4712a0bf0fac062105cd1308d73d13a49d16c;hpb=952d6b6fecfb976c0c113f013ed2b8980af3d190;p=jalview.git

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index ebd4712..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;
@@ -411,7 +414,7 @@ public class FeatureSettings extends JPanel
     {
       frame = new JInternalFrame();
       frame.setContentPane(this);
-      frame.setFrameIcon(WindowIcons.featuresIcon);
+      frame.setFrameIcon(null);
       Rectangle bounds = af.getFeatureSettingsGeometry();
       String title;
       if (af.getAlignPanels().size() > 1 || Desktop.getAlignmentPanels(
@@ -951,11 +954,69 @@ public class FeatureSettings extends JPanel
     chooser.setResponseHandler(0, () -> {
       File file = chooser.getSelectedFile();
       load(file);
-      return null;
     });
     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
    * 
@@ -963,50 +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
        */
@@ -1020,7 +1052,8 @@ public class FeatureSettings extends JPanel
       }
     } catch (Exception ex)
     {
-      System.out.println("Error loading User Colour File\n" + ex);
+      jalview.bin.Console
+              .outPrintln("Error loading User Colour File\n" + ex);
     }
   }
 
@@ -1609,7 +1642,7 @@ public class FeatureSettings extends JPanel
     {
       Color newColor = gcol.getMaxColour();
       comp.setBackground(newColor);
-      // System.err.println("Width is " + w / 2);
+      // jalview.bin.Console.errPrintln("Width is " + w / 2);
       Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
       comp.setIcon(ficon);
       // tt+="RGB value: Max (" + newColor.getRed() + ", "
@@ -1788,11 +1821,15 @@ public class FeatureSettings extends JPanel
     {
       FeatureMatcherSetI theFilter = (FeatureMatcherSetI) filter;
       setOpaque(true);
-      String asText = theFilter.toString();
       setBackground(tbl.getBackground());
-      this.setText(asText);
       this.setIcon(null);
 
+      if (theFilter != null)
+      {
+        String asText = theFilter.toString();
+        this.setText(asText);
+      }
+
       if (isSelected)
       {
         if (selectedBorder == null)
@@ -2116,7 +2153,6 @@ public class FeatureSettings extends JPanel
     refreshDisplay();
   }
 }
-
 class FeatureIcon implements Icon
 {
   FeatureColourI gcol;