X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;fp=src%2Fjalview%2Fgui%2FJalview2XML.java;h=9a9c7b318b7e0456b095da884c3e81660fd7c5b1;hb=0b1c761dfaa8242f122cf868e8897a06ec6eb727;hp=fc96edcbcd908e6ca8f9ecd0a12c574ee5f45705;hpb=8b9c85b131fbaa1b9b29c489b661089c0ea404bd;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index fc96edc..9a9c7b3 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
@@ -71,7 +72,7 @@ import jalview.schemabinding.version2.Viewport;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
@@ -90,6 +91,7 @@ import jalview.ws.params.ArgumentI;
 import jalview.ws.params.AutoCalcSetting;
 import jalview.ws.params.WsParamSetI;
 
+import java.awt.Color;
 import java.awt.Rectangle;
 import java.io.BufferedReader;
 import java.io.DataInputStream;
@@ -1193,34 +1195,32 @@ public class Jalview2XML
                 .getFeatureRenderer().getRenderOrder()
                 .toArray(new String[0]);
 
-        Vector settingsAdded = new Vector();
-        Object gstyle = null;
-        GraduatedColor gcol = null;
+        Vector<String> settingsAdded = new Vector<String>();
         if (renderOrder != null)
         {
           for (int ro = 0; ro < renderOrder.length; ro++)
           {
-            gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+            FeatureColourI gstyle = ap.getSeqPanel().seqCanvas
+                    .getFeatureRenderer()
                     .getFeatureStyle(renderOrder[ro]);
             Setting setting = new Setting();
             setting.setType(renderOrder[ro]);
-            if (gstyle instanceof GraduatedColor)
+            if (!gstyle.isSimpleColour())
             {
-              gcol = (GraduatedColor) gstyle;
-              setting.setColour(gcol.getMaxColor().getRGB());
-              setting.setMincolour(gcol.getMinColor().getRGB());
-              setting.setMin(gcol.getMin());
-              setting.setMax(gcol.getMax());
-              setting.setColourByLabel(gcol.isColourByLabel());
-              setting.setAutoScale(gcol.isAutoScale());
-              setting.setThreshold(gcol.getThresh());
-              setting.setThreshstate(gcol.getThreshType());
+              setting.setColour(gstyle.getMaxColour().getRGB());
+              setting.setMincolour(gstyle.getMinColour().getRGB());
+              setting.setMin(gstyle.getMin());
+              setting.setMax(gstyle.getMax());
+              setting.setColourByLabel(gstyle.isColourByLabel());
+              setting.setAutoScale(gstyle.isAutoScaled());
+              setting.setThreshold(gstyle.getThreshold());
+              // -1 = No threshold, 0 = Below, 1 = Above
+              setting.setThreshstate(gstyle.isAboveThreshold() ? 1
+                      : (gstyle.isBelowThreshold() ? 0 : -1));
             }
             else
             {
-              setting.setColour(ap.getSeqPanel().seqCanvas
-                      .getFeatureRenderer().getColour(renderOrder[ro])
-                      .getRGB());
+              setting.setColour(gstyle.getColour().getRGB());
             }
 
             setting.setDisplay(av.getFeaturesDisplayed().isVisible(
@@ -1236,36 +1236,11 @@ public class Jalview2XML
           }
         }
 
-        // Make sure we save none displayed feature settings
-        Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
-                .getFeatureColours().keySet().iterator();
-        while (en.hasNext())
-        {
-          String key = en.next().toString();
-          if (settingsAdded.contains(key))
-          {
-            continue;
-          }
-
-          Setting setting = new Setting();
-          setting.setType(key);
-          setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
-                  .getColour(key).getRGB());
-
-          setting.setDisplay(false);
-          float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
-                  .getOrder(key);
-          if (rorder > -1)
-          {
-            setting.setOrder(rorder);
-          }
-          fs.addSetting(setting);
-          settingsAdded.addElement(key);
-        }
         // is groups actually supposed to be a map here ?
-        en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+        Iterator<String> en = ap.getSeqPanel().seqCanvas
+                .getFeatureRenderer()
                 .getFeatureGroups().iterator();
-        Vector groupsAdded = new Vector();
+        Vector<String> groupsAdded = new Vector<String>();
         while (en.hasNext())
         {
           String grp = en.next().toString();
@@ -1282,7 +1257,6 @@ public class Jalview2XML
           groupsAdded.addElement(grp);
         }
         jms.setFeatureSettings(fs);
-
       }
 
       if (av.hasHiddenColumns())
@@ -2178,6 +2152,7 @@ public class Jalview2XML
       {
         SwingUtilities.invokeAndWait(new Runnable()
         {
+          @Override
           public void run()
           {
             setLoadingFinishedForNewStructureViewers();
@@ -4352,25 +4327,33 @@ public class Jalview2XML
       af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
       String[] renderOrder = new String[jms.getFeatureSettings()
               .getSettingCount()];
-      Hashtable featureGroups = new Hashtable();
-      Hashtable featureColours = new Hashtable();
-      Hashtable featureOrder = new Hashtable();
+      Map<String, FeatureColourI> featureColours = new Hashtable<String, FeatureColourI>();
+      Map<String, Float> featureOrder = new Hashtable<String, Float>();
 
       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
       {
         Setting setting = jms.getFeatureSettings().getSetting(fs);
         if (setting.hasMincolour())
         {
-          GraduatedColor gc = setting.hasMin() ? new GraduatedColor(
-                  new java.awt.Color(setting.getMincolour()),
-                  new java.awt.Color(setting.getColour()),
-                  setting.getMin(), setting.getMax()) : new GraduatedColor(
-                  new java.awt.Color(setting.getMincolour()),
-                  new java.awt.Color(setting.getColour()), 0, 1);
+          FeatureColourI gc = setting.hasMin() ? new FeatureColour(
+                  new Color(setting.getMincolour()), new Color(
+                          setting.getColour()), setting.getMin(),
+                  setting.getMax()) : new FeatureColour(new Color(
+                  setting.getMincolour()), new Color(setting.getColour()),
+                  0, 1);
           if (setting.hasThreshold())
           {
-            gc.setThresh(setting.getThreshold());
-            gc.setThreshType(setting.getThreshstate());
+            gc.setThreshold(setting.getThreshold());
+            int threshstate = setting.getThreshstate();
+            // -1 = None, 0 = Below, 1 = Above threshold
+            if (threshstate == 0)
+            {
+              gc.setBelowThreshold(true);
+            }
+            else if (threshstate == 1)
+            {
+              gc.setAboveThreshold(true);
+            }
           }
           gc.setAutoScaled(true); // default
           if (setting.hasAutoScale())
@@ -4386,8 +4369,8 @@ public class Jalview2XML
         }
         else
         {
-          featureColours.put(setting.getType(),
-                  new java.awt.Color(setting.getColour()));
+          featureColours.put(setting.getType(), new FeatureColour(
+                  new Color(setting.getColour())));
         }
         renderOrder[fs] = setting.getType();
         if (setting.hasOrder())
@@ -4404,7 +4387,7 @@ public class Jalview2XML
           fdi.setVisible(setting.getType());
         }
       }
-      Hashtable fgtable = new Hashtable();
+      Map<String, Boolean> fgtable = new Hashtable<String, Boolean>();
       for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
       {
         Group grp = jms.getFeatureSettings().getGroup(gs);