X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=965770ce5a7bbc4f7a57821d2f365b94ca089951;hb=0ebbad305e982eeda562a1842362dc415c36cc8d;hp=e89c1c2998ecdf210b8f03b7490b5c997b9663c5;hpb=3da878124135ff033f42d19d8733891b09e953cd;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index e89c1c2..965770c 100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -20,15 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.GraphLine;
-import jalview.datamodel.SequenceGroup;
-import jalview.gui.JalviewColourChooser.ColourChooserListener;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -48,13 +39,20 @@ import javax.swing.JInternalFrame;
 import javax.swing.JLayeredPane;
 import javax.swing.JPanel;
 
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceGroup;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
 import net.miginfocom.swing.MigLayout;
 
 @SuppressWarnings("serial")
 public class AnnotationColourChooser extends AnnotationRowFilter
 {
-  private static final int ONETHOUSAND = 1000;
-
   private ColourSchemeI oldcs;
 
   private JButton defColours;
@@ -75,6 +73,12 @@ public class AnnotationColourChooser extends AnnotationRowFilter
 
   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
   {
+    this(av, ap, null);
+  }
+
+  public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap,
+          AnnotationColourGradient initSettings)
+  {
     super(av, ap);
     oldcs = av.getGlobalColourScheme();
     if (av.getAlignment().getGroups() != null)
@@ -89,6 +93,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       }
     }
     frame = new JInternalFrame();
+    frame.setFrameIcon(null);
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     Desktop.addInternalFrame(frame,
@@ -107,9 +112,29 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     setDefaultMinMax();
 
     adjusting = true;
-    if (oldcs instanceof AnnotationColourGradient)
+    if (oldcs instanceof AnnotationColourGradient && initSettings == null)
+    {
+      // init from oldcs
+      initialiseFrom((AnnotationColourGradient) oldcs);
+    }
+    else
+    {
+      // use initial colour gradient - if any..
+      initialiseFrom(initSettings);
+    }
+
+    jbInit();
+    adjusting = false;
+
+    updateView();
+    frame.invalidate();
+    frame.pack();
+  }
+
+  private void initialiseFrom(AnnotationColourGradient acg)
+  {
+    if (acg != null)
     {
-      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
       useOriginalColours.setSelected(
               acg.isPredefinedColours() || acg.getBaseColour() != null);
       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
@@ -126,10 +151,15 @@ public class AnnotationColourChooser extends AnnotationRowFilter
 
     populateThresholdComboBox(threshold);
 
-    if (oldcs instanceof AnnotationColourGradient)
+    if (acg != null)
     {
-      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
       String label = getAnnotationMenuLabel(acg.getAnnotation());
+      // TODO: workaround below shouldn't be necessary - there's a bug in
+      // getAnnotationMenuLabel!
+      if (acg.isSeqAssociated())
+      {
+        label = acg.getAnnotation().label;
+      }
       annotations.setSelectedItem(label);
       switch (acg.getAboveThreshold())
       {
@@ -147,15 +177,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter
                 "error.implementation_error_dont_know_about_threshold_setting"));
       }
       thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
-      thresholdValue.setText("" + acg.getAnnotationThreshold());
+      thresholdValue.setText(String.valueOf(acg.getAnnotationThreshold()));
     }
-
-    jbInit();
-    adjusting = false;
-
-    updateView();
-    frame.invalidate();
-    frame.pack();
   }
 
   @Override
@@ -329,7 +352,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       {
         updateView();
       }
-      getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+      getCurrentAnnotation().threshold.value = getSliderValue();
       propagateSeqAssociatedThreshold(updateAllAnnotation,
               getCurrentAnnotation());
       ap.paintAlignment(false, false);
@@ -358,9 +381,10 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       return;
     }
 
+    int selIndex = annotations.getSelectedIndex();
+    int annIndex = annmap[selIndex];
     setCurrentAnnotation(
-            av.getAlignment().getAlignmentAnnotation()[annmap[annotations
-                    .getSelectedIndex()]]);
+            av.getAlignment().getAlignmentAnnotation()[annIndex]);
 
     int selectedThresholdItem = getSelectedThresholdItem(
             getThreshold().getSelectedIndex());
@@ -369,6 +393,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     thresholdValue.setEnabled(true);
     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 
+    final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
     {
       slider.setEnabled(false);
@@ -377,33 +402,26 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       thresholdIsMin.setEnabled(false);
     }
     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
-            && getCurrentAnnotation().threshold == null)
+            && currentAnnotation.threshold == null)
     {
-      getCurrentAnnotation().setThreshold(new GraphLine(
-              (getCurrentAnnotation().graphMax
-                      - getCurrentAnnotation().graphMin) / 2f,
+      currentAnnotation.setThreshold(new GraphLine(
+              (currentAnnotation.graphMax - currentAnnotation.graphMin)
+                      / 2f,
               "Threshold", Color.black));
     }
 
     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
     {
       adjusting = true;
-      float range = getCurrentAnnotation().graphMax * ONETHOUSAND
-              - getCurrentAnnotation().graphMin * ONETHOUSAND;
-
-      slider.setMinimum(
-              (int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
-      slider.setMaximum(
-              (int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
-      slider.setValue(
-              (int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
-      thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
-      slider.setMajorTickSpacing((int) (range / 10f));
+      setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
+              currentAnnotation.threshold.value);
       slider.setEnabled(true);
+
+      setThresholdValueText();
       thresholdValue.setEnabled(true);
       adjusting = false;
     }
-    colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
+    colorAlignmentContaining(currentAnnotation, selectedThresholdItem);
 
     ap.alignmentChanged();
   }
@@ -444,8 +462,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
         {
           continue;
         }
-        sg.setColourScheme(
-                acg.getInstance(av, sg));
+        sg.setColourScheme(acg.getInstance(av, sg));
       }
     }
   }
@@ -456,4 +473,41 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     super.sliderDragReleased();
     ap.paintAlignment(true, true);
   }
+
+  /**
+   * construct and display a colourchooser for a given annotation row
+   * 
+   * @param av
+   * @param ap
+   * @param alignmentAnnotation
+   * @param perseq
+   *          - when true, enable per-sequence if alignment annotation is per
+   *          sequence
+   */
+  public static void displayFor(AlignViewport av, AlignmentPanel ap,
+          AlignmentAnnotation alignmentAnnotation, boolean perSeq)
+  {
+    ColourSchemeI global = av.getGlobalColourScheme();
+    AnnotationColourGradient newCS = new AnnotationColourGradient(
+            alignmentAnnotation, global,
+            alignmentAnnotation.threshold != null
+                    ? AnnotationColourGradient.ABOVE_THRESHOLD
+                    : AnnotationColourGradient.NO_THRESHOLD);
+    if (alignmentAnnotation.sequenceRef != null)
+    {
+      newCS.setSeqAssociated(perSeq);
+    }
+    for (int i = 0; i < alignmentAnnotation.annotations.length; i++)
+    {
+      Annotation ann = alignmentAnnotation.annotations[i];
+      if (ann != null && ann.colour != null
+              && !ann.colour.equals(Color.white))
+      {
+        newCS.setPredefinedColours(true);
+        break;
+      }
+    }
+    AnnotationColourChooser achooser = new AnnotationColourChooser(av, ap,
+            newCS);
+  }
 }