X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColumnChooser.java;h=3a7188ea47d3aa8966a830ed9032bec812a17ad1;hb=1810df9d010000e434975a8a4e68dcbda238f7f1;hp=4b67bbf7c5f011178a6f77114c5344b9cc179708;hpb=3ba37699f5f799d357e0cb6f041f32fc490b6eda;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java
index 4b67bbf..3a7188e 100644
--- a/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@ -21,7 +21,7 @@
 package jalview.appletgui;
 
 import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.util.MessageManager;
 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
@@ -46,7 +46,7 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.TextEvent;
 import java.awt.event.TextListener;
-import java.util.Iterator;
+import java.util.ArrayList;
 import java.util.Vector;
 
 //import javax.swing.JPanel;
@@ -110,7 +110,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
   private int actionOption = ACTION_OPTION_SELECT;
 
-  private ColumnSelection oldColumnSelection;
+  private HiddenColumns oldHiddenColumns;
 
   public AnnotationColumnChooser()
   {
@@ -140,9 +140,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     {
       return;
     }
-    setOldColumnSelection(av.getColumnSelection());
+    setOldHiddenColumns(av.getAlignment().getHiddenColumns());
     adjusting = true;
-    Vector<String> list = new Vector<String>();
+    Vector<String> list = new Vector<>();
     int index = 1;
     for (int i = 0; i < anns.length; i++)
     {
@@ -167,20 +167,22 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     }
 
     populateThresholdComboBox(threshold);
-
+    AnnotationColumnChooser lastChooser = av
+            .getAnnotationColumnSelectionState();
     // restore Object state from the previous session if one exists
-    if (av.getAnnotationColumnSelectionState() != null)
+    if (lastChooser != null)
     {
-      currentSearchPanel = av.getAnnotationColumnSelectionState()
+      currentSearchPanel = lastChooser
               .getCurrentSearchPanel();
-      currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
+      currentStructureFilterPanel = lastChooser
               .getCurrentStructureFilterPanel();
-      annotations.select(av.getAnnotationColumnSelectionState()
+      annotations.select(lastChooser
               .getAnnotations().getSelectedIndex());
-      threshold.select(av.getAnnotationColumnSelectionState()
+      threshold.select(lastChooser
               .getThreshold().getSelectedIndex());
-      actionOption = av.getAnnotationColumnSelectionState()
+      actionOption = lastChooser
               .getActionOption();
+      percentThreshold.setState(lastChooser.percentThreshold.getState());
     }
 
     try
@@ -243,10 +245,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     ngStructureFilterPanel = new StructureFilterPanel(this);
 
     thresholdPanel.setTitle("Threshold Filter");
-    thresholdPanel.add(percentThreshold);
     thresholdPanel.add(getThreshold());
     thresholdPanel.add(slider);
     thresholdPanel.add(thresholdValue);
+    thresholdPanel.add(percentThreshold);
 
     actionPanel.add(ok);
     actionPanel.add(cancel);
@@ -287,27 +289,28 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
   @SuppressWarnings("unchecked")
   public void reset()
   {
-    if (this.getOldColumnSelection() != null)
+    if (this.getOldHiddenColumns() != null)
     {
       av.getColumnSelection().clear();
 
       if (av.getAnnotationColumnSelectionState() != null)
       {
-        ColumnSelection oldSelection = av
+        HiddenColumns oldHidden = av
                 .getAnnotationColumnSelectionState()
-                .getOldColumnSelection();
-        if (oldSelection != null && oldSelection.getHiddenColumns() != null
-                && !oldSelection.getHiddenColumns().isEmpty())
+                .getOldHiddenColumns();
+        if (oldHidden != null)
         {
-          for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
-                  .iterator(); itr.hasNext();)
+          ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopy();
+          for (int[] positions : regions)
           {
-            int positions[] = itr.next();
             av.hideColumns(positions[0], positions[1]);
           }
         }
-        av.setColumnSelection(oldSelection);
+        // TODO not clear why we need to hide all the columns (above) if we are
+        // going to copy the hidden columns over wholesale anyway
+        av.getAlignment().setHiddenColumns(oldHidden);
       }
+      av.sendSelection();
       ap.paintAlignment(true);
     }
 
@@ -318,7 +321,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
   {
     if (!adjusting)
     {
-      thresholdValue.setText((slider.getValue() / 1000f) + "");
+      setThresholdValueText();
       valueChanged(!sliderDragging);
     }
   }
@@ -404,12 +407,14 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     slider.setEnabled(true);
     thresholdValue.setEnabled(true);
+    percentThreshold.setEnabled(true);
 
     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
     {
       slider.setEnabled(false);
       thresholdValue.setEnabled(false);
       thresholdValue.setText("");
+      percentThreshold.setEnabled(false);
       // build filter params
     }
     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
@@ -424,8 +429,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       }
 
       adjusting = true;
-      float range = getCurrentAnnotation().graphMax * 1000
-              - getCurrentAnnotation().graphMin * 1000;
+      // float range = getCurrentAnnotation().graphMax * 1000
+      // - getCurrentAnnotation().graphMin * 1000;
 
       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
@@ -434,6 +439,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       // slider.setMajorTickSpacing((int) (range / 10f));
       slider.setEnabled(true);
       thresholdValue.setEnabled(true);
+      percentThreshold.setEnabled(true);
       adjusting = false;
 
       // build filter params
@@ -499,10 +505,13 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       }
     }
 
+    // show hidden columns here, before changing the column selection in
+    // filterAnnotations, because showing hidden columns has the side effect of
+    // adding them to the selection
+    av.showAllHiddenColumns();
     av.getColumnSelection().filterAnnotations(
             getCurrentAnnotation().annotations, filterParams);
 
-    av.showAllHiddenColumns();
     if (getActionOption() == ACTION_OPTION_HIDE)
     {
       av.hideSelectedColumns();
@@ -510,19 +519,20 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     filterParams = null;
     av.setAnnotationColumnSelectionState(this);
+    av.sendSelection();
     ap.paintAlignment(true);
   }
 
-  public ColumnSelection getOldColumnSelection()
+  public HiddenColumns getOldHiddenColumns()
   {
-    return oldColumnSelection;
+    return oldHiddenColumns;
   }
 
-  public void setOldColumnSelection(ColumnSelection currentColumnSelection)
+  public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
   {
-    if (currentColumnSelection != null)
+    if (currentHiddenColumns != null)
     {
-      this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
+      this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
     }
   }
 
@@ -890,19 +900,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
   @Override
   public void actionPerformed(ActionEvent evt)
   {
-    if (evt.getSource() == thresholdValue)
-    {
-      try
-      {
-        float f = new Float(thresholdValue.getText()).floatValue();
-        slider.setValue((int) (f * 1000));
-        adjustmentValueChanged(null);
-      } catch (NumberFormatException ex)
-      {
-      }
-    }
 
-    else if (evt.getSource() == ok)
+    if (evt.getSource() == ok)
     {
       ok_actionPerformed(null);
     }